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Dataset Title:  Cell size and chemical characteristics of five strains of coccolithophore
Emiliania huxleyi (Protist signaling project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_684883)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files
Variable ?   Optional
Constraint #1 ?
Constraint #2 ?
   Minimum ?
   Maximum ?
 data_type (unitless) ?          "Calcifying"    "Replicate determin..."
 CCMP1516 (unitless) ?          "0.014"    "no"
 CCMP3268 (unitless) ?          "0.015"    "no"
 CCMP3266 (unitless) ?          "0.056"    "yes"
 CCMP2668 (unitless) ?          "0.009"    "yes"
 NEZH (unitless) ?          "0.18"    "yes"
Server-side Functions ?
 distinct() ?
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File type: (more info)

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  data_type {
    String bcodmo_name "datatype";
    String description "Description of the type of data found in the corresponding row.";
    String long_name "Data Type";
    String units "unitless";
  CCMP1516 {
    String bcodmo_name "sample";
    String description "Data for strain CCMP1516";
    String long_name "CCMP1516";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  CCMP3268 {
    String bcodmo_name "sample";
    String description "Data for strain CCMP3268";
    String long_name "CCMP3268";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  CCMP3266 {
    String bcodmo_name "sample";
    String description "Data for strain CCMP3266";
    String long_name "CCMP3266";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  CCMP2668 {
    String bcodmo_name "sample";
    String description "Data for strain CCMP2668";
    String long_name "CCMP2668";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  NEZH {
    String bcodmo_name "sample";
    String description "Data for strain NEZH";
    String long_name "NEZH";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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
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.";
    String awards_0_award_nid "614837";
    String awards_0_award_number "OCE-1434842";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1434842";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "David L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Emiliania huxleyi biochem data 
  S. Strom 
  Version 5 April 2017";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2017-03-20T16:51:34Z";
    String date_modified "2019-04-03T20:12:49Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.684883.1";
    String history 
"2024-04-24T00:52:08Z (local files)
2024-04-24T00:52:08Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_684883.html";
    String infoUrl "https://www.bco-dmo.org/dataset/684883";
    String institution "BCO-DMO";
    String instruments_0_acronym "Gas Chromatograph";
    String instruments_0_dataset_instrument_description "Used to measure Dimethylsulfoniopropionate (DMSP)";
    String instruments_0_dataset_instrument_nid "684896";
    String instruments_0_description "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)";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB02/";
    String instruments_0_instrument_name "Gas Chromatograph";
    String instruments_0_instrument_nid "661";
    String instruments_0_supplied_name "Shimadzu GC-14A gas chromatograph";
    String instruments_1_dataset_instrument_description "Used to determine cell size";
    String instruments_1_dataset_instrument_nid "684898";
    String instruments_1_description "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\".";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
    String instruments_1_instrument_name "Microscope-Optical";
    String instruments_1_instrument_nid "708";
    String instruments_1_supplied_name "Leica DM5500 B microscope";
    String instruments_2_dataset_instrument_description "Used to measure fluorescent reaction";
    String instruments_2_dataset_instrument_nid "684897";
    String instruments_2_description "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 µL 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.";
    String instruments_2_instrument_name "plate reader";
    String instruments_2_instrument_nid "528693";
    String instruments_2_supplied_name "BioTek Synergy M plate reader";
    String keywords "bco, bco-dmo, biological, ccmp1516, ccmp2668, ccmp3266, ccmp3268, chemical, data, data_type, dataset, dmo, erddap, management, nezh, oceanography, office, preliminary, type";
    String license "https://www.bco-dmo.org/dataset/684883/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/684883";
    String param_mapping "{'684883': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/684883/parameters";
    String people_0_affiliation "Western Washington University - Shannon Point Marine Center";
    String people_0_affiliation_acronym "SPMC";
    String people_0_person_name "Suzanne Strom";
    String people_0_person_nid "50471";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Woods Hole Oceanographic Institution";
    String people_1_affiliation_acronym "WHOI BCO-DMO";
    String people_1_person_name "Hannah Ake";
    String people_1_person_nid "650173";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String project "Protist signaling";
    String projects_0_acronym "Protist signaling";
    String projects_0_description 
"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.";
    String projects_0_end_date "2017-08";
    String projects_0_geolocation "Salish Sea: 48.5, -122.75";
    String projects_0_name "Environmental stress and signaling based on reactive oxygen species among planktonic protists";
    String projects_0_project_nid "614838";
    String projects_0_start_date "2014-09";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Cell size and chemical characteristics of five strains of coccolithophore Emiliania huxleyi (Protist signaling project)";
    String title "Cell size and chemical characteristics of five strains of coccolithophore Emiliania huxleyi (Protist signaling project)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";


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