Results for “elution” — Page 7

DOE OSTI2024

Label-free single-vesicle based surface enhanced Raman spectroscopy: A robust approach for investigating the biomolecular composition of small extracellular vesicles

Small extracellular vesicles (sEVs) are cell-released vesicles ranging from 30-150nm in size. They have garnered increasing attention because of their potential for both the diagnosis and treatment of disease. The diversity of sEVs derives from their biological composition and cargo content. Currently, the isolation of sEV subpopulations is primarily based on bio-physical and affinity-based approaches. Since a standardized definition for sEV subpopulations is yet to be fully established, it is important to further investigate the correlation between the biomolecular composition of sEVs and their physical properties. In this study, we employed a platform combining single-vesicle surface-enhanced Raman spectroscopy (SERS) and machine learning to examine individual sEVs isolated by size-exclusion chromatography (SEC). The biomolecular composition of each vesicle examined was reflected by its corresponding SERS spectral features (biomolecular “fingerprints”), with their roots in the composition of their collective Raman-active bonds. Origins of the SERS spectral features were validated through a comparative analysis between SERS and mass spectrometry (MS). SERS fingerprinting of individual vesicles was effective in overcoming the challenges posed by EV population averaging, allowing for the possibility of analyzing the variations in biomolecular composition between the vesicles of similar and/or different sizes. Using this approach, we uncovered that each of the size-based fractions of sEVs contained particles with predominantly similar SERS spectral features. Indeed, more than 84% of the vesicles residing within a particular group were clearly distinguishable from that of the other EV sub-populations, despite some spectral variations within each sub-population. Our results suggest the possibility that size-based EV fractionation methods produce samples where similarly eluted sEVs are correlated with their respective biochemical contents, as reflected by their SERS spectra. Our findings therefore highlight the possibility that the biogenesis and respective biological functionalities of the various sEV fractions may be inherently different.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Utilization of traceable standards to validate plutonium isotopic purification and separation of plutonium progeny using AG MP-1M resin for nuclear forensic investigations

Radio-chronometric studies on plutonium (Pu) materials require independent measurement of the Pu (parent) content and isotopic distribution as well as concentration and isotopic distribution of the plutonium isotopic decay products. We performed a series of experiments to demonstrate the consistency of separations using the Lewatit MP 800 macroporous anion exchange resin and the AG MP-1M resin with traceable Pu isotopic certified reference material (CRM) standards 136, 137, 138, and 126-A. Two different mesh-sizes of the AG MP-1M resin were tested and the 50–100 mesh size resin was found to work more efficiently for the separation task. Both Lewatit and AG MP-1M resins were found to perform satisfactorily for quantitatively extracting the americium (Am) and uranium (U) progeny as well as gallium (Ga) present as a tracer in the Pu material. Both resins were effective in removing isobaric interferences from the Pu fraction used in isotopic measurements by thermal ionization mass spectrometry (TIMS). To address the co-elution of uranium and gallium, Alizarin red S (ARS) was used as a colorimetric dye to determine the behavior of UO 2 2+ and Ga 3+ on AG MP-1M resin with various acidic solutions as eluents using UV–vis spectra. Poor resolution of these peaks complicated quantitative analysis by UV–vis spectroscopy, but these results were informative in planning automated separation experiments by HPLC. LA-UR-24-28919.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2020

Recycling Isotopically Enriched Mo from the RadioGenix Waste Stream

NorthStar’s RadioGenix generator utilizes an aqueous biphasic extraction chromatography column to separate Tc from low-specific-activity 99 Mo. During this separation process, a fraction of the source Mo material can be found in the waste. This is not of concern when natural Mo targets are used. However, the introduction of isotopically enriched 98 Mo for neutron capture or 100 Mo for accelerator-based production requires recovery of this valuable enriched Mo material. The generator waste is absorbed and solidified in a superabsorbent hydrogel polymer. In this contribution, we report results from our small-scale experimental study on development of a separation process for recovery of molybdenum from the polymeric gel waste using common chemicals and simple chemical techniques. Our investigation confirms that the acidic deswelling of the alkaline hydrogel with concentrated hydrochloric acid converts the occluded molybdate to a neutral molybdenyl dichloride species that is freely released from the gel. Mo can then be concentrated on a commercial tri-n-butyl phosphate resin, eluted with ammonium hydroxide, and crystallized as ammonium heptamolybdate for conversion back to Mo metal. Typical Mo recoveries are 90-95%.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

