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High-throughput Three-dimensional Gel Electrophoresis for Versatile Utilities: A Stacked Slice-gel System for Separation and Reactions (4SR)

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Genomics, Proteomics & Bioinformatics 2006年第1期4卷 26-33页

作者： Md. Salimullah Masaki Mori Koichi Nishigaki Department of Functional Materials Science Saitama University Saitama 338-8570 Japan Rational Evo-lutionary Design of Advanced Biomolecules (REDS) Group Saitama Small Enterprise Promotion CorporationSKIP City Kawaguchi 333-0844 Japan.

A novel high-throughput system, called the stacked slice-gel system for separation and reactions （4SR）, was developed for the analysis of DNA/RNA and protein/peptide. The system provides a novel three-dimensional gel electrophoresis approach that exploits the property of stacked slice gels. It allows multiple samples simultaneously to react as well as to be separated, offering a two-dimensional （m×n） sample loading system. For this purpose, high-throughput multi-micro vessels （MMVs） containing variable numbers of wells （100 wells in this paper） have been used, which are made of 25 mm square-size polyacrylamide gels. Furthermore, after electrophoretic separation, a slice gel containing a desired sample can be easily removed and proceeded to the next step. Different biological reactions as well as successive separation of products were effectively carried out dealing with DNA/RNA and protein/peptide. It shows that this system has a diversity of potentials to be developed.

关键词： three-dimensional polyacrylamide gel electrophoresis （3D-PAGE） high-throughput screening three-dlmensional separation microarray technology

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microarrays and transcriptome analysis in renal transplantation

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NATURE CLINICAL PRACTICE NEPHROLOGY 2006年第1期2卷 2-3页

作者： Halloran, PF Einecke, G Univ Alberta Div Nephrol & Transplantat Immunol Alberta Transplant Inst Edmonton AB T6G 2S2 Canada

Transcriptome-based assessment of blood, urine or biopsy tissue could have a powerful impact on the management of renal transplants, with the potential to detect injurious mechanisms before graft injury is established. This Viewpoint article explores the promise held by transcriptomics and high-density microarrays, and examines the challenges of applying these new technologies in renal transplant recipients.

关键词： Renal Kidney Transplantation Human Analysis of substances microarray technology 肾移植 microarray technology Kidney Transplantation microarray Kidney Human Kidney Diseases renal graft dysfunction Gene Expression Profiling transcriptomics

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Oligonucleotide microarrays for studying the effects of Ras signal transduction on the genetic program

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Signal Transduction 2006年第3期6卷 209-218页

作者： Tchernitsa, Oleg I. Sers, Christine Geflitter, Anita Schäfer, Reinhold Laboratories of Molecular Tumor Pathology and of Functional Genomics Charité Universitätsmedizin Berlin Berlin Germany Institute of Pathology Charité Campus Mitte D-10117 Berlin Schumannstr. 20/21 Germany

Cytoplasmic signal transduction processes are tightly coupled with the transcriptional regulation of genes executing cellular phenotypes in normal conditions and in disease. A major challenge in signal transduction research is to understand how the specificity of the transcriptional response is determined by complex networks of signaling effectors and transcription factors. The Ras signal transduction pathway belongs to the few characterized pathways triggering malignant phenotypes both in experimental and human cancer. We have developed an array-based tool which permits analysis of Ras signaling on transcription under various experimental conditions as well as in tumor specimens. The composition of targets represented on the Ras signaling target array (RASTA) is based on previously validated gene expression profiles and published functional studies. The Ras signaling target array was used to compare the transcriptional response toward oncogenic Ras in fibroblasts and epithelial cells and to assess the time-dependent deregulation of target genes. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.

