http://www.lsis.com/goto/r259/rss 2010-06-23T11:13:03+01:00 text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FB%1D%7B%7Fs OBJECTIVE: Rheumatoid arthritis (RA) is associated with increased production of adipokines, cytokine-like mediators that are mainly produced in adipose tissue but also by synovial cells. As RA synovial fibroblasts (SF), lymphocytes, endothelial cells and chondrocytes are key players in the pathophysiology of RA, we analyzed the effects of the key adipokine adiponectin on pro-inflammatory and pro-destructive synovial effector cells. METHODS: Lymphocytes were in part activated prior to stimulation. All cells were stimulated with adiponectin and changes in gene and protein expression were determined by Affymetrix and protein arrays. mRNA and protein levels were confirmed using (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FB%10uz%7B Intramuscular fat, the total lipid deposited within skeletal muscle, has been regarded as a potential factor responsible for meat quality in animal production and insulin resistance in humans. The objective of present study was to identify candidate genes which control intramuscular fat accumulation through using animal models. PIC pigs (lean-type) and Rongchang pigs (obese-type) were used. By scanning the mRNA samples of longissimus dorsi muscle with Affymetrix Gene-Chip microarray technology, sus scrofa chloride intracellular channel 5 (CLIC5) was isolated, and its mRNA abundance and protein expression level were reversely related with the intramuscular fat content of pigs. Furthermore, (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FB%10yvs Gene expression profiles were determined for 12 cutaneous squamous cell carcinomas (SCC) removed from sun-exposed sites on nonimmunosuppressed patients. Gene expression in each SCC was compared to that in sun-exposed skin from the same patient using the Affymetrix HGU133 2.0 PlusGeneChip. We identified 440 genes with increased expression in SCC and 738 with decreased expression; overall we identified a large number of small changes in gene expression rather than a few marked changes that distinguished SCC from sun-exposed skin. Analyzing this robust data set according to biofunctional pathways using DAVID, transcriptional control elements using oPOSSUM, and chromosomal location using GSEA (…) text/html http://www.businesswire.com Business Wire http://www.lsis.com/goto/v259/%3B%97f%FB%11tv%7D SAN DIEGO-(BUSINESS WIRE)-TrovaGene, Inc. (TROV.PK), formerly Xenomics, Inc. (XNOM.PK), a developer of transrenal molecular diagnostics, announced today that Skyline Diagnostics BV, a company which develops and commercializes diagnostic microarrays for oncology, has licensed its NPM1 technology to be included in one of its microarray products. Skyline Diagnostics plans to initially offer this product as a laboratory testing service in Europe and will eventually expand this testing service to markets outside of Europe. We are pleased that Skyline Diagnostics will be providing our NPM1 technology in an innovative microarray product as a laboratory testing service œWe are pleased that (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FB%16xvr Chip based high throughput genotyping has facilitated genome-wide studies of genetic diversity. Many studies have utilized these large data sets to make inferences about the demographic history of human populations, using measures of genetic differentiation such as F(ST) or principal component analyses. However, the SNP chip data suffer from ascertainment biases caused by the SNP discovery process in which a small number of individuals from selected populations are used as discovery panels. In this study, we investigate the effect of the ascertainment bias on inferences regarding genetic differentiation among populations in one of the common genome-wide genotyping platforms. We generate (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FB%15x%7F%7B The purpose of this study was to pool information in epithelial ovarian cancer by combining studies using Affymetrix expression microarray datasets made at different laboratories to identify novel biomarkers. Epithelial microarray expression information across laboratories was screened and combined after preprocessing raw microarray data, then ANOVA and unpaired T test statistical analysis was performed for identifying differentially expressed genes (DEGs), followed by clustering and pathway analysis for these DEGs. In this work, we performed a combination analysis on microarrays from three different laboratories using gene expression data on ovarian cancer and obtained a list of (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FB%15x%7C%7F