http://lod.bco-dmo.org/id/dataset/670442
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)
Analysis of temporal dynamics of three virus types persistently co-infecting Pleurochrysis carterae CCMP645 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/670442
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) Analysis of temporal dynamics of three virus types persistently co-infecting Pleurochrysis carterae CCMP645 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/670442 [access date]
Analysis of temporal dynamics of three virus types (ssDNA PcCV, dsDNA PLV, dsDNA PsEV) persistently co-infecting P. carterae CCMP645 Dataset Description: <p>This dataset contains temporal dynamics information for viruses co-infecting <em>Pleurochrysis carterae</em>, a coccolithophorid&nbsp;alga. &nbsp;Parameters included in this dataset are the number of virus droplets used, number of virus genomes per milliliter of culture, droplet normalization factors used, and the normalized number virus droplets used.</p>
<p><strong>Related datasets:</strong><br />
* <a href="https://www.bco-dmo.org/dataset/670431" target="_blank">Pleurochrysis carterae growth</a><br />
*&nbsp;&nbsp;<a href="https://www.bco-dmo.org/dataset/670450" target="_blank">Virus dPCR assay primers</a><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670912">Accession numbers (P. carterae viruses and field samples)</a><br />
* <a href="https://www.bco-dmo.org/dataset/670714" target="_blank">TEM Pleurochrysis carterae thin section images</a><br />
* <a href="https://www.bco-dmo.org/dataset/670706" target="_blank">TEM Pleurochrysis carterae virion images</a></p> Methods and Sampling: <p><em>Pleurochrysis carterae </em>CCMP645 cells in mid-exponential growth phase were transferred (10% v/v) into flasks containing either F/2 (Guillard, 1975) [1] or L1 (Guillard and Hargraves, 1993) [2] media, in duplicate. Virus production in each flask was monitored by digital PCR (dPCR) for a 106-day period. The frequency of sampling varied throughout the period of the study as indicated in the excel data file. At each sampling point, 0.5 ml samples were collected and stored at -80C without the addition of any fixatives for further quantification of viral abundances. Prior to analysis, the samples were thawed at room temperature, diluted 1:1 in nuclease-free water. &nbsp;Cellular debris was removed by centrifugation at maximum speed for 5 seconds. Two microliter aliquots were taken from the supernatant and put directly into digital PCR (dPCR) reactions to quantify the abundance of co-infecting virus genotypes. Specifically, probes and primers were designed to target genotypes: <em>P. carterae </em>endemic virus genotypes 2 and 1b (PsEV2 and PsEV1b, respectively; dsDNA viruses); <em>P. carterae </em>Polinton-like viruses (PleuroPLV; dsDNA viruses); and <em>P. carterae </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; For more information about primers used in these experiments see the&nbsp;&nbsp;<a href="https://www.bco-dmo.org/dataset/670450" target="_blank">Virus dPCR assay primer</a>&nbsp;dataset.</p>
<p>Specific primer/probe assays for all samples were multiplexed as follows:<br />
* Multiplex Assay 1 – PsEV2 and PsEV1b probes were TET-labelled and multiplexed with PcCV-1 Rep and Cap probes (FAM labelled).<br />
*&nbsp; Multiplex Assay 2 – For the second dPCR multiplex assay, the same samples were thawed again, diluted and spun out as before, and 2 ul of the supernatant was put into multiplex reaction with PleuroPLV assay (probe was FAM-labelled) and same 2 PsEV assays as an internal control to see how the repeated freeze-thaw cycles impacted the counts.</p>
