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     data   graph     files  public Partitioning of iron and plutonium in exopolymeric substances and intracellular biopolymers:
a comparison study between the coccolithophore Emiliania huxleyi and the diatom Skeletonema
costatum
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_764480

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 The seawater (< 1 kDa) was enriched with f/2 nutrients, trace metals and
vitamins, and autoclaved in pre-combusted and seawater-preconditioned clear
glassware. Known activity of 59Fe (gamma emitting radionuclide) and 238Pu
(alpha emitting radionuclide) were added into the seawater in pre-combusted
and seawater-preconditioned clear glassware.\u00a0
After checking the pH of each radiolabeled medium to be 8.0, laboratory
axenic Skeletonema costatum (UTEX LB 2308) and Emiliania huxleyi (CCMP 371)
was added to 100 mL of media and incubated at a temperature of
19\u00b11\u00baC with a light:dark cycle of 14 h:10 h under an irradiation
condition of 100 \u00b5mol-quanta/m2/s.
The sequential chemical extraction scheme for obtaining individual fractions
from S. costatum and E. huxleyi followed the procedures described in Chuang et
al. (2015) and Lin et al. (2017), with a few exceptions. For the extracellular
biopolymers excreted by the phytoplankton, non-attached exopolymeric
substances (NAEPS) in the surrounding seawater and attached EPS (AEPS)
associated with cellular surface, were harvested. Laboratory cultures were
centrifuged at 3000 x g for 30 min, followed by filtration of the supernatant
which was further concentrated and desalted with nanopure water (18.2 \u03a9)
in 3 kDa Microsep centrifugal filter tubes (Milipore) to obtain the NAEPS
fraction, while the resultant pellet from the centrifugation was resuspended
by 50 mL 3% NaCl solution and stirred gently overnight at 4\u00baC to extract
EPS from the cellular surface. The solution was also centrifuged, and the
supernatant containing the AEPS was then filtered to remove residual cells
before further desalting via the 3 kDa ultrafiltration centrifugation tubes.
The final volume of concentrated solution of each biopolymer fraction (>3 kDa)
was 2 mL.
For the S. costatum cultures, 10 mL of 100 mM EDTA (pH 8.0) solution was
added to the diatom cells from the previous AEPS extraction step. The diatom
cells were resuspended at 4\u00baC overnight to extract the intracellular
material after diatom cell lysis and the supernatant was collected after
centrifugation to obtain the EDTA-extractable intracellular biopolymers. Then,
the resultant pellet was further resuspended in 10 mL of 1% SDS/10 mM Tris (pH
6.8) solution and heated at 95\u00baC for 1 hr. The centrifuged supernatant
was also collected and defined as SDS-extractable biopolymer in S. costatum
cells.\u00a0
To access the diatom frustule-associated biopolymers, 5 mL of 52% HF was
then added to the frustules and incubated on ice for 1 hr. After the
separation of HF-insoluble pellet, the HF-soluble fraction was evaporated
under N2 stream and neutralized, followed by the 3 kDa centrifugal filtration
to collect the digested frustule silica fraction (<3 kDa) and HF-soluble
frustule-associated biopolymer (>3 kDa). Lastly, the residue biopolymer in the
HF-insoluble pellet was collected with the resuspension in a 2 mL of 100 mM
ammonium acetate solution and sonication. Similar to NAEPS and AEPS, all the
S. costatum cellular biopolymers were concentrated and desalted with nanopure
water in 3 kDa Microsep centrifugal filter tubes (Milipore).
The coccosphere of the E. huxleyi cells was first dissolved before the
extraction of intracellular biopolymers. In brief, the pellet from the
previous AEPS extraction step was digested in 0.44 M acetic acid (HAc) (weak
acidity and non-oxidizing nature to avoid the breakage of cells) plus 0.1 M
NaCl solution at 4\u00baC for 8 hr. After the digestion, the mixed solution
was centrifuged and filtered, followed by ultrafiltration of the supernatant
with 3 kDa Microsep centrifugal filter tubes. The retentate (>3 kDa) was
defined as coccosphere-associated biopolymers, and the permeate fraction (<3
kDa) was also collected to obtain the fraction of digested biogenic calcite.