ABSTRACT: BACKGROUND: Pancreatic cancer is still associated with devastating prognosis. Real progress in its treatment has still not been achieved. Therefore new models to investigate this deadly malignancy are urgently needed. As a part of this process we have established and characterized a new human pancreatic cancer cell line. METHODS: The newly established pancreatic cancer cell line PaCa 5061 was characterized for its morphology, growth rate, chromosomal analysis and mutational analysis for K-ras, EGFR and p53 genes. Gene-amplification and RNA expression profile were obtained using Affymetrix microarray and overexpression was validated by IHC analysis. Tumorigenicity and spontaneous (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FC%1C%7C%7F%7C Affymetrix microarrays measure gene expression based on the intensity of hybridization of a panel of oligonucleotide probes (probe set) with mRNA. The signals from all probes within a probe set are converted into a single measure that represents the expression value of a gene. This step diminishes the number of independently measured parameters and eliminates from consideration individual "good-working" probes. We propose a new feature selection algorithm (Probe Level Universal Search or PLUS algorithm) for probe-level analysis of gene expression datasets. The algorithm evaluates the intensities of perfect-match Affymetrix probes individually and selects probes that allow one to (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FC%1D%7Cx%7F Excessive cell proliferation and genetic changes such as loss of an allele (loss of heterozygosity (LOH) or amplifications or deletions of parts of chromosomes (copy number variations (CNV) are common findings in cancers. It is unknown whether these changes are also present in patients with overgrowth syndromes, although the presence of small-scale CNVs (such as duplication of 11p15 in Beckwith-Wiedemann syndrome), excessive cell proliferation and an increased frequency of tumors have all been reported in these patients. We present results of a genome-wide scan for LOH and CNV in Proteus syndrome (PS), a severely disfiguring overgrowth syndrome. We investigated CNV and LOH in DNA derived (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FC%10yw%7E Objective: 22q11.2 Deletion Syndrome (22q11.2 DS), also known as DiGeorge Syndrome Type 1 (DGS1), occurs in approximately 1:3000 live births. 75% of children with DGS1 have severe congenital heart disease requiring early intervention. The gold standard for detection of DGS1 is fluorescence in situ hybridization (FISH) with a probe at the TUPLE1 gene. However, FISH has a high false negative rate, is costly, and requires several days to perform. As a result, FISH is under-utilized and the diagnosis of 22q11.2 DS is frequently delayed, often resulting in profound clinical consequences. The goal of this study was to determine if multiplexed, quantitative, real-time PCR (MQPCR), could be used (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FC%14z%7Fs Alopecia areata (AA) is a non-scarring inflammatory hair loss disease with a complex autoimmune etiopathogenesis that is poorly understood. In order to investigate the pathogenesis of AA at the molecular level, we examined the gene expression profiles in skin samples from lesional (n=10) and non-lesional sites (n=10) of AA patients using Affymetrix Hu95A-v2 arrays. 363 genes were found to be differentially expressed in AA skin compared to non-lesional skin; 97 were up-regulated and 266 were down-regulated. Functional classification of the differentially expressed genes (DEGs) provides evidence for T-cell mediated immune response (CCL5, CXCL10, CD27, ICAM-2 and-3, IL7R, FKN), and a possible (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FC%14%7E%7Cx Abstract Genome wide association studies rely upon segregating natural genetic variation, particularly the patterns of polymorphism and correlation between adjacent markers. To facilitate association studies in the model legume Medicago truncatula, we present a genome scale polymorphism scan using existing Affymetrix microarrays. We develop and validate a method that uses a simple information-criteria algorithm to call polymorphism from microarray data without reliance on a reference genotype. We genotype 12 inbred M. truncatula lines sampled from 4 wild Tunisian populations and find polymorphisms at approximately 7% of features, comprising 31,419 probes. Only approximately 3% of these (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FC%15uy%7C In addition to KIT and PDGFRA mutations, sequential accumulation of other genetic events is involved in the