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At least 397 records · Page 22

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DOE OSTI2023

Direct selection of functional fluorescent-protein antibody fusions by yeast display

Antibodies are important reagents for research, diagnostics, and therapeutics. Many examples of chimeric proteins combining the specific target recognition of antibodies with complementing functionalities such as fluorescence, toxicity or enzymatic activity have been described. However, antibodies selected solely on the basis of their binding specificities are not necessarily ideal candidates for the construction of chimeras. Here, we describe a high throughput method based on yeast display to directly select antibodies most suitable for conversion to fluorescent chimera. A library of scFv binders was converted to a fluorescent chimeric form, by cloning thermal green protein into the linker between VH and VL, and directly selecting for both binding and fluorescent functionality. This allowed us to directly identify antibodies functional in the single chain TGP format, that manifest higher protein expression, easier protein purification, and one-step binding assays.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format

Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes ( e . g ., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5–2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Single-nuclei transcriptome analysis of channel catfish spleen provides insight into the immunome of an aquaculture-relevant species

The catfish industry is the largest sector of U.S. aquaculture production. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied and has provided crucial information on innate and adaptive immune function during disease progression. To further examine the channel catfish immune system, we performed single-cell RNA sequencing on nuclei isolated from whole spleens, a major lymphoid organ in teleost fish. Libraries were prepared using the 10X Genomics Chromium X with the Next GEM Single Cell 3’ reagents and sequenced on an Illumina sequencer. Each demultiplexed sample was aligned to the Coco_2.0 channel catfish reference assembly, filtered, and counted to generate feature-barcode matrices. From whole spleen samples, outputs were analyzed both individually and as an integrated dataset. The three splenic transcriptome libraries generated an average of 278,717,872 reads from a mean 8,157 cells. The integrated data included 19,613 cells, counts for 20,121 genes, with a median 665 genes/cell. Cluster analysis of all cells identified 17 clusters which were classified as erythroid, hematopoietic stem cells, B cells, T cells, myeloid cells, and endothelial cells. Subcluster analysis was carried out on the immune cell populations. Here, distinct subclusters such as immature B cells, mature B cells, plasma cells, γδ T cells, dendritic cells, and macrophages were further identified. Differential gene expression analyses allowed for the identification of the most highly expressed genes for each cluster and subcluster. This dataset is a rich cellular gene expression resource for investigation of the channel catfish and teleost splenic immunome.

Science & Technology - Other Topics↗

DOE OSTI2019

Understanding the Interactions of Seawater Ions with Amidoxime through X-Ray Crystallography

Insoluble polymer substrates functionalized with the amidoxime (R-C(NH 2 )=NOH) functional group have been demonstrated as a technically feasible platform for extracting uranium from seawater, a potential source of extremely abundant uranium for use as nuclear fuel. While it is possible to isolate macroscopic amounts of uranium from the ocean with a positive energy return on investment using these materials, both the economic and energetic costs are many times greater than those of terrestrial uranium mining. Currently, the major contribution to this cost is the production of the sorbent itself, so being able to recycle the sorbent even a small number of times will have a huge impact on lowering the cost of their use. However, amidoxime resins show capacity fading when stripped by strong acids, presently limiting their recyclability. Both alternative extractants and alternative elution chemistries are under development with promising results but are yet at too early a stage to make predictions about their ultimate success. Given the potentially huge impact of a successful recycling process on the viability of seawater extraction of uranium, there is a strong need to pursue additional routes to elution chemistry. During the course of this project, we studied the interactions of amidoxime-containing small molecules with the abundant metal ions in seawater, including Li, Na, K, Mg, Ca, Fe, Cu, and V, to understand the interactions of [UO 2 ] 2+ with amidoxime. By using small molecules with multiple adjacent functional groups, we crystallized the resulting metal complexes and used single crystal X-ray diffraction (SCXRD) as our primary tool for structural characterization. We also investigated the use of solutions of hydroxylammonium salts in weak acids as eluents for stripping and recycling amidoxime-based sorbents. The replacement of strong acids, which react with and destroy the amidoxime functional groups, with weak acids based on hydroxylammonium, a reagent that is actually used to make the amidoxime groups, is expected to avoid capacity loss on recycling and possibly even regenerate functionality that was lost due to exposure to the marine environment.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2020

