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DOE OSTI2023

A standardized quantitative analysis strategy for stable isotope probing metagenomics

ABSTRACT Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg , an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, “who is eating what?” and “who is active?” within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism’s taxonomic identity and genome composition while providing quantitative estimates of the microorganism’s isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

NSUF Rad-AFM: Nanoscale Material Property Measurements of Radioactive Materials

Many advances in our understanding of radiation induced damage mechanisms are due to imaging techniques including transmission electron microscopy and scanning electron microscopy. However, the effect of these radiation induced defects characterized on the atomic to micrometer scale are often interpreted by changes in bulk material properties measured in the hundreds of microns to cm scale. In order to bridge this gap, additional tools need to be developed for use with radioactive materials. To this end a new Asylum Infinity multimodal atomic force microscope (AFM) has been added to the library of Nuclear Science User Facility (NSUF) instruments for use on radioactive materials. This instrument is housed in the Radiochemical Processing Laboratory (RPL) which is a Department of Energy Hazard Category II Non-Reactor Nuclear Facility operated by Battelle at Pacific Northwest National Laboratory. This allows for the handling, sample preparation, and characterization of highly radioactive materials providing a unique capability to understand fundamental properties of nuclear materials and the effects of radiation induced damage.

Riechers, Shawn L.↗

DOE OSTI2017

Scoping study to expedite development of a field deployable and portable instrument for UF6 enrichment assay

The primary objective of the present study is to identity the most promising, viable technologies that are likely to culminate in an expedited development of the next-generation, field-deployable instrument for providing rapid, accurate, and precise enrichment assay of uranium hexafluoride (UF6). UF6 is typically involved, and is arguably the most important uranium compound, in uranium enrichment processes. As the first line of defense against proliferation, accurate analytical techniques to determine the uranium isotopic distribution in UF6 are critical for materials verification, accounting, and safeguards at enrichment plants. As nuclear fuel cycle technology becomes more prevalent around the world, international nuclear safeguards and interest in UF6 enrichment assay has been growing. At present, laboratory-based mass spectrometry (MS), which offers the highest attainable analytical accuracy and precision, is the technique of choice for the analysis of stable and long-lived isotopes. Currently, the International Atomic Energy Agency (IAEA) monitors the production of enriched UF6 at declared facilities by collecting a small amount (between 1 to 10 g) of gaseous UF6 into a sample bottle, which is then shipped under chain of custody to a central laboratory (IAEA’s Nuclear Materials Analysis Laboratory) for high-precision isotopic assay by MS. The logistics are cumbersome and new shipping regulations are making it more difficult to transport UF6. Furthermore, the analysis is costly, and results are not available for some time after sample collection. Hence, the IAEA is challenged to develop effective safeguards approaches at enrichment plants. In-field isotopic analysis of UF6 has the potential to substantially reduce the time, logistics and expense of sample handling. However, current laboratory-based MS techniques require too much infrastructure and operator expertise for field deployment and operation. As outlined in the IAEA Department of Safeguards Long-Term R&D Plan, 2012–2023, one of the IAEA long-term R&D needs is to “develop tools and techniques to enable timely, potentially real-time, detection of HEU (Highly Enriched Uranium) production in LEU (Lowly Enriched Uranium) enrichment facilities” (Milestone 5.2). Because it is common that the next generation of analytical instruments is driven by technologies that are either currently available or just now emerging, one reasonable and practical approach to project the next generation of chemical instrumentation is to track the recent trends and to extrapolate them. This study adopted a similar approach, and an extensive literature review on existing and emerging technologies for UF6 enrichment assay was performed. The competitive advantages and current limitations of different analytical techniques for in-field UF6 enrichment assay were then compared, and the main gaps between needs and capabilities for their field use were examined. Subsequently, based on these results, technologies for the next-generation field-deployable instrument for UF6 enrichment assay were recommended. The study was organized in a way that a suite of assessment metric was first identified. Criteria used in this evaluation are presented in Section 1 of this report, and the most important ones are described briefly in the next few paragraphs. Because one driving force for in-field UF6 enrichment assay is related to the demanding transportation regulation for gaseous UF6, Section 2 contains a review of solid sorbents that convert and immobilized gaseous UF6 to a solid state, which is regarded as more transportation friendly and is less regulated. Furthermore, candidate solid sorbents, which show promise in mating with existing and emerging assay technologies, also factor into technology recommendations. Extensive literature reviews on existing and emerging technologies for UF6 enrichment assay, covering their scientific principles, instrument options, and current limitations are detailed in Sections 3 and 4, respectively. In Section 5, the technological gaps as well as start-of-the-art and commercial off-the-shelf components that can be adopted to expedite the development of a fieldable or portable UF6 enrichment-assay instrument are identified and discussed. Finally, based on the results of the review, requirements and recommendations for developing the next-generation field-deployable instrument for UF6 enrichment assay are presented in Section 6.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Structural Stability Study of Crystalline Silicotitanate Dispersed in Caustic Solutions for Extended Periods

