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Microarray Technology (microarray + technology)
Kinds of Microarray Technology Selected AbstractsBook Review: Applying Genomic and Proteomic Microarray Technology in Drug Discovery.PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 14 2005By Robert S. Matson No abstracts. [source] 2243: Update on inherited ocular developmental diseaseACTA OPHTHALMOLOGICA, Issue 2010GCM BLACK Purpose To provide an overview of progress in understanding of the genetics of developmental ocular disease. Methods A systematic review, including case presentations, to illustrate insights into genes underlying developmental ocular disorders: Results Studies suggest that, in developed countries, between a third and a half of the diagnoses underlying childhood blind or partial-sighted registration are genetic while a number of other ,non-genetic' conditions also have a substantial genetic contribution. Such a figure is likely to be an underestimate. Although most of these conditions are rare, many of the issues regarding diagnosis and counselling apply to the group as a whole and it is therefore possible to consider a common approach to many aspects of their clinical management. An important challenge, for example, is to improve genetic counselling for patients affected by, and at risk of, disorders that may be caused by a genetic change in one of many possible genes, which typifies many inherited conditions associated with blindness (developmental ocular disorders, early-onset retinal dystrophies, congenital cataract). Most diagnostic genetic testing currently being undertaken focuses on single genes; this will be illustrated for ocular conditions such as retinoblastoma, Norrie disease and microphthalmia. However future prospects will focus upon use of new higher throughput technologies (e.g Microarray technologies). Conclusion The recent identification of genes underlying, for example, anophthalmia/microphthalmia spectrum (e.g. VSX2, SOX2, BCOR), anterior segment dysgenesis (e.g. PITX2, FOXC1, FOXE3) and early,onset retinal disorders (e.g. ADVIRC, RPE65) has shed light on the pathways and processes underlying a range of the biological processes underlying ocular development. [source] A microarray's view of life in the desert: adding a powerful evolutionary genomics tool to the packrat's middenMOLECULAR ECOLOGY, Issue 11 2009MARJORIE D MATOCQ Identifying the genetic architecture of adaptive traits is fundamental to understanding how organisms respond to their environment, over both ecological and evolutionary timeframes. Microarray technology that allows us to capture the simultaneous expression of thousands of genes provides unparalleled insight into how organisms cope with their environment at the transcriptional level. Recent studies in Molecular Ecology demonstrate how microarrays can rapidly identify which genes and pathways allow organisms to face some of the most fundamental physiological challenges posed by the environment, including compensation for the hypoxic and thermal stress of high-altitudes (Cheviron et al. 2008) and, in this issue, the biotransformation of toxic plant secondary compounds by mammals (Magnanou et al. 2009). Microarrays (Ekins et al. 1989; Fodor et al. 1991) are glass slides affixed with hundreds to thousands of oligonucleotide or cDNA sequences (probes). Messenger RNA transcripts (typically reverse transcribed to cDNA) are isolated from a tissue/sample of interest and hybridized to the array. Binding to specific probes indicates that a particular gene was transcriptionally active at or near the time of sampling and thus provides a potentially comprehensive measure of gene expression. Although a tremendously powerful tool, commercially produced oligonucleotide arrays are only available for a handful of model organisms. Nonetheless, evolutionary ecologists have exploited this resource by using a cross-species hybridization approach (e.g. Saetre et al. 2004), that is, hybridizing a model organism array with a nonmodel sample (Bar-Or et al. 2007). Magnanou et al. (2009) present a novel example of using a model muroid microarray (Agilent Technologies, Rattus) to study physiological response in a wild, nonmodel muroid, Neotoma. [source] Expression and chromosomal organization of mouse meiotic genesMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 3 2010Hiba Waldman Ben-Asher Microarray technology which enables large scale analysis of gene expression and thus comparison between transcriptomes of different cell types, cells undergoing different treatments or cells at different developmental stages has also been used to study the transcriptome involved with spermatogenesis. Many new germ cell-specific genes were determined, and the resulting genes were classified according to different criteria. However, the biological significance of these classifications and their clustering according to developmental transcriptional patterns during spermatogenesis have not yet been addressed. In this study we utilized mouse testicular transcriptome analysis at five distinct post-natal ages (Days 7, 10, 12, 14, and 17), representing distinct meiotic stages, in an attempt to better understand the biological significance of genes clustered into similar expression patterns during this process. Among 790 sequences that showed an expression level change