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NASA NTRS2018

Developing a Community of Practice for Applied Uses of Future PACE Data to Address Food Security Challenges

Ocean color satellite measurements have yielded valuable information about the base of the marine food web for over 20 years. The Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission is building an advanced spectrometer to further refine ecosystem monitoring. Higher spectral resolution data from PACE will enable identification of additional marine biological indicators and their response to multiple stressors to guide sustainable management. Seafood is an important source of protein for a significant number of people. Wild catches cannot match increasing demand and their sustainability is in question. Aquaculture is an ever more important industry to feed the world's population. We share early efforts to engage a community of practice around food security to increase satellite data product use in support of resource management, business decisions, and policy analysis. Understanding the needs of applied scientists as well as non-traditional users of satellite data early in the PACE mission process will improve planning and preparation for a broader user base and hopefully help to mitigate food insecurity.

Schollaert Uz, Stephanie↗

NASA NTRS2018

NASA Guidelines for Promoting Scientific and Research Integrity

The National Aeronautics and Space Administration (NASA) seeks to explore and expand human knowledge of the Earth, solar system, and universe and to enable the development of aeronautical and space exploration systems. NASA's ability to achieve these purposes depends on the integrity of the research and technology activities the agency conducts and supports. The NASA workforce - as well as all external entities who review proposals for or receive NASA funding - must maintain the highest standards of scientific integrity. These responsibilities include selecting the most meritorious research activities through open and fair competition, peer review and other appropriate merit review processes, and avoidance of actual and perceived conflicts of interest; avoiding fabrication, falsification, or plagiarism in proposing, performing, or reviewing research, or in reporting research results; openly sharing results and methods not subject to classification or privacy standards; disclosing assumptions and biases in sharing and applying scientific information and data; and acting honestly and transparently in using and serving on advisory committees and in engaging in professional development activities.

Guidelines↗

NASA NTRSDate not supplied

Enabling Open and Interoperable Science: Multi-Omics Data Processing Platform with NASA GeneLab Standardized Bioinformatics Workflows for Space and Earth Research

Multi-omics biological data continues to be generated at an astounding pace. Genomics, transcriptomics, metabolomics, and proteomics, or collectively known as multi-omics data, are used to assess biological functions, and provide invaluable insights into human, animal, plant, and environmental health both on Earth and in Space. Despite the abundance of these valuable data, the need for bioinformatics expertise, particularly as it relates to the niche filed of space biology, and a lack of accessible resources for processing these data limit their usefulness in deriving biological insights. The NASA Open Science Data Repository (OSDR) provides access to omics data from various spaceflight and analog studies. To enhance the accessibility and reusability of these data, GeneLab (part of OSDR) designs and implements standardized, community-driven, open-source bioinformatics workflows to transform raw omics data into standardized processed data. Currently, GeneLab-processed data from hundreds of space studies have been reused for meta-analyses. This has led to new insights and scientific publications that extend beyond the initial research, thereby enriching our understanding of molecular-scale biological responses to the space environment. To make these bioinformatics workflows open and accessible, GeneLab teamed up with DOE-funded initiatives, including the National Microbiome Data Collaborative (NMDC), to create the NASA EDGE [Empowering the Development of Genomics Expertise] Bioinformatics web-based platform. NASA EDGE utilizes shared compute resources to run the GeneLab standardized bioinformatics workflows, which eliminates the need for researchers to have their own high performance computing cluster. The web-based platform makes complicated biological analyses incredibly easy to perform, thus expanding the reach of these analyses to bioinformatics novices, students, and even citizen scientists enabling them to contribute to scientific discoveries and progress. The authors will demonstrate how the NASA EDGE platform can be used to process microbial omics data hosted on OSDR as well as user-generated omics datasets using GeneLab’s standard workflows.

