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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Brachiopod δ 34 S CAS microanalyses indicate a dynamic, climate-influenced Permo-Carboniferous sulfur cycle

Early isotopic studies of sulfate in carbonate minerals (carbonate associated sulfate; CAS) suggested that carbonates can provide a reliable, well-dated archive of the marine sulfur cycle through time. However, subsequent research has shown that diagenetic alteration can impose highly heterogeneous CAS sulfur isotopic compositions (δ 34 S CAS ) among different carbonate phases within sediments. Such alteration necessitates targeted sampling of well-preserved, primary carbonate phases. Here, we present a new record of Carboniferous and Early Permian brachiopod δ 34 S CAS generated from over 130 measurements of microsampled brachiopod shells. Our record refines existing brachiopod δ 34 S CAS records and confirms a large, ~6.5‰ δ 34 S CAS decrease in the Early Carboniferous. Importantly, the record also features a novel 3–5‰ increase in δ 34 S CAS near the Serpukhovian-Bashkirian boundary (323.4 Ma) that coincides with carbonate δ 13 C and δ 18 O increases. Variability in δ 34 S CAS is minor both within (≤0.3‰) and among (≤2‰) individual co-depositional brachiopod specimens. A taxon-specific δ 34 S CAS offset is present one species (Composita subtilita) that also exhibits a δ 13 C offset, supporting the existence of biological “vital effects” on δ 34 S CAS . Geologic evidence and mathematical modeling of the Permo-Carboniferous carbon and sulfur cycles suggest that changes in the burial ratio of organic carbon to pyrite sulfur (R C:S ) are insufficient to explain the observed mid-Carboniferous δ 34 S CAS record. We find that changes in the 34 S depletion of pyrite relative to seawater sulfate ( 34 ε) or in the δ 34 S of the input to the ocean (δ 34 S in ) are also needed. Large additions of O 2 from organic carbon burial during the Permo-Carboniferous cannot be entirely compensated for with sulfur cycle changes; lower than modern late Visean pO 2 and/or additional O 2 sinks are needed to keep pO 2 at plausible levels. Based on the geologic context surrounding our record's mid-Carboniferous δ 34 S CAS increase, we advocate for simultaneous changes in pyrite burial, 34 ε, and δ 34 S in , driven by sea level or tectonically induced changes in environments of sulfur burial, as a viable mechanism to produce rapid seawater δ 34 S changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences

Abstract RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a ‘Quick’ method to generate a single PAM prediction or in a ‘Comprehensive’ method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Abstract There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Selective Sorbent Design: CaS Aerogel for Rapid Remediation of Aqueous Pb (II)

Heavy metals are a persistent environmental problem due to their high toxicity, even at very low concentrations (parts per billion, ppb). The removal of such diluted heavy metals is challenging because of the competition the counterions (Ca 2+ , Na + , Mg 2+ , etc.) present in natural water bodies. The design of sorbents capable of removing ions below the action limit (15 ppb for Pb 2+ ) requires a strong driving force for selective uptake and rapid removal. In this work, we report the synthesis of porous CaS aerogels (surface area = 143.6 m 2 /g) by oxidative assembly of CaS nanoparticles and describe their use in selective Pb 2+ ion remediation from water. Despite the presence of amorphous CaCO 3 (up to 50 wt %) in the gel network, the gels demonstrated a capacity of 17.1 mmol Pb/g aerogel (3543 mg/g), and this could be augmented to 22.5 mmol Pb/g aerogel (4593 mg/g) by modifying the synthesis to reduce CaCO 3 content to ca. 15 wt %. Moreover, the selectivity of CaS aerogels toward Pb 2+ ions is high, as evidenced by little-to-no change in the distribution constant (K d ∼ 10 4 ) in the presence of competing ions (1 M) such as Na + , Mg 2+ , and Ca 2+ . During remediation with low concentrations (100 ppb) of Pb 2+ with CaS aerogels, the level of Pb 2+ dropped to 5.4 ppb (below the 15 ppb EPA limit) within 1 h with a 95.4% removal efficiency. In contrast to the CO 2 supercritically dried aerogels, lower surface area ambient dried gels (xerogels) only remove 40% of the lead ions from a 100 ppb solution, saturating within 1 h. The efficiency and rapidity of selective Pb 2+ uptake using CdS aerogels arise from a combination of a strong thermodynamic driving force for cation exchange (K eq = 2.5 × 10 27 ) and chemisorption along with favorable kinetics associated with the high surface area porous architecture. These results show that formation of high surface area metal chalcogenide aerogels by oxidative assembly to form nanocrystalline architectures, as previously demonstrated for II−VI and IV−VI semiconductors, can be extended to the more highly ionic alkaline earth sulfides.

