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     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 (external link) RSS 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 (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 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/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv.pl v1.0
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
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.764688.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/764688 (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 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 (� 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_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, dissolved, dissolved nutrients, 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, nutrients, ocean, oceanography, oceans, office, preliminary, science, sea, seawater, silicate, water
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
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/764688 (external link)
attribute NC_GLOBAL param_mapping String {'764688': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/764688/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 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() v1.0-alpha
variable Group   String  
attribute Group description String component group
attribute Group ioos_category String Unknown
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 description String exopolymeric substance extracted from diatoms cultured under Si-replete (f/2 medium) conditions
attribute EPS_Si_plus ioos_category String Dissolved Nutrients
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 description String exopolymeric substance extracted from diatoms cultured under Si-depleted (f/2-Si medium) conditions
attribute EPS_Si_minus ioos_category String Dissolved Nutrients
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, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.


 
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