Particle size of several plutonium-238 oxide fuel samples from oxalate precipitation processes

Particle size of 238 PuO 2 powders is an important factor in determining the structural integrity of fuel pellets hot-pressed from the oxide powder. Understanding the evolution of particle size during aqueous processing is a first step in assuring control of particle size throughout the pellet formation process. Measured particle sizes are reported here, and discussed in terms of measured particle size changes occurring during calcining, observed aggregation of particulate, and particle morphology. Morphology and aggregation are related to surface energy, which governs granule formation and hot pressing behavior. Results are discussed in terms of reported dependence of oxide morphology on process temperatures and reagent concentrations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

The Activation of Hydrogen by First-Row Transition-Metal Complexes. Final Report

We have assigned the vibrational spectra of Os 1 and Os 2 complexes of propene, butene, and acetylene, and have used them for the assignment of the vibrational frequencies of surface alkenes and alkynes. We have measured the rates of H• transfer from (C 5 R 5 )Cr(CO) 3 H to olefins of many structural types, and have learned that even one substituent on the carbon to which the H• is transferred slows down the reaction considerably. We have shown that these Cr hydrides are useful catalysts for chain transfer during radical polymerization reactions. We have determined the strengths of several M–H bonds (in particular Cr–H ones), and have confirmed that the hydrides of first-row transition metals are particularly useful for generating radicals. We have used H• transfer to terminal methylenes to generate radicals that cyclize. We have shown that (C 5 R 5 )Cr(CO) 3 H can be regenerated under H 2 and is therefore catalytic, but that (P–P)V(CO) 4 H cannot be regenerated from H 2 and therefore can only be used stoichiometrically for radical generation. (The V-H bonds are weaker than the Cr–H ones, and the H• transfer to an olefin is therefore faster.) We have found that, under five atm of H 2 pressure, cobaloximes catalyze H• transfer; they efficiently remove an H• from cyclized radicals, and therefore can be used to catalyze the cycloisomerization of some olefins. We have explored the one- and two-electron oxidation of (Ph 3 P) 6 Cu 6 H 6 . One-electron oxidation (which is reversible) generates a cation radical, whereas two-electron oxidation generates loss of a hydride (i.e., two electrons and a proton). We have found that the hydricity of (Ph 3 P) 6 Cu 6 H 6 is between 36 and 50 kcal/mol. We have shown that uncongested organic radicals (i.e., TEMPO) can catalyze H• transfer from (C 5 R 5 )Cr(CO) 3 H to congested radicals like Ar 3 C•. We have examined the one-electron oxidation of [CpV(CO 3 H] – , and have inferred from the results that the reduction of alkyl iodides with [CpV(CO 3 H] – occurs by one-electron transfer. We have been able to use that reagent to catalyze radical cyclizations from H 2 and appropriate alkyl iodides.

08 HYDROGEN↗

DOE OSTI2020

Technology Summary DNATRAX

DNATrax (DNA Tagged Reagents for Aerosol eXperiments) was developed to provide a safe simulant for understanding the transport and dispersion of pathogens. Specifically, it was developed as a safe surrogate for the Bacillus anthrasis spore bioagent, since most naturally occurring spores are not safe for public release. As DNA-tagged sugar particles, DNATrax aerosols are safe for public release. Scientists can add unique DNA barcode sequences to the sugar particles to produce a wide variety of test particles that can be easily differentiated, making it possible to release and test them simultaneously. The unique barcodes also eliminate the need to conduct decontamination between tests, dramatically reducing the cost and time to run experiments. Additionally, the surrogate offers a high-sensitivity detection method to understand key public health issues. We conducted both lab-based and largescale field studies using DNATrax to validate its capabilities for use as a pathogen surrogate. We have demonstrated the ability to produce DNATrax in a range of sizes, adjusting the microparticles to simulate different sized pathogens with ability to create unique sequences of DNA bases, enabling them to create a nearly unlimited variety of test particles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Study of Poly(ether ketone ketone) (PEKK): Outgassing Characteristics and Likely Residual Synthesis Impurities