Aerogels↗
DOE OSTI2021

Implementation of an Orographic Drag Scheme Considering Orographic Anisotropy in All Flow Directions in the Earth System Model CAS‐ESM 2.0

Abstract A reasonable representation of orographic anisotropy in earth system models is vital for improving weather and climate modeling. In this study, we implement the orographic drag scheme, including 3‐D orographic anisotropy (3D‐AFD), into the Chinese Academy of Sciences Earth System Model version 2 (CAS‐ESM 2.0). Three groups of simulations named sensitivity run, medium‐range forecast, and seasonal forecast respectively are conducted using the updated CAS‐ESM model and validated against station observation and reanalysis data. These simulations are run using the three schemes—3D‐AFD scheme, the 3D orographic anisotropy scheme for the eight‐direction (3D‐8x), and the 2D isotropic scheme (2D)—to compare their performance in CAS‐ESM 2.0. Sensitivity runs show that the 3D‐AFD provide more continuous transition of calculated drag as function of wind direction than the 3D‐8x, while the drag calculated using the 2D scheme show no variation with change of wind direction. Enhanced drag in the medium range and seasonal forecast using the updated CAS‐ESM alleviates part of the winter wind speed bias over the Tibetan Plateau (TP) and the cold bias over TP and the Siberian polar region. It is shown that the 3D‐AFD scheme alleviates more bias than that of the 3D‐8x scheme (by wind speed reduction of 1 ∼ 2 m/s and temperature of 1 ∼ 2 K) especially in the seasonal forecast. The results suggest that reasonable representation of the orographic anisotropy is important in climate modeling.

Xie, Jinbo↗
DOE OSTI2020

Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR–Cas complex revealed by cryo-EM

Prokaryotes and viruses have fought a long battle against each other. Prokaryotes use CRISPR–Cas-mediated adaptive immunity, while conversely, viruses evolve multiple anti-CRISPR (Acr) proteins to defeat these CRISPR–Cas systems. The type I-F CRISPR–Cas system in Pseudomonas aeruginosa requires the crRNA-guided surveillance complex (Csy complex) to recognize the invading DNA. Although some Acr proteins against the Csy complex have been reported, other relevant Acr proteins still need studies to understand their mechanisms. As such, here, we obtain three structures of previously unresolved Acr proteins (AcrF9, AcrF8, and AcrF6) bound to the Csy complex using electron cryo-microscopy (cryo-EM), with resolution at 2.57 Å, 3.42 Å, and 3.15 Å, respectively. The 2.57-Å structure reveals fine details for each molecular component within the Csy complex as well as the direct and water-mediated interactions between proteins and CRISPR RNA (crRNA). Our structures also show unambiguously how these Acr proteins bind differently to the Csy complex. AcrF9 binds to key DNA-binding sites on the Csy spiral backbone. AcrF6 binds at the junction between Cas7.6f and Cas8f, which is critical for DNA duplex splitting. AcrF8 binds to a distinct position on the Csy spiral backbone and forms interactions with crRNA, which has not been seen in other Acr proteins against the Csy complex. Our structure-guided mutagenesis and biochemistry experiments further support the anti-CRISPR mechanisms of these Acr proteins. Our findings support the convergent consequence of inhibiting degradation of invading DNA by these Acr proteins, albeit with different modes of interactions with the type I-F CRISPR–Cas system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Csx3 is a cyclic oligonucleotide phosphodiesterase associated with type III CRISPR–Cas that degrades the second messenger cA 4

