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Microarray Sensors

A special issue of Sensors (ISSN 1424-8220).

Deadline for manuscript submissions: closed (31 August 2014) | Viewed by 62446

Special Issue Editor


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Guest Editor
1. Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550, USA
2. Davis Medical Center, Department of Radiation Oncology, University of California, 4501 X Street, Suite G-140, Sacramento, CA 95817, USA
Interests: microarray; nucleic acid array; protein array; chemical array; analyte sensors; multiplex detection

Special Issue Information

Dear Colleagues,

The technological advances resulting from the multitude of genome projects have propelled the scientific community into a new era of post-genomic science. This is especially true regarding array-based technology platforms for research. Microarrays, whether printed on a glass slide or incorporated in to a microfluidic or nanotechnology platform, still offer several distinct advantages over competing conventional analytical technologies. Also, microarrays are no longer limited to just nucleic acid-based detection. Protein microarrays, hybrid nucleic acid-protein microarrays, antibody microarray and chemical compound microarrays have all now been produced on varied substrates for monitoring both biological and chemical processes. Along with the expansion of types of arrays there has been a large growth in the methods and instruments used for detection.

This special issue will cover all topics relevant to the science, technology and applications of array-based detection sensors. Areas of interest include, but not limited to,

• Array-based detection platforms at the micro and nanoscale
• Label free and label-based sensors
• Electrical and chemical sensors
• Automation of detection and data analysis
• Development of multiple target analyte sensors, as well as array-based applications for both qualitative and quantitative microarray detection

Dr. Matthew A. Coleman
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Sensors is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (7 papers)

