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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Improved Characterization of Soil Organic Matter by Integrating FT-ICR MS, Liquid Chromatography Tandem Mass Spectrometry, and Molecular Networking: A Case Study of Root Litter Decay under Drought Conditions

Understanding of how soil organic matter (SOM) chemistry is altered in a changing climate has advanced considerably; however, most SOM components remain unidentified, impeding the ability to characterize a major fraction of organic matter and predict what types of molecules, and from which sources, will persist in soil. Here we present a novel approach to better characterize SOM extracts by integrating information from three types of analyses, and we deploy this method to characterize decaying root-detritus soil microcosms subjected to either drought or normal conditions. To observe broad differences in composition, we employed direct infusion Fourier-transform ion cyclotron resonance mass spectrometry (DI-FT-ICR MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectral cosine similarity scores to relate unknowns and library matches through molecular networks. This integrated approach allowed us to corroborate DI-FT-ICR MS molecular formulas using library matches, which included fungal metabolites and related polyphenolic compounds. We also inferred structures of unknowns from molecular networks and improved LC-MS/MS annotation rates from ~5 to 35% by considering DI-FT-ICR MS molecular formula assignments. Under drought conditions, we found greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas and lower average nominal oxidation state of carbon, suggesting reduced decomposition of SOM and/or microbes under stress. Our integrated approach provides a framework for enhanced annotation of SOM components that is more comprehensive than performing individual data analyses in parallel.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

Global Reference Atmospheric Model (GRAM) Advancements and Additions

Introduction:The Global Reference Atmospheric Model (GRAM) is one of the most widely used engineering models of the atmosphere. GRAM development and maintenance has been led by NASA Marshall Space Flight Center (MSFC). The NASA Science Mission Directorate (SMD) has provided funding support to upgrade the GRAMs since Fiscal Year 2018. NASA Langley Research Center has been working with MSFC on the upgrades.This presentation will provide details regarding the upgrades that have been made to the existing GRAMs, the development of new GRAMs, as well as the ongoing objectives, tasks, and milestones re-lated to the GRAM upgrades funded by NASA SMD. GRAM: The GRAMs are engineering-oriented atmospheric models that estimate mean values and statistical variations of the atmospheric properties for numerous planetary destinations.They provide mean values and variability for any point in the atmosphere as well as seasonal, geographic, and altitude variations. GRAM outputs include atmospheric density, temperature, pressure, winds, and chemical composition along a user-defined path.Theyhave been widely used by the engineering community because of their ability to create realistic dispersions. GRAMs have been integrated into high fidelity flight dynamic simulations of launch, entry, descent and landing (EDL), aerobraking and aerocapture. MSFC has been developing and updating GRAMs since 1974; GRAMs are currently available for Earth, Mars, Venus, Neptune, and Titan. GRAM Upgrade Status: Code Moderization.The planetary GRAMs are being rearchitected from Fortran to a common object-ori-entedC++ framework called the GRAM Suite. This new architecture creates a common GRAM library of data models and utilities. The first C++ releases of the existing planetary GRAMs (Mars, Venus, Neptune, and Titan-GRAM) in the GRAM Suite are straight conversions from the latest Fortran version. Model Upgrades.The focus of the model upgrade task is to improve the atmosphere models in the existing GRAMs and to establish a foundation for developing GRAMs for additional destinations. The GRAM ephemerishas been upgraded to the NASA Navigation and Ancillary Information Facility (NAIF) SPICE toolkit (version N0066). The calculation of the speed of sound has also been improved in the GRAMs. The GRAM team has received updated Mars General Circulation Model (MGCM) datasets from NASA Ames Research Center. Mars Global Ionosphere-Thermosphere Model (M-GITM) data is being obtained toreplace the Mars Thermospheric General Circulation Model (MTGCM) data in legacy Mars-GRAM. M-GITM and updated MGCM data will be incorporated into a future GRAM Suite release.Twoprojects that will improve the atmospheric model data in the GRAMs have been funded by the GRAM team since Fiscal Year 2020. Sanjay Limaye and Patrick Fry at the University of Wisconsin are reanalyzing the Venus Express radio occultation observations and analyzing the Akatsukiradio occultation observations.This will lead tothe calculation of number density, temperature, and pressure profiles for the 40-90 km altitude range. Kunio Sayanagi, Justin Garland, and Ryan McCabeat Hampton University are developing empirical global models for Venus,Jupiter, Saturn, Uranus, Neptune, and Titan that incorporates the latest data available for each of these planetary destinations. Upgraded GRAM Releases. GRAM Suite Version 1.0 was released in May 2020 and contains the rearchitected Neptune-GRAM, including the common GRAM framework and planet–specific code. GRAM Suite Version 1.1 was released in September 2020 and addedthe rearchitected Titan-GRAM to the GRAM Suite. A User Guide and Programmer’s Manualarereleased with all GRAMs. The rearchitected Mars and Venus-GRAMs will be released in upcomingversions of the GRAM Suite. New GRAM Releases. New GRAMs have been de-veloped for Uranus and Jupiter. Uranus-GRAM is based on an individual profile generated by Gary Allen (ARC) from Voyager 2 occultation data and will be released in GRAM Suite Version 1.2. Jupiter-GRAM is based on individual profile produced from Al Seiff’s Ju-piter model[1].Jupiter-GRAM will be released in GRAM Suite Version 1.3. Saturn-GRAM is currently under development and will be released in a future version of the GRAM Suite. Conclusions: GRAMs are vital and frequently used toolsets. Releases of the GRAM Suite, upgrades of the existing planetary GRAMs, and development of new planetary GRAMs are ongoing. NASA SMD funding has been essential to addressing current limitations and accomplishing GRAM developmental goals. Continua-tion ofSMD fundingwill ensure the development, up-grades, and maintenance of the GRAMs. References: [1] Seiff, A., et al. (1998) JGR, 103, 22,857-22,889. Acknowledgments: The authors gratefully acknowledge support from the NASA SMD