Cas10 is the signature gene for type III CRISPR–Cas surveillance complexes. Unlike type I and type II systems, type III systems do not require a protospacer adjacent motif and target nascent RNA associated with transcriptionally active DNA. Further, target RNA recognition activates the cyclase domain of Cas10, resulting in the synthesis of cyclic oligoadenylate second messengers. These second messengers are recognized by ancillary Cas proteins harboring CRISPR-associated Rossmann fold (CARF) domains and regulate the activities of these proteins in response to invading nucleic acid. Csx3 is a distant member of the CARF domain superfamily previously characterized as a Mn 2+ -dependent deadenylation exoribonuclease. However, its specific role in CRISPR–Cas defense remains to be determined. Here we show that Csx3 is strongly associated with type III systems and that Csx3 binds cyclic tetra-adenylate (cA 4 ) second messenger with high affinity. Further, Csx3 harbors cyclic oligonucleotide phosphodiesterase activity that quickly degrades this cA 4 signal. In addition, structural analysis identifies core elements that define the CARF domain fold, and the mechanistic basis for ring nuclease activity is discussed. Overall, the work suggests that Csx3 functions within CRISPR–Cas as a counterbalance to Cas10 to regulate the duration and amplitude of the cA 4 signal, providing an off ramp from the programmed cell death pathway in cells that successfully cure viral infection.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling

Understanding CRISPR-Cas systems—the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks—is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical ‘rich-get-richer’ mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chapter 20: Advances and Application of CRISPR-Cas Systems

A new gene-editing technique called clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins have revolutionized genome engineering because of its high efficiency, relatively low cost, and ease of use compared with other techniques such as zinc-finger nucleases and transcription activator-like effector nucleases. CRISPR-Cas systems have transformed biological research, quickly becoming the preferred method for engineering specific genome sequences in industrially relevant microbes, important food crops, and human cells. This powerful new tool has the potential for limitless applications ranging from the treatment of human diseases to improving food security to the generation of renewable and sustainable bioproducts and biofuels. In this chapter, we will discuss advances and applications for these CRISPR-Cas systems in biological engineering.

bacterial↗
DOE OSTI2021

CRISPR-Cas Genome Editing in the Cellulolytic Bacterium Clostridium thermocellum (C. thermocellum)

Clostridium thermocellum is an anaerobic thermophile that can efficiently degrade lignocellulosic biomass and directly convert it into value-added products such as ethanol. The cellulolytic and ethanologenic capabilities of C. thermocellum make it an excellent candidate for consolidated bioprocessing (CBP) for industrial production, where biomass degradation and fermentation occur simultaneously. In this organism, strain development for effective CBP has traditionally been hindered by the lack of genetic tools. Here, we detail our efficient two-step CRISPR-Cas genome editing protocol for C. thermocellum, using both the native Type I-B CRISPR-Cas system and an exogenous Type-II CRISPR system from Geobacillus stearothermophilus. As recombination is limiting in C. thermocellum genome engineering, we highlight effective thermophilic recombinases necessary to improve genome editing in these systems. We additionally provide design rules for the repair template and synthetic guide RNA (gRNA) for each system. Using these newly developed CRISPR and recombineering tools, targeted C. thermocellum engineering will substantiate efforts toward CBP strain development in industrial applications.

anaerobe↗
DOE OSTI2026

Production of Heavy α -Elements and 44 Ti in Cas A: Comparison to Abundances from 1D Core-collapse Supernova Models and Evidence for Carbon–Oxygen Shell Mergers

The merger between the carbon (C) and oxygen (O) shells hours to days before the collapse of a massive star significantly changes its nucleosynthesis, which is reflected in the elemental ratios observed in supernova remnants (SNRs). We present a nucleosynthesis study of 44 Ti production in core-collapse supernovae (CCSNe), highlighting large silicon (Si), sulfur (S), calcium (Ca), and, most importantly, argon (Ar) to neon (Ne) ratios as diagnostics for carbon–oxygen (C–O) shell mergers. We compare yields from eight different sets of CCSNe models to observations of Cassiopeia A (Cas A), and show that C–O shell mergers are consistently the models that best match X-ray and infrared observations. These models produce high Ar/Ne ratios (≳0.1), due to 20 Ne depletion and production of 36 Ar and 38 Ar, while lower ratios are obtained from nonmerger cases. Based on the Ar/Ne diagnostic, we compare the range of expected 44 Ti produced by C–O shell mergers, which is up to ∼20%–30% of the overall 44 Ti, but expected to be located outside the reverse shock. Based on the sets of models considered, the photon flux expected from the 44 Ti synthesized in the C–O shell merger in Cas A is below the NuSTAR and COSI detection limits, compatible with current limits locating most of the 44 Ti interior to the reverse shock, but might be detectable from proposed missions like ASCENT. Finally, for the SNR of 1987A, a dominant C–O merger origin of the observed 44 Ti is unlikely based on the observed redshift in its 44 Ti line.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Materials Data on CaS by Materials Project

