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Dataset Title:  Percent amount of organic fractions from diatoms that bind with radionuclides   RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_764860)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  substance {
    String description "type of substance";
    String ioos_category "Unknown";
    String long_name "Substance";
    String units "unitless";
  Protein {
    Float32 _FillValue NaN;
    Float32 actual_range 3.2, 33.4;
    String description "percent amount of Protein";
    String ioos_category "Unknown";
    String long_name "Protein";
    String units "unitless (percent)";
  TCHO {
    Float32 _FillValue NaN;
    Float32 actual_range 5.2, 36.4;
    String description "percent amount of total carbohydrates";
    String ioos_category "Unknown";
    String long_name "TCHO";
    String units "unitless (percent)";
  URA {
    Float32 _FillValue NaN;
    Float32 actual_range 2.9, 55.7;
    String description "percent amount of uronic acids";
    String ioos_category "Unknown";
    String long_name "URA";
    String units "unitless (percent)";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Radiolabeled Diatom Cultures  
 Natural seawater with a salinity of 35, collected from the Gulf of Mexico,
was sequentially filtered through a  
 0.2 \\u03bcm polycarbonate cartridge and ultrafiltered with a 1000 amu cutoff
membrane to remove particulate  
 and colloidal organic matter [Guo et al., 1995; Roberts et al., 2009]. The
<1000 amu ultrafiltrate fraction was  
 then used for later experiments. The 234Th tracer was milked and purified
from a 238U solution [Alvarado  
 Quiroz et al., 2006; Quigley et al., 2002]; 233Pa, in equilibrium with
237Np, was obtained from Pacific Northwest  
 National Laboratory; 210Pb, in 1 mol L-1 nitric acid (HNO3), was purchased
from Eckert & Ziegler Isotope  
 Products, and the 7Be tracer solution (in 0.1 mol L-1 hydrochloric acid,
HCl) was manufactured at the Paul  
 Scherrer Institute, Switzerland [Schumann et al., 2013].  
 Autoclaved f/2 media (50 ml) were added to preconditioned clear polyethylene
containers, and then ~10 to  
 15 Bq of each radionuclide tracer (234Th, 233Pa, 210Pb, and 7Be) was added.
In each radiolabeled medium, 1ml  
 of laboratory axenic culture, Phaeodactylum tricornutum (UTEX 646), was then
added and incubated at a temperature of 19 \\u00b1 1\\u00b0C with a light:dark
cycle of 14 h:10 h under an irradiance of 100 \\u03bcmol quanta m-2 s-1.  
 Incubation experiments were carried out in duplicate. The growth status of
P. tricornutum was monitored  
 by changes in optical density at 750nm (OD750) in a parallel nonlabeled
culture. When P. tricornutum reached the stationary phase observed by its
OD750, cells were harvested for further extraction and analyses. The total
 time was 35 days.  
 Exopolymeric Substance (AEPS and NAEPS) Extraction  
 AEPS and NAEPS extractions were performed following the procedures described
in Chuang et al. [2014, 2015]. Briefly, for NAEPS, laboratory cultures were
centrifuged (2694 g, 30 min) and filtered (0.2 \\u03bcm). The filtrate was
desalted via diafiltration with a 1000 amu cutoff cross-flow ultrafiltration
membrane, followed by freeze drying  
 for later use. For the AEPS extraction, diatom cells were collected after
centrifugation from the previous step. Then,  
 the pellet was soaked with 0.5mol L -1\\u00a0 sodium chloride (NaCl) solution
for 10 min, followed by centrifugation at  
 2000 g for 15 min to remove the medium and weakly bound organic material on
the cells. The pellet was  
 then resuspended in a fresh 100 ml, 0.5mol L-1 NaCl solution and stirred
gently overnight at 4\\u00b0C. The resuspended  
 particle solution was ultracentrifuged at 12,000 g (30 min, 4\\u00b0C), and
the supernatant was then filtered through a 0.2 \\u03bcm polycarbonate
membrane. The filtrate was further desalted via diafiltration with a 1000 amu
cutoff ultrafiltration membrane and subsequently freeze dried for later
Intracellular and Frustule BF Extraction  
 Procedures for frustule biopolymers extraction adapted from Scheffel et al.