atmospheric models↗
DOE OSTI2021

Particle track classification using quantum associative memory

Pattern recognition algorithms are commonly employed to simplify the challenging and necessary step of track reconstruction in sub-atomic physics experiments. Aiding in the discrimination of relevant interactions, pattern recognition seeks to accelerate track reconstruction by isolating signals of interest. In high collision rate experiments, such algorithms can be particularly crucial for determining whether to retain or discard information from a given interaction even before the data is transferred to tape. As data rates, detector resolution, noise, and inefficiencies increase, pattern recognition becomes more computationally challenging, motivating the development of higher efficiency algorithms and techniques. Quantum associative memory is an approach that seeks to exploits quantum mechanical phenomena to gain advantage in learning capacity, or the number of patterns that can be stored and accurately recalled. Here, we study quantum associative memory based on quantum annealing and apply it to the particle track classification. We focus on discrimination models based on Ising formulations of quantum associative memory model (QAMM) recall and quantum content-addressable memory (QCAM) recall. We characterize classification performance of these approaches as a function detector resolution, pattern library size, and detector inefficiencies, using the D-Wave 2000Q processor as a testbed. Discrimination criteria is set using both solution-state energy and classification labels embedded in solution states. We find that energy-based QAMM classification performs well in regimes of small pattern density and low detector inefficiency. In contrast, state-based QCAM achieves reasonably high accuracy recall for large pattern density and the greatest recall accuracy robustness to a variety of detector noise sources.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines

Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Theoretical framework for new magnetic materials for quantum computing and information storage. Final report for the Award No. DE-SC0018910

The focus of this grant was on molecular magnetic materials for information storage and quantum computing. We have been developing robust, first-principle methods for computing relevant electronic and magnetic properties of molecular building blocks (SMMs) of novel magnetic materials and quantum computers. These tools enable theoretical modeling of SMMs’ behavior, facilitating the interpretation of experimental studies and aiding the design of novel magnetic materials. Our strategy is based on the spin-flip (SF) approach, which extends the hierarchy of black-box single-reference methods to strongly correlated systems. Specifically, we developed general scalable algorithms and computer codes for calculating molecular properties, with an emphasis on spin-related properties, such as zero-field splittings, hyperfine couplings, and g-tensors. While our primary focus was on SF wave functions and SF-TDDFT, the underlying theory and computer codes were formulated using reduced density matrices, such that these tools are applicable to a broader class of methods. To extend the scope of applicability of wave-function-based SF methods to larger systems, we developed reduced-scaling approaches for the equation-of-motion coupled-cluster (EOM-CC) methods and continue developing libtensor (our open-source general tensor contraction library for many-body methods). We carried out extensive benchmarks and also carried out several applications.