The purpose of this study was to determine if pretreated engineered crystalline silicotitanate (CST) utilized in the Tank Cesium Closure Removal (TCCR) process would aggregate when contacted with sodium hydroxide (NaOH) or simulated tank waste solutions over an extended period. The aggregation of CST could be problematic for the TCCR process as it may lead to increased pressure drops across the columns, due to column plugging. Multiple prior studies have been completed on the agglomeration of CST stored in caustic simulants for prolonged periods showing evidence of clumping especially at elevated temperatures. For this study, pretreated CST was combined with various concentrations of sodium hydroxide and SRS simulant, in both glass and plastic storage containers, and monitored for an extended period. The samples were monitored for signs of agglomeration for a period of 8 months. After 7 months weak agglomeration was observed in the sample stored in SRS simulant, while no signs of clumping were observed in the samples stored in 2, 3, or 4 M NaOH. This is consistent with previous work where agglomeration of CST was not observed in simple salt solutions, only in simulants containing Al. In addition, the clumping observed for the sample stored in SRS simulant was not replicated in the duplicate sample stored in a plastic (as opposed to glass) vial, indicating leaching of Si from the glass may have contributed. It was also noted during the study that the solution above the CST stored in 4 M NaOH became opaque. The most likely cause of the opaque solution is the presence of micro-CST particles that may have been generated through sample handling, although this has not been confirmed by analysis.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q1

Microbes play key roles in our biosphere, from driving global nutrient cycling to impacting plant, animal and human health and disease. Complex data from microbial genomes, proteins, and metabolites provide a window into these tiny engines that drive life on our planet. Yet these data are dispersed among researchers’ laboratories and various repositories, making it difficult to access. This calls for new ways of managing data, improving data interoperability, advancing community standards, and creating an infrastructure where data are shared efficiently. We have built the National Microbiome Data Collaborative (NMDC) to advance how scientists create, use, and reuse data to redefine the way we understand and harness the power of microbes. The vision of the National Microbiome Data Collaborative (NMDC) is to drive a microbiome data sharing network connecting data, people, and ideas to advance microbiome innovation and discovery. The NMDC was launched in 2019 and brought together DOE National Laboratories to collaborate across resources, capabilities, and expertise. The NMDC team was strategically assembled to include software developers, microbial researchers, metadata experts, and multi-omics specialists. The diversity of the NMDC team reflects the inherently interdisciplinary nature of microbiome science, and we leverage the strengths of the DOE National Laboratory system. Towards BER’s goal of advancing an iterative systems biology approach to the understanding of microbial genomes, the NMDC serves as a foundation for infrastructure, data standards, and community building. Together with the flagship DOE User Facilities, the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), we are developing core capabilities in metadata standards for environmental descriptors and sample handling and processing; standardized bioinformatic workflows; an interface for data search and access; and robust community engagement activities. The NMDC production platform supports long-term data infrastructure and community building for BER’s bioenergy and environmental research goals. Our approach leverages lessons learned and an ambitious framework for collaborative, interdisciplinary data infrastructure to support microbiome research. The NMDC supports data, information, and knowledge access through three defined software tools – the Submission Portal, NMDC EDGE, and the Data Portal – driven by community needs. Herein, we describe the value proposition for the microbiome research community, our overarching strategy, and challenges and opportunities for developing the NMDC as both an infrastructure and community engagement program.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1

Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to “mine” information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O -formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling). Interesting cleavages and modifications (e.g., S -cyanylation and trimethylation) were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N -termini recovered by concanavalin A binding or from a previous study, only M. mazei S -layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more. This study supplements limited, existing experimental datasets of mature archaeal N -termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Resurgence of a Nation’s Radiation Science Driven by Its Nuclear Industry Needs

This article describes the radiation facilities and associated sample preparation, management, and analysis equipment currently in place at the Dalton Cumbrian Facility, a facility which opened in 2011 to support the UK’s nuclear industry. Examples of measurements performed using these facilities are presented to illustrate their versatility and the breadth of research they make possible. Results are presented from research which furthers our understanding of radiation damage to polymeric materials, radiolytic yield of gaseous products in situations relevant to nuclear materials, radiation chemistry in light water reactor cooling systems, material chemistry relevant to immobilization of nuclear waste, and radiation-induced corrosion of fuel cladding elements. Applications of radiation chemistry relevant to health care are also described. Research concerning the mechanisms of radioprotection by dietary carotenoids is reported. An ongoing open-labware project to develop a suite of modular sample handling components suited to radiation research is described, as is the development of a new neutron source able to provide directional beams of neutrons.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NASA NTRS1983

Electronic Dilatometer

Nonclamping micrometer measures small strains. Electronic dilatometer measures minute dimensional changes caused by moisture absorption in graphite/ epoxy composites. Instrument handles sample 6 inches (15 cm) long and has strain resolution of 0.1 micro-inch/inch (0.1 micron/meter). Possible to predict humidity-induced dimensional changes in items constructed of sample material.

Stroope, C. R.↗

NASA NTRS1984

High pressure cosmochemistry applied to major planetary interiors: Experimental studies

Progress is reported on a project to determine the properties and boundaries of high pressure phases of the H2-He-H2O-NH3-CH4 system that are needed to constrain theoretical models of the interiors of the major planets. This project is one of the first attempts to measure phase equilibria in binary fluid-solid systems in diamond anvil cells. Vibrational spectroscopy, direct visual observations, and X-ray diffraction crystallography of materials confined in externally heated cells are the primary experimental probes. Adiabats of these materials are also measured in order to constrain models of heat flow in these bodies and to detect phase transitions by thermal anomalies. Initial efforts involve the NH3-H2O binary. This system is especially relevant to models for surface reconstruction of the icy satellites of Jupiter and Saturn. Thermal analysis experiments were completed for the P-X space, p4GPa:0 or = 0.50, near room temperature. The cryostat, sample handling equipment, and optics needed to extend the optical P-T-X work below room temperature was completed.

Nicol, M. F.↗

NASA NTRS1988

Mars rover/sample return mission requirements affecting space station

The possible interfaces between the Space Station and the Mars Rover/Sample Return (MRSR) mission are defined. In order to constrain the scope of the report a series of seven design reference missions divided into three major types were assumed. These missions were defined to span the probable range of Space Station-MRSR interactions. The options were reduced, the MRSR sample handling requirements and baseline assumptions about the MRSR hardware and the key design features and requirements of the Space Station are summarized. Only the aspects of the design reference missions necessary to define the interfaces, hooks and scars, and other provisions on the Space Station are considered. An analysis of each of the three major design reference missions, is reported, presenting conceptual designs of key hardware to be mounted on the Space Station, a definition of weights, interfaces, and required hooks and scars.

