http://lod.bco-dmo.org/id/dataset/870161
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
2022-02-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cell volumes were calculated for 8 species of marine cryptophytes grown under full-spectrum, blue, green, or red light during laboratory-based growth experiments in 2018
2022-02-22
publication
2022-02-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-03-10
publication
https://doi.org/10.26008/1912/bco-dmo.870161.1
Tammi Richardson
University of South Carolina
principalInvestigator
Jeffry L. Dudycha
University of South Carolina
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: Richardson, T., Dudycha, J. L. (2022) Cell volumes were calculated for 8 species of marine cryptophytes grown under full-spectrum, blue, green, or red light during laboratory-based growth experiments in 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-02-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.870161.1 [access date]
Methods and Sampling: Full details are available in Heidenreich & Richardson (2020).
Cell volumes were calculated using a Nikon Eclipse TS100 inverted microscope at 200x magnification using live cells that were left on the stage for a period of time to slow their swimming speed.
Cell sizes were performed using non-preserved cells. We found that preserving these cryptophytes caused them to shrink or swell; response was unpredictable among species.
We assumed the shape was a prolate spheroid; where V = pi/6 * Length * width^2
Light treatments (all with 30 umol m^-2 s^-1 light intensity):
Full = Full Spectrum
Blue = Blue only
Green = Green only
Red = Red only
Each row in the data table corresponds to measurements from one cell within one of the light treatments.
Species List:
ScientificName,Strain,AphiaID,LSID
Chroomonas mesostigmatica, CCMP 1168,573826,urn:lsid:marinespecies.org:taxname:573826
Guillardia theta, CCMP 327,590566,urn:lsid:marinespecies.org:taxname:590566
Hemiselmis andersenii, CCMP 644,623449,urn:lsid:marinespecies.org:taxname:623449
Hemiselmis cryptochromatica, CCMP 1181,623450,urn:lsid:marinespecies.org:taxname:623450
Hemiselmis tepida, CCMP 443,623452,urn:lsid:marinespecies.org:taxname:623452
Proteomonas sulcata, CCMP 1175,573956,urn:lsid:marinespecies.org:taxname:573956
Rhodomonas salina, CCMP 1319,106316,urn:lsid:marinespecies.org:taxname:106316
Storeatula sp., CCMP 1868,573984,urn:lsid:marinespecies.org:taxname:573984
Funding provided by NSF Division of Environmental Biology (NSF DEB) Award Number: DEB-1542555 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1542555
completed
Tammi Richardson
University of South Carolina
803-777-2269
College of Arts and Sciences, Biological Sciences 715 Sumter Street (Room CLS 401)
Columbia
SC
29208
USA
richardson@biol.sc.edu
pointOfContact
Jeffry L. Dudycha
University of South Carolina
(803) 777-3987
715 Sumter Street Room CLS 608
Columbia
SC
29208
USA
dudycha@biol.sc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Date
Species
Strain
Treatment
Replicate
Length
Width
Volume
Nikon Eclipse TS100
theme
None, User defined
date
species scientific name (binomial)
sample description
treatment
replicate
length
width
volume
featureType
BCO-DMO Standard Parameters
Inverted Microscope
instrument
BCO-DMO Standard Instruments
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Dimensions: Links Between Spectral Irradiance and Cryptophyte Biodiversity in Environments from Ponds to Oceans
https://osprey.bco-dmo.org/project/655542
Dimensions: Links Between Spectral Irradiance and Cryptophyte Biodiversity in Environments from Ponds to Oceans
<p>In aquatic environments, microscopic algae known as phytoplankton are important primary producers. Through photosynthesis, these organisms fix carbon dioxide into the organic carbon molecules that fuel life in ponds, rivers, lakes and oceans. The color of light available for photosynthesis varies among environments, e.g., the deep blue ocean vs. a black water river. In order to live in a particular environment, phytoplankton must have photosynthetic pigments that are tuned to absorbing the colors of light available. This project focuses on the cryptophytes, a relatively uncharacterized group of phytoplankton, that are abundant in a wide range of aquatic habitats ranging from small ponds to oceans. Cryptophytes use phycobilin pigments to capture light energy; these pigments allow cryptophytes to photosynthesize in light environments that are poorly exploited by other types of algae. The project goals are: (1) to characterize the ecological distribution and taxonomic diversification of cryptophyte species, (2) to determine the effectiveness of their light capture in different light environments, and (3) to characterize the molecular evolutionary pathways of critical light capture genes. Understanding these links is important to predicting how changes in land-use (like deforestation and urbanization, both of which impact the color of light in downstream watersheds) will affect aquatic productivity. This project will provide training for a post-doc, 2-4 graduate students, and 10 undergraduates. Through a partnership with Morris College and other University of South Carolina programs, underrepresented minorities will be recruited into summer fellowships. Novel cryptophyte strains will be deposited in living culture collections for use by other researchers.</p>