36 MATERIALS SCIENCE↗
NASA NTRS2024

Qualitative Headspace GCMS Analysis of Lunar Regolith and Volatile Simulant Mixtures

Introduction: Future Artemis missions aim to return the volatile-bearing samples collected near lunar polar craters. We, as advanced curation scientists, are responsible for developing techniques and methodologies for preserving the integrity of returned samples and the science value those samples contain. The extent to which that preservation is possible, and the trade-offs preservation requires (e.g. monetary costs, sample volume limitations) all must be considered. Even less-than pristine volatile-bearing samples will be of tremendous value to the scientific community seeking to unravel the history of lunar surface volatiles and, more broadly, volatiles in the solar system. A sample collected on the lunar surface will experience at least five distinctive periods during which any changes here referred to as “alteration” will certainly occur at some scale: collection on the lunar surface; transportation back to Earth; long-term storage; curatorial processing; and allocation/distribution. The Planetary Exploration and Astromaterials Research Lab (PEARL) seeks to understand temperature and pressure effects on returned volatile samples by working with high-fidelity volatile-containing regolith simulants, setting the foundation for the future of cold curation. This abstract is focused on gas-surface interactions between LCROSS volatiles and readily available lunar regolith simulants. Experiments involved analyzing differences in headspace gas composition for various combinations of volatile and regolith simulants using gas chromatography/mass spectrometry (GC/MS). Experimental Procedure: The volatile simulants were chosen based on the molecules detected during the LCROSS mission.1 Stock solutions of condensed lunar volatile analytes were: methanol, 7 N ammonia in methanol, and 0.4% hydrogen sulfide in water. The regolith simulants used were primarily JSC-1A and NU-LHT-4M. Additional regolith simulant control studies were conducted with <150 μm sieved sand and KBr. A nested vial sample preparation approach separated the liquid stock solutions from the regolith, eliminating potential matrix effects between liquid and solid phases. Fifteen microliter aliquots of liquid volatile simulants were added to a 2 mL liquid GC vial and capped in atmosphere. An 18G needle punctured the 2 mL GC vial immediately before being transferred and sealed in a 20 mL GC vial containing 0-0.3 g of regolith simulant, see Figure 1. Separating the analytes ensures any changes observed in the total headspace gases is a result of gas-surface and/or gas-gas interactions. Equipment and Method: Initial GC/MS method development for the separation and identification of relevant headspace gases can be found in Amick, et al. 2023.2 The only hardware change is a different column: a TG-1701MS 30 m × 0.25 mm × 1.00 μm column. The vials were sampled at 10°C, room temperature (~25°C) and 50°C. Low temperature samples were kept in a chilled autosampler stage for at least 1 hour prior to sampling. High temperature samples were agitated at 50°C for 5 minutes immediately prior to injection onto the column. Headspace chromatograms were collected for each combination of temperature, regolith, and volatile simulant, including controls without one or both types of analytes, in triplicate. The chromatogram elution window for each analyte or significant atmospheric gas was identified using the peak mass spectrum cross-referenced with Figure 1.Picture of the nested vial set-up. a NIST MS library search. Each analyte peak was integrated after filtering the mass spectrum trace for the parent or most unique mass-to-charge ratio. For example, the mass-to-charge ratio used to identify, filter for, and integrate the carbon dioxide peak was centered around 44 m/z. Results: Figure 2 shows the integrated peak area for hydrogen sulfide in all combinations of regolith simulants, temperatures, and the addition of ammonia in methanol solution. Multiple repeat experiments with H2S and regolith simulants have confirmed hydrogen sulfide is removed from the headspace within 1 hour when exposed to JSC-1A, NU-LHT-4M and sand (not pictured). The consumption of H2S by lunar regolith simulants at different temperatures indicates surface chemistry will be an integral component in sample integrity and preservation. It is important to note that while the effect of surface chemistry on gaseous hydrogen sulfide is intriguing, further investigation into more chemically accurate regolith simulants is necessary and ongoing. The sulfur in hydrogen sulfide is in its most reduced state while off-the-shelf, terrestrially sourced JSC-1A and NU-LHT-4M are more oxidized than most lunar materials,3which likely leads to different oxidation-reduction reactions than would be expected in lunar regolith. Figure 3 shows the integrated peak area of carbon dioxide for each sample combination that contained ammonia in methanol solution. The addition of ammonia to the GC vials results in a consistent and reproducible decrease in carbon dioxide gas, even at 50°C. The effect became more pronounced when JSC-1A or NU-LHT-4M were present. This set of experiments demonstrated that the sample composition will affect the chemical and physical state of each component present. Future spectroscopic and microscopy experiments will be geared towards identifying the cause for the CO2(g) concentration decrease and the consumption of hydrogen sulfide. As cold and volatile curation scientists, this information provides necessary insight on how to appropriately handle and analyze volatile bearing returned samples, as well as predict the effect chemical composition has on the various sample phases we will analyze upon return to Earth. Unlike traditional curation of geologic materials, the molecules in a sample cannot be identified or processed using the naked eye or even an optical microscope. Volatile curation will require a combination of analytical techniques, including but not limited to highly sensitive gas and solid/condensed phase spectroscopy. This set of experiments has demonstrated the need for more detailed studies of volatile mixtures with mineralogically and geochemically analogous lunar regolith simulants to prepare for the curation of volatile-rich lunar samples from the south polar region of the Moon. References: [1] Colaprete, A., et al. (2010) Science, 330, (463-468). [2] Amick, C. L., et al.(2023) Houston, Texas, [3] Heiken, G. H., et al.(1991) (778-778)