关键词： Experimental cancer Gene regulation microarray technology Ras oncogenes

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Automation of cDNA microarray hybridization and washing yields improved data quality

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JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2005年第1期64卷 69-75页

作者： Yauk, C Berndt, L Williams, A Douglas, GR Hlth Canada Environm & Occupat Toxicol Div Ottawa ON K1A 0L2 Canada Hlth Canada Biostat & Epidemiol Div Ottawa ON K1A 0L2 Canada

microarray technology allows the analysis of whole-genome transcription within a single hybridization, and has become a standard research tool. It is extremely important to minimize variation in order to obtain high quality microarray data that can be compared among experiments and laboratories. The majority of facilities implement manual hybridization approaches for microarray studies. We developed an automated method for cDNA microarray hybridization that uses equivalent pre-hybridization, hybridization and washing conditions to the suggested manual protocol. The automated method significantly decreased variability across microarray slides compared to manual hybridization. Although normalized signal intensities for buffer-only spots across the chips were identical, significantly reduced variation and inter-quartile ranges were obtained using the automated workstation. This decreased variation led to improved correlation among technical replicates across slides in both the Cy3 and Cy5 channels. Crown Copyright (c) 2005 Published by Elsevier B.V. All rights reserved.

关键词： cDNA microarrays automated hybridization signal intensities microarray technology

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Sensitivity and specificity of metal surface-immobilized "molecular beacon" biosensors

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2005年第21期127卷 7932-7940页

作者： Du, H Strohsahl, CM Camera, J Miller, BL Krauss, TD Univ Rochester Dept Dermatol Rochester NY 14627 USA Univ Rochester Dept Biochem & Biophys Rochester NY USA Univ Rochester Dept Chem Rochester NY USA Univ Rochester Ctr Future Hlth Rochester NY USA

The separate developments of microarray patterning of DNA oligonucleotides, and of DNA hairpins as sensitive probes for oligonucleotide identification in solution, have had a tremendous impact on basic biological research and clinical applications. We have combined these two approaches to develop arrayable and label-free biological sensors based on fluorescence unquenching of DNA hairpins immobilized on metal surfaces. The thermodynamic and kinetic response of these sensors, and the factors important in hybridization efficiency, were investigated. Hybridization efficiency was found to be sensitive to hairpin secondary structure, as well as to the surface distribution of DNA hairpins on the substrate. The identity of the bases used in the hairpin stem as well as the overall loop length significantly affected sensitivity and selectivity. Surface-immobilized hairpins discriminated between two sequences with a single base-pair mismatch with high sensitivity (over an order of magnitude difference in signal) under identical assay conditions (no change in stringency). This represents a significant improvement over other microarray-based techniques.

关键词： DNA-HAIRPINS NANOPARTICLE PROBES NUCLEIC-ACID STAPHYLOCOCCUS-AUREUS microarray technology SECONDARY STRUCTURE ELECTRON-TRANSFER CDNA ARRAYS HYBRIDIZATION KINETICS

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microarrays: The technology, analysis and application

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ENGINEERING IN LIFE SCIENCES 2005年第3期5卷 215-222页

作者： Kumar, A Goel, G Fehrenbach, E Puniya, AK Singh, K Natl Dairy Res Inst Dairy Microbiol Div Karnal 132001 Haryana India Univ Klinikum Tubingen Abt Transfusionsmed D-72076 Tubingen Germany

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.

关键词： technology analysis DNA genetic parameters Scanner Point Mutation microarray technology DNA microarray Analysis microarray functional/structural genomics

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The results of the expression array studies correlate and enhance the known genetic basis of gastric and colorectal cancer

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CYTOMETRY PART B-CLINICAL CYTOMETRY 2005年第1期68B卷 1-17页

作者： Galamb, O Sipos, F Fischer, K Tulassay, Z Molnar, B Semmelweis Univ Dept Med 2 Fac Med H-1088 Budapest Hungary