<p>This project's central question is deceptively simple: How do functional, genetic, and phylogenetic diversity interact in the ecological diversification of cryptophytes with respect to light environment? The researchers will conduct an integrative research program on the biodiversity of cryptophytes to understand how environmental variation in spectral irradiance is associated with the physiological diversity of light capture in cryptophytes in the context of their historical diversification. This work integrates several components: (1) Field sampling in water bodies ranging from small ponds to oceans to identify the specific light environments in which strains live, to determine the pigments that cryptophytes produce in those habitats, and to identify novel species; (2) Phenotypic studies to determine how variation in spectral irradiance (light color) influences light capture, photosynthesis, and growth of diverse taxa. These will also determine spectral absorption of phycobilins in strains throughout the cryptophyta; (3) Construction of a well-supported phylogeny based on sequencing nucleomorph genomes of ~200 strains; (4) Analyses of molecular evolution of key light capture genes, in particular those that encode the alpha and beta subunits of the cryptophyte phycobiliproteins, and those involved in the phycobilin synthesis pathway; (5) Experimental evolution to test the ability of diverse strains of cryptophytes to evolve into new light niches; (6) Experimental transcriptomics to identify the functional responses of diverse strains to variation in spectral irradiance; and (7) Phylogenetically-informed tests of the associations between habitat, molecular evolution, organismal performance, and spectral absorbance. Ultimately, this work should be a transformative contribution to our understanding of the diversification of photosynthesis and the role of that diversification in the ecological distribution of cryptophytes.</p>
Spectral Irradiance and Cryptophyte Biodiversity
largerWorkCitation
project
eng; USA
oceans
2018-02-01
2018-02-12
Ponds, lakes, estuaries and oceans globally
0
BCO-DMO catalogue of parameters from Cell volumes were calculated for 8 species of marine cryptophytes grown under full-spectrum, blue, green, or red light during laboratory-based growth experiments in 2018
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/870609.rdf
Name: Date
Units: unitless
Description: <p>Cell measurement date in ISO8601 format YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/870610.rdf
Name: Species
Units: unitless
Description: <p>Scientific name (Genus species) of the cell measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/870611.rdf
Name: Strain
Units: unitless
Description: <p>Strain of the cell measured (e.g. CCMP 1168)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870612.rdf
Name: Treatment
Units: unitless
Description: <p>Light treatment (Full = Full Spectrum; Blue = Blue only; Green = Green only; Red = Red only). See methodology.</p>
http://lod.bco-dmo.org/id/dataset-parameter/870613.rdf
Name: Replicate
Units: unitless
Description: <p>Replicate number for each strain and treatment (unique for strain and light treatment).</p>
http://lod.bco-dmo.org/id/dataset-parameter/870614.rdf
Name: Length
Units: micrometers (um)
Description: <p>Cell length (longest axis)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870615.rdf
Name: Width
Units: micrometers (um)
Description: <p>Cell width (shortest axis)</p>
http://lod.bco-dmo.org/id/dataset-parameter/870616.rdf
Name: Volume
Units: cubic micrometers (um^3)
Description: <p>Cell volume (calculated, see methodology)</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
411433
https://darchive.mblwhoilibrary.org/bitstream/1912/28081/1/dataset-870161_cryptophyte-cell-volumes__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.870161.1
download
onLine
dataset
Full details are available in Heidenreich & Richardson (2020).
Cell volumes were calculated using a Nikon Eclipse TS100 inverted microscope at 200x magnification using live cells that were left on the stage for a period of time to slow their swimming speed.
Cell sizes were performed using non-preserved cells. We found that preserving these cryptophytes caused them to shrink or swell; response was unpredictable among species.
We assumed the shape was a prolate spheroid; where V = pi/6 * Length * width^2
Light treatments (all with 30 umol m^-2 s^-1 light intensity):
Full = Full Spectrum
Blue = Blue only
Green = Green only
Red = Red only
Each row in the data table corresponds to measurements from one cell within one of the light treatments.
Species List:
ScientificName,Strain,AphiaID,LSID
Chroomonas mesostigmatica, CCMP 1168,573826,urn:lsid:marinespecies.org:taxname:573826
Guillardia theta, CCMP 327,590566,urn:lsid:marinespecies.org:taxname:590566
Hemiselmis andersenii, CCMP 644,623449,urn:lsid:marinespecies.org:taxname:623449
Hemiselmis cryptochromatica, CCMP 1181,623450,urn:lsid:marinespecies.org:taxname:623450
Hemiselmis tepida, CCMP 443,623452,urn:lsid:marinespecies.org:taxname:623452
Proteomonas sulcata, CCMP 1175,573956,urn:lsid:marinespecies.org:taxname:573956
Rhodomonas salina, CCMP 1319,106316,urn:lsid:marinespecies.org:taxname:106316
Storeatula sp., CCMP 1868,573984,urn:lsid:marinespecies.org:taxname:573984
Specified by the Principal Investigator(s)
<p>Infinity Analyze program (V6.5.4; Lumenera Corporation,&nbsp;Nepean, Ontario, Canada).</p>
<div>BCO-DMO Data Manager Processing Notes:<br />
* Data from 8 Excel source files (one file per strain) Sheet1 were imported into the BCO-DMO data system. Original sheets had 4 data tables per sheet (one per light treatment).&nbsp;&nbsp;<br />
* Strategy for formatting data developed with the data submitter.<br />
* The separate strain and light treatment tables were concatenated into one data table with added columns to capture Treatment (Full, Red, Green, Blue), Replicate (within treatment)&nbsp;and what strain the treatment was for.&nbsp; Each row in the table corresponds to measurements from one cell.<br />
* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See <a href="https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions">https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions</a><br />
* Date column added from metadata preceding each table in the excel file (added in ISO 8601 format YYYY-MM-DD)</div>
<div>* Species names checked using the&nbsp;World Register of Marine Species taxa match tool.&nbsp; All names matched exactly to a currently accepted name (as of 2022-02-22). Species list, strain name,&nbsp;LSID and AphiaID added to metadata text.<br />
* Data table sorted by {Date}{Species}{Strain}{Treatment}{Replicate}</div>
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
Nikon Eclipse TS100
Nikon Eclipse TS100
PI Supplied Instrument Name: Nikon Eclipse TS100 PI Supplied Instrument Description:Cell sizes performed on Nikon Eclipse TS100 inverted microscope at 200x magnification using non-preserved cells. Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/