Cecilia L Amick↗
NASA NTRS2013

ISSM: Ice Sheet System Model

In order to have the capability to use satellite data from its own missions to inform future sea-level rise projections, JPL needed a full-fledged ice-sheet/iceshelf flow model, capable of modeling the mass balance of Antarctica and Greenland into the near future. ISSM was developed with such a goal in mind, as a massively parallelized, multi-purpose finite-element framework dedicated to ice-sheet modeling. ISSM features unstructured meshes (Tria in 2D, and Penta in 3D) along with corresponding finite elements for both types of meshes. Each finite element can carry out diagnostic, prognostic, transient, thermal 3D, surface, and bed slope simulations. Anisotropic meshing enables adaptation of meshes to a certain metric, and the 2D Shelfy-Stream, 3D Blatter/Pattyn, and 3D Full-Stokes formulations capture the bulk of the ice-flow physics. These elements can be coupled together, based on the Arlequin method, so that on a large scale model such as Antarctica, each type of finite element is used in the most efficient manner. For each finite element referenced above, ISSM implements an adjoint. This adjoint can be used to carry out model inversions of unknown model parameters, typically ice rheology and basal drag at the ice/bedrock interface, using a metric such as the observed InSAR surface velocity. This data assimilation capability is crucial to allow spinning up of ice flow models using available satellite data. ISSM relies on the PETSc library for its vectors, matrices, and solvers. This allows ISSM to run efficiently on any parallel platform, whether shared or distrib- ISSM: Ice Sheet System Model NASA's Jet Propulsion Laboratory, Pasadena, California uted. It can run on the largest clusters, and is fully scalable. This allows ISSM to tackle models the size of continents. ISSM is embedded into MATLAB and Python, both open scientific platforms. This improves its outreach within the science community. It is entirely written in C/C++, which gives it flexibility in its design, and the power/speed that C/C++ allows. ISSM is svn (subversion) hosted, on a JPL repository, to facilitate its development and maintenance. ISSM can also model propagation of rifts using contact mechanics and mesh splitting, and can interface to the Dakota software. To carry out sensitivity analysis, mesh partitioning algorithms are available, based on the Scotch, Chaco, and Metis partitioners that ensure equal area mesh partitions can be done, which are then usable for sampling and local reliability methods.