of twofold or more in any of the five key stages that were monitored, relative to the geometric average of all stages, about 40% peaked and about 30% were specifically suppressed at post-natal day 14 (representing the early pachytene stage of spermatocytes), reflecting tight transcriptional regulation at this stage. We also found that each of the six main transcription clusters that were determined was characterized by statistically significant representation of genes related to specific biological processes. Finally, our results indicated that genes important for meiosis are not randomly distributed along the mouse genome but rather preferentially located on specific chromosomes, suggesting for the first time that chromosomal location might be a regulating factor of meiotic gene expression. Mol. Reprod. Dev. 77: 241,248, 2010. © 2009 Wiley-Liss, Inc. [source] De novo synthesis and assembly of multiplex riboswitches in vitroBIOTECHNOLOGY PROGRESS, Issue 5 2009Hao-Hua Sun Abstract Pools of short synthetic oligonucleotides (oligos) are required in the multiplex and parallel DNA construction. Microarray technology provides a fast and economical mean for massive parallel synthesis of oligos. The method of oligo synthesis with the programmable microfluidic PicoArray could simultaneously synthesize the designed oligos for multiple riboswitch genes. The synthetic oligos were recovered and purified as a pool of oligo mixture (OligoMix). Three temperature steps were employed to denature, anneal and extend the designed OligoMix until, after multiple rounds of thermocycling, the riboswitches with the desired length are obtained. The OligoMix was amplified using this PCR-based technique and the flanking adapter segments were cleaved for following assembly. Based on these oligos derived from 197 riboswitch sequences, the method of simultaneous assembling multiplex riboswitches (SAMRs) showed high fidelity by sequence identification. The resultant error rate was determined to be 2.78,. With the templates from SAMRs, in vitro transcription was applied to produce milligram amounts of biologically active riboswitches. With the verification of biological activity based on the high specificity of recognizing small-molecule metabolites as well as the DNA sequence redivivus by RT-PCR, the assembled riboswitches can be used for further gene operation and biological application. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Microarray technology for surgeonsBRITISH JOURNAL OF SURGERY (NOW INCLUDES EUROPEAN JOURNAL OF SURGERY), Issue 4 2005A. M. Thompson Continuing the Journal's 2005 series of leading articles highlighting areas where laboratory science meets clinical practice, Professor Alastair Thompson of Dundee outlines the present and future prospects for microarray technology. Copyright © 2005 British Journal of Surgery Society Ltd. Published by John Wiley & Sons, Ltd. [source] Role of ancillary techniques in diagnosing and subclassifying non-Hodgkin's lymphomas on fine needle aspiration cytologyCYTOPATHOLOGY, Issue 5 2006P. DeyArticle first published online: 8 SEP 200 Non-Hodgkin's lymphomas (NHL) are tumours of the lymphoid cells. During the process of development of lymphoid cells, neoplasia may evolve at any point. Neoplastic cells usually carry the imprint of cell of origin at the stage of origin. Various types of NHL may have similar morphology with wide variation in origin, immunophenotype and other biological features. Different ancillary laboratory techniques may help to overcome the limitations of morphology in this aspect. The commonly used ancillary techniques in lymphomas are immunocytochemistry (IC), flow cytometry, Southern blot (SB) technique, polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH). In addition, laser scanning cytometry (LSC) and DNA microarray technologies are in the research phase. Various laboratory techniques are used for immunophenotyping, demonstration of monoclonality, identification of chromosomal translocation, assessment of cell kinetics and expression of mRNA in the tumour cells. Flow cytometry helps in rapid immunophenotying of NHL and it has an added advantage over IC in recognizing the co-expression of CD markers. Fine needle aspiration cytology (FNAC) combined with flow immunophenotyping may help us to diagnose and subclassify certain NHLs, such as follicular lymphoma and mantle cell lymphoma, which were previously recognized as pure morphological entities. Loss of morphology is one of the important limitations of flow cytometry. LSC can overcome this limitation by studying morphology along with the immunophenotyping pattern of individual cells. Chromosomal changes in NHL can be identified by SB, PCR and FISH. Molecular diagnosis of NHL helps in diagnosis, subclassification, prognostic assessment and even in planning of therapy. DNA microarray is a relatively newer and promising technology. It gives information about the expression of several thousands of genes in a tumour in a single experiment. In the near future, FNAC combined with ancillary techniques may play a major role in diagnosis, subclassification and management of lymphomas. [source] The Japanese toxicogenomics project: Application of toxicogenomicsMOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue 2 2010Takeki Uehara Abstract Biotechnology advances have provided novel methods for the