Data Access Form

Dataset Title:	[coccolithophore-associated biopolymers for radionuclides] - Coccolithophore- associated organic biopolymers for fractionating particle-reactive radionuclides (234Th, 233Pa, 210Pb, 210Po, and 7Be) (Biopolymers as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores)
Institution:	BCO-DMO (Dataset ID: bcodmo_dataset_738772)
Information:	Summary \| License \| ISO 19115 \| Metadata \| Background \| Files \| Make a graph

To work correctly, this web page requires that JavaScript be enabled in your browser. Please:
1) Enable JavaScript in your browser:
      • Chrome: "Settings : Advanced : Privacy and security : Site Settings : JavaScript"
      • Firefox: (it should be always on!)"
      • Opera: "Settings : Websites : JavaScript"
      • Safari: "Safari : Preferences : Security : Enable JavaScript"
2) Reload this web page.

Variable	Minimum	Maximum
Biopolymer_Fraction (unitless)	"AEPS"	"Shell associated b..."
Th234_Activity (unitless)	"2"	"n.d."
Pa233_Activity (unitless)	"1"	"n.d."
Pb210_Activity (unitless)	"3"	"n.d."
Po210_Activity (unitless)	"1"	"n.d."
Be7_Activity (unitless)	"0.3"	"n.d."
Protein_Amount (microMole Carbon (uM-C))	"-"	"n.d."
TCHO_Amount (microMole Carbon (uM-C))	1.0	25.7
URA_Amount (microMole Carbon (uM-C))	0.2	38.2
Protein_C_TCHO_C (unitless)	0.0	6.2
URA_pcnt_TCHO (unitless)	13	100

Server-side Functions

distinct()

Hover here to see a list of options. Click on an option to select it.

File type: (more information)

(Documentation / Bypass this form )

(Please be patient. It may take a while to get the data.)

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Biopolymer_Fraction {
    String bcodmo_name "sample_descrip";
    String description "biopolymer fraction of E. huxleyi cells";
    String long_name "Biopolymer Fraction";
    String units "unitless";
  }
  Th234_Activity {
    String bcodmo_name "radioactive_isotope_conc";
    String description "percentage of 234Th activity (%)";
    String long_name "Th234 Activity";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/WRAD/";
    String units "unitless";
  }
  Pa233_Activity {
    String bcodmo_name "radioactive_isotope_conc";
    String description "percentage of 233Pa activity (%)";
    String long_name "Pa233 Activity";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/WRAD/";
    String units "unitless";
  }
  Pb210_Activity {
    String bcodmo_name "radioactive_isotope_conc";
    String description "percentage of 210Pb activity (%)";
    String long_name "Pb210 Activity";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/WRAD/";
    String units "unitless";
  }
  Po210_Activity {
    String bcodmo_name "radioactive_isotope_conc";
    String description "percentage of 210Po activity (%)";
    String long_name "Po210 Activity";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/WRAD/";
    String units "unitless";
  }
  Be7_Activity {
    String bcodmo_name "radioactive_isotope_conc";
    String description "percentage of 7Be activity (%)";
    String long_name "Be7 Activity";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/WRAD/";
    String units "unitless";
  }
  Protein_Amount {
    String bcodmo_name "proteins";
    String description "amount of organic protein component";
    String long_name "Protein Amount";
    String units "microMole Carbon (uM-C)";
  }
  TCHO_Amount {
    Float32 _FillValue NaN;
    Float32 actual_range 1.0, 25.7;
    String bcodmo_name "carbohydrates";
    String description "amount of organic total carbohydrate component";
    String long_name "TCHO Amount";
    String units "microMole Carbon (uM-C)";
  }
  URA_Amount {
    Float32 _FillValue NaN;
    Float32 actual_range 0.2, 38.2;
    String bcodmo_name "unknown";
    String description "amount of organic Uronic acid component";
    String long_name "URA Amount";
    String units "microMole Carbon (uM-C)";
  }
  Protein_C_TCHO_C {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 6.2;
    String bcodmo_name "unknown";
    String description "ratio of proteins to total carbohydrates";
    String long_name "Protein C TCHO C";
    String units "unitless";
  }
  URA_pcnt_TCHO {
    Byte _FillValue 127;
    String _Unsigned "false";
    Byte actual_range 13, 100;
    String bcodmo_name "unknown";
    String description "the percentage of the uronic acid in the bulk total carbohydrates pool";
    String long_name "URA Pcnt TCHO";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"The seawater (< 1 kDa) was enriched with f/2 nutrients, trace metals and
vitamins, and autoclaved in pre-combusted and seawater-preconditioned clear
glassware. Then, ~50 Bq of each gamma emitting radionuclide, including 234Th,
233Pa, 210Pb and 7Be, was added. Since 210Po emits no gamma radiation, 210Po
was added separately into the seawater. After checking the pH of each
radiolabeled medium to be 8.0, 2 mL of laboratory axenic Emiliania huxleyi
(CCMP 371) was added to 100 mL of media and incubated at a temperature of
19\\u00b11\\u00baC with a light:dark cycle of 14 h:10 h under an irradiation
condition of 100 \\u00b5mol-quanta/m2/s.
 