Larour, Eric↗
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 OSTI2025

Spectroscopy of the Hamburg Meteorite, Michigan H4

Spectroscopic studies of the Hamburg (Michigan H4) meteorite using visible–near-infrared (VNIR), mid-infrared (MIR), Raman, and Mössbauer data reproduce the results of more conventional laboratory measurements of petrology and geochemistry. This combination provides general information on the mineral modes of silicates, although spectroscopy was performed on different splits of this meteorite, and varying results may be explained by heterogeneity that is typical of ordinary chondrites. Raman also detects small features assigned to first-order D and G carbon bands, while Mössbauer data show the presence of Fe oxides and carbides. The electron microprobe (EMPA) composition of olivine in this meteorite is accurately measured to be Fo 81.3 , while MIR and Raman closely agree with Fo 80 and Fo 82 , respectively, and Mössbauer, at Fo 60 − Fo 70 , is in the ballpark. Similarly, P. R. Heck et al. report pyroxenes with compositions of Fs 16 Wo 1 , while Raman suggests a somewhat similar composition of Fs 28 Wo 0 . Both VNIR and MIR detect the presence of small amounts of feldspar, while EMPA identifies its composition as An 14 Ab 8 Or 5 . VNIR data were matched to spectral libraries of meteorite and asteroid data and shown to closely match other L and H meteorites. The best spectral matches to the Michigan H4 meteorite are to asteroid classes L/H/LL/URE, EH/EL/AUB, and CO/CV from M. D. Dyar et al.; objects in this group are intermediate in semimajor axis lengths for their orbits. The results highlight the strengths and weaknesses of each technique and show their collective strength when applied together to a single meteorite sample.

58 GEOSCIENCES↗
NASA NTRSDate not supplied

Venus Global Reference Atmospheric Model (Venus-GRAM) Upgrades

Introduction: The Venus Global Reference Atmospheric Model (Venus-GRAM) is one of the most widely used engineering models of Venus’ atmosphere. The Venus-GRAM upgrades are being developed by NASA Marshall Space Flight Center (MSFC) and NASA Langley Research Center (LaRC). This presentation will provide details regarding the upgrades that have been made to Venus-GRAM and the ongoing objectives, tasks, and milestones related to the GRAM upgrades funded by the NASA Science Mission Directorate (SMD). Venus-GRAM: Venus-GRAM is an engineering-oriented atmospheric model that estimates mean values and statistical variations of the atmospheric properties of Venus. Venus-GRAM provides mean values and variability for any point in the atmosphere as well as seasonal, geographic, and altitude variations. Venus-GRAM outputs include atmospheric density, temperature, pressure, winds, and chemical composition along a user-defined path. It is extensively used by the engineering community because of its ability to create realistic dispersions. GRAMs have been integrated into high fidelity flight dynamic simulations of launch, entry, descent and landing (EDL), aerobraking and aerocapture. GRAMs are currently available for Earth, Mars, Venus, Neptune, Titan, and Uranus. The lower atmosphere model in Venus-GRAM (up to 250 km) is based on the Venus International Reference Atmosphere (VIRA) [1]. The Venus-GRAM thermosphere (250 to 1000 km) is based on a MSFC-developed model [2] which assumes an isothermal temperature profile initialized using VIRA conditions at 250 km [3]. The VIRA version included in Venus-GRAM includes Pioneer Venus Orbiter and Probe data as well as Venera probe data, but it does not include a solid planet model or a high-resolution gravity model [4]. Venus-GRAM Upgrade Status: Code Modernization. Venus-GRAM has been rearchitected from Fortran to a common object-oriented C++ framework called the GRAM Suite. This new architecture creates a common GRAM library of data models and utilities. The first C++ release of the rearchitected Venus-GRAM is a straight conversion from the latest Fortran version. Model Upgrades. The focus of the model upgrade task is to improve the atmosphere models in the existing GRAMs and to establish a foundation for developing GRAMs for additional destinations. The GRAM ephemeris has been upgraded to the NASA Navigation and Ancillary Information Facility (NAIF) SPICE toolkit (version N0066). The calculation of the speed of sound has also been improved in the GRAMs. In FY20, the GRAM project established contracts to improve the model data within Venus-GRAM. Hampton University is developing an empirical global model for Venus. The University of Wisconsin is reanalyzing the Venus Express radio occultation observations and analyzing the Akatsuki thermal imaging data. Upgraded Venus-GRAM Release. GRAM Suite Version 1.3 will be released in September 2021 and will contain the rearchitected Venus-GRAM, including the common GRAM framework and planet–specific code. A User Guide and Programmer’s Manual are released with all GRAMs. Conclusions: GRAMs are frequently used toolsets and vital in assessing effects of atmospheres on interplanetary spacecraft during the program life cycle process. Releases of the GRAM Suite, upgrades of the existing planetary GRAMs, and development of new planetary GRAMs are ongoing. Venus-GRAM atmosphere model upgrades will be included in the next phase of GRAM tasks. References: [1] Kliore, A. J. et al. (1985) ASR, 5, 11, 1-304. [2] Justh, H. L. et al. (2006) AIAA/AAS Astrodynamics Specialist Conference & Exhibit, Abstract AIAA-2006-6394. [3] Guide to Reference and Standard Atmosphere Models, BSR/AIAA G-003-2010. [4] Limaye, S. S. (2012), LPSC VEXAG Townhall Meeting. Acknowledgments: The authors gratefully acknowledge support from the NASA SMD.