development and progression of gastrointestinal stromal tumors (GISTs). Until recently, the significance of these other alterations has not been thoroughly investigated. We report the first study that integrates gene expression profiling and high-resolution genomic copy number analyses in GIST. Fresh tissue specimens from 25 patients with GIST were collected, and gene expression profiling and high-resolution genomic copy number analyses were performed, using Affymetrix U133Plus and SNP array 6.0. We found that all 21 mutant GIST patients showed both macroscopic cytogenetic (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FC%15x%7B%7E ABSTRACT: BACKGROUND: Signal transduction processes mediated by phosphatidyl inositol phosphates affect a broad range of cellular processes such as cell cycle progression, migration and cell survival. The protein kinase AKT is one of the major effectors in this signaling network. Chronic AKT activation contributes to oncogenic transformation and tumor development. Therefore, analogs of phosphatidyl inositol phosphates (PIAs) were designed as new small drugs to block AKT activity for cancer treatment. Here we characterize the biological effects of the PIAs SH-5 and SH-6 in colorectal cancer cell lines. METHODS: Serum-starved or serum-supplemented human colorectal cancer cell lines SW480, (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FD%1D%7Ex%7F A multiplatform approach, including conventional cytogenetic techniques, BAC array comparative genomic hybridization, and Affymetrix 500K SNP arrays, was applied to the study of the tumor genomes of 25 follicular lymphoma biopsy samples with paired normal DNA samples to characterize balanced translocations, copy number imbalances, and copy-neutral loss of heterozygosity (cnLOH). In addition to the t(14;18), eight unique balanced translocations were found. Commonly reported FL-associated copy number regions were revealed including losses of 1p32-36, 6q, and 10q, and gains of 1q, 6p, 7, 12, 18, and X. The most frequent regions affected by copy-neutral loss of heterozygosity were 1p36.33 (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FD%13%7D%7By To identify a novel amplified cancer gene a systematic screen of 975 human cancer DNA samples, 750 cell lines and 225 primary tumors, using the Affymetrix 10K SNP microarray was undertaken. The screen identified 193 amplicons. A previously uncharacterized amplicon located on 6p21.2 whose 1 Mb minimal common amplified region contained eight genes (GLO1, DNAH8, GLP1R, C6orf64, KCNK5, KCNK17, KCNK16, and C6orf102) was further investigated to determine which gene(s) are the biological targets of this amplicon. Real time quantitative PCR (qPCR) analysis of all amplicon 6p21.2 genes in 618 human cancer cell lines identified GLO1, encoding glyoxalase 1, to be the most frequently amplified gene (…) text/html http://www.biospace.com BioSpace http://www.lsis.com/goto/v259/%3B%97f%FD%11yyz REDWOOD CITY, Calif.-(BUSINESS WIRE)-Pathwork Diagnostics Inc., a molecular diagnostics company focused on oncology, today announced the U.S. Food and Drug Administration (FDA) cleared the Pathwork Tissue of Origin Test for formalin-fixed, paraffin-embedded (FFPE) tissues. The FDA clearance allows the Tissue of Origin Test to be broadly utilized on common clinical FFPE tumor specimens from both community and research hospitals and paves the way for additional FFPE-based cancer tests on the Pathwork platform. With some metastatic and poorly differentiated tumors, identifying the tumor s origin is complex and can make diagnosis and treatment difficult. The Pathwork Tissue of Origin Test (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FD%16t%7B%7C Although inherited mitochondrial genetic variation can cause human disease, no validated methods exist for control of confounding due to mitochondrial population stratification (PS). We sought to identify a reliable method for PS assessment in mitochondrial medical genetics. We analyzed mitochondrial SNP data from 1513 European American individuals concomitantly genotyped with the use of a previously validated panel of 144 mitochondrial markers as well as the Affymetrix 6.0 (n = 432), Illumina 610-Quad (n = 458), or Illumina 660 (n = 623) platforms. Additional analyses were performed in 938 participants in the Human Genome Diversity Panel (HGDP) (Illumina 650). We compared the following (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FD%16z%7B%7B ABSTRACT: BACKGROUND: Lymphotropism in oral squamous cell carcinoma (OSCC) is one of the most important prognostic factors of 5-year survival. In an effort to identify genes that may be responsible for the initiation