In May-June, 2020, a study was conducted to characterize the outgassing properties of a series PEKK (Poly(ether ketone ketone)) samples using cryo-GC/MS headspace analysis. Three sets of samples were interrogated: sample group 1 consisted of 2 additively manufactured PEKK samples (PEKK "ole and "New") prepared by KCNSC from powder material from Solvay Specialty Polymers USA, LLC. Sample groups 2 and 3 consist of 5 PEKK powder types (used as feedstock for additive manufacturing processes) and 4 additively-manufactured PEKK material lots, respectively. Contrary to expectations, all samples of PEKK material were observed to outgas sulfur-containing compounds. Other analyses (EDS/EMA, GC-TOF/MS of PEKK sample extractions) confirmed the presence of sulfur in the PEKK bulk material. Specifically, Diphenyl sulfone (used as a reagent or high-temperature solvent in the synthesis of Polyaryletherketone or PAEK polymers) was observed in three of the powders and in both the PEKK "Old" and "New" samples, suggesting that the source of the sulfur can be traced to impurities in the material left over from the synthesis process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Validation of pooling strategies of clinical COVID-19 samples for more efficient diagnostic testing

Pooling of COVID-19 clinical samples can offer significant reduction in reagents, time, and labor needed to test large numbers of clinical samples. Especially for testing asymptomatic and return-towork/ school cases, where the prevalence of COVID-19 may be relatively low, large groups of clinical samples can be classified as negative with a single test, with no need to test every sample individually. LANL has performed validation for two different pooling strategies to assess diagnostic assay sensitivity in pooled samples compared to the clinical positive sample alone. (1) Pooling study - Determine diagnostic assay sensitivity in pooled samples with ratios of 1:5, 1:10, 1:20, and 1:30 positive to negative clinical samples. (2) Reloading study - Determine diagnostic assay sensitivity in reloading of multiple clinical samples through a Qiagen column in 5x, 10, and 20x sample volumes (1 positive plus 4, 9, and 19 negative samples).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Recovery of Rare Earth Elements from Bioleachates by Precipitation

Rare earth elements are essential components in electronic devices, however because of the limited imports and mining capabilities in the US, recycling these rare earths is crucial. Common practices used to recover REEs including hydrometallurgy and pyrometallurgy are harmful to the environment. Bioleaching, a form of biohydrometallurgy, is an emerging process that uses organic acids synthesized by microorganisms and can leach REEs at comparable efficiencies to less environmentally conscious processes. Once the REEs are leached by the bio-lixiviant produced by microorganisms, the REEs are suspended in the solution and need to precipitate out in order to be harvested for reuse. Common chemicals used for rare earth precipitation in hydrometallurgy processes include sodium sulfate and oxalic acid. These two reagents were tested at varying stoichiometric excess concentrations in bio-leachate derived from smart phone speaker magnets and bio-lixiviant. Following the precipitation reactions, it was observed that the oxalic acid reaction precipitated an abundance of iron (II) oxalate, an REE contaminate. This is most likely due to the bio-leachate having a higher pH compared to the hydrometallurgical leachates. Therefore, it was determined that sodium sulfate is a better candidate for REE precipitation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Handheld Biosensor for COVID-19 Screening

