ERDDAP > info > bcodmo_dataset_764688

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	Experiments evaluating protein size distribution pattern in EPS Si+ and EPS Si2 using sodium dodecyl sulfate\u2013polyacrylamide gel electrophoresis		I   M	background			BCO-DMO	bcodmo_dataset_764688

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	Diatom cultures, sample preparation, and EPS extraction P. tricornutum (UTEX 646) was selected for culturing in autoclaved f/2 and f/2-Si media (salinity of 26) at a temperature of 19 + 1 oC with a light cycling of 14 h : 10 h under a saturating irradiance of 100 umol quanta m-2 s-1. In order to deplete the diatom of Si supply, cultures were transferred into f/2-Si medium over at least six generations by harvesting cells (2694 g, 30 min) and resuspending them in fresh f/2-Si medium. Sterile polycarbonate bottles were also used to prevent Si supply from glassware. The growth status of P. tricornutum was monitored by changes in optical density at 750 nm. Cells, frustules, and EPS were collected when P. tricornutum reached the stationary phase. Laboratory cultures of P. tricornutum were centrifuged (2694 x g, 30 min) and filtered (0.2 um) to collect the whole cells. The frustules were repeatedly treated by using a hydrogen peroxide (30%, room temperature) treatment until bubbles were no longer generated, followed by concentrated nitric acid (HNO3) digestion (85oC, 1 h) to remove organic matter adopted from Robinson et al. (2004).\u00a0 The resulting organic carbon (C), nitrogen (N), and sulfur (S) contents of the cleaned frustules were measured using a Perkin Elmer CHNS 2400 analyzer to ensure the removal of organic materials using cysteine as a standard according to Guo and Santschi (1997). EPS extraction was followed the procedures described in Xu et al. (2011b), which minimize cell rupture and molecular alterations and maximize extraction efficiency. EPS here is referring to those biopolymers that are attached on the diatom frustules. Hereafter, EPS Si+ and EPS Si2 denote the EPS extracted from diatoms cultured under Si-replete (f/2 medium) and Si-depleted (f/2-Si medium) conditions, respectively. Briefly, laboratory cultures were centrifuged (2694 x g, 30 min) and filtered (0.2 um) when diatoms reached stationary phase. The diatom cells were soaked with 0.5 mol L-1 sodium chloride (NaCl) solution for 10 min and followed by centrifugation at 2000 x g for 15 min to remove the medium and weakly bound organic material on the cells. The pellet from previous step was resuspended in a new 100 mL 0.5 mol L-1 NaCl solution and stirred gently overnight at 4oC. The resuspended particle solution was ultracentrifuged at 12,000 x g (30 min, 4uC), and the supernatant was then filtered through a 0.2 um polycarbonate membrane. The filtrate was desalted and collected with a 1 kDa cutoff cross-flow ultrafiltration and diafiltration membrane and then freeze-dried for later use. Characterization of exopolymeric substances After partitioning EPS collected from lab cultures into aliquots for freeze- drying, subsamples were analyzed for individual components. Concentration of total carbohydrate (TCHO) concentration was determined by the TPTZ (2,4,6-tripyridyl-s-triazine) method using glucose as the standard, and uronic acids were measured by the meta-hydroxyphenyl method using glucuronic acid as the standard (Hung and Santschi 2001). Protein content was determined using a modified Lowry protein assay, using bovine serum albumin (BSA) as the standard (Pierce, Thermo Scientific). C, N, and S contents were determined as described above. Iron was measured using an atomic absorption spectrometer (Varian) after overnight digestion with 12 mol L-1 HNO3 at 85oC (Von Loon 1985). To evaluate the protein size distribution pattern in EPS Si+ and EPS Si2, sodium dodecyl sulfate\u2013polyacrylamide gel electrophoresis (SDS-PAGE) was carried out according to Sambrook et al. (1989) using standard molecular weight markers (Dual Xtra Standards, Bio-Rad).\u00a0 Fourier transform infrared spectroscopy (FTIR) was used to characterize samples using a Varian 3100 model interfaced with a single reflection horizontal attenuated total reflectance (ATR) accessory (PIKE Technologies). A diamond plate was used as the internal reflection element. A freeze-dried EPS sample was mounted at the surface of the diamond. Absorbance spectra from 800 to 2000 cm21 were collected and integrated using Varian Resolution Pro 4.0 software. ATR-FTIR spectroscopy provides a noninvasive way to quickly gain information about the contents of major secondary structures of biopolymers (Xu et al. 2011b; Jiang et al. 2012). Major infrared (IR) peaks were assigned according to Xu et al. (2011b) and Jiang et al. (2012). Characteristic bands found in the IR spectra of proteins and polypeptides include the amide I (1652\u20131648 cm-1) and amide II (1550\u20131548 cm-1) band. The absorption associated with the amide I band leads to stretching vibrations of the C=O bond of the amide, and absorption associated with the amide II band leads primarily to bending vibrations of the N-H and C-N bond. The symmetric stretching peak due to deprotonated carboxyl groups is observed at 1400 cm-1 along with the CH2 bending mode at 1455 cm-1. In the 800\u20131200 cm-1 regions, responses from C-O, C-O-C, P-O-P, C-O-P, and ring vibrations of the main polysaccharide functional groups are present in polysaccharide mixtures. The peaks at 1241 and 1113 cm-1 correspond to P-O stretching in phosphate groups.