Non-attached exopolymeric substances (NAEPS) and exopolymeric substances
attached on the coccolithophore cellular surface (AEPS) were extracted
followed the procedures described in Chuang et al. (2015) and Xu et al.
(2011). In brief, laboratory cultures were centrifuged at 3000 \\u00d7g for 30
min, and then the supernatant for the NAEPS fraction was filtered, followed by
the concentration and extensive desalting of supernatant against nanopure
water (18.2 \\u03a9) with 3 kDa Microsep centrifugal filter tubes (Milipore).
For AEPS extraction, the resultant pellet from the centrifugation was
resuspended by 50 mL 3% NaCl solution and stirred gently overnight at
4\\u00baC. Lastly, the solution was centrifuged, and the supernatant containing
the AEPS was then filtered before further desalting via the 3 kDa
ultrafiltration centrifugation tubes. The pellet from the previous step was
thus further digested in the 0.44 M HAc + 0.1 M NaCl solution at 4\\u00baC for
8 h. After the digestion, the mixed solution was centrifuged and filtered,
followed by ultrafiltration of the supernatant with 3 kDa Microsep centrifugal
filter tubes. The retentate (> 3 kDa) was defined as coccosphere-associated
biopolymers. The permeate (<3 kDa), defined as the fraction of digested
biogenic calcite. Cells remaining from the last step was further heated in 20
mL of 1% SDS containing 10 mM Tris solution (pH 6.8) at 95 \\u00baC for 1 h.
The supernatant was also collected through centrifugation and filtration,
followed by desalting and concentration with 3 kDa Microsep centrifugal filter
tubes. Subsequently, the pellet was further digested by 0.04 M NH2OH HCl +
4.35 M HAc mixture at 96 \\u00baC for 6 h, with occasional agitation to obtain
the intracellular Fe-Mn associated metabolitic biopolymer. The sum of these
two fractions represents the intracellular biopolymers after cell breakage.
 
Subsamples were taken from the concentrated biopolymers for the analysis of
protein, total carbohydrate (TCHO) and uronic acid (URA), respectively. In
brief, the protein abundance was measured through a modified Lowry protein
assay, using bovine serum albumin (BSA) as the standard. For the
concentrations of TCHO, samples were hydrolyzed by 0.09 M HCl (final
concentration) at 150\\u00baC for 1 h. After neutralization with NaOH solution,
the hydrolysate was measured by the 2,4,6-tripyridyl-triazine (TPTZ) method
(Hung et al., 2001), with glucose as the standard. URA concentrations were
determined by the metahydroxyphenyl method using glucuronic acid as the
standard (Hung and Santschi, 2001).\\u00a0
 