of OSCC lymphotropism, we examined DNA copy number gains and losses and corresponding gene expression changes from tumor cells in metastatic lymph nodes of patients with OSCC. RESULTS: We performed integrative analysis of DNA copy number alterations (CNA) and corresponding mRNA expression from OSCC cells isolated from metastatic lymph nodes of 20 patients using Affymetrix 250K Nsp I SNP and U133 Plus 2.0 arrays, respectively. Overall, genome CNA accounted for expression (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FD%17%7Cwy ABSTRACT: BACKGROUND: A main goal in understanding cell mechanisms is to explain the relationship among genes and related molecular processes through the combined use of technological platforms and bioinformatics analysis. High throughput platforms, such as microarrays, enable the investigation of the whole genome in a single experiment. There exist different kind of microarray platforms, that produce different types of binary data (images and raw data). Moreover, also considering a single vendor, different chips are available. The analysis of microarray data requires an initial preprocessing phase (i.e. normalization and summarization) of raw data that makes them suitable for use on (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FD%14%7C%7C%7E OBJECTIVES: The aim of this study was to identify new prognostic factors in metastatic renal cell carcinoma (RCC) based on the analysis of precisely defined metastatic tissue. METHODS: Expression profiling was done on 26 snap-frozen samples of clear-cell RCC metastases with complete follow-up (up to 116 months) using laser microdissection and oligonucleotide microarrays (Affymetrix). A prognosis-associated gene signature was determined using the semi-supervised principal components analysis method. Validation was performed with quantitative RT-PCR on samples of normal renal tissue (n = 6), RCC primary tumor (n = 57), and RCC metastases (n = 59). Immunohistochemistry (IHC) was done to (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FD%15y%7D%7F ABSTRACT: BACKGROUND: Peroxisome proliferator-activated receptor gamma (PPAR gamma) is a nuclear receptor whose activation has been shown to modulate macrophage and T cell-mediated inflammation. The objective of this study was to investigate the mechanisms by which the deletion of PPAR gamma in T cells modulates immune cell distribution and colonic gene expression and the severity of experimental IBD. METHODS: PPAR gamma flfl; CD4 Cre+ (CD4cre) and Cre- (WT) mice were challenged with 2.5% dextran sodium sulfate in their drinking water for 0, 2, or 7 days. Mice were scored on disease severity both clinically and histopathologically. Flow cytometry was used to assess lymphocyte and (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FE%1Duy%7C Background: Recently, in genome-wide analyses of DNA copy number abnormalities using single nucleotide polymorphism (SNP) microarrays, genetic alterations targeting PAX5 were identified in over 30% of pediatric acute lymphoblastic leukemia (ALL) patients. So far the occurrence of PAX5 alterations and their clinical correlation have not been investigated in adults with BCR-ABL1-positive ALL. Patients and methods: To characterize the rearrangements on 9p involving PAX5 and their clinical significance in adult BCR-ABL1-positive ALL.Eighty-nine patients with de novo adult BCR-ABL1-positive ALL were enrolled into institutional (n = 15) or GIMEMA (Gruppo Italiano Malattie EMatologiche (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FE%1D%7B%7F%7E In this study, we assess 34 of the most replicated genetic associations for Alzheimer's disease using data generated on Affymetrix SNP 6.0 arrays and imputed at over 5.7 million markers from a unique cohort of over 1600 neuropathologically defined Alzheimer's disease cases and controls (1019 cases and 591 controls). Testing the top genes from the AlzGene meta-analysis, we confirm the well known association with APOE single nucleotide polymorphisms (SNPs), the CLU, PICALM and CR1 SNPs recently implicated in unusually large data sets, and previously implicated CST3 and ACE SNPs. In the cases of CLU, PICALM and CR1, as well as in APOE, the odds ratios we find are slightly larger than those (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FE%13%7E%7Er MOTIVATION: Current algorithms for estimating DNA copy numbers (CNs) borrow concepts from gene expression analysis methods. However, single nucleotide polymorphism (SNP) arrays have special characteristics that, if taken into account, can improve the overall performance. For example, cross hybridization between alleles occurs in SNP probe pairs. In