risk assessment of chemicals. The application of microarray technologies to toxicology, known as toxicogenomics, is becoming an accepted approach for identifying chemicals with potential safety problems. Gene expression profiling is expected to identify the mechanisms that underlie the potential toxicity of chemicals. This technology has also been applied to identify biomarkers of toxicity to predict potential hazardous chemicals. Ultimately, toxicogenomics is expected to aid in risk assessment. The following discussion explores potential applications and features of the Japanese Toxicogenomics Project. [source] Pilot Study Examining the Utility of Microarray Data to Identify Genes Associated with Weight in Transplant RecipientsNURSING & HEALTH SCIENCES, Issue 2 2006Ann Cashion Purpose/Methods:, Obesity, a complex, polygenic disorder and a growing epidemic in transplant recipients, is a risk factor for chronic diseases. This secondary data analysis identified if microarray technologies and bioinformatics could find differences in gene expression profiles between liver transplant recipients with low Body Mass Index (BMI < 29; n = 5) vs. high (BMI > 29; n = 7). Blood was hybridized on Human U133 Plus 2 GeneChip (Affymetrix) and analyzed using GeneSpring Software. Results:, Groups were similar in age and race, but not gender. Expression levels of 852 genes were different between the low and high BMI groups (P < 0.05). The majority (562) of the changes associated with high BMI were decreases in transcript levels. Among the 852 genes associated with BMI, 263 and 14 genes were affected greater than 2- or 5-fold, respectively. Following functionally classification using Gene Ontology (GO), we found that 19 genes (P < 0.00008) belonged to defense response and 15 genes (P < 0.00006) belonged to immune response. Conclusion:, These data could point the way toward therapeutic interventions and identify those at-risk. These results demonstrate that we can (1) extract high quality RNA from immunosuppressed patients; (2) manage large datasets and perform statistical and functional analysis. [source] Applications of protein microarrays for biomarker discoveryPROTEOMICS - CLINICAL APPLICATIONS, Issue 10-11 2008Niroshan Ramachandran Abstract The search for new biomarkers for diagnosis, prognosis, and therapeutic monitoring of diseases continues in earnest despite dwindling success at finding novel reliable markers. Some of the current markers in clinical use do not provide optimal sensitivity and specificity, with the prostate cancer antigen (PSA) being one of many such examples. The emergence of proteomic techniques and systems approaches to study disease pathophysiology has rekindled the quest for new biomarkers. In particular the use of protein microarrays has surged as a powerful tool for large-scale testing of biological samples. Approximately half the reports on protein microarrays have been published in the last two years especially in the area of biomarker discovery. In this review, we will discuss the application of protein microarray technologies that offer unique opportunities to find novel biomarkers. [source] DNA Microarray Experiments: Biological and Technological AspectsBIOMETRICS, Issue 4 2002Danh V. Nguyen Summary. DNA microarray technologies, such as cDNA and oligonucleotide microarrays, promise to revolutionize biological research and further our understanding of biological processes. Due to the complex nature and sheer amount of data produced from microarray experiments, biologists have sought the collaboration of experts in the analytical sciences, including statisticians, among others. However, the biological and technical intricacies of microarray experiments are not easily accessible to analytical experts. One aim for this review is to provide a bridge to some of the relevant biological and technical aspects involved in microarray experiments. While there is already a large literature on the broad applications of the technology, basic research on the technology itself and studies to understand process variation remain in their infancy. We emphasize the importance of basic research in DNA array technologies to improve the reliability of future experiments. [source] DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial SystemsBIOTECHNOLOGY PROGRESS, Issue 5 2004Yandi Dharmadi DNA microarrays are currently used to study the transcriptional response of many organisms to genetic and environmental perturbations. Although there is much room for improvement of this technology, its potential has been clearly demonstrated in the past 5 years. The general consensus is that the bottleneck is now located in the processing and analysis of transcriptome data and its use for purposes other than the quantification of changes in gene expression levels. In this article we discuss technological aspects of DNA microarrays, statistical and biological issues pertinent to the design of microarray experiments, and statistical tools for microarray data analysis. A review on applications of DNA microarrays in the study of bacterial systems is presented. Special attention is given to studies in the following areas: (1) bacterial response to environmental changes; (2) gene identification, genome organization, and transcriptional regulation; and (3) genetic and metabolic engineering. Soon, the use of DNA