The E. huxleyi cells after the removal of shells were further heated in 20
mL of 1% SDS/10 mM Tris mixed solution (pH 6.8) at 95 \u00baC for 1 hr. The
supernatant was also collected through centrifugation and filtration, followed
by desalting with 3 kDa Microsep centrifugal filter tubes. Subsequently, the
remaining pellet was further digested by 0.04 M NH2OH\u2022HCl/4.35 M HAc
mixture at 96 \u00baC for 6 hr to obtain the intracellular metabolitic
biopolymer. The sum of these two fractions represents the intracellular
biopolymers in E. huxleyi cells.
All the solutions from the different extraction steps, including the >3 kDa
biopolymer fractions and the permeate (< 3 kDa, i.e., frustule and
coccosphere), were counted to determine the activity of 59Fe and 238Pu. 59Fe
activity was directly obtained from a Canberra ultrahigh purity germanium well
gamma detector at the decay energies of 1099 kev. All the solutions for the
gamma counting had the same volume and geometry to avoid geometry corrections,
and all the data were decay corrected.\u00a0
238Pu activities were determined by alpha-spectroscopy (Xu et al., 2016).
Briefly, a known activity of 242Pu was spiked to trace the yield of 238Pu
during the extraction steps. The samples were oven-dried, then heated at 600
\u00baC overnight in a ceramic crucible. The resulting ash fraction was then
digested in Teflon tubes overnight in concentrated HNO3 and HCl (1:1) at
85\u00baC. The remaining solid residual fraction was collected by
centrifugation and discarded, and the supernatant was further evaporated to
incipient dryness. To convert all Pu ions to Pu(IV), a FeSO4\u20227H2O (0.2
g/mL) solution, followed by 0.25 g of NaNO2, were added to each sample to
achieve a final volume of 3 mL for each sample. Samples were then passed
through an UTEVA column (Cat. # UT-C50-A, Eichrom, USA) to separate Pu from
other alpha-emitting radionuclides (e.g., 238U, 241Am). After washing the
column with an 8 M HNO3 solution, the Pu was eluted using freshly-prepared
0.02 M NH2OH\u2022HCl/0.02 M ascorbic acid in 2 M HNO3. The Pu-containing
eluent was evaporated and re-constituted in 0.4 M (NH4)2SO4 (pH~2.6) for
electroplating onto a stainless steel planchet at 0.6 Amps current for 2 hr.
Sample-bearing planchets were then analyzed via alpha spectroscopy for at
least one week to obtain counting errors (1 sigma) lower than 5%.

