Accessing BCO-DMO data
log in    
Brought to you by BCO-DMO    

ERDDAP > info > bcodmo_dataset_738772

Title Sum-
Institution Dataset ID
     data   graph     files  public Coccolithophore-associated organic biopolymers for fractionating particle-reactive
radionuclides (234Th, 233Pa, 210Pb, 210Po, and 7Be)
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_738772

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 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.
attribute NC_GLOBAL awards_0_award_nid String 735995
attribute NC_GLOBAL awards_0_award_number String OCE-1356453
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1356453 (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 Henrietta N Edmonds
attribute NC_GLOBAL awards_0_program_manager_nid String 51517
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String 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
AEPS = Attached exopolymeric substances
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 version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2018-06-18T18:14:36Z
attribute NC_GLOBAL date_modified String 2019-03-28T13:14:47Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.738772.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/738772 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String LSC
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Beckman Model 8100 Liquid Scintillation Counter
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 738804
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB21/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Liquid Scintillation Counter
attribute NC_GLOBAL instruments_0_instrument_nid String 624
attribute NC_GLOBAL instruments_0_supplied_name String Beckman Model 8100 Liquid Scintillation Counter
attribute NC_GLOBAL instruments_1_acronym String Spectrometer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String UV-Visible spectrometer, BioTek Instruments Inc Model EPOCH
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 738781
attribute NC_GLOBAL instruments_1_description String A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Spectrometer
attribute NC_GLOBAL instruments_1_instrument_nid String 667
attribute NC_GLOBAL instruments_1_supplied_name String UV-Visible spectrometer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Beckman Coulter Allegra X-12 centrifuge
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 738805
attribute NC_GLOBAL instruments_2_description String 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.
attribute NC_GLOBAL instruments_2_instrument_name String Centrifuge
attribute NC_GLOBAL instruments_2_instrument_nid String 629890
attribute NC_GLOBAL instruments_2_supplied_name String Beckman Coulter Allegra X-12 centrifuge
attribute NC_GLOBAL instruments_3_dataset_instrument_description String Canberra ultrahigh purity germanium well gamma detector Model GCW3024
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 738780
attribute NC_GLOBAL instruments_3_description String Instruments measuring the relative levels of electromagnetic radiation of different wavelengths in the gamma-ray waveband.
attribute NC_GLOBAL instruments_3_instrument_name String Gamma Ray Spectrometer
attribute NC_GLOBAL instruments_3_instrument_nid String 670659
attribute NC_GLOBAL instruments_3_supplied_name String Canberra ultrahigh purity germanium well gamma detector
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/738772/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/738772 (external link)
attribute NC_GLOBAL param_mapping String {'738772': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/738772/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Texas A&M, Galveston
attribute NC_GLOBAL people_0_affiliation_acronym String TAMUG
attribute NC_GLOBAL people_0_person_name String Peter Santschi
attribute NC_GLOBAL people_0_person_nid String 735998
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 Texas A&M, Galveston
attribute NC_GLOBAL people_1_affiliation_acronym String TAMUG
attribute NC_GLOBAL people_1_person_name String Antonietta Quigg
attribute NC_GLOBAL people_1_person_nid String 736000
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Texas A&M, Galveston
attribute NC_GLOBAL people_2_affiliation_acronym String TAMUG
attribute NC_GLOBAL people_2_person_name String Kathleen Schwehr
attribute NC_GLOBAL people_2_person_nid String 736002
attribute NC_GLOBAL people_2_role String Co-Principal Investigator
attribute NC_GLOBAL people_2_role_type String originator
attribute NC_GLOBAL people_3_affiliation String Texas A&M, Galveston
attribute NC_GLOBAL people_3_affiliation_acronym String TAMUG
attribute NC_GLOBAL people_3_person_name String Chen Xu
attribute NC_GLOBAL people_3_person_nid String 736004
attribute NC_GLOBAL people_3_role String Co-Principal Investigator
attribute NC_GLOBAL people_3_role_type String originator
attribute NC_GLOBAL people_4_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_4_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_4_person_name String Mathew Biddle
attribute NC_GLOBAL people_4_person_nid String 708682
