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A microarray Biosensor for Multiplexed Detection of Microbes Using Grating-Coupled Surface Plasmon Resonance Imaging

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ENVIRONMENTAL SCIENCE & technology 2012年第1期46卷 348-359页

作者： Marusov, Gregory Sweatt, Andrew Pietrosimone, Kathryn Benson, David Geary, Steven J. Silbart, Lawrence K. Challa, Sreerupa Lagoy, Jacqueline Lawrence, David A. Lynes, Michael A. Univ Connecticut Dept Mol & Cell Biol Storrs CT 06269 USA Univ Connecticut Dept Pathobiol Storrs CT 06269 USA Univ Connecticut Dept Allied Hlth Sci Storrs CT 06269 USA Univ Connecticut Ctr Excellence Vaccine Res Storrs CT 06269 USA New York Dept Hlth Wadsworth Ctr Albany NY 12208 USA

Grating-coupled surface plasmon resonance imaging (GCSPRI) utilizes an optical diffraction grating embossed on a gold-coated sensor chip to couple collimated incident light into surface plasmons. The angle at which this coupling occurs is sensitive to the capture of analyte at the chip surface. This approach permits the use of disposable biosensor chips that can be mass-produced at low cost and spotted in microarray format to greatly increase multiplexing capabilities. The current GCSPRI instrument has the capacity to simultaneously measure binding at over 1000 unique, discrete regions of interest (ROIs) by utilizing a compact microarray of antibodies or other specific capture molecules immobilized on the sensor chip. In this report, we describe the use of GCSPRI to directly detect multiple analytes over a large dynamic range, including soluble protein toxins, bacterial cells, and viruses, in near real-time. GCSPRI was used to detect a variety of agents that would be useful for diagnostic and environmental sensing purposes, including macromolecular antigens, a nontoxic form of Pseudomonas aeruginosa exotoxin A (ntPE), Bacillus globigii, Mycoplasma hyopneumoniae, Listeria monocytogenes, Escherichia coli, and M13 bacteriophage. These studies indicate that GCSPRI can be used to simultaneously assess the presence of toxins and pathogens, as well as quantify specific antibodies to environmental agents, in a rapid, label-free, and highly multiplexed assay requiring nanoliter amounts of capture reagents.

关键词： BIOSENSORS microarray technology SURFACE plasmon resonance DIFFRACTION gratings PATHOGENIC microorganisms -- Detection PROTEIN microarrays

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microarray-to-microarray Transfer of Reagents by Snapping of Two Chips for Cross-Reactivity-Free Multiplex Immunoassays

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ANALYTICAL CHEMISTRY 2012年第11期84卷 4776-4783页

作者： Li, Huiyan Bergeron, Sebastien Juncker, David McGill Univ Biomed Engn Dept Montreal PQ H3A 1A4 Canada McGill Univ Genome Quebec Innovat Ctr Montreal PQ H3A 1A4 Canada McGill Univ Dept Neurol & Neurosurg Montreal PQ H3A 1A4 Canada

Whereas microarray and microfluidic technologies have progressed on many fronts, servicing microchips with minute amounts of reagents still constitutes an important challenge for many applications. Recently, chip-to-chip reagent transfer methods were introduced that simplify the delivery of reagents but required manual, visual alignment, custom-built microwells, and only showed the reaction of a single sample with multiple chemicals. Here, we present the snap chip, which uses common glass slides for transfer, back-side alignment for achieving precise alignment in spite of mirroring, and a snap-apparatus for facile transfer of arrays of chemicals at once by snapping the two slides together. We recently established that cross-reactivity was a significant problem in multiplex assays both theoretically and experimentally and found that it can be eliminated by avoiding mixing, but which necessitates delivering each detection antibody to a single spot with the cognate capture antibody.(18) Using the snap chip, multiplexed sandwich immunoassays without mixing were performed: a slide with multiple arrays of 10 different capture antibodies was incubated with a sample, and then all detection antibodies transferred at once by snapping, each to the single cognate spot. All binding curves were established and limits of detection in the pg/mL range were obtained. Snap chips were stored up to 3 months prior to usage. The snap chip, by dissociating microarray production, which requires expensive equipment, from assay execution, which can be achieved using a hand-held alignment apparatus, will allow for multiplex reactions to be performed using a user-friendly kit. This new liquid handling format can be easily adapted to other applications that require transfer of minute amounts of different reagents in parallel.