addition, most of the current copy-number methods are focused on total copy numbers while it has been shown that allele-specific copy numbers are of paramount importance for some studies. Therefore, we have developed a summarization method which estimates high-quality allele-specific copy numbers. RESULTS: The proposed method estimates the (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%1Cuy%7E Summary This research tests hypotheses aimed at examining the extent of intraspecific variation in the Populus drought transcriptome, using six different Populus balsamifera L. genotypes and Affymetrix GeneChip technology. Although there was a common, shared water-deficit-induced transcriptome level response for P. balsamifera, the amplitude of gene expression for the shared water-deficit transcriptome varied among genotypes. Larger changes in the absolute magnitude of transcript abundance in response to drought were observed for genotypes that had more rapid declines in their physiological status in response to drought. The findings better define within-species variation in the response (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%1C%7Bvy The gene expression changes produced by moderate hypothermia are not fully known, but appear to differ in important ways from those produced by heat shock. We examined the gene expression changes produced by moderate hypothermia and tested the hypothesis that rewarming after hypothermia approximates a heat-shock response. Six sets of human HepG2 hepatocytes were subjected to moderate hypothermia (31 degrees C for 16 h), a conventional in vitro heat shock (43 degrees C for 30 min) or control conditions (37 degrees C), then harvested immediately or allowed to recover for 3 h at 37 degrees C. Expression analysis was performed with Affymetrix U133A gene chips, using analysis of variance-based (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%1Dy%7Cs In plants, isoprene plays a dual role: (a) as thermo-protective agent proposed to prevent degradation of enzymes/membrane structures involved in photosynthesis, and (b) as reactive molecule reducing abiotic oxidative stress. The present work addresses the question whether suppression of isoprene emission interferes with genome wide transcription rates and metabolite fluxes in grey poplar (Populus x canescens) throughout the growing season. Gene expression and metabolite profiles of isoprene emitting wild type plants and RNAi-mediated non-isoprene emitting poplars were compared by using poplar Affymetrix microarrays and non-targeted FT-ICR-MS (Fourier transform ion cyclotron resonance mass (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%1Dxzs Aims Aortic stenosis induces pressure overload and myocardial remodelling with concentric hypertrophy and alterations in extracellular matrix (ECM). Aortic valve replacement leads to reverse remodelling, a process of which knowledge is scarce. The aims of the present study were to examine alterations in myocardial gene expression and subsequently identify molecular alterations important for the early phase of reverse remodelling. Methods and results After 4 weeks of ascending aortic banding, mice were subjected to a debanding operation (DB) and followed for 3, 7, or 14 days. Cardiac function was assessed by echocardiography/tissue Doppler ultrasonography. Myocardial gene expression was (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%1D%7F%7Cr Strains of non-pathogenic pseudomonad bacteria, can elicit host defence responses against pathogenic microorganisms. Pseudomonas fluorescens strain MKB158 can protect cereals from pathogenesis by Fusarium fungi, including Fusarium head blight which is an economically important disease due to its association with both yield loss and mycotoxin contamination of grain. Using the 22 K barley Affymetrix chip, trancriptome studies were undertaken to determine the local effect of P. fluorescens strain MKB158 on the transcriptome of barley head tissue, and to discriminate transcripts primed by the bacterium to respond to challenge by Fusarium culmorum, a causal agent of the economically important (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%1D%7Ezz To investigate whether integration of HPV DNA in cervical carcinoma is responsible for structural alterations of the host genome at the insertion site, a series of 34 primary cervical carcinomas and eight cervical cancer-derived cell lines were analysed. DNA copy number profiles were assessed using the Affymetrix GeneChip Human Mapping 250K Sty array. HPV 16, 18 or 45 integration sites were determined using the DIPS-PCR technique. The genome status at integration sites was classified as follows: