http://lod.bco-dmo.org/id/dataset/670450
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-12-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Primers used for Pleurochrysis carterae virus dPCR assays from laboratory experiments at the Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016
2016-12-15
publication
2016-12-15
revision
BCO-DMO Linked Data URI
2016-12-15
creation
http://lod.bco-dmo.org/id/dataset/670450
Joaquín Martínez Martínez
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Martínez Martínez, J. (2016) Primers used for Pleurochrysis carterae virus dPCR assays from laboratory experiments at the Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-12-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/670450 [access date]
Primers used for Pleurochrysis carterae virus dPCR assays Dataset Description: <p>This dataset includes information for the five primers used in the&nbsp;<a href="http://www.bco-dmo.org/dataset/670442">Pleurochrysis&nbsp;carterae&nbsp;virus production&nbsp;</a>dataset. &nbsp;It contains the&nbsp;primer ID, forward primer, reverse primer, amplicon length, annealing temperature, and probe&nbsp;amplicon sequence.</p>
<p><strong>Related datasets:</strong><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670431" target="_blank">Pleurochrysis carterae growth</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670442">Pleurochrysis carterae virus production</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670912">Accession numbers (P. carterae viruses and field samples)</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670714" target="_blank">TEM Pleurochrysis carterae thin section images</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670706" target="_blank">TEM Pleurochrysis carterae virion images</a></p> Methods and Sampling: <p>Probes and primers were designed to target genotypes:&nbsp;<em>Pleurochrysis carterae&nbsp;</em>endemic virus genotypes 2 and 1b (PsEV2 and PsEV1b, respectively; dsDNA viruses);&nbsp;<em>P. carterae&nbsp;</em>Polinton-like viruses (PleuroPLV; dsDNA viruses); and&nbsp;<em>P. carterae&nbsp;</em>CRESS viruses (PcCV1, ssDNA viruses). For the latter, we designed probes for both the REP and the CAP genes to discriminate viral particles with partial (i.e., amplification for only the REP or the CAP markers from a single dPCR intact drop) or complete genomes (i.e., amplification with both molecular markers from a single dPCR intact drop). &nbsp; <a href="https://doi.org/10.2216/i0031-8884-32-3-234.1" target="_blank"> </a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1346272 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1346272
completed
Joaquín Martínez Martínez
Bigelow Laboratory for Ocean Sciences
410-221-1819
2020 Horns Point Road AREL 239
Cambridge
MD
21613
USA
jmartinez@umces.edu
pointOfContact
asNeeded
Unknown
primer_id
forward_primer
reverse_primer
aplicon_length
annealing_temp
probe
amplicon_sequence
theme
None, User defined
sample identification
sequence
water temperature at measurement depth
featureType
BCO-DMO Standard Parameters
Bigelow_Martinez_2015-2016
service
Deployment Activity
Bigelow Laboratory for Ocean Sciences, Maine
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Persistent Virus Infections in Marine Phytoplankton
https://osprey.bco-dmo.org/project/560443
Persistent Virus Infections in Marine Phytoplankton
<p><em>Description from NSF award abstract:</em><br />
Viruses are prevalent in every part of the environment of our living planet, and yet our understanding of type, distribution, and function is the least well-known aspect of biodiversity. In recent years we have developed an increased appreciation for the role viruses play in driving host evolution in the environment, but fundamental knowledge about the mechanisms involved remain lacking. Additionally, viruses may influence diversity indirectly through "kill the winner" scenarios, as well as through cell lysis and subsequent release of dissolved nutrients, which facilitate restructuring of microbial communities. The majority of research on marine viruses to date has focused on combinations of acutely susceptible host strains with highly virulent virus isolates. However, it is likely that marine viruses also employ a persistent infection life strategy, arguably preferring it to the more widely recognized lytic cycle. The objective of this project is to demonstrate that persistent virus infections occur in marine phytoplankton, and that these are a crucial component of ocean ecosystem function and a key evolutionary driver in primary producers. Using a range of persistent virus:host systems, this project will investigate:<br />
1) how pervasive persistent virus infections are in marine systems; and<br />
2) the role of non-coding RNAs in maintaining host:virus symbiosis.</p>
<p>This is a high risk-high pay research as it involves a radically different approach to the analysis of viruses in marine systems. The investigators plan to apply a suite of molecular (transcriptomics, genomics and development of novel diagnostic markers) techniques to include the analysis of microRNAs to determine the functional importance of persistent viruses in the ocean. The results of this project will be potentially transformative for our understanding of virus-driven phytoplankton evolution and its potential impact on biodiversity in marine phytoplankton, a vital component of the global carbon cycle.</p>
<p>Note: William Wilson (Bigelow Laboratory) was the Former Principal Investigator on this project award.</p>
Marine Chronic Viruses
largerWorkCitation
project
eng; USA
oceans
Bigelow Laboratory for Ocean Sciences, Maine
2016-12-15
0
BCO-DMO catalogue of parameters from Primers used for Pleurochrysis carterae virus dPCR assays from laboratory experiments at the Bigelow Laboratory for Ocean Sciences, Maine from 2015-2016
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/671083.rdf
Name: primer_id
Units: unitless
Description: <p>Primer identifier (see dataset acquisition section for details)</p>
http://lod.bco-dmo.org/id/dataset-parameter/671084.rdf
Name: forward_primer
Units: unitless
Description: <p>Forward primer sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/671085.rdf
Name: reverse_primer
Units: unitless
Description: <p>Reverse primer sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/671086.rdf
Name: aplicon_length
Units: unitless
Description: <p>Number of nucleobases in amplicon</p>
http://lod.bco-dmo.org/id/dataset-parameter/671087.rdf
Name: annealing_temp
Units: degrees Celsius
Description: <p>Annealing temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/671088.rdf
Name: probe
Units: unitless
Description: <p>Probe sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/671089.rdf
Name: amplicon_sequence
Units: unitless
Description: <p>Amplicon sequence</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
1180
https://datadocs.bco-dmo.org/file/GwwAJ6NhOLV31B/VirusAssays.csv
VirusAssays.csv
Primary data file for dataset ID 670450
download
https://osprey.bco-dmo.org/dataset/670450/data/download
download
onLine
dataset
<p>Probes and primers were designed to target genotypes:&nbsp;<em>Pleurochrysis carterae&nbsp;</em>endemic virus genotypes 2 and 1b (PsEV2 and PsEV1b, respectively; dsDNA viruses);&nbsp;<em>P. carterae&nbsp;</em>Polinton-like viruses (PleuroPLV; dsDNA viruses); and&nbsp;<em>P. carterae&nbsp;</em>CRESS viruses (PcCV1, ssDNA viruses). For the latter, we designed probes for both the REP and the CAP genes to discriminate viral particles with partial (i.e., amplification for only the REP or the CAP markers from a single dPCR intact drop) or complete genomes (i.e., amplification with both molecular markers from a single dPCR intact drop). &nbsp; <a href="https://doi.org/10.2216/i0031-8884-32-3-234.1" target="_blank"> </a></p>
from Deployment: Bigelow_Martinez_2015-2016 <p>laboratory experiment</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Manager Processing Notes:</strong><br />
* made primer PcCV-1_Rep sequence uppercase (AGGAGGAG...)to match all other sequence formatting.<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* blank values replaced with no data value 'nd'</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Deployment: Bigelow_Martinez_2015-2016
Bigelow_Martinez_2015-2016
lab Bigelow
laboratory
lab Bigelow
laboratory