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Dataset Title:  Absorbance from Fourier transform infrared spectroscopy sample
characterization experiments.
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_764546)
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 {
  wavenumber {
    Float32 _FillValue NaN;
    Float32 actual_range 800.46, 2000.2;
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "wavenumber";
    String ioos_category "Statistics";
    String long_name "Wavenumber";
    String units "unitless";
  }
  EPS_Si_plus {
    Float32 _FillValue NaN;
    Float32 actual_range -0.001326, 0.043897;
    String description "absorbance EPS Si+";
    String ioos_category "Dissolved Nutrients";
    String long_name "Mass Concentration Of Silicate In Sea Water";
    String units "per centimeter";
  }
  EPS_Si_minus {
    Float32 _FillValue NaN;
    Float32 actual_range -0.001805, 0.16678;
    String description "absorbance EPS Si-";
    String ioos_category "Dissolved Nutrients";
    String long_name "Mass Concentration Of Silicate In Sea Water";
    String units "per centimeter";
  }
  EPS_Si_diff {
    Float32 _FillValue NaN;
    Float32 actual_range -0.023796, 0.14845;
    Float64 colorBarMaximum 10.0;
    Float64 colorBarMinimum -10.0;
    String description "absorbance difference EPS (Si-)-(Si+)";
    String ioos_category "Dissolved Nutrients";
    String long_name "Mass Concentration Of Silicate In Sea Water";
    String units "per centimeter";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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.
 
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.";
    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 
"Fourier transform infrared spectroscopy sample characterization experiments. 
  PI: Peter H. Santschi 
  Version: 2019-04-09";
    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 "2019-04-10T15:43:31Z";
    String date_modified "2019-04-11T20:02:28Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.764546.1";
    String history 
"2019-06-27T01:13:39Z (local files)
2019-06-27T01:13:39Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_764546.das";
    String infoUrl "https://www.bco-dmo.org/dataset/764546";
    String institution "BCO-DMO";
    String instruments_0_acronym "Spectrometer";
    String instruments_0_dataset_instrument_description "Fourier transform infrared spectroscopy (FTIR) was used to characterize samples using a Varian 3100 Excalibur model interfaced with a single reflection horizontal attenuated total reflectance (ATR) diamond accessory (PIKE Technologies).";
    String instruments_0_dataset_instrument_nid "764549";
    String instruments_0_description "A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/";
    String instruments_0_instrument_name "Spectrometer";
    String instruments_0_instrument_nid "667";
    String instruments_0_supplied_name "Varian 3100 Excalibur";
    String keywords "bco, bco-dmo, biological, chemical, chemistry, concentration, data, dataset, dissolved, dissolved nutrients, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Silicate, EPS_Si_diff, EPS_Si_minus, EPS_Si_plus, erddap, management, mass, mass_concentration_of_silicate_in_sea_water, nutrients, ocean, oceanography, oceans, office, preliminary, science, sea, seawater, silicate, statistics, water, wavenumber";
    String keywords_vocabulary "GCMD Science Keywords";
    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/764546";
    String param_mapping "{'764546': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/764546/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 "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, scavenging, and fractionation of radionuclides would require the application of molecular-level characterization techniques.";
    String title "Absorbance from Fourier transform infrared spectroscopy sample characterization experiments.";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.5-beta";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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