PORFLOW modeling of Vadose zone flow and transport for the E-area intermediate level vault

In support of the E-Area Performance Assessment, a two-dimensional model of water flow and radionuclide transport through the E-Area Intermediate Level Vault (ILV) and local vadose zone has been developed using the PORFLOWTM software. The purpose of the model is to calculate flux to the water table for radionuclides eluted from the ILV during its operational life, the period of institutional control, and times following site closure. Results of model calculations will be used by a three-dimensional PORFLOW model of transport through the aquifer to determine radionuclide concentrations at a hypothetical 100 meter well and at the site boundary where contaminated groundwater could be assessed by members of the public following site closure. While newly developed, the model structure closely follows that used in the 2008 PA while incorporating a refined computational mesh, updated material properties for the vadose zone soil and vault concrete, revised infiltration rates, and new solid-liquid distribution coefficients. The model also addresses degradation of concrete hydraulic properties by blending soil and concrete water retention curves over a 500 year period. That is, the hydraulic properties of ILV concrete start out as fresh concrete at the time of site closure and degrade to soil properties over a 500 year time period. This approach has not been used previously in E-Area PA’s. The model has been used to calculate water flow through the ILV vadose zone and, on a trial basis, transport of a limited number of radionuclides from the waste region inside the ILV to the water table. Figure ES-1 provides a view of the model and an example of water flow after the concrete has substantially degraded. Figure dimensions are in centimeters. The red area in the left hand side figure is the waste disposal region within the ILV. Colored bands in the figures indicate different soil and concrete regions. Figure ES-2 shows a calculation of flux to the water table (mol/yr) for U-234 and its one-year half-life decay chain (U-234 → Th-230 → Ra-226 → Pb-210). Pb-210 flux is too small to show on the same scale used for Th-230 and Ra-226 in Figure ES-2. The model has also been used to make a preliminary evaluation of the release of tritium from TPBAR disposal containers that will be place in the ILV. A separately calculated tritium release rate as a function of time was used as a source in the PORFLOW model. The TPBAR disposal schedule and tritium release rate differ from the values used in the 2008 PA. Results from these initial trial runs are compared to calculations made for the 2008 PA ILV analysis. In brief, a new PORFLOW model of flow and transport through the ILV vadose zone has been developed and tested. The model is ready to be used for PA calculations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

PORFLOW Modeling of Vadose Zone Flow and Transport for the E- Area Low Activity Waste Vault

In support of the E-Area Performance Assessment, a two-dimensional model of water flow and radionuclide transport through the E-Area Low Activity Waste Vault (LAWV) and local vadose zone has been developed using the PORFLOW TM software. The purpose of the model is to calculate flux to the water table for radionuclides eluted from the LAWV during its operational life, the period of institutional control, and times following site closure. Results of model calculations will be used by a three-dimensional PORFLOW model of transport through the aquifer to determine radionuclide concentrations at a hypothetical 100 meter well and at the site boundary where contaminated groundwater could be accessed by members of the public following site closure.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

PORFLOW Modeling of Vadose Zone Flow and Transport for E-Area Intermediate Level Vault

In support of the E-Area Performance Assessment, a two-dimensional model of water flow and radionuclide transport through the E-Area Intermediate Level Vault (ILV) and local vadose zone has been developed using the PORFLOW TM software. The purpose of the model is to calculate flux to the water table for radionuclides eluted from the ILV during its operational life, the period of institutional control, and times following site closure. Results of model calculations will be used by a three-dimensional PORFLOW model of transport through the aquifer to determine radionuclide concentrations at a hypothetical 100 meter well and at the site boundary where contaminated groundwater is accessible to members of the public following site closure.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Developing Inorganic Resins for Radium and Actinium Generators and Purifications

The inorganic, normal-phase sorbents alumina, titania, and zirconia were evaluated and screened for the separation of Ba, La, 228 Ra, 228 Ac, and 212 Pb in a dilute acid matrix. The results show that the sorbents are capable of fractionating the ions between pH 1–8. Acetate and total metal ion concentrations were experimentally evaluated as factors that could affect retention using La and Ba surrogates. Pseudo-second order rate constants were derived and the uptake of La was determined to be endothermic. A stationary zirconia column was used to isolate Ba from La and Ra from Ac/Pb; elution profiles of each separation are presented. The utility and implications of these sorbents are discussed with respects to large-scale production of 225 Ac from radium targets. This work was published in 2020 and in 2022.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2023