All the solutions from the different extraction steps, including the >3 kDa
biopolymer fractions and the permeate (< 3 kDa), were counted for the activity
concentrations of 234Th, 233Pa, 210Pb and 7Be by a Canberra ultrahigh purity
germanium well gamma detector. In addition, the 210Po activity in different
separately incubated fractions was determined by Beckman Model 8100 Liquid
Scintillation Counter.";
    String awards_0_award_nid "735995";
    String awards_0_award_number "OCE-1356453";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1356453";
    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 "Henrietta N Edmonds";
    String awards_0_program_manager_nid "51517";
    String cdm_data_type "Other";
    String comment 
"Coccolithophore-associated organic biopolymers for fractionating particle-reactive radionuclides (234Th, 233Pa, 210Pb, 210Po, and 7Be) 
  PI: Peter H. Santschi 
  Version 2018-05-15 
  Notes: \"n.d.\" denotes lower than detection limit 
         \"-\" denotes data not available 
         NAEPS = Non-attached exopolymeric substances\t 
         AEPS = Attached exopolymeric substances";
    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 "2018-06-18T18:14:36Z";
    String date_modified "2019-03-28T13:14:47Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.738772.1";
    String history 
"2024-11-21T08:35:46Z (local files)
2024-11-21T08:35:46Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_738772.html";
    String infoUrl "https://www.bco-dmo.org/dataset/738772";
    String institution "BCO-DMO";
    String instruments_0_acronym "LSC";
    String instruments_0_dataset_instrument_description "Beckman Model 8100 Liquid Scintillation Counter";
    String instruments_0_dataset_instrument_nid "738804";
    String instruments_0_description "Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB21/";
    String instruments_0_instrument_name "Liquid Scintillation Counter";
    String instruments_0_instrument_nid "624";
    String instruments_0_supplied_name "Beckman Model 8100 Liquid Scintillation Counter";
    String instruments_1_acronym "Spectrometer";
    String instruments_1_dataset_instrument_description "UV-Visible spectrometer, BioTek Instruments Inc Model EPOCH";
    String instruments_1_dataset_instrument_nid "738781";
    String instruments_1_description "A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/";
    String instruments_1_instrument_name "Spectrometer";
    String instruments_1_instrument_nid "667";
    String instruments_1_supplied_name "UV-Visible spectrometer";
    String instruments_2_dataset_instrument_description "Beckman Coulter Allegra X-12 centrifuge";
    String instruments_2_dataset_instrument_nid "738805";
    String instruments_2_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.";
    String instruments_2_instrument_name "Centrifuge";
    String instruments_2_instrument_nid "629890";
    String instruments_2_supplied_name "Beckman Coulter Allegra X-12 centrifuge";
    String instruments_3_dataset_instrument_description "Canberra ultrahigh purity germanium well gamma detector Model GCW3024";
    String instruments_3_dataset_instrument_nid "738780";
    String instruments_3_description "Instruments measuring the relative levels of electromagnetic radiation of different wavelengths in the gamma-ray waveband.";
    String instruments_3_instrument_name "Gamma Ray Spectrometer";
    String instruments_3_instrument_nid "670659";
    String instruments_3_supplied_name "Canberra ultrahigh purity germanium well gamma detector";
    String keywords "activity, amount, bco, bco-dmo, be7, Be7_Activity, biological, biopolymer, Biopolymer_Fraction, chemical, data, dataset, dmo, erddap, fraction, management, oceanography, office, pa233, Pa233_Activity, pb210, Pb210_Activity, pcnt, po210, Po210_Activity, preliminary, protein, Protein_Amount, Protein_C_TCHO_C, tcho, TCHO_Amount, th234, Th234_Activity, ura, URA_Amount, URA_pcnt_TCHO";
    String license "https://www.bco-dmo.org/dataset/738772/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/738772";
    String param_mapping "{'738772': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/738772/parameters";
    String people_0_affiliation "Texas A&M, Galveston";
    String people_0_affiliation_acronym "TAMUG";
    String people_0_person_name "Peter Santschi";
    String people_0_person_nid "735998";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Texas A&M, Galveston";
    String people_1_affiliation_acronym "TAMUG";
    String people_1_person_name "Antonietta Quigg";
    String people_1_person_nid "736000";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Texas A&M, Galveston";
    String people_2_affiliation_acronym "TAMUG";
    String people_2_person_name "Kathleen Schwehr";
    String people_2_person_nid "736002";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Texas A&M, Galveston";
    String people_3_affiliation_acronym "TAMUG";
    String people_3_person_name "Chen Xu";
    String people_3_person_nid "736004";
    String people_3_role "Co-Principal Investigator";
    String people_3_role_type "originator";
    String people_4_affiliation "Woods Hole Oceanographic Institution";
