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IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics (vol 30, pg 1392, 2014)

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BIOINFORMATICS 2016年第16期32卷 2565-2565页

作者： Rosikiewicz, Marta Robinson-Rechavi, Marc

A correction to the article 'IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics' that was published ... 详细信息

关键词： microarray technology QUALITY control MATHEMATICAL models

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A Novel Microbial Source Tracking microarray for Pathogen Detection and Fecal Source Identification in Environmental Systems

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ENVIRONMENTAL SCIENCE & technology 2015年第12期49卷 7319-7329页

作者： Li, Xiang Harwood, Valerie J. Nayak, Bina Staley, Christopher Sadowsky, Michael J. Weidhaas, Jennifer W Virginia Univ Dept Civil & Environm Engn Morgantown WV 26506 USA Univ S Florida Dept Integrat Biol Tampa FL 33620 USA Univ Minnesota Inst Biotechnol St Paul MN 55108 USA Univ Minnesota Inst Biotechnol Dept Soil Water & Climate St Paul MN 55108 USA

Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity Of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitivity (percentage true positives) of MST results in sewage and animal waste samples (21-33%) was lower than specificity (83-90%, percentage of true negatives). Next generation DNA sequencing revealed two dominant bacterial families that were common to all sample types: Ruminococcaceae and Lachnospiraceae. Five dominant phyla and 15 dominant families comprised 97% and 74%, respectively, of sequences from all fecal sources. Phyla and families not represented on the microarray are possible candidates for inclusion in subsequent array designs.

关键词： FECAL contamination GENOMES microarray technology HELICOBACTER pylori CAMPYLOBACTER

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The effect of unequal strand length on short DNA duplex hybridization in a model microarray system: A Monte Carlo simulation study

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CHEMICAL PHYSICS LETTERS 2015年 634卷 230-235页

作者： Cooper, Sarah J. Stubbs, John M. Univ New England Dept Chem & Phys Biddeford ME 04005 USA

Monte Carlo molecular simulations of DNA decamer-hexamer strands were carried out over a range of temperatures, both free in solution and bound to a surface in several possible fashions, to investigate the effect of dangling end nucleotides on hybridization. For comparison, analogous hexamer duplexes were also studied in solution. Duplex stability was analyzed in terms of energetic, hydrogen bonding, and structural properties. Of the systems studied, shorter solution sequences interacting with longer surface-bound sequences generally had weaker interactions than the opposite. (C) 2015 Elsevier B.V. All rights reserved.

关键词： NUCLEIC acid hybridization microarray technology DNA structure HYDROGEN bonding NUCLEOTIDES MONTE Carlo method

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Plain Silver Surface Plasmon Resonance for microarray Application

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ANALYTICAL CHEMISTRY 2015年第3期87卷 1466-1469页

作者： Cheng, Zhiqiang Wang, Zhiyou Gillespie, Doreen E. Lausted, Christopher Zheng, Zheng Yang, Mo Zhu, Jinsong Natl Ctr NanoSci & Technol Beijing 100190 Peoples R China Tsinghua Univ Dept Chem Beijing 100084 Peoples R China Plexera LLC Woodinville WA 98072 USA Inst Syst Biol Seattle WA 98103 USA Beihang Univ Sch Elect & Informat Engn Beijing 100191 Peoples R China

The application scope of surface plasmon resonance (SPR) and SPR imaging (SPRi) is rapidly growing, and tools such as high-performance and low-cost slides could enable more rapid growth of the field. We describe herein a novel silver slide, addressing the inherent instability of plain silver structure by improving adhesion between the glass substrate and the silver layer with a thin buffer layer of gold. Covered by a self-assembled monolayer (SAM) only, SPR characteristics of the slide remain steady for more than 3 months under regular storage. In a bioassay, the slide substantiates the predicted nearly 100% sensitivity improvement over gold slides and exhibits exceptional performance stability as determined by sensitivity and resolution measurements during the extended 40?000 s multicycle experiment. We demonstrate the suitability of this new slide for large-area SPRi, describing analysis results from a 1?296-ligand protein microarray. We predict this slide structure will provide a stable, high-sensitivity solution for high-throughput SPRi applications and other surface analysis platforms.