Source record↗

NASA NTRS1987

Bioseparations - Flight experiment support research

While important principles of electrokinetic technology, such as electrophoresis, have been demonstrated for microgravity environments and promise to be able to alleviate many of the practical limitations imposed by gravity, the minimal crew time and sample-handling facilities available in orbit call for almost total reliance on postflight analysis of separated fractions. Since cell separations are the most difficult to accomplish in 1-g, two model cell types have been studied intensively to determine the basic relationships between cell surface charge and secretory functions. A rationale has been developed for selecting and qualifying new cell types and proteins that warrant processing in microgravity.

Morrison, Dennis R.↗

NASA NTRS1988

Measurement of Seebeck coefficient using a large thermal gradient

The integral method of measuring the Seebeck voltage, V(T), has been applied to short rod-shaped samples. In the present method, one end of the sample is held at a fixed temperature and the other end is automatically varied through a temperature T range of interest, up to a maximum temperature of 1000 C. The Seebeck coefficient is then obtained from the slope of the V(T) vs T curve. The method offers simplicity of sample handling and minimal operator involvement.

Wood, C.↗

NASA NTRS1989

Planetary protection issues for sample return missions

Planetary protection (PP) issues for both a comet nucleus sample return (CNSR) mission and a Mars rover sample return (MRSR) mission are discussed, with special attention given to the PP requirements for such missions, the exobiology science objectives for the CNSR and MRSR missions, and a qualitative PP risk assessment for both mission types. A set of contamination control procedures for both missions is presented, which identify procedures for each of the mission phases (i.e., the prelaunch, launch, sample handling, transit vehicle, and earth return). Recommendations for further research and technology development are discussed.

Devincenzi, D. L.↗

NASA NTRS1989

The measurement of trace elements in interplanetary dust and cometary particles by ultra-high sensitivity INAA

Today the major elemental composition of interplanetary dust particles (IDPs) is routinely determined in many laboratories. These and mineralogical studies have revealed the presence of at least two major types of IDPs, chondritic and refractory. Preliminary results of a successful attempt to determine abundances of a large suite of trace elements from both chondritic and refractory IDPs are reported. The analytical procedure can be used in the grain-by-grain analysis of returned cometary samples. Chondritic and refractory IDPs are characterized by standard scanning electron microscopy and energy dispersive x ray spectroscopy (SEM-EDX) techniques. With this system, detection limits for many elements are well below picogram levels, and some approach femtogram levels. This technique is non-destructive, although some sample handling is required, so particles can be analyzed by other techniques after instrument neutron activation analysis (INAA) is completed. Data is presently being reduced from the analyses of 7 IDPs. These are U2015E10, U2015F1, W7029-A2, W7029-A3, W7013A8, LACl (all chondritic) and 705 (refractory). So far, 17 different major and trace elements were detected and measured in these particles, including rare earths and some very volatile elements (Br and Zn).

Zolensky, M. E.↗

NASA NTRS1992

Simulation of Martian surface-atmosphere interaction in a space-simulator: Technical considerations and feasibility

The Space Simulator of the German Aerospace Research Establishment at Cologne, formerly used for testing satellites, is now, since 1987, the central unit within the research sub-program 'Comet-Simulation' (KOSI). The KOSI team has investigated physical processes relevant to comets and their surfaces. As a byproduct we gained experience in sample-handling under simulated space conditions. In broadening the scope of the research activities of the DLR Institute of Space Simulation an extension to 'Laboratory-Planetology' is planned. Following the KOSI-experiments a Mars Surface-Simulation with realistic minerals and surface soil in a suited environment (temperature, pressure, and CO2-atmosphere) is foreseen as the next step. Here, our main interest is centered on thermophysical properties of the Martian surface and energy transport (and related gas transport) through the surface. These laboratory simulation activities can be related to space missions as typical pre-mission and during-the-mission support of the experiments design and operations (simulation in parallel). Post mission experiments for confirmation and interpretation of results are of great value. The physical dimensions of the Space Simulator (cylinder of about 2.5 m diameter and 5 m length) allows for testing and qualification of experimental hardware under realistic Martian conditions.

