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     data        files  public Cell size and chemical characteristics of five strains of coccolithophore Emiliania
huxleyi (Protist signaling project)
   ?     I   M   background (external link) RSS BCO-DMO bcodmo_dataset_684883

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Cultures of\u00a0\u00a0Emiliania\u00a0huxleyi\u00a0were obtained from the
National Center for Marine Algae and Microbiota at Bigelow Laboratories (all
CCMP strains), or from Dr. D. Iglesias-Rodriguez at UC Santa Barbara (strain
NEZH) and maintained in the Strom laboratory at Shannon Point Marine Center.

Batch cultures were grown in 50-100 ml volumes of seawater (salinity = 30)
amended with f/50 nutrients, at a temperature of 15 deg C and an irradiance of
140-300 umol photons m-2\u00a0s-1\u00a0on a 12L:12D light cycle. Replicate
cultures (n=3) were subsampled for chemical measurements at cell densities of
1.4 to 2.7 x 10^5\u00a0cells ml-1\u00a0(DMSP) and 3.6 to 12.8 x
10^5\u00a0cells ml-1\u00a0(H2O2). Different chemical and size measurements
reported for a given strain were made over the course of several separate
experiments.

Dimethylsulfoniopropionate (DMSP) contained
within\u00a0E.\u00a0huxleyi\u00a0cells was measured using a Shimadzu GC-14A
gas chromatograph and flame photometric detection, following the methods of
Wolfe et al. (2002 J.\u00a0Phycol.\u00a038:\u00a0948-960).\u00a0 Cells were
captured on 25 mm glass fiber filters (effective pore size 0.7 um) and placed
into 3 ml 5N NaOH for hydrolysis.\u00a0Method\u00a0was standardized using
ultrapure DMSP-Cl (standard range 0.625 to 50 nM; r2\u00a0\u22650.998).

Hydrogen peroxide (H2O2) released into the dissolved phase
by\u00a0E.\u00a0huxleyi\u00a0was measured using the Amplex Red \u2013
horseradish peroxidase method, using a kit from Molecular Probes (now part of
Thermo Fisher Scientific) according to kit directions and to Suggett et al.
(2008 J\u00a0Phycol\u00a044:\u00a0948-956).\u00a0Fluorescent\u00a0reaction
product was quantified in a BioTek Synergy M plate reader (565 nm excitation,
585 nm emission). True reagent blanks were obtained by catalase treatment
of\u00a0E.\u00a0huxleyi\u00a0culture filtrate (50 U ml-1, 45 min, room
temperature) following Shaked et al. (2010 Environ Sci
Technol\u00a044:\u00a03238-3244). Method was standardized using ultrapure
H2O2\u00a0(standard range 0.025 to 0.5 uM; r2\u00a0= 0.98)