We have made significant progress toward the development of an integrated nucleic acid amplification system for Autonomous Medical Devices Incorporated (AMDIs) Optikus handheld diagnostic device. In this effort, we developed a set of loop-mediated isothermal amplification (LAMP) primers for SARS-CoV-2 and then demonstrate amplification directly on a surface acoustic wave (SAW) sensor. We built associated hardware and developed a C-code to control the amplification process. The goal of this project was to develop a nucleic amplification assay that is compatible with SAW sensors to enable both nucleic and serological testing in a single handheld diagnostic device. Toward this goal, AMDI is collaborating Sandia National Laboratories to develop a rapid, portable diagnostic screening device that utilizes Sandias unique surface acoustic wave biosensor (SAW) for COVID-19 detection. Previously, the SANDIA- AMDI SAW sensor has successfully detected multiple high-profile bacteria viruses, including Ebola, HIV, Sin Nombre, and Anthrax. Over the last two years, AMDI and SANDIA have significantly improved the sensitivity and detection capability of the SAW biosensor and have also developed a modular hand-held, portable platform called the Optikus, which uses CD microfluidics and handheld instrumentation to automate all sample preparation, reagent introduction, sample delivery, and measurement for a number of different assay targets. We propose to use this platform for the development of a rapid (%3C30 minutes), point-of-care diagnostic test for detection of COVID-19 from nasal swab samples.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

AX Farm and A Farm Third Retrieval Technology Chemical Dissolution Options Evaluation

In response to DOE-ORP direction to prepare a Practicability Evaluation for Waste Tank AX-102, and to address the Washington State Department of Ecology recommendation to evaluate the use of acid reagents for chemical dissolution, an Integrated Project Team (IPT) consisting of retrieval, process chemistry, corrosion, closure and laboratory subject matter experts was assembled to evaluate chemical dissolution options. This document provides a summary of these efforts and is intended to aid in the evaluation and third retrieval technology decision process not only for AX-102, but for all the AX and A Farm tanks, since the tanks contain similar waste and are flat-bottomed with uneven bottom plates.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

19-LW-045 Full Length Final Report. Molecular Mechanisms of Bacterial Pathogenesis: Waging the Arms Race with Superbugs

As the current global pandemic makes abundantly clear, we need a better understanding of infectious disease to safeguard human health, the economy and global security. Modern omics techniques hold the promise of providing a comprehensive understanding of the molecular mechanisms of life, including causes of pathogenesis from infectious disease at the molecular level, but we there is a serious gap in annotation of gene function. For as much as half of the genes and gene products encoded in genomes the molecular and/or cellular function is unknown or only partially understood. Recent innovations in fluorescence microscopy for live cell imaging and genetic engineering make it possible to determine the temporal correlation between molecular events, such as a gene being expressed due to host-pathogen interaction, and cellular events, such as bacterial invasion of immune cells. This is turn allows us to gain new insight as to the molecular and cellular role of individual genes and will enable the discovery and validation of new molecular mechanisms essential for infectious disease. Knowing the molecular mechanisms of disease processes will provide new therapeutic targets or novel countermeasure strategies. We aimed to develop a lattice light sheet fluorescence microscope as a unique resource at LLNL for long time course live cell imaging experiments; to develop the reagents and cell lines needed to monitor molecular events during the course pathogenic bacteria infecting mammalian immune cells; and to demonstrate that we could capture molecular events during an infection. We fully commissioned the LLNL lattice light sheet microscope and conducted initial proof of principle imaging experiments on mammalian immune cells and pathogenic bacteria. It is clear from the experience gained that long time course live cell imaging has tremendous potential to help elucidate molecular mechanisms of host-pathogen interactions and to help annotate gene function, which would establish a basis for new countermeasures. It is also clear that if live cell imaging is to realize its full potential new data processing and analysis tools will need to be developed to facilitate analysis of molecular events within cells; new sample chambers and stages could facilitate studies with a wider range of cell and tissue types; and alternative molecular tagging methods need to be explored to enable more facile engineering of cells labeled with molecular specificity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Imaging APO-BMI with Micro X-ray Computed Tomography (CT)