关键词： microarray technology CHEMICAL tests & reagents IMMUNOASSAY REACTIVITY (Chemistry) MICROFLUIDIC analytical techniques INTEGRATED circuits MULTIPLEXING (Telecommunication)

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Pathway-based visualization of cross-platform microarray datasets

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BIOINFORMATICS 2012年第23期28卷 3021-3026页

作者： Wrzodek, Clemens Eichner, Johannes Zell, Andreas Univ Tubingen Ctr Bioinformat Tuebingen ZBIT D-72076 Tubingen Germany

Motivation: Traditionally, microarrays were almost exclusively used for the genome-wide analysis of differential gene expression. But nowadays, their scope of application has been extended to various genomic features, such as microRNAs (miRNAs), proteins and DNA methylation (DNAm). Most available methods for the visualization of these datasets are focused on individual platforms and are not capable of integratively visualizing multiple microarray datasets from cross-platform studies. Above all, there is a demand for methods that can visualize genomic features that are not directly linked to protein-coding genes, such as regulatory RNAs (e. g. miRNAs) and epigenetic alterations (e. g. DNAm), in a pathway-centred manner. Results: We present a novel pathway-based visualization method that is especially suitable for the visualization of high-throughput datasets from multiple different microarray platforms that were used for the analysis of diverse genomic features in the same set of biological samples. The proposed methodology includes concepts for linking DNAm and miRNA expression datasets to canonical signalling and metabolic pathways. We further point out strategies for displaying data from multiple proteins and protein modifications corresponding to the same gene. Ultimately, we show how data from four distinct platform types (messenger RNA, miRNA, protein and DNAm arrays) can be integratively visualized in the context of canonical pathways.

关键词： microarray technology CELLULAR signal transduction MICRORNA DNA methylation INFORMATION visualization BIOINFORMATICS

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Evaporation-Enhanced Impedance Sensing for Highly-Sensitive Differentiation of dsDNA from ssDNA

Evaporation-Enhanced Impedance Sensing for Highly-Sensitive ...

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Annual Device Research Conference

作者： Aida Ebrahimi Muhammad A. Alam School of Electrical and Computer Engineering Purdue University

ISBN: (纸本)9781479908134

Motivation/Background: The ability to 'read' DNA codes from trace-samples has broad applications in medicine, counter-terrorism, paleontology, archeology, etc. A biosensor reads an unidentified target DNA segment by being able to differentiate the responses of a single stranded receptor DNA (ssDNA) and the double-stranded DNA (dsDNA) after target-receptor hybridization. Traditional methods to detect hybridization, such as gel electrophoresis, membrane blots, and microarray technology require labeling, complex sample preparation, and expensive optical readout. Moreover, these approaches do not scale reliably to ultra-low concentrations. Similarly, label-free impedance sensing is known to provide simpler and cheaper design/fabrication, faster response, and can be combined with IC technology for massively parallel detection [1-3]. And yet, the physical diffusion of the dispersed analytes to the sensing region defines a fundamental trade-off between response time and target ssDNA density [4], thereby defining a lower-limit of practical analyte detection. In this paper, we adopt a radically different approach to beat the diffusion limit through time-dependent evaporation of microliter-sized droplets (containing DNA molecules) pinned onto an array of electroplated nickel electrodes, and thereby achieve highly sensitive, statistically-robust, label-free, non-faradaic impedance-based differentiation of ssDNA vs. dsDNA at femtomolar (～fM) concentration. The proposed approach is ideally suited for integration in a portable, array format, and could be used in real-time point-of-care applications for which highly sensitive, yet selective detection of DNA hybridization is desired. Sample Preparation: The originally purchased DNA solutions are 500 bp synthetic dsDNA molecules with concentration of 1.5 μM in TEx1 (10 mM Tris-EDTA). The DNA molecules are diluted in nuclease-free DI water to desired concentrations;the specification of samples S1 to S5 is summarized in Fig. 1 (a). To