    String people_4_affiliation_acronym "WHOI BCO-DMO";
    String people_4_person_name "Mathew Biddle";
    String people_4_person_nid "708682";
    String people_4_role "BCO-DMO Data Manager";
    String people_4_role_type "related";
    String project "Biopolymers for radionuclides";
    String projects_0_acronym "Biopolymers for radionuclides";
    String projects_0_description 
"NSF Award Abstract:
Particle-associated natural radioisotopes are transported to the ocean floor mostly via silica and carbonate ballasted particles, allowing their use as tracers for particle transport. Th(IV), Pa (IV,V), Po(IV), Pb(II) and Be(II) radionuclides are important proxies in oceanographic investigations, used for tracing particle and colloid cycling, estimating export fluxes of particulate organic carbon, tracing air-sea exchange, paleoproductivity, and/or ocean circulation in paleoceanographic studies. Even though tracer approaches are considered routine, there are cases where data interpretation or validity has become controversial, largely due to uncertainties about inorganic proxies and organic carrier molecules. Recent studies showed that cleaned diatom frustules and pure silica particles, sorb natural radionuclides to a much lower extent (by 1-2 orders of magnitude) than whole diatom cells (with or without shells). Phytoplankton that build siliceous or calcareous shells, such as the diatoms and coccolithophores, are assembled via bio-mineralization processes using biopolymers as nanoscale templates. These templates could serve as possible carriers for radionuclides and stable metals.
In this project, a research team at the Texas A & M University at Galveston hypothesize that radionuclide sorption is controlled by selective biopolymers that are associated with biogenic opal (diatoms), CaCO3 (coccolithophores) and the attached exopolymeric substances (EPS), rather than to pure mineral phase. To pursue this idea, the major objectives of their research will include separation, identification and molecular-level characterization of the individual biopolymers (e.g., polysaccharides, uronic acids, proteins, hydroquinones, hydroxamate siderophores, etc.) that are responsible for binding different radionuclides (Th, Pa, Pb, Po and Be) attached to cells or in the matrix of biogenic opal or CaCO3 as well as attached EPS mixture, in laboratory grown diatom and coccolithophore cultures. Laboratory-scale radiolabeling experiments will be conducted, and different separation techniques and characterization techniques will be applied.
Intellectual Merit : It is expected that this study will help elucidate the molecular basis of the templated growth of diatoms and coccoliths, EPS and their role in scavenging natural radionuclides in the ocean, and help resolve debates on the oceanographic tracer applications of different natural radioisotopes (230,234Th, 231Pa, 210Po, 210Pb and 7,10Be). The proposed interdisciplinary research project will require instrumental approaches for molecular-level characterization of these radionuclides associated carrier molecules.
Broader Impacts: The results of this study will be relevant for understanding biologically mediated ocean scavenging of radionuclides by diatoms and coccoliths which is important for carbon cycling in the ocean, and will contribute to improved interpretation of data obtained by field studies especially through the GEOTRACES program. This new program will enhance training programs at TAMUG for postdocs, graduate and undergraduate students. Lastly, results will be integrated in college courses and out-reach activities at Texas A&M University, including NSF-REU, Sea Camp, Elder Hostel and exhibits at the local science fair and interaction with its after-school program engaging Grade 9-12 students from groups traditionally underrepresented.";
    String projects_0_end_date "2018-02";
    String projects_0_name "Biopolymers as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores";
    String projects_0_project_nid "735996";
    String projects_0_start_date "2014-03";
    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 "Laboratory incubation experiments using the coccolithophore Emiliania huxleyi were conducted in the presence of 234Th, 233Pa, 210Pb, 210Po, and 7Be to differentiate radionuclide uptake to the CaCO3 coccosphere from coccolithophore-associated biopolymers.";
    String title "[coccolithophore-associated biopolymers for radionuclides] - Coccolithophore-associated organic biopolymers for fractionating particle-reactive radionuclides (234Th, 233Pa, 210Pb, 210Po, and 7Be) (Biopolymers as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link)

Data Access Protocol (DAP) (external link)

and its selection constraints (external link)

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

(easy) You can get data by using the dataset's Data Access Form or Subset form. They make the URL for you.
(easy) You can make a graph or map by using the dataset's Make A Graph form. It makes the URL for you.
(not hard) You can bypass the forms and get the data or make a graph or map by generating the URL by hand or with a computer program or script.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.