<p>dPCR reactions contained 900 nM of each primer set and 200 nM probe, except for PsEV1b-TET and PcCV1-REP-FAM, which contained 450 nM primers and 100 nM probe. PCR reaction volumes were parsed into 5 million droplets per sample (RainDrop Source, RainDance Technologies) and then amplified in a C1000 Touch deep-well thermal cycler (Bio-Rad) with the following thermal protocol: 95C for 10 min; 95C for 15 s and then 60C for 60 s, with a ramping rate of 0.5C s−1 for 50 cycles; and final in-activation at 98C for 10 min. The droplets were enumerated on the RainDrop Sense (RainDance Technologies). &nbsp;</p>
<p>Reactions were run on a&nbsp;Bio Rad&nbsp;icycler&nbsp;and data was analyzed following Bio Rad’s Instruction Manual, Catalog Number 170-8740.</p>
<p><strong>References</strong></p>
<p>[1] Guillard, Robert RL. "Culture of phytoplankton for feeding marine invertebrates."&nbsp;<em>Culture of marine invertebrate animals</em>. Springer US, 1975. 29-60.</p>
<p>[2] Guillard, R. R. L., and P. E. Hargraves. "Stichochrysis immobilis is a diatom, not a chrysophyte."&nbsp;<em>Phycologia</em>&nbsp;32.3 (1993): 234-236. <a href="https://doi.org/10.2216/i0031-8884-32-3-234.1" target="_blank">https://doi.org/</a><a href="https://doi.org/10.2216/i0031-8884-32-3-234.1" target="_blank">10.2216/i0031-8884-32-3-234.1</a></p>
<p>&nbsp;</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
assay_id
date_start
date
media
replicate
drops
drops_CAP_FAM
drops_REP_FAM
drops_REP_and_CAP_FAM
drops_PsEV2_TET
drops_PsEV1b_TET
drops_PLV_FAM
drops_norm
PsEV2_norm
PsEV1b_norm
REP_norm
CAP_norm
REP_and_CAP_norm
PLV_norm
PsEV2_conc
PsEV1b_conc
REP_conc
CAP_conc
REP_and_CAP_conc
PLV_conc
sample_id
RainDrop Source
Bio Rad icycler
theme
None, User defined
sample identification
date_start
date
sample description
replicate
count
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Centrifuge
dPCR
Thermal Cycler
instrument
BCO-DMO Standard Instruments
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 Analysis of temporal dynamics of three virus types persistently co-infecting Pleurochrysis carterae CCMP645 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/671057.rdf
Name: assay_id
Units: unitless
Description: <p>Assay identifier (1 or 2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/671058.rdf
Name: date_start
Units: unitless
Description: <p>Start date of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/671059.rdf
Name: date
Units: unitless
Description: <p>Date of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/671060.rdf
Name: media
Units: unitless
Description: <p>Type of media used (L1 or F/2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/671061.rdf
Name: replicate
Units: unitless
Description: <p>Replicate (A or B)</p>
http://lod.bco-dmo.org/id/dataset-parameter/671062.rdf
Name: drops
Units: drop
Description: <p>Number of droplets counted by RainDrop Sense out of 5 mill formed drops</p>
http://lod.bco-dmo.org/id/dataset-parameter/671063.rdf
Name: drops_CAP_FAM
Units: drop
Description: <p>Number of droplets with partial P. carterae CRESS virus genomes; CAP-gene target only</p>
http://lod.bco-dmo.org/id/dataset-parameter/671064.rdf
Name: drops_REP_FAM
Units: drop
Description: <p>Number of droplets with partial P. carterae CRESS virus genomes; REP-gene target only</p>
http://lod.bco-dmo.org/id/dataset-parameter/671065.rdf
Name: drops_REP_and_CAP_FAM
Units: drop
Description: <p>Number of droplets with complete P. carterae CRESS virus genomes; CAP- and REP-gene targets</p>
http://lod.bco-dmo.org/id/dataset-parameter/671066.rdf
Name: drops_PsEV2_TET
Units: drop
Description: <p>Number of droplets with P. cartera endemic virus genotype 2 genomes</p>
http://lod.bco-dmo.org/id/dataset-parameter/671067.rdf
Name: drops_PsEV1b_TET
Units: drop
Description: <p>Number of droplets with P. cartera endemic virus genotype 1b genomes</p>
http://lod.bco-dmo.org/id/dataset-parameter/671068.rdf
Name: drops_PLV_FAM
Units: drop
Description: <p>Number of droplets with P. carterae Polinton-like virus</p>