no change, amplification, transition normal/gain, normal/loss or gain/LOH. A single HPV integration site was found in 34 cases; two sites were found in seven cases; and three sites in one case (51 (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%12yw%7F Solitary fibrous tumour (SFT) is a mesenchymal neoplasm composed of CD34-positive fibroblastic cells. The pathogenesis driving this neoplasm remains unclear, with no recurrent genetic aberrations described to date. Previous reports suggest a role for IGF2 over-expression in the pathogenesis of these tumours, implicated in triggering hypoglycaemia in some patients. The expression profiling of 23 SFTs was investigated using an Affymetrix U133A platform. The transcriptional signature was compared to a set of 34 soft tissue sarcomas spanning seven subtypes. Potential candidate genes were then further investigated for activating mutations or loss of imprinting (LOI). SFT had a distinct (…) text/html http://www.bionity.com Bionity.com http://www.lsis.com/goto/v259/%3B%97f%FF%13u%7C%7D 07.06.2010 - Signature Diagnostics AG announced positive results from its international, prospective, multi-center performance evaluation study showing the diagnostic ability of Predictor C to distinguish between high-risk and low-risk disease progression. Predictor C, a prognostic tissue test for UICC stage II / III colorectal cancer, uses Affymetrix technology to evaluate the expression of 32 genes that are involved in the disease's progression. "Predictor C will have a significant impact on both the diagnosis and treatment of stage II and III colorectal cancer patients. Our multi-gene test enables physicians to predict colorectal cancer progression and thereby provide their patients (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%13xzz BACKGROUND Parthenogenetic embryonic stem cells (PESCs) may have future utilities in cell replacement therapies since they are closely related to the female from which the activated oocyte was obtained. Furthermore, the avoidance of parthenogenetic development in mammals provides the most compelling rationale for the evolution of genomic imprinting, and the biological process of parthenogenesis raises complex issues regarding differential gene expression. METHODS AND RESULTS We describe here homozygous rhesus monkey PESCs derived from a spontaneously duplicated, haploid oocyte genome. Since the effect of homozygosity on PESCs pluripotency and differentiation potential is unknown, we (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%10zy%7E Xenograft survival is a balance between immunological rejection and adaptive changes in the graft. Immunohistochemical analysis of vascular immunoglobulin deposition in heterotopic and orthotopic pig to primate cardiac xenografts shows vascular antibody deposition as early as 30 min after reperfusion and throughout the transplant period in both GT+ and GTKO hearts. Despite the abundance of antibody, graft contractility in heterotopic transplants and the ability of the graft to support orthotopic recipients remained high, with little evidence of microvascular thrombosis for extended periods of time. This suggests that the graft is actively adapting to chronic antibody exposure to forestall (…) text/html http://www.marketwire.com Marketwire http://www.lsis.com/goto/v259/%3B%97f%FF%11xx%7D POTSDAM, GERMANY-(Marketwire - June 4, 2010) - * Study data to be presented on June 6 at the Annual American Society of Clinical Oncology (ASCO) * Product Launch planned for Q4 2010 - Q1 2011 Signature Diagnostics AG announced today positive results from its international, prospective, multi-center performance evaluation study showing the diagnostic ability of Predictor C to distinguish between high-risk and low-risk disease progression. Predictor C, a prognostic tissue test for UICC stage II / III colorectal cancer, uses Affymetrix technology to evaluate the expression of 32 genes that are involved in the disease's progression. The company will present the complete study data at the (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%11%7Cw%7B OBJECTIVES: We have used genome-wide association studies to identify variants that are associated with vulnerability to develop heroin addiction. METHODS: DNA from 325 methadone stabilized, former severe heroin addicts and 250 control individuals were pooled by ethnicity (Caucasian and African-American) and analyzed using the Affymetrix GeneChip Mapping 100 K Set. Genome-wide association tests were conducted. RESULTS: The strongest association with vulnerability to develop heroin addiction, with experiment-wise significance (P=0.035), was found in Caucasians with the