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A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.

ABSTRACT: While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.

SUBMITTER: Paredes CJ

PROVIDER: S-EPMC1932840 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

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A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.

Paredes Carlos J CJ Senger Ryan S RS Spath Iwona S IS Borden Jacob R JR Sillers Ryan R Papoutsakis Eleftherios T ET

Applied and environmental microbiology 20070525 14

While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, inc ...[more]

PMID: 17526797

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Project description:Within One Health, research translation is a dynamic process involving collaboration and communication between the human, animal, and environmental health sectors to create and apply research findings to address health threats at the human-animal-environment interface. Research translation is essential for the creation of evidence-based policies and programs for the prevention and control of infectious diseases and other health threats, and thus is an important component of a robust national capacity to effectively prevent, control, and mitigate biological incidents. However, there is a lack of conceptual guidance and training materials for research translation in a One Health context. To address this need, we developed a novel One Health Research Translation Framework that describes an iterative process for research and policy stakeholders to collaborate to design and implement research applications addressing One Health zoonotic disease challenges. In addition, we developed accompanying training materials to validate the Framework and facilitate capacity building for understanding and applying research translation concepts to zoonotic disease threats. The training materials consist of exercises to map One Health communication pathways and literature-based case studies on research translation to address zoonotic disease concerns. The Framework and training materials were piloted with Egyptian One Health stakeholders at a workshop in Cairo in 2018. The outcomes of the workshop validated the comprehensiveness and applicability of the Framework and training materials, as participants were able to demonstrate a firm understanding of research translation processes and successfully apply research translation and One Health concepts to real-world zoonotic disease scenarios. Overall, the Framework and accompanying training materials address an important gap in capacity building for One Health stakeholders and are valuable tools for strengthening research translation networks that promote development of innovative, evidence-based solutions to One Health zoonotic disease threats.

Dataset Information

A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.

Publications

A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.

Similar Datasets

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