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Research

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1595 KiB  
Article
Regeneration of Recombinant Antigen Microarrays for the Automated Monitoring of Antibodies against Zoonotic Pathogens in Swine Sera
by Verena K. Meyer, Catharina Kober, Reinhard Niessner and Michael Seidel
Sensors 2015, 15(2), 2614-2628; https://doi.org/10.3390/s150202614 - 23 Jan 2015
Cited by 5 | Viewed by 6829
Abstract
The ability to regenerate immobilized proteins like recombinant antigens (rAgs) on surfaces is an unsolved problem for flow-based immunoassays on microarray analysis systems. The regeneration on microarray chip surfaces is achieved by changing the protein structures and desorption of antibodies. Afterwards, reactivation of [...] Read more.
The ability to regenerate immobilized proteins like recombinant antigens (rAgs) on surfaces is an unsolved problem for flow-based immunoassays on microarray analysis systems. The regeneration on microarray chip surfaces is achieved by changing the protein structures and desorption of antibodies. Afterwards, reactivation of immobilized protein antigens is necessary for reconstitution processes. Any backfolding should be managed in a way that antibodies are able to detect the protein antigens in the next measurement cycle. The regeneration of rAg microarrays was examined for the first time on the MCR3 flow-based chemiluminescence (CL) microarray analysis platform. The aim was to reuse rAg microarray chips in order to reduce the screening effort and costs. An antibody capturing format was used to detect antibodies against zoonotic pathogens in sera of slaughtered pigs. Different denaturation and reactivation buffers were tested. Acidic glycine-SDS buffer (pH 2.5) and 8 M guanidinium hydrochloride showed the best results in respect of denaturation efficiencies. The highest CL signals after regeneration were achieved with a carbonate buffer containing 10 mM DTT and 0.1% BSA for reactivation. Antibodies against Yersinia spp. and hepatitis E virus (HEV) were detected in swine sera on one immunochip over 4 days and 25 measurement cycles. Each cycle took 10 min for detection and regeneration. By using the rAg microarray chip, a fast and automated screening of antibodies against pathogens in sera of slaughtered pigs would be possible for zoonosis monitoring. Full article
(This article belongs to the Special Issue Microarray Sensors)
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770 KiB  
Article
A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes
by Alvaro Díaz-Badillo, María De Lourdes Muñoz, Gerardo Perez-Ramirez, Victor Altuzar, Juan Burgueño, Julio G. Mendoza-Alvarez, Jorge P. Martínez-Muñoz, Alejandro Cisneros, Joel Navarrete-Espinosa and Feliciano Sanchez-Sinencio
Sensors 2014, 14(5), 7580-7601; https://doi.org/10.3390/s140507580 - 25 Apr 2014
Cited by 14 | Viewed by 10359
Abstract
Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples [...] Read more.
Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples. Full article
(This article belongs to the Special Issue Microarray Sensors)
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1457 KiB  
Article
Dielectrophoretic Manipulation and Separation of Microparticles Using Microarray Dot Electrodes
by Bashar Yafouz, Nahrizul Adib Kadri and Fatimah Ibrahim
Sensors 2014, 14(4), 6356-6369; https://doi.org/10.3390/s140406356 - 3 Apr 2014
Cited by 62 | Viewed by 9959
Abstract
This paper introduces a dielectrophoretic system for the manipulation and separation of microparticles. The system is composed of five layers and utilizes microarray dot electrodes. We validated our system by conducting size-dependent manipulation and separation experiments on 1, 5 and 15 μm polystyrene [...] Read more.
This paper introduces a dielectrophoretic system for the manipulation and separation of microparticles. The system is composed of five layers and utilizes microarray dot electrodes. We validated our system by conducting size-dependent manipulation and separation experiments on 1, 5 and 15 μm polystyrene particles. Our findings confirm the capability of the proposed device to rapidly and efficiently manipulate and separate microparticles of various dimensions, utilizing positive and negative dielectrophoresis (DEP) effects. Larger size particles were repelled and concentrated in the center of the dot by negative DEP, while the smaller sizes were attracted and collected by the edge of the dot by positive DEP. Full article
(This article belongs to the Special Issue Microarray Sensors)
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862 KiB  
Article
Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays
by Roman Jaksik, Michal Marczyk, Joanna Polanska and Joanna Rzeszowska-Wolny
Sensors 2014, 14(1), 532-548; https://doi.org/10.3390/s140100532 - 31 Dec 2013
Cited by 11 | Viewed by 6032
Abstract
High density oligonucleotide microarrays present a big challenge for statistical data processing methods which aim to separate changes induced by experimental factors from those caused by artifacts and measurement inaccuracies. Despite huge advances in the field of microarray probe design methods, the signal [...] Read more.
High density oligonucleotide microarrays present a big challenge for statistical data processing methods which aim to separate changes induced by experimental factors from those caused by artifacts and measurement inaccuracies. Despite huge advances in the field of microarray probe design methods, the signal variation between probes that target a single transcript is substantially larger than their between-replicate array variability, suggesting a large influence of various probe-specific effects that introduce bias to the data. In this work we present the influence of probe-related design variations on the expression intensities of individual probes, focusing on five potential sources of high probe signal variance: the GC composition of the probe, the distance between individual probe target sites, G-quadruplex formation in the probe sequence, the occurrence of sequence motifs complementary to the oligo(dT) primer, and the specificity of unrecognized alternative splicing probeset assignment. By focusing on two high quality microarray datasets based on two distinct array designs we show the extent of variance between probes that target a specific transcript providing guidelines for the future design of microarrays and data processing methods. Full article
(This article belongs to the Special Issue Microarray Sensors)
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590 KiB  
Article
A Pt-Doped TiO2 Nanotube Arrays Sensor for Detecting SF6 Decomposition Products
by Xiaoxing Zhang, Jing Tie and Jinbin Zhang
Sensors 2013, 13(11), 14764-14776; https://doi.org/10.3390/s131114764 - 30 Oct 2013
Cited by 38 | Viewed by 6769
Abstract
The detection of partial discharge and analysis of SF6 gas components in gas-insulated switchgear (GIS) is important for the diagnosis and operating state assessment of power equipment. The use of a Pt-doped TiO2 nanotube arrays sensor for detecting sulfur hexafluoride (SF [...] Read more.
The detection of partial discharge and analysis of SF6 gas components in gas-insulated switchgear (GIS) is important for the diagnosis and operating state assessment of power equipment. The use of a Pt-doped TiO2 nanotube arrays sensor for detecting sulfur hexafluoride (SF6) decomposition products is proposed in this paper. The electrochemical pulse deposition method is employed to prepare the sensor array. The sensor’s response to the main characteristic gaseous decomposition products of SF6 is evaluated. The gas sensing characteristic curves of the Pt-doped TiO2 nanotube sensor and intrinsic TiO2 nanotube arrays sensor are compared. The mechanism of the sensitive response is discussed. Test results showed that the Pt-doped nanoparticles not only change the gas sensing selectivity of the TiO2 nanotube arrays sensor with respect to the main characteristic SF6 decomposition products, but also reduce the operating temperature of the sensor. Full article
(This article belongs to the Special Issue Microarray Sensors)
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439 KiB  
Article
A Low Density Microarray Method for the Identification of Human Papillomavirus Type 18 Variants
by Thuluz Meza-Menchaca, John Williams, Rocío B. Rodríguez-Estrada, Aracely García-Bravo, Ángel Ramos-Ligonio, Aracely López-Monteon and Rossana C. Zepeda
Sensors 2013, 13(10), 12975-12993; https://doi.org/10.3390/s131012975 - 26 Sep 2013
Cited by 4 | Viewed by 6403
Abstract
We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This [...] Read more.
We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18’s variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings. Full article
(This article belongs to the Special Issue Microarray Sensors)
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Review

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1398 KiB  
Review
Immobilization Techniques for Microarray: Challenges and Applications
by Satish Balasaheb Nimse, Keumsoo Song, Mukesh Digambar Sonawane, Danishmalik Rafiq Sayyed and Taisun Kim
Sensors 2014, 14(12), 22208-22229; https://doi.org/10.3390/s141222208 - 25 Nov 2014
Cited by 132 | Viewed by 15341
Abstract
The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce [...] Read more.
The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided. Full article
(This article belongs to the Special Issue Microarray Sensors)
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