Subsamples were taken from the concentrated biopolymers for the analysis of
protein, total carbohydrate (TCHO) and uronic acid (URA), respectively. In
brief, the protein abundance was measured through a modified Lowry protein
assay, using bovine serum albumin (BSA) as the standard. For the
concentrations of TCHO, samples were hydrolyzed by 0.09 M HCl (final
concentration) at 150\u00baC for 1 h. After neutralization with NaOH solution,
the hydrolysate was measured by the 2,4,6-tripyridyl-triazine (TPTZ) method
(Hung et al., 2001), with glucose as the standard. URA concentrations were
determined by the metahydroxyphenyl method using glucuronic acid as the
standard (Hung and Santschi, 2001).\u00a0
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 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 Partitioning of iron and plutonium in exopolymeric substances and intracellular biopolymers: a comparison study between the coccolithophore Emiliania huxleyi and the diatom Skeletonema costatum
PI: Peter H. Santschi
Version: 2019-04-08
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 version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2019-04-08T17:02:21Z
attribute NC_GLOBAL date_modified String 2019-04-08T19:26:10Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.764480.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/764480 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Spectrometer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Sample-bearing planchets were then analyzed via alpha spectroscopy for at least one week to obtain counting errors (1 sigma) lower than 5%.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 764489
attribute NC_GLOBAL instruments_0_description String A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Spectrometer
attribute NC_GLOBAL instruments_0_instrument_nid String 667
attribute NC_GLOBAL instruments_0_supplied_name String Canberra Quad Alpha Spectrometer Model 7404
attribute NC_GLOBAL instruments_1_acronym String Spectrometer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String UV-Visible spectrometer, BioTek Instruments Inc Model EPOCH
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 764490
attribute NC_GLOBAL instruments_1_description String A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Spectrometer
attribute NC_GLOBAL instruments_1_instrument_nid String 667
attribute NC_GLOBAL instruments_1_supplied_name String UV-Visible spectrometer, BioTek Instruments Inc Model EPOCH
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Beckman Coulter Allegra X-12 centrifuge
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 764491
attribute NC_GLOBAL instruments_2_description String A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
attribute NC_GLOBAL instruments_2_instrument_name String Centrifuge
attribute NC_GLOBAL instruments_2_instrument_nid String 629890
attribute NC_GLOBAL instruments_2_supplied_name String Beckman Coulter Allegra X-12 centrifuge
attribute NC_GLOBAL instruments_3_dataset_instrument_description String Canberra ultrahigh purity germanium well gamma detector Model GCW3024
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 764492
attribute NC_GLOBAL instruments_3_description String Instruments measuring the relative levels of electromagnetic radiation of different wavelengths in the gamma-ray waveband.
attribute NC_GLOBAL instruments_3_instrument_name String Gamma Ray Spectrometer
attribute NC_GLOBAL instruments_3_instrument_nid String 670659
attribute NC_GLOBAL instruments_3_supplied_name String Canberra ultrahigh purity germanium well gamma detector Model GCW3024
attribute NC_GLOBAL keywords String act, bco, bco-dmo, biological, biopolymer, Biopolymer_fraction, cell, Cell_type, chemical, data, dataset, dmo, erddap, fe59, Fe59_act_pcnt, fraction, management, oceanography, office, pcnt, pcnt_URA_TCHO, preliminary, protein, Protein_C_TCHO_C, pu238, Pu238_act_pcnt, tcho, type, ura
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/764480/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/764480 (external link)
attribute NC_GLOBAL param_mapping String {'764480': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/764480/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 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 Iron (Fe), a micronutrient for algal growth, and plutonium (Pu), an anthropogenic radionuclide, share some common features. This includes similar oceanic distributions when different input modes are taken into account, as well as their chemical behavior, such as a high affinity to natural organic matter (NOM). The NOM produced by various phytoplankton communities can potentially influence Fe cycling in the ocean, and likely also influence the transport behavior of Pu. We conducted laboratory incubation experiments using the coccolithophore Emiliania huxleyi and the diatom Skeletonema costatum, in the presence of 59Fe and 238Pu as radiotracers, in order to differentiate Fe and Pu uptake by extracellular exopolymeric substances (EPS) and intracellular biopolymers. The Fe and Pu distributions in select organic compound classes including proteins, total carbohydrates (TCHO) and uronic acids (URA) produced by these two types of phytoplankton were compared. Our results indicated that most of the Fe and Pu (>95%) were found concurrently concentrated in E. huxleyi-derived non-attached EPS, while much less (<2%) was present in the intracellular fraction of E. huxleyi. By contrast, in the diatom S. costatum, both Fe and Pu distribution was EPS > intracellular biopolymers > outer cell covering (i.e., frustule). In fact, over 50% of Fe was concentrated in S. costatum-derived attached EPS and intracellular biopolymers. The diatom derived Fe-EPS complexes were more hydrophobic, with stronger tendency to aggregate in seawater. Fe binding to biopolymers in both E. huxleyi and S. costatum cultures was related to URA concentrations, but the overall distribution of URA between these two phytoplankton species was different. Our findings suggest that the presence of URA in S. costatum cellular surface (i.e., attached EPS) and its intracellular fraction could be an indicator for the Fe transport from the surrounding seawater to the diatom cells. However, for the coccolithophore E. huxleyi, Fe appeared not to be efficiently taken up during its growth. Instead, the more hydrophilic non-attached EPS (i.e., low protein/TCHO ratio) produced by E. huxleyi could have stabilized Fe in the colloidal form as Fe-EPS complexes. Similar partitioning behavior of Fe and Pu suggests that Pu isotopes can potentially serve as a tracer for the Fe biogeochemistry in the ocean.