关键词： DNA DNA DNA hybridization impedance Schematic diagrams Figs Specimen preparation DEIONIZED WATER microarray technology hybridisation

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Multipurpose Instantaneous microarray Detection of Acute Encephalitis Causing Viruses and Their Expression Profiles

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CURRENT MICROBIOLOGY 2012年第3期65卷 290-303页

作者： Singh, Desh Deepak Jain, Amita CSM Med Univ Dept Microbiol Virol Lab Lucknow 226003 Uttar Pradesh India

Detection of multiple viruses is important for global analysis of gene or protein content and expression, opening up new prospects in terms of molecular and physiological systems for pathogenic diagnosis. Early diagnosis is crucial for disease treatment and control as it reduces inappropriate use of antiviral therapy and focuses surveillance activity. This requires the ability to detect and accurately diagnose infection at or close to the source/outbreak with minimum delay and the need for specific, accessible point-of-care diagnosis able to distinguish causative viruses and their subtypes. None of the available viral diagnostic assays combine a point-of-care format with the complex capability to identify a large range of human and animal viruses. microarray detection provides a useful, labor-saving tool for detection of multiple viruses with several advantages, such as convenience and prevention of cross-contamination of polymerase chain reaction (PCR) products, which is of foremost importance in such applications. Recently, real-time PCR assays with the ability to confirm the amplification product and quantitate the target concentration have been developed. Furthermore, nucleotide sequence analysis of amplification products has facilitated epidemiological studies of infectious disease outbreaks and monitoring of treatment outcomes for infections, in particular for viruses that mutate at high frequency. This review discusses applications of microarray technology as a potential new tool for detection and identification of acute encephalitis-causing viruses in human serum, plasma, and cell cultures.

关键词： PROTEIN microarrays ENCEPHALITIS -- Diagnosis POLYMERASE chain reaction microarray technology MICROBIOLOGICAL assay NUCLEOTIDE sequence EPIDEMICS

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microarray based IgE detection in poly-sensitized allergic patients with suspected food allergy - an approach in four clinical cases

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ALLERGOLOGIA ET IMMUNOPATHOLOGIA 2012年第3期40卷 172-180页

作者： Vieira, T. Lopes, C. Pereira, A. M. Araujo, L. Moreira, A. Delgado, L. Hosp Sao Joao EPE Ser Imunoalergol Oporto Portugal Hosp Sao Joao EPE Serv Patol Clin Lab Imunol Oporto Portugal Univ Porto Serv & Lab Imunol Oporto Portugal Univ Porto Fac Med CINTESIS Ctr Res Hlth Technol & Informat Syst Oporto Portugal

Background: Component-resolved diagnosis and microarray technology have been recently introduced into clinical allergy practice, and may be particularly useful in poly-sensitized allergic patients. Methods: We compare the clinical usefulness of a microarray-based IgE detection assay (ISAC (R)) with skin tests and specific IgE with standard allergens (sIgE) or their monocomponents in four case reports of patients poly-sensitized to aeroallergens and food. Results: Case 1: a woman with rhinitis, oral allergy syndrome to several fruits and anaphylaxis to cherry. Diagnostic tests supported non-specific lipid transfer proteins (nsLTPs) primary sensitization. Case 2: a woman with exercise-induced asthma, rhino-conjunctivitis and oral allergy syndrome to fresh fruits of different families. A diagnosis of primary grass and weed pollen allergy with profilin and pathogenesis-related protein family 10 (PR-10) cross-reactive food allergy was proposed. Case 3: a man with atopic eczema, asthma, rhinitis, and multiple anaphylactic episodes with cashew nuts and oral allergy syndrome to fruits. The diagnostic workup supported a primary birch pollen allergy with PR-10 and nsLTPs cross-reactive food allergy. Case 4: a woman with rhino-conjunctivitis, per-operative anaphylaxis due to latex and recent pharyngeal angio-oedema episodes. The diagnosis was a primary grass and weed pollen allergy with equivocal profilin sensitization and no obvious cross-reactivity mediated by nsLTPs sensitization. Conclusions: The possibility to carry out multiple sIgE measurements with single protein allergens, in particular with the microarray technique, is a useful, simple and non-invasive diagnostic tool in complex poly-sensitized allergic patients. (C) 2011 SEICAP. Published by Elsevier Espana, S.L. All rights reserved.