http://lod.bco-dmo.org/id/dataset-parameter/671069.rdf
Name: drops_norm
Units: drop
Description: <p>Droplet normalization factor calculated as intact drops (Count divided by 5 mill total droplets)</p>
http://lod.bco-dmo.org/id/dataset-parameter/671070.rdf
Name: PsEV2_norm
Units: drop
Description: <p>Normalized number of droplets with P. cartera endemic virus genotype 2 genomes</p>
http://lod.bco-dmo.org/id/dataset-parameter/671071.rdf
Name: PsEV1b_norm
Units: drop
Description: <p>Normalized number of droplets with P. cartera endemic virus genotype 1b genomes</p>
http://lod.bco-dmo.org/id/dataset-parameter/671072.rdf
Name: REP_norm
Units: drop
Description: <p>Normalized number of droplets with partial P. carterae CRESS virus genomes; REP-gene target only</p>
http://lod.bco-dmo.org/id/dataset-parameter/671073.rdf
Name: CAP_norm
Units: drop
Description: <p>Normalized number of droplets with partial P. carterae CRESS virus genomes; CAP-gene target only</p>
http://lod.bco-dmo.org/id/dataset-parameter/671074.rdf
Name: REP_and_CAP_norm
Units: drop
Description: <p>Normalized number of droplets with complete P. carterae CRESS virus genomes; CAP- and REP-gene targets</p>
http://lod.bco-dmo.org/id/dataset-parameter/671075.rdf
Name: PLV_norm
Units: drop
Description: <p>Normalized number of droplets with P. carterae Polinton-like virus genomes</p>
http://lod.bco-dmo.org/id/dataset-parameter/671076.rdf
Name: PsEV2_conc
Units: genomes per milliliter
Description: <p>Estimated P. cartera endemic virus genotype 2 genomes per milliliter of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/671077.rdf
Name: PsEV1b_conc
Units: genomes per milliliter
Description: <p>Estimated P. cartera endemic virus genotype 1b genomes per milliliter of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/671078.rdf
Name: REP_conc
Units: genomes per milliliter
Description: <p>Estimated P. carterae CRESS virus REP-gene partial genomes per milliliter of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/671079.rdf
Name: CAP_conc
Units: genomes per milliliter
Description: <p>Estimated P. carterae CRESS virus CAP-gene partial genomes per milliliter of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/671080.rdf
Name: REP_and_CAP_conc
Units: genomes per milliliter
Description: <p>Estimated P. carterae CRESS virus complete genomes per milliliter of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/671081.rdf
Name: PLV_conc
Units: genomes per milliliter
Description: <p>Estimated P. carterae Polinton-like virus genomes per milliliter of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/671082.rdf
Name: sample_id
Units: unitless
Description: <p>sampling day number (1-106) culture media (F/2 or L1) replicate (A or B)</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
22999
https://datadocs.bco-dmo.org/file/KAAGNrls259pNz/PleuroViruses.csv
PleuroViruses.csv
Primary data file for dataset ID 670442
download
https://osprey.bco-dmo.org/dataset/670442/data/download
download
onLine
dataset
<p><em>Pleurochrysis carterae </em>CCMP645 cells in mid-exponential growth phase were transferred (10% v/v) into flasks containing either F/2 (Guillard, 1975) [1] or L1 (Guillard and Hargraves, 1993) [2] media, in duplicate. Virus production in each flask was monitored by digital PCR (dPCR) for a 106-day period. The frequency of sampling varied throughout the period of the study as indicated in the excel data file. At each sampling point, 0.5 ml samples were collected and stored at -80C without the addition of any fixatives for further quantification of viral abundances. Prior to analysis, the samples were thawed at room temperature, diluted 1:1 in nuclease-free water. &nbsp;Cellular debris was removed by centrifugation at maximum speed for 5 seconds. Two microliter aliquots were taken from the supernatant and put directly into digital