关键词： SURFACE plasmon resonance microarray technology MONOMOLECULAR films SURFACES (technology) -- Analysis MAGNETIC resonance imaging

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High-Throughput Dose-Response Measurement Using a Label-Free microarray-in-Microplate Assay Platform

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ANALYTICAL CHEMISTRY 2015年第11期87卷 5640-5648页

作者： Landry, J. P. Malovichko, G. Zhu, X. D. Univ Calif Davis Dept Phys Davis CA 95616 USA

microarray-based binding assays facilitate the discovery of protein ligands from large collections of small molecules. Hundreds of ligands can be identified, yet only a small portion of them have interfering effects (competitive or noncompetitive) on a specific protein-receptor binding reaction. Further efficient screening of ligands for those with specific modifying effect is needed in order to take the full advantage of throughputs of microarray-based assays for drug discovery. We report a label-free microarray-in-microplate assay platform for simultaneous acquisition of at least 32 dose-response curves in a single experiment, each curve having 12 concentration points. When combined with ligand discovery, this makes the microarray-based platform a true high-throughout means of finding inhibitors to specific protein-receptor reactions starting from a large collection of small-molecule libraries.

关键词： microarray technology MICROPLATES LIGANDS SMALL molecules PROTEIN receptors CHEMICAL reactions

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Ag@SiO₂-entrapped hydrogel microarray: a new platform for a metal-enhanced fluorescence-based protein assay

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ANALYST 2015年第10期140卷 3375-3383页

作者： Jang, Eunji Kim, Minsu Koh, Won-Gun Yonsei Univ Dept Chem & Biomol Engn Seoul 120749 South Korea

We developed a novel protein-based bioassay platform utilizing metal-enhanced fluorescence (MEF), which is a hydrogel microarray entrapping silica-coated silver nanoparticles (Ag@SiO2). As a model system, different concentrations of glucose were detected using a fluorescence method by sequential bienzymatic reaction of hydrogel-entrapped glucose oxidase (GOX) and peroxidase (POD) inside a hydrogel microarray. microarrays based on poly(ethylene glycol)(PEG) hydrogels were prepared by photopatterning a solution containing PEG diacrylate (PEG-DA), photoinitiator, enzymes, and Ag@SiO2. The resulting hydrogel microarrays were able to entrap both enzymes and Ag@SiO2 without leaching and deactivation problems. The presence of Ag@SiO2 within the hydrogel microarray enhanced the fluorescence signal, and the extent of the enhancement was dependent on the thickness of silica shells and the amount of Ag@SiO2. Optimal MEF effects were achieved when the thickness of the silica shell was 17.5 nm, and 0.5 mg mL(-1) of Ag@SiO2 was incorporated into the assay systems. Compared with the standard hydrogel microarray-based assay performed without Ag@SiO2, more than a 4-fold fluorescence enhancement was observed in a glucose concentration range between 10(-3) mM and 10.0 mM using hydrogel microarray entrapping Ag@SiO2, which led to significant improvements in the sensitivity and the limit of detection (LOD). The hydrogel microarray system presented in this study could be successfully combined with a microfluidic device as an initial step to create an MEF-based micro-total-analysis-system (mu-TAS).

关键词： PROTEINS -- Analysis microarray technology SILICA HYDROGELS FLUORESCENCE BIOLOGICAL assay SILVER nanoparticles

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Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization

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ANALYST 2015年第3期140卷 912-921页

作者： Girard, Laurie D. Boissinot, Karel Peytavi, Regis Boissinot, Maurice Bergeron, Michel G. Univ Laval Ctr Rech Infectiol CHU Quebec Ctr Rech Quebec City PQ Canada Univ Laval Fac Med Dept Microbiol Infectiol & Immunol Quebec City PQ G1K 7P4 Canada

The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have high complexity and cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotide sequence-dependent segment and a unique "target sequence-independent" 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design o

关键词： microarray technology Sensitivity and Specificity Nucleic Acid Amplification Tests non-sinking support hybridisation Indexing reaction chambers MULTIPLEXOR Oligonucleotides Oligonucleotide Probes

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Cancer Feature Selection and Classification Using a Binary Quantum-Behaved Particle Swarm Optimization and Support Vector Machine

