“Omics”-Enabled Microbial Sensors on Ocean Platforms
“Omics”-Enabled Microbial Sensors on Ocean Platforms
In order to assess the diversity and function of microbial communities most effectively, molecular assays need to be designed that target the phylogenetic markers and functional genes that are key to major ecological processes and microorganisms. A streamlined design process is presented here that designs probes for microarray and quantitative PCR (qPCR) assays, for application on the lab bench or on remote instrumentation. These assays can be used for DNA (genome) and RNA (gene transcription) studies. The pipeline described here establishes a database of environmental sequences, which is then used for the design of molecular probes for microarrays and to inform the design of qPCR assays, which is detailed here along with the assay optimization process. Finally, the process for the design of high-density microarrays is described. The qPCR protocol is currently used for assay optimization on the Environmental Sample Processor, a deployable robotic “genosensor” (http://www.mbari.org/esp). The protocols described here should advance applications in microbial oceanography using robotic instrumentation as well as traditional sampling methods.
Quantitative PCR, Microarray, Biosensors, Environmental microbiology, Ocean platforms, Robotic instrumentation, Microbial oceanography, Genosensor, Environmental sample processor
978-1-61779-914-3
1-32
Robidart, Julie C.
1d72ac92-7dca-49a0-9f9e-26798387e66b
Shilova, Irina N.
5d9ef464-1ab1-4a87-b7ea-5e550ae1ea27
Zehr, Jonathan P.
df07e726-0814-4247-8a74-942c07bd23e2
Tiquia-Arashiro, Sonia M.
2012
Robidart, Julie C.
1d72ac92-7dca-49a0-9f9e-26798387e66b
Shilova, Irina N.
5d9ef464-1ab1-4a87-b7ea-5e550ae1ea27
Zehr, Jonathan P.
df07e726-0814-4247-8a74-942c07bd23e2
Tiquia-Arashiro, Sonia M.
Robidart, Julie C., Shilova, Irina N. and Zehr, Jonathan P.
(2012)
“Omics”-Enabled Microbial Sensors on Ocean Platforms.
In,
Tiquia-Arashiro, Sonia M.
(ed.)
Molecular Biological Technologies for Ocean Sensing.
(Springer Protocols Handbooks)
New York, US.
Humana Totowa, .
(doi:10.1007/978-1-61779-915-0_1).
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Book Section
Abstract
In order to assess the diversity and function of microbial communities most effectively, molecular assays need to be designed that target the phylogenetic markers and functional genes that are key to major ecological processes and microorganisms. A streamlined design process is presented here that designs probes for microarray and quantitative PCR (qPCR) assays, for application on the lab bench or on remote instrumentation. These assays can be used for DNA (genome) and RNA (gene transcription) studies. The pipeline described here establishes a database of environmental sequences, which is then used for the design of molecular probes for microarrays and to inform the design of qPCR assays, which is detailed here along with the assay optimization process. Finally, the process for the design of high-density microarrays is described. The qPCR protocol is currently used for assay optimization on the Environmental Sample Processor, a deployable robotic “genosensor” (http://www.mbari.org/esp). The protocols described here should advance applications in microbial oceanography using robotic instrumentation as well as traditional sampling methods.
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Published date: 2012
Keywords:
Quantitative PCR, Microarray, Biosensors, Environmental microbiology, Ocean platforms, Robotic instrumentation, Microbial oceanography, Genosensor, Environmental sample processor
Organisations:
Ocean Technology and Engineering
Identifiers
Local EPrints ID: 374057
URI: http://eprints.soton.ac.uk/id/eprint/374057
ISBN: 978-1-61779-914-3
PURE UUID: 8b99f58f-2e3f-4329-b0b2-adaf457d2486
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Date deposited: 02 Feb 2015 16:48
Last modified: 14 Mar 2024 19:00
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Contributors
Author:
Julie C. Robidart
Author:
Irina N. Shilova
Author:
Jonathan P. Zehr
Editor:
Sonia M. Tiquia-Arashiro
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