E.\u00a0huxleyi\u00a0cell size was obtained by imaging live cells (n = 23-29)
at 1000x magnification on a Leica DM5500 B microscope, and sizing them with
associated image analysis software. Calcification (i.e. whether a strain
harbored coccoliths) was also confirmed\u00a0during\u00a0microscopy. Note that
the sample of strain CCMP3266 used for size measurement comprised a mixture of
calcifying and non-calcifying cells.
attribute NC_GLOBAL awards_0_award_nid String 614837
attribute NC_GLOBAL awards_0_award_number String OCE-1434842
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1434842 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Dr David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Emiliania huxleyi biochem data
S. Strom
Version 5 April 2017
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv.pl v1.0
attribute NC_GLOBAL date_created String 2017-03-20T16:51:34Z
attribute NC_GLOBAL date_modified String 2019-04-03T20:12:49Z
attribute NC_GLOBAL defaultDataQuery String &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.684883.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/684883 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Gas Chromatograph
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to measure�Dimethylsulfoniopropionate (DMSP)
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 684896
attribute NC_GLOBAL instruments_0_description String Instrument separating gases, volatile substances, or substances dissolved in a volatile solvent by transporting an inert gas through a column packed with a sorbent to a detector for assay. (from SeaDataNet, BODC)
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB02/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Gas Chromatograph
attribute NC_GLOBAL instruments_0_instrument_nid String 661
attribute NC_GLOBAL instruments_0_supplied_name String Shimadzu GC-14A gas chromatograph
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used to determine cell size
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 684898
attribute NC_GLOBAL instruments_1_description String Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB05/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Microscope-Optical
attribute NC_GLOBAL instruments_1_instrument_nid String 708
attribute NC_GLOBAL instruments_1_supplied_name String Leica DM5500 B microscope
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Used to measure fluorescent reaction
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 684897
attribute NC_GLOBAL instruments_2_description String Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 �L per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: https://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
attribute NC_GLOBAL instruments_2_instrument_name String plate reader
attribute NC_GLOBAL instruments_2_instrument_nid String 528693
attribute NC_GLOBAL instruments_2_supplied_name String BioTek Synergy M plate reader
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, ccmp1516, ccmp2668, ccmp3266, ccmp3268, chemical, data, data_type, dataset, dmo, erddap, management, nezh, oceanography, office, preliminary, type
attribute NC_GLOBAL license String The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/684883 (external link)
attribute NC_GLOBAL param_mapping String {'684883': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/684883/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Western Washington University - Shannon Point Marine Center
attribute NC_GLOBAL people_0_affiliation_acronym String SPMC
attribute NC_GLOBAL people_0_person_name String Suzanne Strom
attribute NC_GLOBAL people_0_person_nid String 50471
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Hannah Ake
attribute NC_GLOBAL people_1_person_nid String 650173
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Environmental stress and signaling based on reactive oxygen species among planktonic protists
attribute NC_GLOBAL projects_0_acronym String Protist signaling
attribute NC_GLOBAL projects_0_description String Description from NSF proposal:
This proposal arises from the central premise that the oxidative stress response is an emergent property of phototrophic cellular systems, with implications for nearly every aspect of a phytoplankton cell’s life in the upper ocean. Oxidative stress (OS) arises from the uncompensated production of reactive oxygen species (ROS) within a cell, which can occur in response to a myriad of environmental stressors (e.g. nutrient limitation, temperature extremes, toxins, variable light exposure). In addition to the biochemical damage and physiological impairment that OS can cause, the phytoplankton OS response also includes increased net production and extracellular release of ROS, osmolytes, and other compounds that are known or suspected to be potent signals regulating protist behavior. We hypothesize that, through chemical signaling, oxidative stress acts to govern relationships among environmental variability, phytoplankton condition, and protist predation. Our proposed study of these integrated signaling and response processes has three overarching objectives: 1) Create and characterize oxidatively stressed phytoplankton. We will use light stress (variable exposure to visible light and UV) to create oxidatively stressed phytoplankton in the laboratory. Common coastal taxa with contrasting stress responses will be characterized using an array of fluorescent probes, biochemical measurements, and physiological assays. In addition, intracellular production and extracellular release of ROS and the associated chemical signal DMSP will be quantified. Use of Phaeodactylum tricornutum light stress mutants will add an independent means of connecting OS to signal production and predation response. 2) Examine protist predator responses to oxidatively stressed phytoplankton and associated chemical signals. Responses will be investigated by means of manipulation experiments and thorough characterization of associated signal chemistry. Assessment of predator response will be via predation rate measurements and population aggregation/dispersal behaviors in structured columns. 3) Investigate the prevalence of OS, its environmental correlates, and the microzooplankton predation response in the natural waters of a well-characterized local embayment. Application of ROS probes and OS assays to the natural environment and the design of OS manipulation experiments will be informed by the laboratory experiments using local protist species.
Our work will help to elucidate some of the multiple ways in which the OS response can affect phytoplankton fitness, contributing information that can be used to characterize the position of key coastal species along an OS response spectrum. Ultimately such information could be used in trait-based conceptual and numerical models in a manner analogous to cell size and other 'master traits'. Our research will also inform the relatively new and exciting field of chemical signaling in planktonic communities, exploring DMSP- and ROS-based signaling between two of the most significant groups in the plankton, the eukaryotic phytoplankton and their protist predators. Finally, findings will help elucidate the links between environmental stress, phytoplankton response, and predation in planktonic ecosystems. These links relate to central issues in biological oceanography, including the predator-prey interactions that influence bloom demise, and the mechanisms by which protists feed selectively and thereby structure prey communities. The proposed research is a cross-cutting endeavor that unites subjects usually studied in isolation through a novel conceptual framework. Thus the findings have the potential to generate broadly applicable new insights into the ecological and evolutionary regulation of this key trophic link in planktonic food webs.
attribute NC_GLOBAL projects_0_end_date String 2017-08
attribute NC_GLOBAL projects_0_geolocation String Salish Sea: 48.5, -122.75
attribute NC_GLOBAL projects_0_name String Environmental stress and signaling based on reactive oxygen species among planktonic protists
attribute NC_GLOBAL projects_0_project_nid String 614838
attribute NC_GLOBAL projects_0_start_date String 2014-09
attribute NC_GLOBAL publisher_name String Hannah Ake
attribute NC_GLOBAL publisher_role String BCO-DMO Data Manager(s)
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v29
attribute NC_GLOBAL summary String Cell size and chemical characteristics of five strains of coccolithophore Emiliania huxleyi (Protist signaling project)
attribute NC_GLOBAL title String Cell size and chemical characteristics of five strains of coccolithophore Emiliania huxleyi (Protist signaling project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.0-alpha
variable data_type   String  
attribute data_type description String Description of the type of data found in the corresponding row.
attribute data_type ioos_category String Unknown
attribute data_type long_name String Data Type
attribute data_type units String unitless
variable CCMP1516   String  
attribute CCMP1516 description String Data for strain�CCMP1516
attribute CCMP1516 ioos_category String Unknown
attribute CCMP1516 long_name String CCMP1516
attribute CCMP1516 units String unitless
variable CCMP3268   String  
attribute CCMP3268 description String Data for strain�CCMP3268
attribute CCMP3268 ioos_category String Unknown
attribute CCMP3268 long_name String CCMP3268
attribute CCMP3268 units String unitless
variable CCMP3266   String  
attribute CCMP3266 description String Data for strain�CCMP3266
attribute CCMP3266 ioos_category String Unknown
attribute CCMP3266 long_name String CCMP3266
attribute CCMP3266 units String unitless
variable CCMP2668   String  
attribute CCMP2668 description String Data for strain�CCMP2668
attribute CCMP2668 ioos_category String Unknown
attribute CCMP2668 long_name String CCMP2668
attribute CCMP2668 units String unitless
variable NEZH   String  
attribute NEZH description String Data for strain�NEZH
attribute NEZH ioos_category String Unknown
attribute NEZH long_name String NEZH
attribute NEZH units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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