atmospheric models↗
DOE OSTI2022

evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library

Widespread availability of protein sequence-fitness data would revolutionize both our biochemical understanding of proteins and our ability to engineer them. Unfortunately, even though thousands of protein variants are generated and evaluated for fitness during a typical protein engineering campaign, most are never sequenced, leaving a wealth of potential sequence-fitness information untapped. Primarily, this is because sequencing is unnecessary for many protein engineering strategies; the added cost and effort of sequencing is thus unjustified. It also results from the fact that, even though many lower cost sequencing strategies have been developed, they often require at least some sequencing or computational resources, both of which can be barriers to access. In this work, we present every variant sequencing (evSeq), a method and collection of tools/standardized components for sequencing a variable region within every variant gene produced during a protein engineering campaign at a cost of cents per variant. evSeq was designed to democratize low-cost sequencing for protein engineers and, indeed, anyone interested in engineering biological systems. Execution of its wet-lab component is simple, requires no sequencing experience to perform, relies only on resources and services typically available to biology labs, and slots neatly into existing protein engineering workflows. Analysis of evSeq data is likewise made simple by its accompanying software (found at github.com/fhalab/evSeq, documentation at fhalab.github.io/evSeq), which can be run on a personal laptop and was designed to be accessible to users with no computational experience. Here, low-cost and easy to use, evSeq makes collection of extensive protein variant sequence-fitness data practical.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Phenopacket-tools: Building and validating GA4GH Phenopackets

The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Transcriptomics-Based Points of Departure for Daphnia magna Exposed to 18 Per- and Polyfluoroalkyl Substances

Here, per- and polyfluoroalkyl substances (PFAS) represent a large group of contaminants of concern based on their widespread use, environmental persistence, and potential toxicity. Many traditional models for estimating toxicity, bioaccumulation, and other toxicological properties are not well suited for PFAS. Consequently, there is a need to generate hazard information for PFAS in an efficient and cost-effective manner. In the present study, Daphnia magna were exposed to multiple concentrations of 22 different PFAS for 24 h, in 96-well plate format. Following exposure, whole body RNA was extracted and extracts, each representing five exposed individuals, were subjected to RNA sequencing. Following analytical measurements to verify PFAS exposure concentrations, and quality control on processed cDNA libraries for sequencing, concentration-response modeling was applied to the data sets for 18 of the tested compounds, and the concentration at which a concerted molecular response occurred (transcriptomic point of departure; tPOD) was calculated. The tPODs, based on measured concentrations of PFAS, generally ranged from 0.03-0.58 µM (9.9-350 µg/L; interquartile range). In most cases, these concentrations were two orders of magnitude lower than similarly calculated tPODs for human cell lines exposed to PFAS. They were also lower than apical effect concentrations reported for seven PFAS for which some crustacean or invertebrate toxicity data were available, although there were a few exceptions. Despite being lower than most other available hazard benchmarks, Daphnia magna tPODs were, on average, four orders of magnitude greater than the maximum aqueous concentrations of PFAS measured in Great Lakes tributaries. Overall, this high throughput transcriptomics assay with Daphnia magna holds promise as a component of a tiered hazard evaluation strategy employing new approach methodologies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we present a computational framework, designated Y2H-SCORES, for analyzing high-throughput Y2H screens. Y2H-SCORES considers key aspects of NGIS experimental design and important characteristics of the resulting data that distinguish it from RNA-seq expression datasets. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS enabled us to identify conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeast-based interaction screenings, with an equivalent or superior performance than existing methods. Proof-of-concept was demonstrated by discovery and validation of novel interactions between the barley nucleotide-binding leucine-rich repeat (NLR) immune receptor MLA6, and fourteen proteins, including those that function in signaling, transcriptional regulation, and intracellular trafficking.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Diverse PFAS produce unique transcriptomic changes linked to developmental toxicity in zebrafish