[2011]. Briefly, the  
 clean diatom cells from the previous AEPS extraction step were resuspended
in 10 ml, 100mmol L-1 EDTA  
 (pH 8.0) at 4\\u00b0C overnight. EDTA solution was used to extract the
intracellular material after cell lysis. The supernatant  
 was collected after centrifuging at 3000 g for 10 min, defined as EDTA
extractable BF. Subsequently,  
 the pellet was placed in 10 ml, 1% SDS in 10mmol L-1 Tris (pH 6.8) solution
and heated at 95\\u00b0C for 1 h.  
 The resulting frustules were collected by centrifugation (2500 g, 10 min),
washed with 10 ml milli-Q water 3  
 times, and then were freeze dried for later use. The supernatant from this
step was collected and defined  
 as SDS extractable BF, mostly composed of soluble cell-membrane-associated
materials. These two fractions  
 represent intracellular biopolymers lysed after cell breakage.
HF digestion was applied to help extract the diatom frustule biopolymers. HF
is a nonoxidizing acid commonly  
 used to convert SiO2 to volatile SiF4 during wet digestion [Scheffel et al.,
2011; \\u0160ulcek and Povondra,  
 1989]. Hence, frustule biopolymers could be separated from the digested
solution by a 3 kDa cutoff membrane. However, high-concentration HF would also
liberate A type metal radionuclides (Th, Pa, and Be in  
 this study) from any complex by frustule biopolymers [e.g., Burnett et al.,
1997]. Furthermore, deglycosylation  
 might also have occurred during a HF digestion [Mort and Lamport, 1977].
Therefore, the <3000 amu fraction  
 represents the sum of silica frustules and broken down frustule biopolymer
Subsequently, 5 ml, 52% HF was added to the frustules in a 15ml plastic
centrifugation tube, and the mixture  
 solution was incubated on ice for 1 h. Hydrogen fluoride was then evaporated
under an N2 stream to reduce  
 the volume to dryness. The remaining material was neutralized with 3ml
Tris\\u2013HCl (250mmol L-1, pH 8.0) and  
 followed by centrifugation at 11,000 g for 15 min with 3000 amu Microsep
centrifugal filter tubes (Milipore).  
 The filtrate was collected and defined as the fraction of digested silica
with <3000 amu frustule BF residues.  
 The supernatant (defined as>3000amu HF soluble BF, e.g., silaffin) was
concentrated to 250 \\u03bcL and rinsed with  
 milli-Q water. The pellet from this step was then washed by a 3 ml, 200mmol
L-1 ammonium acetate solution  
 twice with centrifugation at 3000 g for 20 min. The pellet was then
resuspended in a 2 ml, 100mmol L-1  
 ammonium acetate solution and was sonicated for 20 s until the mixture
solution appeared homogenized.  
 After ultracentrifuging the mixture solution at 12,000 g for 5 min, the
pellet (>3000 amu HF insoluble BF,  
 e.g., cingulin) was collected and freeze dried for later use. Combined BF
from all three HF fractions represented  
 frustule-embedded biopolymers.
Activity concentrations of 234Th, 233Pa, 210Pb, and 7Be were measured by
counting the gamma decay energies at 63.5 keV, 312 keV, 46.5 keV, and 477.6
keV, respectively, on a Canberra ultrahigh purity germanium well detector. The
210Po activity was analyzed by liquid scintillation counting (Beckman Model
8100 Liquid Scintillation Counter).  
 Concentrations of total carbohydrate (TCHO) were determined by the TPTZ (2,
4, 6-tripyridyl-s-triazine) method using glucose as the standard and [Hung and
Santschi, 2001]. Protein content was determined using a modified Lowry protein
assay, using bovine serum albumin as the standard (Pierce, Thermo Scientific).
uronic acids (URA) were measured by the metahydroxyphenyl method using
glucuronic acid as the standard [Hung and Santschi, 2001].