microarray technologies in conjunction with other genome/system-wide analyses (e.g., proteomics, metabolomics, fluxomics, phenomics, etc.) will provide a better assessment of genotype-phenotype relationships in bacteria, which serve as a basis for understanding similar processes in more complex organisms. [source] A chip-based miniaturized format for protein-expression profiling: The exploitation of comprehensively produced antibodiesELECTROPHORESIS, Issue 18 2006Hisashi Koga Dr. Abstract Numerous antibodies have been developed and validated in recent years, and show promise for use in novel functional protein assays. Such assays would be an alternative to pre-existing comprehensive assays, such as DNA microarrays. Antibody microarrays are thought to represent those functional protein assays. While a variety of attempts have been made to apply DNA microarray technology to antibody microarrays, a fully optimized protocol has not been established. We have been conducting a project to comprehensively produce antibodies against mouse KIAA ("KI" stands for "Kazusa DNA Research Institute" and "AA" are reference characters) proteins. Using our library of antibodies, we established a novel antibody microarray format that utilizes surface plasmon resonance (SPR) technology. A label-free real-time measurement of protein expression in crude cell lysates was achieved by direct readout of the bindings using SPR. Further refinement of the antibody microarray format enabled us to detect a smaller quantity of target proteins in the lysate without the bulk effect. In this review, we first summarize available antibody array formats and then describe the above-mentioned format utilizing updated SPR technology. [source] Microarrays: The Technology, Analysis and ApplicationENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 3 2005A. Kumar Abstract DNA microarray analysis represents one of the major advances leading to the development of functional genomics and proteomics. It involves the fabrication of DNA either by in situ or on-chip photolithographic synthesis or by inkjet or microjet deposition, as microspots immobilized on the surface of miniaturized substrates like glass or membranes. The immobilized DNA molecules are then allowed to hybridize with labeled complementary DNA. The hybrid DNA so formed is read through scanning devices, such as fluorescence and radioactivity. Further, computational approaches, for example, normalization and clustering allow thousands of genetic parameters in a single experiment to be simultaneously analyzed. This review discusses the fundamental principles and data analysis of the microarray technology, while focusing on its application in gene expression analysis, genotyping for point mutation and diseases diagnostics. [source] EVOLUTION OF INSECT METAMORPHOSIS: A MICROARRAY-BASED STUDY OF LARVAL AND ADULT GENE EXPRESSION IN THE ANT CAMPONOTUS FESTINATUSEVOLUTION, Issue 4 2005Michael A. D. Goodisman Abstract Holometabolous insects inhabit almost every terrestrial ecosystem. The evolutionary success of holometabolous insects stems partly from their developmental program, which includes discrete larval and adult stages. To gain an understanding of how development differs among holometabolous insect taxa, we used cDNA microarray technology to examine differences in gene expression between larval and adult Camponotus festinatus ants. We then compared expression patterns obtained from our study to those observed in the fruitfly Drosophila melanogaster. We found that many genes showed distinct patterns of expression between the larval and adult ant life stages, a result that was confirmed through quantitative reverse-transcriptase polymerase chain reaction. Genes involved in protein metabolism and possessing structural activity tended to be more highly expressed in larval than adult ants. In contrast, genes relatively upregulated in adults possessed a greater diversity of functions and activities. We also discovered that patterns of expression observed for homologous genes in D. melanogaster differed substantially from those observed in C. festinatus. Our results suggest that the specific molecular mechanisms involved in metamorphosis will differ substantially between insect taxa. Systematic investigation of gene expression during development of other taxa will provide additional information on how developmental pathways evolve. [source] Molecular diagnosis in dermatopathology: What makes sense, and what doesn'tEXPERIMENTAL DERMATOLOGY, Issue 1 2009Markus Braun-Falco Abstract:, Molecular techniques have provided us with a wealth of information about biological events in healthy individual, and improved tremendously our understanding about the pathogenesis of a huge variety of cutaneous diseases. Those methods have originally been invented to support basic scientific investigations on a molecular level and are translated increasingly into sophisticated diagnostic tools changing the classic paradigm of diagnostic pathology; among them are immunohistochemistry (IHC), polymerase chain reaction (PCR), G-banding, loss of heterozygosity, fluorescence in situ hybridization (FISH), chromogen in situ hybridization (CISH), comparative genomic hybridization on chromosomes and microarray technology. Some of them such as IHC and PCR have already been standardized to a level that allows its utility