PCR (dPCR) reactions to quantify the abundance of co-infecting virus genotypes. Specifically, probes and primers were designed to target genotypes: <em>P. carterae </em>endemic virus genotypes 2 and 1b (PsEV2 and PsEV1b, respectively; dsDNA viruses); <em>P. carterae </em>Polinton-like viruses (PleuroPLV; dsDNA viruses); and <em>P. carterae </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; For more information about primers used in these experiments see the&nbsp;&nbsp;<a href="https://www.bco-dmo.org/dataset/670450" target="_blank">Virus dPCR assay primer</a>&nbsp;dataset.</p>
<p>Specific primer/probe assays for all samples were multiplexed as follows:<br />
* Multiplex Assay 1 – PsEV2 and PsEV1b probes were TET-labelled and multiplexed with PcCV-1 Rep and Cap probes (FAM labelled).<br />
*&nbsp; Multiplex Assay 2 – For the second dPCR multiplex assay, the same samples were thawed again, diluted and spun out as before, and 2 ul of the supernatant was put into multiplex reaction with PleuroPLV assay (probe was FAM-labelled) and same 2 PsEV assays as an internal control to see how the repeated freeze-thaw cycles impacted the counts.</p>
<p>dPCR reactions contained 900 nM of each primer set and 200 nM probe, except for PsEV1b-TET and PcCV1-REP-FAM, which contained 450 nM primers and 100 nM probe. PCR reaction volumes were parsed into 5 million droplets per sample (RainDrop Source, RainDance Technologies) and then amplified in a C1000 Touch deep-well thermal cycler (Bio-Rad) with the following thermal protocol: 95C for 10 min; 95C for 15 s and then 60C for 60 s, with a ramping rate of 0.5C s−1 for 50 cycles; and final in-activation at 98C for 10 min. The droplets were enumerated on the RainDrop Sense (RainDance Technologies). &nbsp;</p>
<p>Reactions were run on a&nbsp;Bio Rad&nbsp;icycler&nbsp;and data was analyzed following Bio Rad’s Instruction Manual, Catalog Number 170-8740.</p>
<p><strong>References</strong></p>
<p>[1] Guillard, Robert RL. "Culture of phytoplankton for feeding marine invertebrates."&nbsp;<em>Culture of marine invertebrate animals</em>. Springer US, 1975. 29-60.</p>
<p>[2] Guillard, R. R. L., and P. E. Hargraves. "Stichochrysis immobilis is a diatom, not a chrysophyte."&nbsp;<em>Phycologia</em>&nbsp;32.3 (1993): 234-236. <a href="https://doi.org/10.2216/i0031-8884-32-3-234.1" target="_blank">https://doi.org/</a><a href="https://doi.org/10.2216/i0031-8884-32-3-234.1" target="_blank">10.2216/i0031-8884-32-3-234.1</a></p>
<p>&nbsp;</p>
from Deployment: Bigelow_Martinez_2015-2016 <p>laboratory experiment</p>
Specified by the Principal Investigator(s)
<p>Standard procedures based on Cq value were followed to quantify gene copies in each sample. We followed general guidance from Bio Rad’s Instruction Manual, Catalog Number 170-8740.&nbsp;</p>
<p><strong>BCO-DMO Data Manager Processing Notes:</strong><br />
* Added date column from start date 2015-10-07 and date information in sample ID.<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'<br />
* Date format converted to ISO Date format</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
PI Supplied Instrument Name: Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
RainDrop Source
RainDrop Source
PI Supplied Instrument Name: RainDrop Source PI Supplied Instrument Description:RainDrop Source from RainDance Technologies Instrument Name: dPCR Instrument Short Name:dPCR Instrument Description: Digital Polymerase Chain Reaction (dPCR)
Bio Rad icycler
Bio Rad icycler
PI Supplied Instrument Name: Bio Rad icycler PI Supplied Instrument Description:Reactions were run on a Bio Rad icycler and data was analyzed following Bio Rad’s Instruction Manual, Catalog Number 170-8740. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: Bigelow_Martinez_2015-2016
Bigelow_Martinez_2015-2016
lab Bigelow
laboratory
lab Bigelow
laboratory