Amanda M. Saravia-Butler↗

NASA NTRSDate not supplied

Evaluating the Efficacy of Conditional Variational Autoencoders in Generating Synthetic Single Nuclei RNA-Seq Data for Space Biology Research

Astronauts are subject to unique stressors during spaceflight, leading to changes in their cellular function. However, neither astronauts nor model organisms respond the same to spaceflight, and research implicates a contribution of omics components in differential responses. Understanding how gene expression affects astronaut health is critical for the success of long-term space missions, prompting interest in developing personalized predictive models leveraging artificial intelligence (AI) and machine learning (ML) techniques. Developing such models requires extensive data, which is challenging to obtain and share. This study explores the use of conditional variational autoencoders (CVAEs) to synthetically generate single-nuclei RNA-seq (snRNA-seq) data. CVAEs build on standard variational autoencoders (VAEs) by conditioning data generation on covariates like sample identity and mission parameters, enhancing the relevance of generated data for specific contexts. For our work, we built two CVAEs with varying degrees of sparsity to optimize both interpretability and generative power. We train and validate models on existing snRNA-seq data collected from the brain tissue of mice subjected to spaceflight conditions and their ground control counterparts. We evaluate model performance using statistical tests and visualizations to compare synthetic data to real data. We aim to demonstrate that these prototype CVAE architectures could be used in future space biology work and that this is a method worth further exploring.

Sarah Golts↗

DOE OSTI2016

The new Zintl phases Eu{sub 21}Cd{sub 4}Sb{sub 18} and Eu{sub 21}Mn{sub 4}Sb{sub 18}

Crystals of two new Zintl compounds, Eu{sub 21}Mn{sub 4}Sb{sub 18} and Eu{sub 21}Cd{sub 4}Sb{sub 18} have been synthesized using the molten metal flux method, and their structures have been established by single-crystal X-ray diffraction. Both compounds are isotypic and crystallize in the monoclinic space group C2/m (No. 12, Z=4). The structures are based on edge- and corner-shared MnSb{sub 4} or CdSb{sub 4} tetrahedra, which make octameric [Mn{sub 8}Sb{sub 22}] or [Cd{sub 8}Sb{sub 22}] polyanions. Homoatomic Sb–Sb bonds are present in both structures. The Eu atoms take the role of Eu{sup 2+}cations with seven unpaired 4f electrons, as suggested by the temperature-dependent magnetization measurements. The magnetic susceptibilities of Eu{sub 21}Mn{sub 4}Sb{sub 18} and Eu{sub 21}Cd{sub 4}Sb{sub 18} indicate that both phases order anti-ferromagnetically with Néel temperatures of ca. 7 K and ca. 10 K, respectively. The unpaired 3d electrons of the Mn atoms in Eu{sub 21}Mn{sub 4}Sb{sub 18} do contribute to the magnetic response, however, the bulk magnetization measurements do not provide evidence for long-range ordering of the Mn spins down to 5 K. Electrical resistivity measurements suggest that both compounds are narrow band gap semiconductors. - Graphical abstract: Eu{sub 21}Mn{sub 4}Sb{sub 18} and Eu{sub 21}Cd{sub 4}Sb{sub 18} have complex monoclinic structures, based on MnSb{sub 4} and CdSb{sub 4} tetrahedra, both edge- and corner-shared. A perspective of the crystal structure is shown, as viewed along the b axis. Display Omitted - Highlights: • Eu{sub 21}Mn{sub 4}Sb{sub 18} and Eu{sub 21}Cd{sub 4}Sb{sub 18} are novel compounds in the respective ternary phase diagrams. • For both structures, the Zintl-Klemm rules are followed, and both are small gap semiconductors. • Eu{sub 21}Mn{sub 4}Sb{sub 18} and Eu{sub 21}Cd{sub 4}Sb{sub 18} are air-stable Zintl phases and could be new thermoelectric materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Evidence for d -wave superconductivity of infinite-layer nickelates from low-energy electrodynamics

The discovery of superconductivity in infinite-layer nickelates established another category of unconventional superconductors that shares structural and electronic similarities with cuprates. However, key issues of the superconducting pairing symmetry, gap amplitude and superconducting fluctuations are yet to be addressed. Here we utilize static and ultrafast terahertz spectroscopy to address these. We demonstrate that the equilibrium terahertz conductivity and non-equilibrium terahertz responses of an optimally Sr-doped nickelate film (superconducting transition temperature of T c = 17 K) are in line with the electrodynamics of d-wave superconductivity in the dirty limit. The gap-to-T c ratio (2Δ/k B T c ) is found to be 3.4, indicating that the superconductivity falls in the weak coupling regime. In addition, we observed substantial superconducting fluctuations near T c that do not extend into the deep normal state as the optimally hole-doped cuprates do. In conclusion, our results support a d-wave system that closely resembles the electron-doped cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2010

International perspectives on mitigating laboratory biorisks.

