The Flow-thru Chip A Miniature, Three-Dimensional Biochip Platform

Steel, Adam B.; Torres, Matthew P.; Hartwell, John A.; Yu, Yifan; Ting, Nan; Hoke, Glenn D.; Yang, Hongjun

doi:10.1201/9780203908006.ch11

Cited by 12 publications

(19 citation statements)

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“…However, one area that sets current cDNA-microarrays apart from membrane-based arrays is that they are not generally reusable (Desprez et al, 1998;Baldwin et al, 1999), though a newer slide derivatization purports to make this possible (Beier and Hoheisel, 1999). Other systems in development for improving hybridization kinetics and signal detection have been recently reviewed (Steel et al, 2000;Blohm and Guiseppi-Elie, 2001). Nanogen has produced a chip where the probes are independently, electronically activated Edman et al, 1997).…”

Section: Hybridi Zation Conditionsmentioning

confidence: 99%

Comprehensive gene expression analysis by transcript profiling

Donson

Fang

Espiritu-Santo

et al. 2002

Functional Genomics

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AbslraelAfter the completion of the genomic seq uence of Arabidopsis tha liana ; it is now a priority to identify all the genes, their patterns of expression and functions. Transcript profiling is playing a substantial role in annotating and determining gene functions, having advanced from one-gene-at-a-time methods to technologies that provide a holistic view of the genome. In this review. comprehensive transcript profiling methodologies are described, includ ing two that arc used extensively by the authors. cDNA-APLP and eDNA microarraying. Both these technologie s illustrate the require ment to integrate molecular biology. automation, LlMS and data analysis. With so much uncharted territory in the Ara bidopsis genome. and the desire to tackle complex biological traits, such integra ted systems will provide a rich source of data for the correlative, functional annotation of genes.Abbreviations: c DNA-AFLP, eDNA amplified fragmen t length polymorp hism; EST, expressed sequence tag; LlMS, laboratory information management system; MPSS. massively parallel signature seq uencing; PCR, polymerase chain reaction; RDA, rep resentational difference analysis; SAGE, serial analysis of gene expression; SSH, suppression subtractive hybridization -..J -..J

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Section: Hybridi Zation Conditionsmentioning

confidence: 99%

Comprehensive gene expression analysis by transcript profiling

Donson

Fang

Espiritu-Santo

et al. 2002

Functional Genomics

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“…We have chosen a novel three-dimensional FTC due to its potential for enhanced performance over planar substrates. When FTC is applied to gene expression analysis, it has shown an improved responsiveness and an improved dynamic range due to the increased surface area relative to that for a flat-surface geometry, as well as reduced assay times due to dynamic fluid delivery to the chip (3,6,23). Enhanced mass transport leading to shorter hybridization times is the primary advantage of the FTC system in gene expression applications with RNA products transcribed in vitro, so it may be possible that such an advantage was mitigated in the present application by the use of PCR for amplification.…”

Section: Discussionmentioning

confidence: 99%

Use of the DNA Flow-Thru Chip, a Three-Dimensional Biochip, for Typing and Subtyping of Influenza Viruses

Keßler

Ferraris

Palmer³

et al. 2004

J Clin Microbiol

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100

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Influenza A viruses, which are further subtyped on the basis of antigenic differences in external hemagglutinin and neuraminidase glycoproteins, and influenza B viruses are prominent among the viral causes of respiratory diseases and can cause a wide spectrum of illness. Each year these viruses are responsible for recurrent epidemics, frequently in association with genetic variation. There is a requirement for sensitive and rapid diagnostic techniques in order to improve both the diagnosis of infections and the quality of surveillance systems. A new three-dimensional biochip platform (Flow-Thru Chip; MetriGenix) was used to develop a rapid and reliable molecular method for the typing and subtyping of influenza viruses. Oligonucleotide probes immobilized in microchannels of a silicon wafer were selected to recognize multiple fragments of the influenza A virus matrix protein gene; the influenza B virus NS gene; the H1, H3, and H5 hemagglutinin genes; and the N1 and N2 neuraminidase genes. Biotinylated amplicons resulting from either multiplex or random reverse transcription-PCR were hybridized to arrayed oligonucleotides on the influenza virus chip before they were stained with horseradish peroxidase-streptavidin and were imaged by use of a chemiluminescent substrate. The chip analysis procedure, from the time of pipetting of the sample into the chip cartridge to the time of analysis of the results, was performed in less than 5 h. The random PCR exhibited a higher level of performance than the multiplex PCR in terms of the specificity of product hybridization to the influenza virus chip. Analysis of influenza A viruses (H1N1, H3N2, H1N2, and H5N1) and influenza B viruses showed that this microarraybased method is capable of the rapid and unambiguous identification of all types and subtypes of viruses by use of random PCR products. The redundancy of the probes designed for each gene selected yielded an additional criterion of confidence for the subtyping of viruses which are known for antigenic variations in some of their components.

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“…Gene Logic offers the Flow-Thru Chip™ (FTC) in which molecular interaction occurs within the 3-D volumes of po-rous substrates (44,68,69). The FTC is a uniformly porous glass or silicon wafer, in contrast to flat, impenetrable materials used in traditional microarrays.…”

Section: Review Rapid Detection and Identification Of Infectious Disease Agentsmentioning

confidence: 99%

Nucleic acid approaches for detection and identification of biological warfare and infectious disease agents

et al. 2003

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Biological warfare agents are the most problematic of the weapons of mass destruction and terror. Both civilian and military sources predict that over the next decade the threat from proliferation of these agents will increase significantly. In this review we summarize the state of the art in detection and identification of biological threat agents based on PCR technology with emphasis on the new technology of microarrays. The advantages and limitations of real-time PCR technology and a review of the literature as it applies to pathogen and virus detection are presented. The paper covers a number of issues related to the challenges facing biological threat agent detection technologies and identifies critical components that must be overcome for the emergence of reliable PCR-based DNA technologies as bioterrorism countermeasures and for environmental applications. The review evaluates various system components developed for an integrated DNA microchip and the potential applications of the next generation of fully automated DNA analyzers with integrated sample preparation and biosensing elements. The article also reviews promising devices and technologies that are near to being, or have been, commercialized.

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The Flow-thru Chip A Miniature, Three-Dimensional Biochip Platform

Cited by 12 publications

References 0 publications

Comprehensive gene expression analysis by transcript profiling

Comprehensive gene expression analysis by transcript profiling

Use of the DNA Flow-Thru Chip, a Three-Dimensional Biochip, for Typing and Subtyping of Influenza Viruses

Nucleic acid approaches for detection and identification of biological warfare and infectious disease agents

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