in daily routine diagnostics for several dermatological diseases. For others like array-based technologies, their optimal indications await to be fully determined. These ancillary methods have the great potential to contribute important new information to challenging cases, and will help to improve diagnostic accuracy particularly in cases in which conventional histopathology is ambiguous. Thus, they will broaden our armamentarium for diagnostic pathology. Herein, some key techniques will be reviewed and their applicability towards the diagnosis of dermatological diseases critically discussed. [source] Cationic Polyelectrolyte Amplified Bead Array for DNA Detection with Zeptomole Sensitivity and Single Nucleotide Polymorphism SelectivityADVANCED FUNCTIONAL MATERIALS, Issue 16 2010Chun Wang Abstract A highly sensitive strand specific DNA assay, which consists of a peptide nucleic acid (PNA) probe, a cationic conjugated polymer (PFVP), and self-assembled polystyrene beads in microwell arrays on silicon chip, is reported. PFVP, as an efficient signal amplifier and signal reporter, has been specially designed and synthesized to be compatible with commercial confocal microscopes for sensing on solid substrates. The assay operates on the net increase in negative charge at the PNA surface that occurs upon single-stranded DNA hybridization, which subsequently allows complex formation with the positively charged PFVP to favor energy transfer between the polymer and Cy5-labeled target. With maximized surface contact provided by bead arrays and signal amplification provided by PFVP, this assay allows detection of ,300 copies of Cy5-labeled DNA using a commercial confocal microscope. In addition, the same strategy is also extended for label-free DNA detection with a detection sensitivity of 150 attomole. Excellent discrimination against single nucleotide polymorphism (SNP) is also demonstrated for both Cy5-labeled and label-free target detection. This study indicates that cationic conjugated polymers have great potential to be incorporated into the widely used microarray technology for simplified process with improved detection sensitivity. [source] Expression of organic cation transporters OCT1 (SLC22A1) and OCT3 (SLC22A3) is affected by genetic factors and cholestasis in human liver,HEPATOLOGY, Issue 4 2009Anne T. Nies An important function of hepatocytes is the biotransformation and elimination of various drugs, many of which are organic cations and are taken up by organic cation transporters (OCTs) of the solute carrier family 22 (SLC22). Because interindividual variability of OCT expression may affect response to cationic drugs such as metformin, we systematically investigated genetic and nongenetic factors of OCT1/SLC22A1 and OCT3/SLC22A3 expression in human liver. OCT1 and OCT3 expression (messenger RNA [mRNA], protein) was analyzed in liver tissue samples from 150 Caucasian subjects. Hepatic OCTs were localized by way of immunofluorescence microscopy. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and genome-wide single-nucleotide polymorphism microarray technology served to genotype 92 variants in the SLC22A1-A3/OCT1-3 gene cluster. Transport of metformin by recombinant human OCT1 and OCT3 was compared using transfected cells. OCT1 mRNA and protein expression varied 113- and 83-fold, respectively; OCT3 mRNA expression varied 27-fold. OCT1 transcript levels were on average 15-fold higher compared with OCT3. We localized the OCT3 protein to the basolateral hepatocyte membrane and identified metformin as an OCT3 substrate. OCT1 and OCT3 expression are independent of age and sex but were significantly reduced in liver donors diagnosed as cholestatic (P , 0.01). Several haplotypes for OCT1 and OCT3 were identified. Multivariate analysis adjusted for multiple testing showed that only the OCT1-Arg61Cys variant (rs12208357) strongly correlated with decreased OCT1 protein expression (P < 0.0001), and four variants in OCT3 (rs2292334, rs2048327, rs1810126, rs3088442) were associated with reduced OCT3 mRNA levels (P = 0.03). Conclusion: We identified cholestasis and genetic variants as critical determinants for considerable interindividual variability of hepatic OCT1 and OCT3 expression. This indicates consequences for hepatic elimination of and response to OCT substrates such as metformin. (HEPATOLOGY 2009.) [source] Large-Scale Arrays of Aligned Single VirusesADVANCED MATERIALS, Issue 1 2010Daniel J. Solis The fabrication of single virus arrays is demonstrated using direct printing of unmodified anti-M13 bacteriophage antibodies onto silicon with nanometer resolution (see image), widely variable feature pitch, and flow alignment of the viruses. Organization of virus-based systems into functional, addressable arrays has many technological applications including microarray technology and bottom-up nanoassemblies. [source] Radiation-induced gene expression profile of human cells deficient in 8-hydroxy-2,-deoxyguanine glycosylaseINTERNATIONAL JOURNAL OF CANCER, Issue 3 2006M. Ahmad Chaudhry Abstract The human OGG1 gene encodes a DNA glycosylase that is involved in the base excision repair of 8-hydroxy-2,-deoxyguanine (8-OH-dG) from oxidatively damaged DNA. Cellular 8-OH-dG levels accumulate in the absence of this activity and could be deleterious for the cell. To assess the role of 8-oxoguanine