attribute NC_GLOBAL title String Partitioning of iron and plutonium in exopolymeric substances and intracellular biopolymers: a comparison study between the coccolithophore Emiliania huxleyi and the diatom Skeletonema costatum
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable type   String  
attribute type bcodmo_name String sample_descrip
attribute type description String type
attribute type long_name String Type
attribute type units String unitless
variable Biopolymer_fraction   String  
attribute Biopolymer_fraction bcodmo_name String sample_descrip
attribute Biopolymer_fraction description String Biopolymer fraction type
attribute Biopolymer_fraction long_name String Biopolymer Fraction
attribute Biopolymer_fraction units String unitless
variable Cell_type   String  
attribute Cell_type bcodmo_name String sample_descrip
attribute Cell_type description String cell type
attribute Cell_type long_name String Cell Type
attribute Cell_type units String unitless
variable Fe59_act_pcnt   String  
attribute Fe59_act_pcnt bcodmo_name String unknown
attribute Fe59_act_pcnt description String Activity percentage
attribute Fe59_act_pcnt long_name String Fe59 Act Pcnt
attribute Fe59_act_pcnt units String unitless (%)
variable Pu238_act_pcnt   String  
attribute Pu238_act_pcnt bcodmo_name String unknown
attribute Pu238_act_pcnt description String Activity percentage
attribute Pu238_act_pcnt long_name String Pu238 Act Pcnt
attribute Pu238_act_pcnt units String unitless (%)
variable Protein   String  
attribute Protein bcodmo_name String unknown
attribute Protein description String amount of protein
attribute Protein long_name String Protein
attribute Protein units String microMole Carbon (uM-C)
variable TCHO   float  
attribute TCHO _FillValue float NaN
attribute TCHO actual_range float 1.0, 38.2
attribute TCHO bcodmo_name String unknown
attribute TCHO description String amount of TCHO-total carbohydrate
attribute TCHO long_name String TCHO
attribute TCHO units String microMole Carbon (uM-C)
variable URA   float  
attribute URA _FillValue float NaN
attribute URA actual_range float 0.2, 38.2
attribute URA bcodmo_name String unknown
attribute URA description String amount of URA-uronic acid
attribute URA long_name String URA
attribute URA units String microMole Carbon (uM-C)
variable Protein_C_TCHO_C   float  
attribute Protein_C_TCHO_C _FillValue float NaN
attribute Protein_C_TCHO_C actual_range float 0.0, 7.8
attribute Protein_C_TCHO_C bcodmo_name String unknown
attribute Protein_C_TCHO_C description String amount of protein to total carbohydrates
attribute Protein_C_TCHO_C long_name String Protein C TCHO C
attribute Protein_C_TCHO_C units String microMole Carbon (uM-C)
variable pcnt_URA_TCHO   byte  
attribute pcnt_URA_TCHO _FillValue byte 127
attribute pcnt_URA_TCHO actual_range byte 13, 100
attribute pcnt_URA_TCHO bcodmo_name String unknown
attribute pcnt_URA_TCHO description String percent uronic acid to total carbohydrates
attribute pcnt_URA_TCHO long_name String Pcnt URA TCHO
attribute pcnt_URA_TCHO units String microMole Carbon (uM-C)

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.


 
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