http://lod.bco-dmo.org/id/dataset/670431
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)
Growth rate of Pleurochrysis carterae CCMP645 cells as measured by flow cytometry in laboratory experiments
2016-12-15
publication
2016-12-15
revision
BCO-DMO Linked Data URI
2016-12-15
creation
http://lod.bco-dmo.org/id/dataset/670431
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) Growth rate of Pleurochrysis carterae CCMP645 cells as measured by flow cytometry in laboratory experiments. 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/670431 [access date]
Growth rate of Pleurochrysis carterae CCMP645 cells as measured by flow cytometry Dataset Description: <p>Laboratory-based experiment using flow cytometry of coccolithophorid&nbsp;alga clonal culture isolates (Pleurochrysis&nbsp;carterae). All work was carried out at Bigelow Laboratory for Ocean Sciences,&nbsp;Maine.</p>
<p><strong>Related datasets:</strong><br />
*&nbsp;<a href="https://www.bco-dmo.org/dataset/670442">Pleurochrysis carterae virus production</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 />
*&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><em>Pleurochrysis carterae </em>CCMP645 cells in mid-exponential growth phase were transferred (10% v/v) into flasks containing either F/2 (Guillard, 1975) or L1 (Guillard and Hargraves, 1993) media, in duplicate. Host abundance in each flask was monitored by flow cytometry (FCM) on a BD FACScan(TM) System 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 time point 1 ml volume sample was collected from each flask and preserved in 0.5% paraformaldehyde, then snap frozen in liquid nitrogen and stored at -80C until ready for FCM analysis. Flow cytometry sample acquisition time was one minute for all samples. &nbsp;FCM analysis was carried out as described in Marie et al. 2005. &nbsp;</p>
<p><strong>References</strong></p>
<p>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>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>Marie, Dominique, Nathalie Simon, and Daniel Vaulot. "Phytoplankton cell counting by flow cytometry."&nbsp;<em>Algal culturing techniques</em>&nbsp;(2005): 253-267. &nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1346272 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1346272
completed
Joaquín Martínez Martínez
Bigelow Laboratory for Ocean Sciences
207-315-2567
60 Bigelow Drive
East Boothbay
ME
04544
USA
jmartinez@bigelow.org
pointOfContact
asNeeded
Unknown
date
sample_id
counts
flow_rate
cell_conc
acquisition_time
BD FACScan(TM) System
theme
None, User defined
date
sample identification
count
flow rate
cell_concentration
time_elapsed
featureType
BCO-DMO Standard Parameters
Flow Cytometer
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://www.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
biota
Bigelow Laboratory for Ocean Sciences, Maine
2016-12-15
0
BCO-DMO catalogue of parameters from Growth rate of Pleurochrysis carterae CCMP645 cells as measured by flow cytometry in laboratory experiments
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/670931.rdf
Name: date
Units: unitless
Description: sample date in format yyyy-mm-dd
http://lod.bco-dmo.org/id/dataset-parameter/670932.rdf
Name: sample_id
Units: unitless
Description: sample identifier made up of day the experiment; media used; and replicate (A or B)
http://lod.bco-dmo.org/id/dataset-parameter/670933.rdf
Name: counts
Units: count
Description: flow cytometry cell count for 1ml volume sample
http://lod.bco-dmo.org/id/dataset-parameter/670934.rdf
Name: flow_rate
Units: microliters per minute (ul/min)
Description: flow cytometry flow rate
http://lod.bco-dmo.org/id/dataset-parameter/670935.rdf
Name: cell_conc
Units: cells per milliliter
Description: cell concentration
http://lod.bco-dmo.org/id/dataset-parameter/671143.rdf
Name: acquisition_time
Units: unitless
Description: flow cytometry sample acquisition time in minutes
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
3487
https://datadocs.bco-dmo.org/file/JEE1M6ktpoqyyk/PleuroGrowth.csv
PleuroGrowth.csv
Primary data file for dataset ID 670431
download
https://www.bco-dmo.org/dataset/670431/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) or L1 (Guillard and Hargraves, 1993) media, in duplicate. Host abundance in each flask was monitored by flow cytometry (FCM) on a BD FACScan(TM) System 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 time point 1 ml volume sample was collected from each flask and preserved in 0.5% paraformaldehyde, then snap frozen in liquid nitrogen and stored at -80C until ready for FCM analysis. Flow cytometry sample acquisition time was one minute for all samples. &nbsp;FCM analysis was carried out as described in Marie et al. 2005. &nbsp;</p>
<p><strong>References</strong></p>
<p>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>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>Marie, Dominique, Nathalie Simon, and Daniel Vaulot. "Phytoplankton cell counting by flow cytometry."&nbsp;<em>Algal culturing techniques</em>&nbsp;(2005): 253-267. &nbsp;</p>
from Deployment: Bigelow_Martinez_2015-2016 <p>laboratory experiment</p>
Specified by the Principal Investigator(s)
<p>FCM data were analyzed with BD Cell QuestTM Pro, v. 5.2.1.</p>
<p><strong>BCO-DMO Data Manager Processing Notes:</strong><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
BD FACScan(TM) System
BD FACScan(TM) System
PI Supplied Instrument Name: BD FACScan(TM) System PI Supplied Instrument Description:Host abundance in each flask was monitored by flow cytometry (FCM) on a BD FACScan(TM) System for a 106-day period. Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Deployment: Bigelow_Martinez_2015-2016
Bigelow_Martinez_2015-2016
lab Bigelow
laboratory
lab Bigelow
laboratory