Moehlmann, D.↗

NASA NTRS1992

Geology of the Apollo 17 site

The Apollo 17 landing site was unique in several aspects: (1) it was the only site that was not selected from telescopic-based geologic interpretation--interest in the site was generated by the visual observations of Al Worden, Apollo 15 Command Module pilot, who interpreted dark-haloed craters as possible cinder cones; (2) instead of 20-m-resolution photographs, as was the norm for all earlier missions, this site had Apollo 15 panoramic camera photography coverage that had 2-m resolution; and (3) it had a geologist-astronaut aboard who was intimately involved in all stages of planning and mission operation, and was also instrumental in the design of a long-handled sample bag holder that eliminated the need for crew to dismount before collecting a sample, which then permitted sampling between major stations. Details of site geology, sample description, and geologic synthesis of the site as viewed from studies through 1976 are summarized.

Muehlberger, W. R.↗

NASA NTRS1992

Commercial researcher perspective

Protein crystallography--a research tool used to study the structure of the complex building blocks of living systems--has a lot to gain from space-based research. In order to know how a protein works in the human body, researchers must understand its molecular structure. Researchers have identified 150,000 different proteins in the body, but they now know the structure of less than a third of them. The only viable technique for analyzing the structure of these proteins is x-ray diffraction of the proteins in their crystal form. The better the quality of a protein crystal, the more useful it is to researchers who are trying to delineate its structure. The microgravity environment of space allows protein crystals to grow nearly undisturbed by convection and other gravity-driven forces that cause flaws to form in them on the ground. In space, lack of convection enables protein crystals to grow more slowly than they do on Earth, and the slower a protein crystal grows, the fewer flaws it will have. Protein crystal growth experiments have already flown on 14 Space Shuttle missions. This year's USML-1 Spacelab mission included protein crystal growth experiments conducted for commercial researchers. The results of protein crystal experiments flown thus far have been larger crystals with more uniform morphologies. The Center for Macromolecular Crystallography (A NASA-cosponsored CCDS) currently builds flight hardware to meet researchers' needs and handles sample loading and retrieval for flight experiments. Protein crystallography enables 'rational drug design': the development of drugs that bind only with the target protein and, hence, do not cause side effects. For example, pharmaceutical companies presently are interested in developing drugs that can inhibit purine nucleoside phosphorylase (PNP), a protein that plays a role in auto-immune diseases. To continue these kinds of investigations, researchers need a constant supply of protein crystals that are as free of flaws as possible. Space Station Freedom will provide the kind of research environment that will enable the production of such supplies. In addition, Freedom will provide the kind of long-duration facility required by protein crystal researchers: 40 percent of proteins require more than two weeks to crystallize.

Delucas, Larry↗

NASA NTRS2000

Effect of Air and Vacuum Storage on the Tensile Properties of X-Ray Exposed Aluminized-FEP

Metallized Teflon(Registered Trademark) FEP (fluorinated ethylene propylene), a common spacecraft thermal control material, from the exterior layer of the Hubble Space Telescope (HST) has become embrittled and suffers from extensive cracking. Teflon samples retrieved during Hubble servicing missions and from the Long Duration Exposure Facility (LDEF) indicate that there may be continued degradation in tensile properties over time. An investigation has been conducted to evaluate the effect of air and vacuum storage on the mechanical properties of x-ray exposed FEP. Aluminized-FEP (Al-FEP) tensile samples were irradiated with 15.3 kV Cu x-rays and stored in air or under vacuum for various time periods. Tensile data indicate that samples stored in air display larger decreases in tensile properties than for samples stored under vacuum. Air-stored samples developed a hazy appearance, which corresponded to a roughening of the aluminized surface. Optical property changes were also characterized. These findings indicate that air exposure plays a role in the degradation of irradiated FEP, therefore proper sample handling and storage is necessary with materials retrieved from space.

deGroh, Kim K.↗