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

ERDDAP > info > bcodmo_dataset_764860

Grid
DAP
Data
Sub-
set
Table
DAP
Data
Make
A
Graph
W
M
S
Source
Data
Files
Acces-
sible
?
Title Sum-
mary
ISO,
Metadata
Back-
ground
Info
RSS Institution Dataset ID
     data   graph     files  public Percent amount of organic fractions from diatoms that bind with radionuclides    ?     I   M   background (external link) RSS BCO-DMO bcodmo_dataset_764860

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 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
incubation
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
use.\u00a0

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
residues.

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.
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 Dr 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 Percent amount of organic fractions from diatoms that bind with radionuclides
PI: Peter H. Santschi
Version: 2019-04-11
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 2.2d 13 Jun 2019
attribute NC_GLOBAL date_created String 2019-04-11T18:54:07Z
attribute NC_GLOBAL date_modified String 2019-04-11T19:52:35Z
attribute NC_GLOBAL defaultDataQuery String &time
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.764860.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/764860 (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 The 210Po activity was analyzed by liquid scintillation counting (Beckman Model 8100 Liquid Scintillation Counter).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 764882
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 (� 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 CHN_EA
attribute NC_GLOBAL instruments_1_dataset_instrument_description String 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.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 764869
attribute NC_GLOBAL instruments_1_description String 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.
attribute NC_GLOBAL instruments_1_instrument_name String CHN Elemental Analyzer
attribute NC_GLOBAL instruments_1_instrument_nid String 625
attribute NC_GLOBAL instruments_1_supplied_name String Perkin Elmer CHN 2400 analyzer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String 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.
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 764881
attribute NC_GLOBAL instruments_2_description String Instruments measuring the relative levels of electromagnetic radiation of different wavelengths in the gamma-ray waveband.
attribute NC_GLOBAL instruments_2_instrument_name String Gamma Ray Spectrometer
attribute NC_GLOBAL instruments_2_instrument_nid String 670659
attribute NC_GLOBAL instruments_2_supplied_name String Canberra ultrahigh purity germanium well detector
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, management, oceanography, office, preliminary, protein, substance, tcho, ura
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/764860 (external link)
attribute NC_GLOBAL param_mapping String {'764860': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/764860/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 as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores
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 Mathew Biddle
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 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.
attribute NC_GLOBAL title String Percent amount of organic fractions from diatoms that bind with radionuclides
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5-beta
variable substance   String  
attribute substance description String type of substance
attribute substance ioos_category String Unknown
attribute substance long_name String Substance
attribute substance units String unitless
variable Protein   float  
attribute Protein _FillValue float NaN
attribute Protein actual_range float 3.2, 33.4
attribute Protein description String percent amount of Protein
attribute Protein ioos_category String Unknown
attribute Protein long_name String Protein
attribute Protein units String unitless (percent)
variable TCHO   float  
attribute TCHO _FillValue float NaN
attribute TCHO actual_range float 5.2, 36.4
attribute TCHO description String percent amount of total carbohydrates
attribute TCHO ioos_category String Unknown
attribute TCHO long_name String TCHO
attribute TCHO units String unitless (percent)
variable URA   float  
attribute URA _FillValue float NaN
attribute URA actual_range float 2.9, 55.7
attribute URA description String percent amount of uronic acids
attribute URA ioos_category String Unknown
attribute URA long_name String URA
attribute URA units String unitless (percent)

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.


 
ERDDAP, Version 1.82
Disclaimers | Privacy Policy | Contact