Per- and polyfluoroalkyl substances (PFAS) are a widespread and persistent class of contaminants posing significant environmental and human health concerns. Comprehensive understanding of the modes of action underlying toxicity among structurally diverse PFAS is mostly lacking. To address this need, we recently reported on our application of developing zebrafish to evaluate a large library of PFAS for developmental toxicity. In the present study, we prioritized 15 bioactive PFAS that induced significant morphological effects and performed RNA-sequencing to characterize early transcriptional responses at a single timepoint (48 h post fertilization) after early developmental exposures (8 h post fertilization). Internal concentrations of 5 of the 15 PFAS were measured from pooled whole fish samples across multiple timepoints between 24–120 h post fertilization, and additional temporal transcriptomics at several timepoints (48–96 h post fertilization) were conducted for Nafion byproduct 2. A broad range of differentially expressed gene counts were identified across the PFAS exposures. Most PFAS that elicited robust transcriptomic changes affected biological processes of the brain and nervous system development. While PFAS disrupted unique processes, we also found that similarities in some functional head groups of PFAS were associated with the disruption in expression of similar gene sets. Body burdens after early developmental exposures to select sulfonic acid PFAS, including Nafion byproduct 2, increased from the 24–96 h post fertilization sampling timepoints and were greater than those of sulfonamide PFAS of similar chain lengths. In parallel, the Nafion byproduct 2-induced transcriptional responses increased between 48 and 96 h post fertilization. PFAS characteristics based on toxicity, transcriptomic effects, and modes of action will contribute to further prioritization of PFAS structures for testing and informed hazard assessment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Opening doors to physical sample tracking and attribution in Earth and environmental sciences

Physical samples and their associated data and metadata underpin scientific discoveries across disciplines and can enable new science when appropriately archived. However, there are significant gaps in current practices and infrastructure that prevent accurate provenance tracking, reproducibility, and attribution. For most samples, descriptive metadata are often sparse, inaccessible, or absent. Samples and associated data and metadata may also be scattered across numerous physical collections, data repositories, laboratories, data files, and papers with no clear linkage or provenance tracking as new information is generated over time. The Earth Science Information Partners (ESIP) Physical Samples Curation Cluster has therefore developed guidance for scientific authors on ‘Publishing Open Research Using Physical Samples.’ This involved synthesizing existing practices, gathering community feedback, and assessing real-world examples. We identified improvements needed to enable authors to efficiently cite and link Earth science samples and related data, and track their use. Our goal is to help improve discoverability, interoperability, and reuse of physical samples, and associated data and metadata. Though primarily focused on the needs of Earth and environmental sciences, these guidelines are broadly applicable.

58 GEOSCIENCES↗
DOE OSTI2020

Hindsight logging for model training

In modern Machine Learning, model training is an iterative, experimental process that can consume enormous computation resources and developer time. To aid in that process, experienced model developers log and visualize program variables during training runs. Exhaustive logging of all variables is infeasible, so developers are left to choose between slowing down training via extensive conservative logging, or letting training run fast via minimalist optimistic logging that may omit key information. As a compromise, optimistic logging can be accompanied by program checkpoints; this allows developers to add log statements post-hoc, and "replay" desired log statements from checkpoint---a process we refer to as hindsight logging. Unfortunately, hindsight logging raises tricky problems in data management and software engineering. Done poorly, hindsight logging can waste resources and generate technical debt embodied in multiple variants of training code. In this paper, we present methodologies for efficient and effective logging practices for model training, with a focus on techniques for hindsight logging. Our goal is for experienced model developers to learn and adopt these practices. To make this easier, we provide an open-source suite of tools for Fast Low-Overhead Recovery (flor) that embodies our design across three tasks: (i) efficient background logging in Python, (ii) adaptive periodic checkpointing, and (iii) an instrumentation library that codifies hindsight logging for efficient and automatic record-replay of model-training. Model developers can use each flor tool separately as they see fit, or they can use flor in hands-free mode, entrusting it to instrument their code end-to-end for efficient record-replay. Our solutions leverage techniques from physiological transaction logs and recovery in database systems. Evaluations on modern ML benchmarks demonstrate that flor can produce fast checkpointing with small user-specifiable overheads (e.g. 7%), and still provide hindsight log replay times orders of magnitude faster than restarting training from scratch.

Computer Science↗