attribute NC_GLOBAL people_4_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_4_role_type String related
attribute NC_GLOBAL project String Biopolymers for radionuclides
attribute NC_GLOBAL projects_0_acronym String Biopolymers for radionuclides
attribute NC_GLOBAL projects_0_description String 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.
attribute NC_GLOBAL projects_0_end_date String 2018-02
attribute NC_GLOBAL projects_0_name String Biopolymers as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores
attribute NC_GLOBAL projects_0_project_nid String 735996
attribute NC_GLOBAL projects_0_start_date String 2014-03
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String 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.
attribute NC_GLOBAL title String Coccolithophore-associated organic biopolymers for fractionating particle-reactive radionuclides (234Th, 233Pa, 210Pb, 210Po, and 7Be)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Biopolymer_Fraction   String  
attribute Biopolymer_Fraction bcodmo_name String sample_descrip
attribute Biopolymer_Fraction description String biopolymer fraction of E. huxleyi cells
attribute Biopolymer_Fraction long_name String Biopolymer Fraction
attribute Biopolymer_Fraction units String unitless
variable Th234_Activity   String  
attribute Th234_Activity bcodmo_name String radioactive_isotope_conc
attribute Th234_Activity description String percentage of 234Th activity (%)
attribute Th234_Activity long_name String Th234 Activity
attribute Th234_Activity nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/WRAD/ (external link)
attribute Th234_Activity units String unitless
variable Pa233_Activity   String  
attribute Pa233_Activity bcodmo_name String radioactive_isotope_conc
attribute Pa233_Activity description String percentage of 233Pa activity (%)
attribute Pa233_Activity long_name String Pa233 Activity
attribute Pa233_Activity nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/WRAD/ (external link)
attribute Pa233_Activity units String unitless
variable Pb210_Activity   String  
attribute Pb210_Activity bcodmo_name String radioactive_isotope_conc
attribute Pb210_Activity description String percentage of 210Pb activity (%)
attribute Pb210_Activity long_name String Pb210 Activity
attribute Pb210_Activity nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/WRAD/ (external link)
attribute Pb210_Activity units String unitless
variable Po210_Activity   String  
attribute Po210_Activity bcodmo_name String radioactive_isotope_conc
attribute Po210_Activity description String percentage of 210Po activity (%)
attribute Po210_Activity long_name String Po210 Activity
attribute Po210_Activity nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/WRAD/ (external link)
attribute Po210_Activity units String unitless
variable Be7_Activity   String  
attribute Be7_Activity bcodmo_name String radioactive_isotope_conc
attribute Be7_Activity description String percentage of 7Be activity (%)
attribute Be7_Activity long_name String Be7 Activity
attribute Be7_Activity nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/WRAD/ (external link)
attribute Be7_Activity units String unitless
variable Protein_Amount   String  
attribute Protein_Amount bcodmo_name String proteins
attribute Protein_Amount description String amount of organic protein component
attribute Protein_Amount long_name String Protein Amount
attribute Protein_Amount units String microMole Carbon (uM-C)
variable TCHO_Amount   float  
attribute TCHO_Amount _FillValue float NaN
attribute TCHO_Amount actual_range float 1.0, 25.7
attribute TCHO_Amount bcodmo_name String carbohydrates
attribute TCHO_Amount description String amount of organic total carbohydrate component
attribute TCHO_Amount long_name String TCHO Amount
attribute TCHO_Amount units String microMole Carbon (uM-C)
variable URA_Amount   float  
attribute URA_Amount _FillValue float NaN
attribute URA_Amount actual_range float 0.2, 38.2
attribute URA_Amount bcodmo_name String unknown
attribute URA_Amount description String amount of organic Uronic acid component
attribute URA_Amount long_name String URA Amount
attribute URA_Amount units String microMole Carbon (uM-C)
variable Protein_C_TCHO_C   float  
attribute Protein_C_TCHO_C _FillValue float NaN
attribute Protein_C_TCHO_C actual_range float 0.0, 6.2
attribute Protein_C_TCHO_C bcodmo_name String unknown
attribute Protein_C_TCHO_C description String ratio of proteins to total carbohydrates
attribute Protein_C_TCHO_C long_name String Protein C TCHO C
attribute Protein_C_TCHO_C units String unitless
variable URA_pcnt_TCHO   byte  
attribute URA_pcnt_TCHO _FillValue byte 127
attribute URA_pcnt_TCHO actual_range byte 13, 100
attribute URA_pcnt_TCHO bcodmo_name String unknown
attribute URA_pcnt_TCHO description String the percentage of the uronic acid in the bulk total carbohydrates pool
attribute URA_pcnt_TCHO long_name String URA Pcnt TCHO
attribute URA_pcnt_TCHO units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

ERDDAP, Version 2.02
Disclaimers | Privacy Policy | Contact