Gastric and colorectal cancers belong to the most frequent cancer types in the world today. This fact emphasizes the importance of identification of useful diagnostic and prognostic markers, in the earliest stage of the disease. The examination of gene expression profile in gastric and colorectal cancer may develop the bases of early diagnosis and of individual therapeutic strategies. In the microarray examinations done so far for these types of cancers, the expression of hundreds and thousands of genes were studied, however, both the sample collection and the results showed wide variations. The diversity of expression array methods and data analysis makes the comparison of microarray results difficult. Beside the exposition of the practical aspects of the chip technology, our aims are the systematization of data that are currently available in the international scientific literature and the description of the results in a comprehensive way. microarray results show that the gene expression pattern, detected in gastric and colon cancers, highly depends on the histological type and heterogeneity of the sample, array type, and softwares, used for data analysis. Recent experiments point out not just the changes of the alterations of tumor suppression, apoptosis, cell-cycle regulation, and signal transduction, but tumor cell metabolism and cell-microenvironment interactions also. Results show connection to and make more complete the already known molecular background of gastric and colorectal cancers. Based on the accumulation of recent and further data, such kind of multifunctional diagnostic microarrays that can be suited for completing the conventional histological diagnostics and subtypization will certainly become available in the near future. (c) 2005 International Society for Analytical Cytology.

关键词： gastric cancer colorectal cancer microarray technology gene expression

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Proteomic: New advances in the diagnosis of rheumatoid arthritis

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CLINICA CHIMICA ACTA 2005年第2期357卷 219-225页

作者： Tampoia, M Brescia, V Fontana, A Maggiolini, P Zucano, A Pansini, N Azienda Osped Policlin Lab Patol Clin 1 I-70124 Bari Italy

Background: Rheumatoid arthritis (RA) is a chronic autoimmune disease affecting the joints. A number of novel treatment modalities have been introduced over the past years, and rheumatologists are now attempting to institute optimal treatment in recent-onset arthritis. To facilitate diagnosis during the early stages of disease, when often not all clinical symptoms are manifest, a good serological marker is needed. Methods: Antibodies directed to citrullinated proteins provide this ability. The most sensitive assay for detecting these antibodies is the so-called anti-cyclic citrullinated peptide, second generation (CCP 11) enzyme-linked immunosorbent assay (ELISA). Results: The diagnostic and prognostic potential of anti-CCP antibodies and the availability of a fully automated assay method lead us to conclude that the test is satisfactory for routine use as a serological marker of RA. In addition, we consider the potential of multiplex autoantibody assays, including miniaturized, high-throughput microarray technology, to improve diagnosis and prognostication in early onset arthritis patients. (c) 2005 Elsevier B.V All rights reserved.

关键词： rheumatoid arthritis (RA) early arthritis rheumatoid factor (RF) citrullinated peptide (CCP) enzyme linked immunosorbent assay (ELISA) microarray technology

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Gene expression induced by drugs of abuse

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CURRENT OPINION IN PHARMACOLOGY 2005年第1期5卷 26-33页

作者： Rhodes, JS Crabbe, JC VA Med Ctr Portland OR 97239 USA

The transition from infrequent drug use to addiction (i.e. the loss of control over consumption of a drug) probably involves changes in gene expression that restructure neural circuits in the brain. The number of genes that have been demonstrated to change expression in response to drugs has increased rapidly in recent years owing to microarray technology, which allows measurement of thousands of genes at one time. It is now important to identify which of these changes are causally related to the compulsive behavior associated with drug addiction, and which are non-specific changes related to general features of arousal or other physiological responses (e.g. stress, altered body temperature or energy metabolism).

关键词： Gene Expression g microarray technology neural circuits 基因表达

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Gene expression profiling of melanoma cells - searching the haystack

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JOURNAL OF TRANSLATIONAL MEDICINE 2005年第1期3卷 1-2页

作者： Brafford, P Herlyn, M Wistar Inst Anat & Biol Philadelphia PA 19104 USA

Cancer is being increasingly recognized as a very heterogeneous disease, both within an individual tumor and within a tumor type and among tumor types. This heterogeneity is manifested both at the genetic and phenotypic level and determines the progression of disease and response to therapy. It is possible to see the heterogeneity in examples of differential disease progression and response to therapy of the same tumor type, as morphology does not always reveal underlying biology. The diagnosis of tumors by histopathological and morphological criteria cannot fully account for the variability seen in prognosis and therapy outcome. Here we review some recent concepts that have emerged from the genetic analysis of metastatic melanoma.

关键词： Melanoma Renal Cell Carcinoma Gene Expression Profile microarray technology Vasculogenic Mimicry

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