Elemental contents of carbon (C) and nitrogen (N), were determined by a Perkin
Elmer CHN 2400 analyzer, using cysteine (29.99% C, 11.67% N) as a standard.";
    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 "Dr Henrietta N Edmonds";
    String awards_0_program_manager_nid "51517";
    String cdm_data_type "Other";
    String comment 
"Percent amount of organic fractions from diatoms that bind with radionuclides  
  PI: Peter H. Santschi 
  Version: 2019-04-11";
    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 2.2d  13 Jun 2019";
    String date_created "2019-04-11T18:54:07Z";
    String date_modified "2019-04-11T19:52:35Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.764860.1";
    String history 
"2019-10-16T05:09:56Z (local files)
2019-10-16T05:09:56Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_764860.das";
    String infoUrl "https://www.bco-dmo.org/dataset/764860";
    String institution "BCO-DMO";
    String instruments_0_acronym "LSC";
    String instruments_0_dataset_instrument_description "The 210Po activity was analyzed by liquid scintillation counting (Beckman Model 8100 Liquid Scintillation Counter).";
    String instruments_0_dataset_instrument_nid "764882";
    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 (� 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 "CHN_EA";
    String instruments_1_dataset_instrument_description "Elemental contents of carbon (C) and nitrogen (N), were determined by a Perkin Elmer CHN 2400 analyzer, using cysteine (29.99% C, 11.67% N) as a standard.";
    String instruments_1_dataset_instrument_nid "764869";
    String instruments_1_description "A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and  nitrogen content in organic and other types of materials, including  solids, liquids, volatile, and viscous samples.";
    String instruments_1_instrument_name "CHN Elemental Analyzer";
    String instruments_1_instrument_nid "625";
    String instruments_1_supplied_name "Perkin Elmer CHN 2400 analyzer";
    String instruments_2_dataset_instrument_description "Activity concentrations of 234Th, 233Pa, 210Pb, and 7Be were measured by counting the gamma decay energies at 63.5 keV, 312 keV, 46.5 keV, and 477.6 keV, respectively, on a Canberra ultrahigh purity germanium well detector.";
    String instruments_2_dataset_instrument_nid "764881";
    String instruments_2_description "Instruments measuring the relative levels of electromagnetic radiation of different wavelengths in the gamma-ray waveband.";
    String instruments_2_instrument_name "Gamma Ray Spectrometer";
    String instruments_2_instrument_nid "670659";
    String instruments_2_supplied_name "Canberra ultrahigh purity germanium well detector";
    String keywords "bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, management, oceanography, office, preliminary, protein, substance, tcho, ura";
    String license 
"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.";
    String metadata_source "https://www.bco-dmo.org/api/dataset/764860";
    String param_mapping "{'764860': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/764860/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 as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores";
    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 "Mathew Biddle";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v29";
    String summary "In order to investigate the importance of biogenic silica associated biopolymers on the scavenging of radionuclides, the diatom Phaeodactylum tricornutum was incubated together with the radionuclides 234Th, 233Pa, 210Pb, and 7Be during their growth phase. Normalized affinity coefficients were determined for the radionuclides bound with different organic compound classes (i.e., proteins, total carbohydrates, uronic acids) in extracellular (nonattached and attached exopolymeric substances), intracellular (ethylene diamine tetraacetic acid and sodium dodecyl sulfate extractable), and frustule embedded biopolymeric fractions (BF). Results indicated that radionuclides were mostly concentrated in frustule BF. Among three measured organic components, Uronic acids showed the strongest affinities to all tested radionuclides. Confirmed by spectrophotometry and two-dimensional heteronuclear single quantum coherence-nuclear magnetic resonance analyses, the frustule BF were mainly composed of carboxyl-rich, aliphatic-phosphoproteins, which were likely responsible for the strong binding of many of the radionuclides. Results from this study provide evidence for selective absorption of radionuclides with different kinds of diatom-associated biopolymers acting in concert rather than as a single compound. This clearly indicates the importance of these diatom-related biopolymers, especially frustule biopolymers, in the scavenging and fractionation of radionuclides used as particle tracers in the ocean.";
    String title "Percent amount of organic fractions from diatoms that bind with radionuclides";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.5-beta";


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