关键词： Component-resolved diagnosis microarray technology Allergy Poly-sensitization

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UbcH10 and Its Emerging Role in Systemic Carcinogenesis

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INTERNATIONAL JOURNAL OF SURGICAL PATHOLOGY 2013年第5期21卷 538-538页

作者： Kapoor, Shailendra 2400 Crossing St Mechanicsville VA USA

A letter to the editor is presented in response to the article 'UbcH10 expression in benign, hyperplastic, and malignant endometrial curetted materials: a tissue microarray study' by M. Kefeli and colleagues i... 详细信息

关键词： CANCER microarray technology

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Proteome- wide Detection of Abl1 SH3-binding Peptides by Integrating Computational Prediction and Peptide microarray

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MOLECULAR & CELLULAR PROTEOMICS 2012年第1期11卷 O111-O111页

作者： Xu, Zheng Hou, Tingjun Li, Nan Xu, Yang Wang, Wei Univ Calif San Diego Dept Chem & Biochem La Jolla CA 92093 USA Univ Calif San Diego Div Biol Sci La Jolla CA 92093 USA Soochow Univ Inst Funct Nano & Soft Mat FUNSOM Suzhou 215123 Jiangsu Peoples R China Soochow Univ Jiangsu Key Lab Carbon Based Funct Mat & Devices Suzhou 215123 Jiangsu Peoples R China

Protein-protein interactions are essential for regulating almost all aspects of cellular functions. Many of these interactions are mediated by weak and transient protein domain-peptide binding, but they are often under-represented in high throughput screening of protein-protein interactions using techniques such as yeast two-hybrid and mass spectrometry. On the other hand, computational predictions and in vitro binding assays are valuable in providing clues of in vivo interactions. We present here a systematic approach that integrates computer modeling and a peptide microarray technology to identify binding peptides of the SH3 domain of the tyrosine kinase Abl1 in the human proteome. Our study provides a comprehensive list of candidate interacting partners for the Abl1 protein, among which the presence of numerous methyl-transferases and RNA splicing proteins may suggest a novel function of Abl1 in chromatin remodeling and RNA processing. This study illustrates a powerful approach for integrating computational and experimental methods to detect protein interactions mediated by domain-peptide recognition. Molecular & Cellular Proteomics 11: 10.1074/mcp.O111.010389, 1- 2, 2012.

关键词： Experimental Methods High-Throughput Screening Assays RNA Splicing Chromatin Remodeling Peptides microarray technology protein domain SH3 Domain microarray Protein-Protein Interaction

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microarray analysis reveals age-related differences in gene expression during the development of osteoarthritis in mice

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ARTHRITIS AND RHEUMATISM 2012年第3期64卷 705-717页

作者： Loeser, Richard F. Olex, Amy L. McNulty, Margaret A. Carlson, Cathy S. Callahan, Michael F. Ferguson, Cristin M. Chou, Jeff Leng, Xiaoyan Fetrow, Jacquelyn S. Wake Forest Univ Bowman Gray Sch Med Winston Salem NC 27157 USA Univ Minnesota St Paul MN 55108 USA