glycosylase (OGG1) in the cellular defense mechanism in a specific DNA repair defect background, we set out to determine the expression pattern of base excision repair genes and other cellular genes not involved in the base excision pathway in OGG1-deficient human KG-1 cells after ionizing radiation exposure. KG-1 cells have lost OGG1 activity due to a homozygous mutation of Arg229Gln. Gene expression alterations were monitored at 4, 8, 12 and 24 hr in 2 Gy irradiated cells. Large-scale gene expression profiling was assessed with DNA microarray technology. Gene expression analysis identified a number of ionizing radiation-responsive genes, including several novel genes. There were 2 peaks of radiation-induced gene induction or repression: one at 8 hr and the other at 24 hr. Overall the number of downregulated genes was higher than the number of upregulated genes. The highest number of downregulated genes was at 8 hr postirradiation. Genes corresponding to cellular, physiologic, developmental and extracellular processes were identified. The highest number of radiation-induced genes belonged to the signal transduction category, followed by genes involved in transcription and response to stress. Microarray gene expression data were independently validated by relative quantitative RT-PCR. Surprisingly, none of the genes involved in the base excision repair of radiation-induced DNA damage showed altered expression. © 2005 Wiley-Liss, Inc. [source] Toxicogenomics: a pivotal piece in the puzzle of toxicological researchJOURNAL OF APPLIED TOXICOLOGY, Issue 4 2007Elisavet T. Gatzidou Abstract Toxicogenomics, resulting from the merge of conventional toxicology with functional genomics, being the scientific field studying the complex interactions between the cellular genome, toxic agents in the environment, organ dysfunction and disease state. When an organism is exposed to a toxic agent the cells respond by altering the pattern of gene expression. Genes are transcribed into mRNA, which in turn is translated into proteins that serve in a variety of cellular functions. Toxicogenomics through microarray technology, offers large-scale detection and quantification of mRNA transcripts, related to alterations in mRNA stability or gene regulation. This may prove advantageous in toxicological research. In the present review, the applications of toxicogenomics, especially to mechanistic and predictive toxicology are reported. The limitations arising from the use of this technology are also discussed. Additionally, a brief report of other approaches, using other -omic technologies (proteomics and metabonomics) that overcome limitations and give global information related to toxicity, is included. Copyright © 2007 John Wiley & Sons, Ltd. [source] Identification of genes regulated by nanog which is involved in ES cells pluripotency and early differentiationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2008Na Liu Abstract Nanog plays an important role in embryonic stem (ES) cells pluripotency and self-renewal, yet the precise mechanism through which Nanog accomplishes this important function remains unclear. To understand comprehensive molecular mechanism by which Nanog mediates, we identified genome-wide molecular changes upon silencing Nanog in ES cells by using microarray technology. In order to downregulate Nanog expression efficiently, four siRNAs were designed on the basis of the conserved Nanog sequence and their effects on the Nanog expression were tested. Among these four siRNAs, Nanog-siRNA-P1 was found to be most effective. Once Nanog was downregulated, ES cells underwent differentiation by showing morphological change and decreased proliferation rate. Microarray analysis was then used to identify the altered gene expression after Nanog was silenced. A series of differentially expressed genes due to reduced expression of Nanog was identified as Nanog-related genes. These genes identified here could provide insights into the roles of Nanog in ES cells self-renewal and early differentiation. J. Cell. Biochem. 104: 2348,2362, 2008. © 2008 Wiley-Liss, Inc. [source] Immunosuppressive drug-free operational immune tolerance in human kidney transplant recipients: Part I. blood gene expression statistical analysisJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2008Christophe Braud Abstract Survival of solid organ grafts depends on life-long immunosuppression, which results in increased rates of infection and malignancy. Induction of tolerance to allografts would represent the optimal solution for controlling both chronic rejection (CR) and side effects of immunosuppression. Although spontaneous "operational tolerance" can occur in human kidney transplantation, the lack of noninvasive peripheral blood biological markers of this rare phenomenon precludes the identification of potentially tolerant patients in whom immunosuppression could be tapered as well as the development of new tolerance inducing strategies. Here, the potential of high throughput microarray technology to decipher complex pathologies allowed us to study the peripheral blood specific gene expression profile and corresponding EASE molecular pathways associated to operational tolerance in a cohort of human kidney graft recipients. In comparison with patients with CR, tolerant patients displayed a set of 343 differentially expressed genes, mainly immune and defense genes, in their peripheral blood mononuclear cells (PBMC), of which 223 were also different from healthy volunteers. Using the expression pattern of these 343 genes, we were able to classify correctly >80% of the patients in a cross-validation experiment and classified correctly all of the samples over time. Collectively, this study identifies a unique PBMC gene signature associated with human operational tolerance in kidney transplantation by a classical statistical microarray analysis and, in the second part, by a nonstatistical analysis. J. Cell. Biochem. 