http://lod.bco-dmo.org/id/dataset/764546
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2019-04-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Absorbance from Fourier transform infrared spectroscopy sample characterization experiments.
2019-04-10
publication
2019-04-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-04-11
publication
https://doi.org/10.1575/1912/bco-dmo.764546.1
Peter Santschi
Texas A&M, Galveston
principalInvestigator
Antonietta Quigg
Texas A&M, Galveston
principalInvestigator
Kathleen Schwehr
Texas A&M, Galveston
principalInvestigator
Chen Xu
Texas A&M, Galveston
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Santschi, P., Quigg, A., Schwehr, K., Xu, C. (2019) Absorbance from Fourier transform infrared spectroscopy sample characterization experiments. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-04-10 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.764546.1 [access date]
Laboratory studies of radionuclides (234Th, 233Pa, 210Po, 210Pb, and 7Be) binding with fractions from cultured diatom, Phaeodactylum tricornutum Dataset Description: <p>Laboratory studies were conducted to examine the sorption of selected radionuclides (234Th, 233Pa, 210Po,<br />
210Pb, and 7Be) onto inorganic (pure silica and acid-cleaned diatom frustules) and organic (diatom cells with or<br />
without silica frustules) particles in natural seawater and the role of templating biomolecules and exopolymeric<br />
substances (EPS) extracted from the same species of diatom, Phaeodactylum tricornutum, in the sorption process.<br />
The range of partition coefficients (Kd, reported as logKd) of radionuclides between water and the different<br />
particle types was 4.78–6.69 for 234Th, 5.23–6.71 for 233Pa, 4.44–5.86 for 210Pb, 4.47–4.92 for 210Po, and 4.93–7.23 for 7Be, similar to values reported for lab and field determinations. The sorption of all radionuclides was<br />
significantly enhanced in the presence of organic matter associated with particles, resulting in Kd one to two<br />
orders of magnitude higher than for inorganic particles only, with highest values for 7Be (logKd of 7.2). Results<br />
further indicate that EPS and frustule-embedded biomolecules in diatom cells are responsible for the sorption<br />
enhancement rather than the silica shell itself. By separating radiolabeled EPS via isoelectric focusing, we found<br />
that isoelectric points are radionuclide specific, suggesting that each radionuclide binds to specific biopolymeric<br />
functional groups, with the most efficient binding sites likely occurring in acid polysaccharides, iron hydroxides,<br />
and proteins. Further progress in evaluating the effects of diatom frustule–related biopolymers on binding,<br />
scavenging, and fractionation of radionuclides would require the application of molecular-level characterization<br />
techniques.</p> Methods and Sampling: <p>Diatom cultures, sample preparation, and EPS extraction<br />
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.</p>
<p>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).&nbsp;</p>
<p>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).</p>
<p>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.</p>
<p>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<br />
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 (1652–1648 cm-1) and amide II (1550–1548 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<br />
CH2 bending mode at 1455 cm-1. In the 800–1200 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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1356453 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1356453
completed
Peter Santschi
Texas A&M, Galveston
4097404476
200 Seawolf Pkwy
Galveston
TX
77553
US
santschi@tamug.edu
pointOfContact
Antonietta Quigg
Texas A&M, Galveston
409-740-4990
200 Seawolf Pkwy
Galveston
TX
77553
quigga@tamug.edu
pointOfContact
Kathleen Schwehr
Texas A&M, Galveston
200 Seawolf Pkwy
Galveston
TX
77553
pointOfContact
Chen Xu
Texas A&M, Galveston
409-354-8312
200 Seawolf Pkwy
Galveston
TX
77553
xuc@tamug.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
wavenumber
EPS_Si_plus
EPS_Si_minus
EPS_Si_diff
Varian 3100 Excalibur
theme
None, User defined
No BCO-DMO term
absorbance
featureType
BCO-DMO Standard Parameters
Spectrometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Biopolymers as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores
https://osprey.bco-dmo.org/project/735996
Biopolymers as carrier phases for selected natural radionuclides (of Th, Pa, Pb, Po, Be) in diatoms and coccolithophores
<p><span style="background-color:transparent; color:rgb(0, 0, 0); font-family:arial; font-size:11pt">NSF Award Abstract:</span></p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
Biopolymers for radionuclides
largerWorkCitation
project
eng; USA
oceans
2019-04-10
0
BCO-DMO catalogue of parameters from Absorbance from Fourier transform infrared spectroscopy sample characterization experiments.
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/764550.rdf
Name: wavenumber
Units: unitless
Description: <p>wavenumber</p>
http://lod.bco-dmo.org/id/dataset-parameter/764551.rdf
Name: EPS_Si_plus
Units: per centimeter
Description: <p>absorbance EPS Si+</p>
http://lod.bco-dmo.org/id/dataset-parameter/764552.rdf
Name: EPS_Si_minus
Units: per centimeter
Description: <p>absorbance EPS Si-</p>
http://lod.bco-dmo.org/id/dataset-parameter/764553.rdf
Name: EPS_Si_diff
Units: per centimeter
Description: <p>absorbance difference EPS (Si-)-(Si+)</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
22044
https://darchive.mblwhoilibrary.org/bitstream/1912/24005/1/dataset-764546_atrftirabsorbance__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.764546.1
download
onLine
dataset
<p>Diatom cultures, sample preparation, and EPS extraction<br />
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.</p>
<p>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).&nbsp;</p>
<p>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).</p>
<p>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.</p>
<p>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<br />
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 (1652–1648 cm-1) and amide II (1550–1548 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<br />
CH2 bending mode at 1455 cm-1. In the 800–1200 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.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
-&nbsp;added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Varian 3100 Excalibur
Varian 3100 Excalibur
PI Supplied Instrument Name: Varian 3100 Excalibur PI Supplied 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). Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/