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COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2016年第1期2016卷 3572705-3572705页

作者： Xi, Maolong Sun, Jun Liu, Li Fan, Fangyun Wu, Xiaojun Wuxi Inst Technol Dept Control Technol Wuxi 214121 Jiangsu Peoples R China Jiangnan Univ Dept Comp Sci Wuxi 214122 Jiangsu Peoples R China Jiangnan Univ Affiliated Hosp Wuxi 214062 Jiangsu Peoples R China

This paper focuses on the feature gene selection for cancer classification, which employs an optimization algorithm to select a subset of the genes. We propose a binary quantum-behaved particle swarm optimization (BQPSO) for cancer feature gene selection, coupling support vector machine (SVM) for cancer classification. First, the proposed BQPSO algorithm is described, which is a discretized version of original QPSO for binary 0-1 optimization problems. Then, we present the principle and procedure for cancer feature gene selection and cancer classification based on BQPSO and SVM with leave-one-out cross validation (LOOCV). Finally, the BQPSO coupling SVM(BQPSO/SVM), binary PSO coupling SVM(BPSO/SVM), and genetic algorithm coupling SVM (GA/SVM) are tested for feature gene selection and cancer classification on five microarray data sets, namely, Leukemia, Prostate, Colon, Lung, and Lymphoma. The experimental results show that BQPSO/SVM has significant advantages in accuracy, robustness, and the number of feature genes selected compared with the other two algorithms.

关键词： PARTICLE swarm optimization SUPPORT vector machines CANCER genetics GENETIC algorithms microarray technology

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Controlled proliferation and screening of mammalian cells on a hydrogel-functionalized small molecule microarray

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CHEMICAL COMMUNICATIONS 2015年第52期51卷 10431-10434页

作者： Zhu, Biwei Jiang, Bo Na, Zhenkun Yao, Shao Q. Natl Univ Singapore Dept Chem Singapore 117543 Singapore

A hydrogel-functionalized small molecule microarray has been developed, on which PC-3 cancer cells were selectively grown. Subsequent controlled release of immobilized bioactive compounds enabled cell-based screening ... 详细信息

关键词： HYDROGELS RESEARCH CANCER cells BIOACTIVE compounds microarray technology MOLECULES

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HIV microarray for the mapping and characterization of HIV-specific antibody responses

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LAB ON A CHIP 2015年第6期15卷 1574-1589页

作者： Gallerano, Daniela Wollmann, Eva Lupinek, Christian Schlederer, Thomas Ebner, Daniel Harwanegg, Christian Niespodziana, Katarzyna Schmetterer, Klaus Pickl, Winfried Puchhammer-Stoeckl, Elisabeth Sibanda, Elopy Valenta, Rudolf Med Univ Vienna Dept Pathophysiol & Allergy Res Ctr Pathophysiol Infectiol & Immunol Div Immunopathol A-1090 Vienna Austria Phadia Austria GmbH Thermo Fisher Sci ImmunoDiagnost Vienna Austria Med Univ Vienna Dept Lab Med Vienna Austria Med Univ Vienna Dept Immunol Vienna Austria Med Univ Vienna Dept Virol Vienna Austria Parirenyatwa Univ Teaching Hosp Allergy Asthma & Immune Dysfunct Clin Harare Zimbabwe

We used the microarray technology to develop chips containing a comprehensive set of proteins and peptides covering the proteome of HIV-1 clade C, which is the HIV-1 subtype that causes the majority of infections worldwide. We demonstrate that the HIV microarray allows simultaneous, sensitive and specific detection of antibody responses for the major immunoglobulin classes (IgG, IgA, IgM, IgE) and subclasses (IgG1-4) with minute amounts of serum samples towards a large number of HIV antigens and peptides. Furthermore, we show that the HIV chip can be used for the monitoring of antibody responses during the course of the disease and during treatment. The HIV microarray should be useful to study antibody responses to multiple HIV antigens and epitopes in HIV-infected patients to explore pathomechanisms of the disease, for diagnosis and for monitoring of treatment and of vaccine trials.

关键词： microarray technology PROTEOMICS IMMUNOGLOBULINS ANTIGENS PEPTIDES ANTIGENIC determinants VACCINES -- Testing

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