NDLI: Underwater Application of Quantitative PCR on an Ocean Mooring

Content Provider	PubMed Central
Author	Preston, Christina M. Harris, Adeline Ryan, John P. Roman, Brent Marin, Roman Jensen, Scott Everlove, Cheri Birch, James Dzenitis, John M. Douglas, Pargett Adachi, Masao Turk, Kendra Zehr, Jonathon P. Scholin, Christopher A.
Editor	Zhao, Zhongming
Copyright Year	2011
Abstract	The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.
Related Links	http://dx.doi.org/10.1371/journal.pone.0022522
Starting Page	22522
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	8
Volume Number	6
Language	English
Publisher	Public Library of Science
Publisher Date	2011-08-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

A Mechanistic Model of PCR for Accurate Quantification of Quantitative PCR Data

An Autonomous Underwater Recorder Based on a Single Board Computer

Development of a Neutralization Assay for Influenza Virus Using an Endpoint Assessment Based on Quantitative Reverse-Transcription PCR

Comparative Analysis of Gene Expression Level by Quantitative Real-Time PCR Has Limited Application in Objects with Different Morphology

Rapid Diagnosis of Aneuploidy Using Segmental Duplication Quantitative Fluorescent PCR

SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the Distribution of the Imperiled Delta Smelt

Correction: SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the Distribution of the Imperiled Delta Smelt

Quantitative Analysis of Food and Feed Samples with Droplet Digital PCR

Correction: Comparative Analysis of Gene Expression Level by Quantitative Real-Time PCR Has Limited Application in Objects with Different Morphology

Underwater Application of Quantitative PCR on an Ocean Mooring

Similar Documents

A Mechanistic Model of PCR for Accurate Quantification of Quantitative PCR Data

An Autonomous Underwater Recorder Based on a Single Board Computer

Development of a Neutralization Assay for Influenza Virus Using an Endpoint Assessment Based on Quantitative Reverse-Transcription PCR

Comparative Analysis of Gene Expression Level by Quantitative Real-Time PCR Has Limited Application in Objects with Different Morphology

Rapid Diagnosis of Aneuploidy Using Segmental Duplication Quantitative Fluorescent PCR

SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the Distribution of the Imperiled Delta Smelt

Correction: SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the Distribution of the Imperiled Delta Smelt

Quantitative Analysis of Food and Feed Samples with Droplet Digital PCR

Correction: Comparative Analysis of Gene Expression Level by Quantitative Real-Time PCR Has Limited Application in Objects with Different Morphology

Underwater Application of Quantitative PCR on an Ocean Mooring