CaS is Halite, Rock Salt structured and crystallizes in the cubic Fm-3m space group. The structure is three-dimensional. Ca2+ is bonded to six equivalent S2- atoms to form a mixture of edge and corner-sharing CaS6 octahedra. The corner-sharing octahedral tilt angles are 0°. All Ca–S bond lengths are 2.86 Å. S2- is bonded to six equivalent Ca2+ atoms to form a mixture of edge and corner-sharing SCa6 octahedra. The corner-sharing octahedral tilt angles are 0°.

36 MATERIALS SCIENCE↗
DOE OSTI2020

CRISPR-Cas “Non-Target” Sites Inhibit On-Target Cutting Rates

CRISPR-Cas systems have become ubiquitous for genome editing in eukaryotic as well as bacterial systems. Cas9 forms a complex with a guide RNA (gRNA) and searches DNA for a matching sequence (target site) next to a protospacer adjacent motif (PAM). Once found, Cas9 cuts the DNA. Cas9 is revolutionary for the ability to change the RNA sequence and target a new site easily. However, while algorithms have been developed to predict gRNA-specific Cas9 activity, a fundamental biological understanding of gRNA-specific activity is lacking. Here, the number of PAM sites in the genome is effectively a large pool of inhibitory substrates, competing with the target site for the Cas9/gRNA complex. We demonstrate that increasing the number of non-target sites for a given gRNA reduces on-target activity in a dose-dependent manner. Furthermore, we show that the use of Cas9 mutants with increased PAM specificity toward a smaller subset of PAMs (or smaller pool of competitive substrates) improves cutting rates, while increased PAM promiscuity decreases cutting rates. Decreasing the potential search space by increasing PAM specificity provides a path toward improving on-target activity for slower high-fidelity Cas9 variants. Engineering improved PAM specificity to reduce the competitive search space offers an alternative strategy to engineer Cas9 variants with increased specificity and maintained on-target activity.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Zagamiite, CaAl2Si3.5O11, the Hexagonal High-Pressure CAS Phase with Dominant Si, as a Mineral from Mars

Within the Ca-Al-silicate system, dense, layered hexagonal phases occur at high temperatures and pressures between 20 and 23 GPa. They have been observed both in nature and in experiments. In this study, we describe the endmember with a dominant sixfold coordinated Si as a mineral zagamiite (IMA 2015-022a). This new mineral identified in Martian meteorites has a general formula of (Ca,Na)(Al,Fe,Mg)2(Si,Al,□)4O11, thus defining CaAl2Si3.5O11 as a previously unknown endmember of the hexagonal CAS phases. Zagamiite assumes space group P63/mmc with a unit cell of a = 5.403(2) Å, c = 12.77(3) Å, V = 322.9(11) Å3, and Z = 2. Zagamiite contains significant Fe and Mg and a substantial deficit of Na relative to plagioclase of an equivalent Al/Si, suggesting that it was formed through crystallization from a melt that was derived from a plagioclase-dominant mixture of plagioclase and clinopyroxene above the solidus beyond 20 GPa.

Ma, Chi (ORCID:0000000218287033)↗
DOE OSTI2023

CRISPR-Cas based system for targeting single-stranded sequences

The present invention relates to a CRISPR-Cas based system for targeting nucleic acid sequences. In part, the invention relates to synthetic guiding components for targeting single-stranded sequences, as well as design principles for constructing such components. Also described herein are methods of employing such components, e.g., to repress or activate a desired target within the subject.

Negrete, Oscar↗
DOE OSTI2022

CAS Operator Training Simulator

SAND2022-1525 O The Central Alarm System (CAS) training simulator is a standalone application that will work on any Alarm Control and Display (AC&D) System. Designed to be used by an instructor in a classroom environment, this software plays back scenario alarms and videos usually exported out of Scribe3D or any software that can produce scenario-based videos. Users can select from an array of different scenarios to play. The alarms are sent to an AC&D controller and the videos are sent to a Video Management Server (VMS). Both alarms and associated videos displayed by the intended AC&D system. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Le, Tam↗
DOE OSTI2023

ERM-CAS Integration

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ERM = Enterprise Risk Management CAS = Contractor ↗