variant rs10494334, a variant in an unannotated region of the genome (1q23.3). In African Americans, the variant most (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97f%FF%11%7D%7F%7C Prolactin and progesterone act together to regulate mammary alveolar development, and both hormones have been implicated in breast cancer initiation and progression. Here we show that Elf5, a prolactin-induced ETS transcription factor that specifies the mammary secretory cell lineage, is also induced by progestins in breast cancer cells via a direct mechanism. To define the transcriptional response to progestin elicited via Elf5, we made an inducible Elf5 short hairpin-RNA knock-down model in T47D breast cancer cells and used it to prevent the progestin-induction of Elf5. Functional analysis of Affymetrix gene expression data using Gene Ontologies and Gene Set Enrichment Analysis showed (…) text/html http://www.biospace.com BioSpace http://www.lsis.com/goto/v259/%3B%97f%FF%14%7E%7B%7C POTSDAM, GERMANY-(Marketwire - June 04, 2010) - * Study data to be presented on June 6 at the Annual American Society of Clinical Oncology (ASCO) * Product Launch planned for Q4 2010 - Q1 2011 POTSDAM, Germany, June 4, 2010 - Signature Diagnostics AG announced today positive results from its prospective, multi-center clinical study validating Detector C, its in-vitro diagnostic screening product. Detector C is a non-invasive, blood-based screening test for the early detection of colorectal cancer. The test uses Affymetrix technology to evaluate the expression of 202 genes that are active in white blood cells in response to tumor formation and growth. The test showed a consistently high (…) text/html http://www.biospace.com BioSpace http://www.lsis.com/goto/v259/%3B%97f%FF%14%7E%7Bx SANTA CLARA, Calif.-(BUSINESS WIRE)-Affymetrix, Inc. (NASDAQ: AFFX) today announced the webcast of its presentation at the Jefferies 2010 Global Life Sciences Conference in New York City. text/html http://www.businesswire.com Business Wire http://www.lsis.com/goto/v259/%3B%97f%FF%15u%7Dr SANTA CLARA, Calif.-(BUSINESS WIRE)-Affymetrix, Inc. (NASDAQ: AFFX) today announced the webcast of its presentation at the Jefferies 2010 Global Life Sciences Conference in New York City. Doug Farrell, Vice President of Investor Relations and Treasury, will present on Friday June 11th at 9:00a ET. To hear a live webcast of the presentation, visit the investor relations page on the Company's Web site at www.affymetrix.com. An archived webcast will be available for 30 days. About Affymetrix Affymetrix technology is used by the world s top pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government, and nonprofit research institutes. More than 1,900 (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F6%1Cty%7C Objective: To study the expression changes of matrix metalloproteinases (MMPs) in traumatic deep vein thrombosis (TDVT) in a rat model with the aid of gene chip technology and to explore the roles of MMPs in TDVT. Methods: Totally 150 Sprague Dawley rats were randomly divided into control group (n equal to 10) and model group (n equal to 140). Rat models of TDVT were established by clamping the femoral vein and fixing the bilateral hind limbs. Then fixation of the hip spica with plaster bandage was conducted. According to the observation phases and/or biological situations of the femoral vein thrombosis, the model rats were further divided into 7 groups. Vascular tissues were obtained from (…) text/html http://www.biospace.com BioSpace http://www.lsis.com/goto/v259/%3B%97g%F6%12zw%7E Craigavon Northern Ireland (03 June 2010) Almac today announced the launch of XCEL ¢ array, a biomarker discovery platform that enables the identification of biomarkers within multiple disease areas. Almac s propriety XCEL ¢ array contains 92,000 transcripts, significantly more than is available on any other platform and the technology is optimised for use with Formalin Fixed Paraffin Embedded (FFPE) tissue. XCEL ¢ array is a high density transcriptome based microarray based on the industry standard Affymetrix GeneChip platform. The content of XCEL has been derived from high quality proprietary sequence data, as well as mining public gene expression and sequence databases. The design (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F6%13uvx Alternative splicing is an important mechanism for increasing protein diversity. However, its functional effects are largely unknown. Here, we present our new software workflow composed of the open-source application AltAnalyze and the Cytoscape plugin DomainGraph. Both programs provide an intuitive and comprehensive end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains, microRNA