Adapting LEU-Modified Cintichem Process for Processing Up to 750 Grams of Uranium Targets

Argonne National Laboratory (Argonne) developed a low-enriched uranium (LEU)-modified Cintichem (LMC) process to enable production and purification of fission-produced molybdenum-99 (Mo-99) from LEU foil targets. This separation scheme starts with nitric acid (HNO 3 ) dissolution of irradiated LEU foil targets that yields an approximate final volume of 2 L. The dissolved uranium solution containing fission products, including Mo-99, is then treated by loading the solution on a titania-based recovery column to separate Mo-99 from bulk uranium. After several washing steps, Mo and other fission products are stripped from the titania column using sodium hydroxide (NaOH). The eluate is then acidified using nitric acid and subsequently processed for final purification using the LMC process. Uranium and most fission products are not adsorbed on the titania column but are eluted (i.e., removed using a solvent) during the wash steps; they can be purified and recycled into new uranium targets.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2022

Ion Exchange Processing of AP-105 Hanford Tank Waste through Crystalline Silicotitanate in a Staged 2- then 3-Column System (Rev.1)

The Tank Side Cesium Removal (TSCR) system, under development by Washington River Protection Solutions LLC (WRPS), will send initial low-activity Hanford waste tank supernate feeds to the Hanford Waste Treatment and Immobilization Plant (WTP) Low-Activity Waste (LAW) Facility. In addition to entrained solids removal from the supernate, the primary goal of TSCR is to remove cesium-137 ( 137 Cs) by ion exchange, allowing contact handling of the liquid effluent product at the WTP. Crystalline silicotitanate (CST) ion exchange media, manufactured by Honeywell UOP, LLC (product IONSIVTM R9140-B), was selected as the ion exchange media at TSCR. CST is a non-elutable inorganic material that has demonstrated robust chemical, physical, and radiation tolerance while maintaining functionality. However, exchange kinetics of Cs onto CST is slow, resulting in low utilization of the CST Cs load capacity before unacceptable Cs breakthrough. Two process flow designs have been tested, as follows. 1. Lead-lag column processing: The lead column was removed after the lag column effluent reached the waste acceptance criteria (WAC) limit, the lag column was moved into the lead position, and a new lag column was installed. This format used ~52% Cs load capacity on the lead column. 2. Lead-lag-polish column processing: The processing was stopped when the polish column effluent reached the WAC limit. This format resulted in 81% Cs load capacity on the lead column. Testing with diluted feed from Hanford tank AP-105 (AP-105DF) incorporated a nuanced change to the lead-lag-polish column system where the polish column was inserted when the lag column effluent reached WAC limit. A 10.9-L volume of AP-105DF (diluted to 5.6 M Na) was processed through the Direct Feed Test Platform system, established at Pacific Northwest National Laboratory to support small-scale waste qualification efforts. The columns consisted of 10-mL CST beds (CST Lot 2002009604, sieved to screen out >30-mesh particles) placed in 1.5-cm-inner-diameter columns. Feed was processed at 1.83 bed volumes (BV) per hour; the flowrate, in terms of contact time with the CST bed, matched the expected flowrate at TSCR. The <30-mesh CST sieve cut was expected to provide appropriate performance scaling to a full-height column. The installation of the polish column later in processing (after processing 523 BVs) did not appear to fundamentally change the utilization of the lead column for Cs exchange nor did it extend the total feed processing volume when compared to the previous test with AP-107 feed. Table ES.1 and Figure ES.1 summarize the measured AP-105DF Cs load performance.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Cesium Removal from 5.5 and 7.0 M Na AP-105 Using Crystalline Silicotitanate