Objective To better understand the contribution of age to the development of osteoarthritis (OA). Methods. Surgical destabilization of the medial meniscus (DMM) was used to model OA in 12-week-old and 12-month-old male C57BL/6 mice. OA severity was evaluated histologically. RNA used for microarray and real-time polymerase chain reaction analysis was isolated from joint tissue collected from the medial side of the joint, including cartilage, meniscus, subchondral bone, and the joint capsule with synovium. Computational analysis was used to identify patterns of gene expression, and immunohistochemistry was used to evaluate tissue distribution of selected proteins. Results. OA was more severe in older mice than in young mice. Only 55 genes showed a similar expression with DMM-induced OA in the 2 age groups, while 493 genes showed differential expression, the majority having increased expression in older mice. Functional categories for similarly expressed genes included extracellular matrix-and cell adhesion-related genes;differentially expressed genes included those related to muscle structure and development and immune response genes. Comparison of expression in sham-operated control joints revealed an age-related decrease in matrix gene expression and an increase in immune and defense response gene expression. Interleukin-33 was present in multiple joint tissue cells, while CCL21 was more localized to chondrocytes and meniscal cells. Periostin was found in the extracellular matrix of cartilage and meniscus. Conclusion. Age affects both the basal pattern of gene expression in joint tissues and the response to surgically induced OA. Examining tissue from the joint beyond only cartilage revealed novel genes and proteins that would be important to consider in OA.

关键词： OSTEOARTHRITIS AGE distribution (Demography) ANALYSIS of variance ANIMAL experimentation GENE expression IMMUNOHISTOCHEMISTRY KNEE MICE POLYMERASE chain reaction FINANCING of research EQUIPMENT & supplies DATA analysis software microarray technology GENETIC aspects

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An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection

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BIOINFORMATICS 2012年第19期28卷 2534-2536页

作者： Wang, Xingbin Kang, Dongwan D. Shen, Kui Song, Chi Lu, Shuya Chang, Lun-Ching Liao, Serena G. Huo, Zhiguang Tang, Shaowu Ding, Ying Kaminski, Naftali Sibille, Etienne Lin, Yan Li, Jia Tseng, George C. Henry Ford Hlth Syst Detroit MI 48202 USA Univ Pittsburgh Dept Human Genet Pittsburgh PA 15261 USA Univ Calif Berkeley Lawrence Berkeley Natl Lab Genom Div Berkeley CA 94720 USA Univ Pittsburgh Magee Womens Res Inst Pittsburgh PA USA Univ Pittsburgh Dept Biostat Pittsburgh PA 15261 USA PharmaNet I3 Hunt Valley MD 21031 USA Univ Pittsburgh Dept Computat & Syst Biol Pittsburgh PA USA Univ Pittsburgh Div Pulm Allergy & Crit Care Med Pittsburgh PA USA Univ Pittsburgh Dept Psychiat Pittsburgh PA USA

With the rapid advances and prevalence of high-throughput genomic technologies, integrating information of multiple relevant genomic studies has brought new challenges. microarray meta-analysis has become a frequently used tool in biomedical research. Little effort, however, has been made to develop a systematic pipeline and user-friendly software. In this article, we present MetaOmics, a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides a quantitative and objective tool to assist study inclusion/exclusion criteria for meta-analysis. MetaDE and MetaPath were developed for candidate marker and pathway detection, which provide choices of marker detection, meta-analysis and pathway analysis methods. The system allows flexible input of experimental data, clinical outcome (case-control, multi-class, continuous or survival) and pathway databases. It allows missing values in experimental data and utilizes multi-core parallel computing for fast implementation. It generates informative summary output and visualization plots, operates on different operation systems and can be expanded to include new algorithms or combine different types of genomic data. This software suite provides a comprehensive tool to conveniently implement and compare various genomic meta-analysis pipelines.

关键词： microarray technology META-analysis GENE expression QUALITY control GENOMICS BIOINFORMATICS

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