The International Perspectives on Mitigating Laboratory Biorisks workshop, held at the Renaissance Polat Istanbul Hotel in Istanbul, Republic of Turkey, from October 25 to 27, 2010, sought to promote discussion between experts and stakeholders from around the world on issues related to the management of biological risk in laboratories. The event was organized by Sandia National Laboratories International Biological Threat Reduction program, on behalf of the US Department of State Biosecurity Engagement Program and the US Department of Defense Cooperative Biological Engagement Program. The workshop came about as a response to US Under Secretary of State Ellen O. Tauscher's statements in Geneva on December 9, 2009, during the Annual Meeting of the States Parties to the Biological Weapons Convention (BWC). Pursuant to those remarks, the workshop was intended to provide a forum for interested countries to share information on biorisk management training, standards, and needs. Over the course of the meeting's three days, participants discussed diverse topics such as the role of risk assessment in laboratory biorisk management, strategies for mitigating risk, measurement of performance and upkeep, international standards, training and building workforce competence, and the important role of government and regulation. The meeting concluded with affirmations of the utility of international cooperation in this sphere and recognition of positive prospects for the future. The workshop was organized as a series of short presentations by international experts on the field of biorisk management, followed by breakout sessions in which participants were divided into four groups and urged to discuss a particular topic with the aid of a facilitator and a set of guiding questions. Rapporteurs were present during the plenary session as well as breakout sessions and in particular were tasked with taking notes during discussions and reporting back to the assembled participants a brief summary of points discussed. The presentations and breakout sessions were divided into five topic areas: 'Challenges in Biorisk Management,' 'Risk Assessment and Mitigation Measures,' 'Biorisk Management System Performance,' 'Training,' and 'National Oversight and Regulations.' The topics and questions were chosen by the organizers through consultation with US Government sponsors. The Chattham House Rule on non-attribution was in effect during question and answer periods and breakout session discussions.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2013

Analysis of Microbial Activity Under a Supercritical CO 2 Atmosphere

Because the extent and impact of microbial activity in deep saline aquifers during geologic sequestration is unknown, the objectives of this proposal were to: (1) characterize the growth requirements and optima of a biofilm-producing supercritical CO 2 -tolerant microbial consortium (labeled MIT0212) isolated from hydrocarbons recovered from the Frio Ridge, TX carbon sequestration site; (2) evaluate the ability of this consortium to grow under simulated reservoir conditions associated with supercritical CO 2 injection; (3) isolate and characterize individual microbial strains from this consortium; and (4) investigate the mechanisms of supercritical CO 2 tolerance in isolated strains and the consortium through genome-enabled studies. Molecular analysis of genetic diversity in the consortium MIT0212 revealed a predominance of sequences closely related to species of the spore-forming genus Bacillus. Strain MIT0214 was isolated from this consortium and characterized by physiological profiling and genomic analysis. We have shown that the strain MIT0214 is an aerobic spore-former and capable of facultative anaerobic growth under both reducing N 2 and CO 2 atmospheres by fermentation and possibly anaerobic respiration. Strain MIT0214 is best adapted to anaerobic growth at pressures of 1 atm but is able to growth at elevated pressures After 1 week growth was observed at pressures as high as 27 atm (N 2 ) or 9 atm (CO 2 ) and after 26-30 days growth can be observed under supercritical CO 2 . In addition, we have determined that spores of strain B. cereus MIT0214 are tolerant of both direct and indirect exposure to supercritical CO 2 . Additional physiological characterization under aerobic conditions have revealed MIT0214 is able to grow from temperature of 21 to 45 °C and salinities 0.01 to 40 g/L NaCl with optimal growth occurring at 30°C and from 1 - 5 g NaCl/L. The genome sequence of B. cereus MIT0214 shared 89 to 91% of genes with other genome-sequenced strains with 93.3 to 97.8% nucleotide identity among shared genes. Comparison of the sequence of MIT0214 or a B. cereus strain isolated from an oil well in China to B. cereus isolates from surface environments revealed a higher proportion of genes involved in Cell wall and capsule biosynthesis and metabolism, metabolism of aromatic compounds, and stress response. Since Bacillus species, including B. cereus strains, have commonly been recovered from other “extreme” environments including the deep subsurface – the scCO 2 tolerance of spores and growth under high pCO 2 conditions is consistent with persistence in a subsurface environment after CO 2 injection.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