binding sites, molecular interactions and pathways. Our software tools include easy-to-use graphical user interfaces, rigorous statistical methods (FIRMA, MiDAS and DABG filtering) and do not require prior (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F6%11%7B%7E%7D ABSTRACT: BACKGROUND: Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for most common laboratory models, transcriptome analysis in non-traditional model species still remains a challenge. Indeed, the signal resulting from heterologous hybridization is low and difficult to interpret because of the weak complementarity between probe and target sequences, especially when no microarray dedicated to a genetically close species is available. RESULTS: We show here that transcriptome analysis in a species genetically distant from laboratory (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F6%11%7E%7C%7F Background: Mild hypothermia (32-34 degrees C) improves resistance to ischemia-reperfusion (I/R) injury. However, the mechanisms by which it affects human cellular function are not fully elucidated. To further test for hypothermic modulation of global biological processes, we used DNA microarray technique to detect the overall gene expression profile. Methods: Human umbilical endothelial cells (HUVECs) were incubated under control condition (37 degrees C) or mild hypothermia (33 degrees C) for 2 hours after stimulated ischemia. Detection of differentially expressed genes was performed with Affymetrix U133 plus 2.0 arrays and PARTEK software. We used DAVID and KEGG Pathways database to (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F6%16%7Fzz ABSTRACT: BACKGROUND: Several molecular changes occur following axotomy, such as gene up-regulation and down-regulation. In our previous study using Affymetrix arrays, it was found that after the axotomy of sciatic nerve, there were many novel genes with significant expression changes. Among them, neuronatin (Nnat) was the one which expression was significantly up-regulated. Nnat was identified as a gene selectively expressed in neonatal brains and markedly reduced in adult brains. The present study investigated whether the expression of Nnat correlates with symptoms of neuropathic pain in adult rats with transected sciatic nerve. METHODS: Western blotting, immunohistochemistry, and the (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F6%15%7By%7D Aim: We sought to determine whether triclosan (2,4,4'-trichloro-2'-hydroxydiphenylether), an extensively used anti-plaque agent with broad-spectrum anti-microbial activity, with reported anti-inflammatory effects via inhibition of prostaglandin E2 and interleukin 1 (IL-1)beta, could also more broadly suppress multiple inflammatory gene pathways responsible for the pathogenesis of gingivitis and periodontitis. Materials and Methods: As an exploratory study, the effects of triclosan on the inflammatory gene expression profile were assessed ex vivo using peripheral whole blood samples from eight periodontally healthy donors. Ten-millilitres whole blood aliquots were incubated 2 h with 0.3 (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F7%1Cuvr Context: Exposure to particulate matter (PM) is associated with systemic health effects, but the cellular and molecular mechanisms are unclear. Objective: We hypothesized that, if circulating mononuclear cells play an important role in mediating systemic effects of PM, they would show gene expression changes following exposure. Materials and methods: Peripheral blood samples were collected before (0 h) and at 24 h from healthy subjects exposed to filtered air (FA) and ultrafine carbon particles (UFPs, 50 mug/m(3) for 2 h in a previous study (n = 3 each). RNA from mononuclear cell fraction ( 85% lymphocytes) was extracted, amplified and hybridized to Affymetrix HU133 plus 2 microarrays. (…) text/html http://www.ncbi.nlm.nih.gov NCBI PubMed http://www.lsis.com/goto/v259/%3B%97g%F7%1Cuys ABSTRACT: BACKGROUND: Pollen development from the microspore involves a series of coordinated cellular events, and the resulting mature pollen has a specialized function to quickly germinate, produce a polar-growth pollen tube derived from the vegetative cell, and deliver two sperm cells into the embryo sac for double fertilization. The gene expression profiles of developing and germinated pollen have been characterised by use of the eudicot model plant Arabidopsis. Rice, one of the most important cereal crops, has been used as an excellent monocot model. A comprehensive analysis of transcriptome profiles of developing and germinated pollen in rice is important to understand the conserved (…)