ERDDAP > info > bcodmo_dataset_764885

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	E mail	Institution	Dataset ID
		data	graph		files	public	Percent activity of organic fractions from diatoms that bind with radionuclide		I   M	background			BCO-DMO	bcodmo_dataset_764885

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
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	Percent activity of organic fractions from diatoms that bind with radionuclide 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/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2019-04-11T19:14:56Z
attribute	NC_GLOBAL	date_modified	String	2019-04-11T19:52:12Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.764885.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/764885
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	764895
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/
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	764893
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	764894
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	aeps, amu, bco, bco-dmo, biological, chemical, data, dataset, dmo, edta, erddap, frequency, HF, HF_insoluble, HF_soluble, high, insoluble, lt_3000_amu, management, naeps, oceanography, office, preliminary, radionuclide, sds, soluble
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/764885/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/764885
attribute	NC_GLOBAL	param_mapping	String	{'764885': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/764885/parameters
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	Percent amount of organic fractions from diatoms that bind with radionuclide. 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 activity of organic fractions from diatoms that bind with radionuclide
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	radionuclide		String
attribute	radionuclide	bcodmo_name	String	unknown
attribute	radionuclide	description	String	radionuclide
attribute	radionuclide	long_name	String	Radionuclide
attribute	radionuclide	units	String	unitless
variable	NAEPS		float
attribute	NAEPS	_FillValue	float	NaN
attribute	NAEPS	actual_range	float	3.13, 36.8
attribute	NAEPS	bcodmo_name	String	unknown
attribute	NAEPS	description	String	non-attached exopolymeric substance
attribute	NAEPS	long_name	String	NAEPS
attribute	NAEPS	units	String	unitless (percent)
variable	AEPS		float
attribute	AEPS	_FillValue	float	NaN
attribute	AEPS	actual_range	float	5.06, 18.04
attribute	AEPS	bcodmo_name	String	unknown
attribute	AEPS	description	String	attached exopolymeric substance
attribute	AEPS	long_name	String	AEPS
attribute	AEPS	units	String	unitless (percent)
variable	HF_soluble		float
attribute	HF_soluble	_FillValue	float	NaN
attribute	HF_soluble	actual_range	float	0.43, 8.69
attribute	HF_soluble	bcodmo_name	String	unknown
attribute	HF_soluble	description	String	hydrofluoric acid
attribute	HF_soluble	long_name	String	HF Soluble
attribute	HF_soluble	units	String	unitless (percent)
variable	HF_insoluble		float
attribute	HF_insoluble	_FillValue	float	NaN
attribute	HF_insoluble	actual_range	float	6.53, 23.9
attribute	HF_insoluble	bcodmo_name	String	unknown
attribute	HF_insoluble	description	String	hydrofluoric acid insoluble
attribute	HF_insoluble	long_name	String	HF Insoluble
attribute	HF_insoluble	units	String	unitless (percent)
variable	lt_3000_amu		float
attribute	lt_3000_amu	_FillValue	float	NaN
attribute	lt_3000_amu	actual_range	float	1.35, 19.48
attribute	lt_3000_amu	bcodmo_name	String	unknown
attribute	lt_3000_amu	description	String	less than 3000 atomic mass units
attribute	lt_3000_amu	long_name	String	Lt 3000 Amu
attribute	lt_3000_amu	units	String	unitless (percent)
variable	EDTA		float
attribute	EDTA	_FillValue	float	NaN
attribute	EDTA	actual_range	float	21.78, 37.39
attribute	EDTA	bcodmo_name	String	unknown
attribute	EDTA	description	String	ethylene diamine tetraacetic acid
attribute	EDTA	long_name	String	EDTA
attribute	EDTA	units	String	unitless (percent)
variable	SDS		float
attribute	SDS	_FillValue	float	NaN
attribute	SDS	actual_range	float	2.54, 25.15
attribute	SDS	bcodmo_name	String	unknown
attribute	SDS	description	String	sodium dodecyl sulfate
attribute	SDS	long_name	String	SDS
attribute	SDS	units	String	unitless (percent)

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.