The Tank Side Cesium Removal (TSCR) system, currently operational by Washington River Protection Solutions LLC (WRPS), prepares initial low-activity Hanford waste tank supernate feeds for the Hanford Waste Treatment and Immobilization Plant (WTP) Low-Activity Waste (LAW) Facility. In addition to entrained solids removal from the supernate, the primary goal of TSCR is to remove cesium-137 ( 137 Cs) by ion exchange, allowing contact handling of the liquid effluent product at the WTP as governed by a waste acceptance criterion (WAC). Specific to 137 Cs, this requirement is < 3.18E-5 Ci 137 Cs/mole of Na. Crystalline silicotitanate (CST) ion exchange media, manufactured by Honeywell UOP, LLC (product IONSIVTM R9140-B), has been selected as the ion exchange media for TSCR. CST is a non-elutable inorganic material that has demonstrated robust chemical, physical, and radiation tolerance while maintaining functionality. However, testing to date on actual tank waste samples has been limited to Na concentrations between 5 and 6 M Na (Fiskum et al. 2019a, 2021b and Westesen et al. 2021a, 2021b, 2022) while actual tank conditions can reach upwards of 9 M Na. Testing with feed from Hanford tank AP-105 incorporated testing at both 5.5 and 7 M Na in order to evaluate the impact of Na concentration on volume of waste processed before reaching the WAC. A 6-L volume of 5.5 M Na AP-105 and an 8-volume of 7 M Na AP-105 was processed through the Radioactive Waste Test Platform system, established at Pacific Northwest National Laboratory to support small-scale waste qualification efforts. The columns consisted of 6- to 9-mL CST beds (CST Lot 2002009604, sieved to screen out >30-mesh particles) placed in 1.5-cm-inner-diameter columns. Feed was processed at 1.9 bed volumes (BV) per hour; the flowrate, in terms of contact time with the CST bed, matched the expected flowrate at TSCR. Table S.1 and Figure S.1 summarize the measured AP-105 Cs load performance for each feed condition.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Multi-functional Sorbent Development for Separation of Critical Minerals and Pollutants

Critical Metals (CMs), including Rare Earth Elements (REEs), aluminum, manganese, cobalt, and others outlined by the U.S. Department of the Interior’s Geological Survey are essential to the national and economic security of the US, and whose supply chain is susceptible to disruption. Because of the negative environmental impacts inherent with the conventional mining and processing of solid ores for CMs, adsorption-based recovery of naturally dissolved species from coal wastewaters is appealing. Acid mine drainage (AMD) remains a relatively untapped source that can be rich in REEs, and especially in Al, Mn, and other CMs. NETL’s Multi-functional Sorbent Technology (MUST) has been developed originally from the functionalized silica sorbents for carbon capture. Ongoing work aims to find AMD sites enriched with either REEs or other CM, and to perform additional field tests at these sites. Overall, our work shows the viability of recovering CMs from AMD and other coal waste streams, using a fixed-bed adsorption system that can also employ a selective elution technique to achieve highly purified metal resources.

Shi, Fan↗

DOE OSTI2026

Novel Zwitterionic Chromatography to Separate Lithium from Unconventional Resources

Since lithium (Li) is a key element for clean energy technologies, the global lithium demand is anticipated to increase rapidly. As a result, efficient lithium extraction technologies that allow the exploitation of unconventional lithium resources, such as geothermal brines and inland brine streams, are essentially needed to meet the Li demand and keep supply chains stable. However, because of low Li concentration, low ratio of Li/Mg or Li/Ca, and complex feed compositions in these feedstocks, using conventional hydrometallurgy or current Direct Lithium Extraction (DLE) processes are often chemical-intensive, requiring substantial amounts of reagent chemicals to recover Li at scale, resulting in large chemical footprints. Therefore, we developed a novel Zwitterionic Chromatography (ZIC) process to separate Li from these resources. Because Li can be partitioned from divalent salts on ZIC under water elution without using chemicals, exploiting the unconventional resources via a ZIC approach can be environmentally benign and sustainable. In this work, we will present the development of the ZIC process for DLE applications. Simulation studies for the Li separation mechanism in ZIC and the demonstration of a continuous ZIC process to separate Li from domestic inland brine and mining wastewater will be presented. Finally, the chemical and energy footprints of ZIC in comparison to other DLE processes will be discussed.