103: 1681,1692, 2008. © 2007 Wiley-Liss, Inc. [source] Identification of genes involved in radiation-induced G1 arrest,JOURNAL OF CHEMOMETRICS, Issue 10-11 2007Giuseppe Musumarra Abstract The advent of microarray gene expression technology permits the simultaneous analysis of the levels of expression of thousands of genes and provides large dataset requiring multivariate analysis tools. Multiple genetic factors may modulate the occurrence and magnitude of the arrest in the G1 phase of the cell cycle following exposure to ionizing radiation in human tumour cell lines. The ability to G1 arrest after exposure to gamma rays and the global gene expression profile, evaluated by cDNA microarray technology, have been reported for the National Cancer Institute (NCI) 60 tumour cell lines panel. The sensitivity of the tumour cell lines to radiations represents an activity fingerprinting that can be correlated by partial least squares (PLS) to the transcriptional profiles of the same cell lines. VIP values obtained by the PLS method are able to detect transcripts relevant to the radiation-induced G1 arrest. High VIP values were obtained for the basal levels of transcripts such as p21/Waf1/Cip1 and MDM2, that are well known for their roles in G1 arrest after irradiation. Novel functional relationships suggested by high VIP values can be investigated experimentally. As an example, in the present study, we report that the transcript for the FLJ11046 protein is induced dose-dependently by gamma-irradiation in a cell line with mutated p53, but not in cell lines with wild-type p53. Moreover specific silencing of FLJ11046 transcript by RNA interference technology results in a block of cell growth. Copyright © 2007 John Wiley & Sons, Ltd. [source] Overexpression of MLH-1 and psoriasin genes in cutaneous angiofibromas from tuberous sclerosis complex patientsJOURNAL OF CUTANEOUS PATHOLOGY, Issue 9 2006Michelangelo La Placa Background:, Tuberous sclerosis complex (TSC) is associated with mutations in two likely tumor-suppressor genes (TSC1 and TSC2) and characterized by the development of tumor-like growths (angiofibromas) in a variety of tissues and organs, particularly brain and skin. Methods:, Employing a DNA-microarray assay, able to detect mRNA production from 1176 different basic genes, we analyzed the gene-expression levels in a cutaneous hamartoma sample from a TSC patient. Altered gene expressions detected by microarray technology were further checked by quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) in the same material and in cutaneous hamartoma samples obtained from five other TSC patients. Results:, The results obtained by the microarray technology in one hamartoma specimen, confirmed by the RT-PCR results obtained in the same material and in five other hamartoma specimens, demonstrated that TSC-related angiofibromas exhibit significant mRNA overexpression of two genes, represented by MLH-1 and psoriasin. Conclusions:, The overexpression of MLH-1, which codes for a DNA mismatch repair protein, and psoriasin, which codes for a specific chemoattractant factor for CD4+ T cells, implicated in the pathogenesis of inflammatory skin disease, and expressed in excess during abnormal pathways of cell growth, may shed light on the pathogenesis of the proliferative skin lesion. [source] Effect of Guanxin No.2 decoction on gene expression in different areas of the myocardial infarcted heart of rats using microarray technologyJOURNAL OF PHARMACY AND PHARMACOLOGY: AN INTERNATI ONAL JOURNAL OF PHARMACEUTICAL SCIENCE, Issue 2 2009Xiaowei Zeng Abstract Objectives We have used microarray technology to detect the effect of Guanxin No.2 decoction on gene expression in different areas of the myocardial infarcted heart of rats. Methods Male Sprague-Dawley rats (180,200 g) were randomly divided into three groups: sham-operated; coronary artery ligation; and coronary artery ligation plus administration of Guanxin No.2 decoction (10.0 g raw materials/kg per day by gavage). The experiment was carried out on day seven after ligation. Key findings We found that the gene expression using microarray technology showed many differences in the border infarcted left ventricular area compared with the remote noninfarcted left ventricular area after administration of Guanxin No.2 decoction. Conclusions Guanxin No.2 decoction has a long history in treating ischaemic cardiomyopathy in China, but the molecular mechanism has been unclear. In this study we found that some important genes may have contributed to the cardioprotective effect of Guanxin No.2 decoction. [source] Gene expression profile of Huh-7 cells expressing hepatitis C virus genotype 1b or 3a core proteinsLIVER INTERNATIONAL, Issue 5 2009Valerio Pazienza Abstract Background: The liver disease