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	Experiments evaluating protein size distribution pattern in EPS Si+ and EPS Si2 using sodium dodecyl sulfate-polyacrylamide gel electrophoresis PI: Peter H. Santschi Version: 2019-04-10
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	2019-04-10T18:06:10Z
attribute	NC_GLOBAL	date_modified	String	2019-04-11T20:00:33Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.764688.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/764688
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	764697
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_dataset_instrument_description	String	For IEF (isoelectric focusing electrophoresis), a Pharmacia Biotech Multiphor II with a EPS3500 XL power supply was used.
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	764696
attribute	NC_GLOBAL	instruments_1_description	String	General term for an apparatus used in clinical and research laboratories to separate charged colloidal particles (or molecules) of varying size through a medium by applying an electric field.
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Electrophoresis Chamber
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	471592
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Pharmacia Biotech Multiphor II
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Activity concentrations of 234Th, 233Pa, 210Pb, 210Po, and 7Be were measured by gamma counting the 63.5, 312, 46.5, and 477.6 keV lines, respectively, on a Canberra ultra-highpurity germanium well-type detector.
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	764698
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 ultra-highpurity germanium well-type detector
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, chemistry, concentration, data, dataset, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Silicate, EPS_Si_minus, EPS_Si_plus, erddap, group, management, mass, mass_concentration_of_silicate_in_sea_water, ocean, oceanography, oceans, office, preliminary, science, sea, seawater, silicate, water
attribute	NC_GLOBAL	keywords_vocabulary	String	GCMD Science Keywords
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/764688/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/764688
attribute	NC_GLOBAL	param_mapping	String	{'764688': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/764688/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	Laboratory studies were conducted to examine the sorption of selected radionuclides (234Th, 233Pa, 210Po, 210Pb, and 7Be) onto inorganic (pure silica and acid-cleaned diatom frustules) and organic (diatom cells with or without silica frustules) particles in natural seawater and the role of templating biomolecules and exopolymeric substances (EPS) extracted from the same species of diatom, Phaeodactylum tricornutum, in the sorption process. The range of partition coefficients (Kd, reported as logKd) of radionuclides between water and the different particle types was 4.78\u20136.69 for 234Th, 5.23\u20136.71 for 233Pa, 4.44\u20135.86 for 210Pb, 4.47\u20134.92 for 210Po, and 4.93\u20137.23 for 7Be, similar to values reported for lab and field determinations. The sorption of all radionuclides was significantly enhanced in the presence of organic matter associated with particles, resulting in Kd one to two orders of magnitude higher than for inorganic particles only, with highest values for 7Be (logKd of 7.2). Results further indicate that EPS and frustule-embedded biomolecules in diatom cells are responsible for the sorption enhancement rather than the silica shell itself. By separating radiolabeled EPS via isoelectric focusing, we found that isoelectric points are radionuclide specific, suggesting that each radionuclide binds to specific biopolymeric functional groups, with the most efficient binding sites likely occurring in acid polysaccharides, iron hydroxides, and proteins. Further progress in evaluating the effects of diatom frustule\u2013related biopolymers on binding,\r\nscavenging, and fractionation of radionuclides would require the application of molecular-level characterization techniques.
attribute	NC_GLOBAL	title	String	Experiments evaluating protein size distribution pattern in EPS Si+ and EPS Si2 using sodium dodecyl sulfate\u2013polyacrylamide gel electrophoresis
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	Group		String
attribute	Group	bcodmo_name	String	unknown
attribute	Group	description	String	component group
attribute	Group	long_name	String	Group
attribute	Group	units	String	unitless
variable	EPS_Si_plus		float
attribute	EPS_Si_plus	_FillValue	float	NaN
attribute	EPS_Si_plus	actual_range	float	13.34, 104.77
attribute	EPS_Si_plus	bcodmo_name	String	unknown
attribute	EPS_Si_plus	description	String	exopolymeric substance extracted from diatoms cultured under Si-replete (f/2 medium) conditions
attribute	EPS_Si_plus	long_name	String	Mass Concentration Of Silicate In Sea Water
attribute	EPS_Si_plus	units	String	nanomole per miligram (nmol/mg)
variable	EPS_Si_minus		float
attribute	EPS_Si_minus	_FillValue	float	NaN
attribute	EPS_Si_minus	actual_range	float	5.14, 27.48
attribute	EPS_Si_minus	bcodmo_name	String	unknown
attribute	EPS_Si_minus	description	String	exopolymeric substance extracted from diatoms cultured under Si-depleted (f/2-Si medium) conditions
attribute	EPS_Si_minus	long_name	String	Mass Concentration Of Silicate In Sea Water
attribute	EPS_Si_minus	units	String	nanomole per miligram (nmol/mg)

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.