09 BIOMASS FUELS↗

DOE OSTI2022

Current State of 44 Ti/ 44 Sc Radionuclide Generator Systems and Separation Chemistry

We report in recent years, there has been an increased interest in 44Ti/44Sc generators as an onsite source of 44Sc for medical applications without needing a proximal cyclotron. The relatively short half-life (3.97 hours) and high positron branching ratio (94.3%) of 44Sc make it a viable candidate for positron emission tomography (PET) imaging. This review discusses current 44Ti/44Sc generator designs, focusing on their chemistry, drawbacks, post-elution processing, and relevant preclinical studies of the 44Sc for potential PET radiopharmaceuticals.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2024

KBase Narrative - Lachnospiraceae sp. C1.1 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2023

Structural Characterization of Toxicologically Relevant Cd 2+ -L-Cysteine Complexes

The exposure of humans to Cd exerts adverse human health effects at low chronic exposure doses, but the underlying biomolecular mechanisms are incompletely understood. To gain insight into the toxicologically relevant chemistry of Cd 2+ in the bloodstream, we employed an anion-exchange HPLC coupled to a flame atomic absorption spectrometer (FAAS) using a mobile phase of 100 mM NaCl with 5 mM Tris-buffer (pH 7.4) to resemble protein-free blood plasma. The injection of Cd 2+ onto this HPLC-FAAS system was associated with the elution of a Cd peak that corresponded to [CdCl 3 ] - /[CdCl 4 ] 2- complexes. The addition of 0.1–10 mM L-cysteine (Cys) to the mobile phase significantly affected the retention behavior of Cd 2+ , which was rationalized by the on-column formation of mixed CdCysxCly complexes. From a toxicological point of view, the results obtained with 0.1 and 0.2 mM Cys were the most relevant because they resembled plasma concentrations. The corresponding Cd-containing (~30 μM) fractions were analyzed by X-ray absorption spectroscopy and revealed an increased sulfur coordination to Cd 2+ when the Cys concentration was increased from 0.1 to 0.2 mM. The putative formation of these toxicologically relevant Cd species in blood plasma was implicated in the Cd uptake into target organs and underscores the notion that a better understanding of the metabolism of Cd in the bloodstream is critical to causally link human exposure with organ-based toxicological effects.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Resin Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation

Reversible oxidative modifications on protein thiols have recently emerged as important mediators of cellular function. Herein we describe the detailed procedure of a quantitative redox proteomics method that utilizes resin-assisted capture (RAC) in combination with tandem mass tag (TMT) isobaric labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to allow multiplexed stochiometric quantification of oxidized protein thiols at the proteome level. The site-specific quantitative information on oxidized cysteine residues provides additional insight into the functional impacts of such modifications. The workflow is adaptable across many sample types including cultured cells (e.g. mammalian, prokaryotic) and whole tissues (e.g. heart, lung, muscle) which are initially lysed/homogenized with free thiols being alkylated to prevent artificial oxidation. The oxidized protein thiols are then reduced and captured by a thiol affinity resin which streamlines and simplifies the workflow steps by allowing the proceeding digestion, labeling, and washing procedures to be performed without additional transfer of proteins/peptides. Finally, labeled peptides are eluted and analyzed by LC-MS/MS to reveal comprehensive stoichiometric changes related to thiol oxidation across the entire proteome. This method greatly improves our understanding of the role of redox dependent regulation under physiological and pathophysiological states related to protein thiol oxidation.

RAC, TMT, thiol redox proteomics, cysteine, PTM st↗

DOE OSTI2020

ESI-FTICR-MS Analysis of Organic Matter during Incubations with Nitrogen Addition, Teller Road Site, Seward Peninsula, Alaska

This dataset contains the results of the molecular characterization of water-extractable organic matter collected during soil microcosm incubations of tundra soil. The microcosms contained soil collected in April 2017 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (“Toeslope”) and Intensive Site 5 (“Plateau”). The incubations were conducted under an atmosphere of N2 at 8°C for 55 days, with or without addition of ammonium chloride (NH4Cl). Soils were extracted with deionized water and extracted using Bond Elut PPL cartridges prior to analysis. Molecular characterization was performed using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI- FTICR-MS). Two data files are provided with this dataset. The first is the summary, by soil type and treatment, of the mass spectrometry results for formulas (as a % of the total) containing C, H, and O only, and with N, S, and other elements. These formulas were then grouped into nine biochemical classes of compounds based on O:C and H:C ratios. The second file provides soil sample characteristics and the processed high-resolution mass spectrometry results by soil type and treatment.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 10-year research effort (2012-2022) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

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