APO-BMI is a high-strength, high-temperature, and low-density foam comprised of 1,2-bis(2-aminophenylthio) ethane (APO-Link, formerly Apocure-601) and 4,4’-bismaleimidodiphenylmethane (BMI) that is used structural applications within the aerospace and weapons manufacturing sectors. APO-link is the diamine reagent used to synthesize BMI, a thermosetting resin. This resin can remain in a molten, flowing state for an extended period of time before crosslinking, allowing addition of glass or carbon microballoons to form its final structure. A portion of the current project was to observe the thermal effects on the structural integrity of the foam associated with exposure to an ion beam. Features within the foam were imaged using micro X-ray computed tomography (CT). The resulting imaging provided evidence that microballoon structure remained mostly intact at the points of failure, indicating that the failure of the material was occurring in the binder material.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Production and Performance of High Sulfur Concentration Waste Glasses (FY21)

In FY21 Savannah River National Laboratory (SRNL) was tasked to investigate the practical aspects of low activity waste (LAW) glass production with high sulfur loading for the Office of River Protection (ORP). Relationships between sulfur solubility, retention, and melter resonance need to be evaluated to refine waste loading limits and the super saturated melting (triple melt, grind, and wash) methodology. The impact of high sulfur concentration on durability and phase stability (crystallization and liquid-liquid immiscibility) during slow cooling also needs to be further evaluated. To accomplish this, SRNL proposed scaled melter testing using simulants with matched physicochemical properties to melter feed, as opposed to laboratory reagents. This type of testing is expected to validate applicability to design parameters and functional criteria expected during unit operations. This work was expected to commence in FY21, with the first melter tests being performed near the end of the FY. However, reduced access to Savannah River Site and personnel availability during the COVID-19 pandemic significantly reduced the amount of time and resources available to perform the task. This report documents the experimental plan and progress towards this task. The following is a summarized list of scheduled testing that will be performed on feed, condensate, cold cap and glass: 1) Melter runs; 2) Product consistency test (PCT); 3) Inductively coupled plasma optical emission spectroscopy (ICP-OES); and 4) Optical (OM) and scanning electron microscopy (SEM).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Potential for Evaporation and In Situ Reaction of Organic Compounds in Hanford Supplemental LAW

The presence of regulated organic species in Hanford nuclear tank waste is assessed in this report, along with fate of the organics and possible evaporative treatment. A narrowed list of regulated organic species of concern is developed based upon published analyses, chemical properties like aqueous solubility, and chemical reactivity under alkaline conditions. Published analyses include tank headspace and liquid samples, review of chemical reagents formerly used at Hanford, and the Tank Waste Information Network System (TWINS). This work supports possible stabilization of Hanford Supplemental Low Activity Waste (SLAW) by grouting.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Potential for Evaporation and In Situ Reaction of Organic Compounds in Hanford Supplemental LAW

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

In Situ Thermodynamics and Kinetics of Mixed-Valence Inorganic Crystal Formation

We have found that the established methods to discover and produce earth-abundant iron-containing active layers are very inefficient. The prospective new material iron silicon sulfide, Fe 2 SiS 4 , was previously only synthesized by slow reactions of metallic iron, silicon, and sulfur powders, resulting in poor yield. We found that using an ordered iron-silicon alloy as a feedstock results in a much faster reaction at a lower temperature. We could track this reaction using our unique in-situ X-ray diffractometer, which allows us to heat our encapsulated material up to 1000°C while providing a simultaneous picture of how the atoms in the structure rearrange. We are using this powerful new technique to search for new active layers and optimize their formation by creative use of more complex reagents. Our key accomplishments are mechanisms for improving synthesis, and new materials that result from them. We have demonstrated the utility of high-throughput, DOE-developed infrastructure, such as the Materials Project, to accelerate materials discovery and synthesis. We have pioneered new capabilities of user facilities, such as beamlines 6-BM, 17-BM, and 11-BM at the Advanced Photon Source (APS) and POWGEN and NOMAD at the Spallation Neutron Source.

36 MATERIALS SCIENCE↗