expression in chronic hepatitis C patients is variable and may partially depend on the sequence of the infecting viral genotype. Aim: To identify some hepatitis C virus (HCV) genotype-specific virus,host interactions potentially leading to clinically significant consequences. Methods: We compared the gene expression profile of Huh-7 cells transiently expressing the core protein of HCV genotype 1b and 3a using microarray technology. Results: Thirty-two genes were overexpressed in Huh-7 transfected with the HCV genotype 1b core protein and 57 genes in cells transfected with the genotype 3a core protein. On the other hand, we found 20 genes downregulated by core 1b and 31 genes by core 3a. These included genes involved in lipid transport and metabolism, cell cycle, immune response and insulin signalling. Conclusion: The expression of HCV core proteins of different genotypes leads to a specific gene expression profile. This may account for the variable disease expression associated with HCV infection. [source] Differences in lymphocyte gene expression between tolerant and syngeneic liver grafted ratsLIVER TRANSPLANTATION, Issue 3 2004Masayuki Fujino Induction of tolerance to allogeneic donor grafts is a clinically desirable goal in bone marrow and solid organ transplantation. We have taken the advantage of DNA microarray technology to investigate gene expression mechanism in regulatory cells. In the present study, using a tacrolimus (FK506) induced tolerance of the fully mismatched liver allograft rat model, we demonstrated that, in contrast with peripheral blood lymphocytes (PBLs) from syngeneic recipients, PBLs taken from tolerant recipients 100 days after transplantation were able to suppress the in vitro proliferation of allogeneic PBLs and to prolong the survival of second syngeneic recipients. We also compared messenger RNA profiles in PBLs from tolerant recipients with those from syngeneic recipients using a DNA microarray with probe sets corresponding to more than 8000 rat genes. There were 96 up-regulated and 103 down-regulated genes in the tolerant recipients. In the up-regulated group, there were 76 known genes and 20 expressed sequence tags (ESTs). In the down-regulated groups, there were 87 known genes and 16 ESTs. Our data indicated that FK506 treatment induced tolerance and expansion of regulatory cells and the DNA microarray technology was useful for this application and provided many informative insights into the mechanism of lymphocyte regulation. (Liver Transpl 2004;10:379,391.) [source] DNA Microarrays: Their Use and MisuseMICROCIRCULATION, Issue 1 2002Xinmin Li DNA microarray represents one of the major advances in functional genomics. Its ability to study expression of several thousands of genes or even all genes in the entire genome in a single experiment has changed the way in which we address basic biomedical questions. Numerous publications have shown its utility in drug discovery, disease diagnosis, novel gene identification, and understanding complex biological systems. However, there are substantive technical issues associated with the use of this technology that limit the interpretation of microarray data. In this review, we first give an overview of DNA microarray technology and then focus on uncertainty areas of microarray technology that include making microarrays, isolation of RNA and labeling, hybridization and scanning, and data analysis. The center theme of this review is to improve microarray reproducibility by addressing common technical problems. Finally, we briefly summarize microarray's applications in biomedical research. [source] Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related speciesMOLECULAR ECOLOGY RESOURCES, Issue 1 2009JULIA C. ENGELMANN Abstract DNA microarrays are a popular technique for the detection of microorganisms. Several approaches using specific oligomers targeting one or a few marker genes for each species have been proposed. Data analysis is usually limited to call a species present when its oligomer exceeds a certain intensity threshold. While this strategy works reasonably well for distantly related species, it does not work well for very closely related species: Cross-hybridization of nontarget DNA prevents a simple identification based on signal intensity. The majority of species of the same genus has a sequence similarity of over 90%. For biodiversity studies down to the species level, it is therefore important to increase the detection power of closely related species. We propose a simple, cost-effective and robust approach for biodiversity studies using DNA microarray technology and demonstrate it on scenedesmacean green algae. The internal transcribed spacer 2 (ITS2) rDNA sequence was chosen as marker because it is suitable to distinguish all eukaryotic species even though parts of it are virtually identical in closely related species. We show that by modelling hybridization behaviour with a matrix algebra approach, we are able to identify closely related species that cannot be distinguished with a threshold on signal intensity. Thus this proof-of-concept study shows that by adding a simple and robust data analysis step to the evaluation of DNA microarrays, species detection can be significantly improved for closely related species with a high sequence similarity. [source] | |||||||||||||||||||||||||||||||||||||