PHOTOMETRIC MONITORING OF THE COLDEST KNOWN BROWN DWARF WITH THE SPITZER SPACE TELESCOPE

Because WISE J085510.83-071442.5 (hereafter WISE 0855-0714) is the coldest known brown dwarf (∼250 K) and one of the Sun’s closest neighbors (2.2 pc), it offers a unique opportunity to study a planet-like atmosphere in an unexplored regime of temperature. To detect and characterize inhomogeneities in its atmosphere (e.g., patchy clouds, hot spots), we have performed time-series photometric monitoring of WISE 0855-0714 at 3.6 and 4.5 μ m with the Spitzer Space Telescope during two 23 hr periods that were separated by several months. For both bands, we have detected variability with peak-to-peak amplitudes of 4%–5% and 3%–4% in the first and second epochs, respectively. The light curves are semiperiodic in the first epoch for both bands, but they are more irregular in the second epoch. Models of patchy clouds have predicted a large increase in mid-infrared (mid-IR) variability amplitudes (for a given cloud covering fraction) with the appearance of water ice clouds at T {sub eff} < 375 K, so if such clouds are responsible for the variability of WISE 0855-0714, then its small amplitudes of variability indicate a very small deviation in cloud coverage between hemispheres. Alternatively, the similarity in mid-IR variability amplitudes between WISE 0855-0714 and somewhat warmer T and Y dwarfs may suggest that they share a common origin for their variability (i.e., not water clouds). In addition to our variability data, we have examined other constraints on the presence of water ice clouds in the atmosphere of WISE 0855-0714, including the recent mid-IR spectrum from Skemer et al. (2016). We find that robust evidence of such clouds is not yet available.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

EXERGETIC: De-Risking Next-Generation Resilient Geothermal Hybrids via At-Scale Evaluation Using Virtual Emulation Digital Twin Environment for Efficient Operation

The DOE-GTO-funded project, award number 5.1.2.12, entitled "EXERGETIC - De-risking Next Generation Resilient Geothermal Hybrids via at-Scale Evaluation Using a Virtual Emulation Digital Twin Environment for Efficient Operation," advances the solution to these challenges by developing and validating a geothermal co-emulation environment implemented at the National Laboratory of the Rockies (NLR)'s Advanced Research on Integrated Energy Systems (ARIES) platform. This framework enables the de-risking of next-generation geothermal and geothermal hybrid systems through high-fidelity modeling, real-time digital emulation, advanced control strategies, and techno-economic assessment. The project focused on geothermal hybrid configurations that integrate geothermal power plants with concentrated solar power and underground thermal energy storage, enabling enhanced efficiency, flexibility, and grid support capabilities. The main goal of this project was the development of a geothermal digital co-emulation environment to demonstrate the technical and economic value of geothermal hybrid systems and their contribution to grid stability and flexibility. The EXERGETIC framework combined physics-based models, controls, and real assets at ARIES, including digital real-time simulators (DRTS), a 20-MW-scale controllable grid interface (CGI), and a 2-MW conventional generator. Detailed transient models were developed for the key subsystems of a hybrid geothermal plant, including parabolic trough solar collectors, reservoir thermal energy storage (RTES), and a binary Organic Rankine Cycle (ORC) power plant. The ORC model explicitly captured thermal inertia and off-design operation and integrated control strategies to dynamically respond to electric load profiles. The models were validated against published experimental and numerical studies, demonstrating strong agreement and confirming the accuracy and robustness of the modeling approach. The resulting digital twin represents geothermal-solar-storage systems at multiple scales (1 MW to 100 MW) and enables realistic emulation of grid-connected operation. The control architecture allows the geothermal resource to provide stable baseload generation, while solar and stored thermal energy supply flexible, dispatchable support during periods of high demand or variable grid conditions. A key contribution of the EXERGETIC project is the demonstration that geothermal hybrid systems can be designed to be active grid assets rather than passive baseload generators. Using the ARIES platform, the digital twin was evaluated under multiple grid scenarios, including load following, voltage support at the distribution level, and frequency response at the transmission level. Results show that hybrid geothermal systems can respond effectively to dynamic grid conditions, providing inertia-like behavior, primary frequency support, and voltage regulation through coordinated control. In addition to the performance and grid services capability analysis of geothermal and hybrid geothermal systems, the EXERGETIC project also focused on scalability and techno-economic analysis of geothermal hybrid plants. In particular, for the scalability analysis, machine-learning (ML)-based surrogate models were trained using data generated from the geothermal digital twin under different grid-connected scenarios and plant capacities. These ML models demonstrated strong interpolation and extrapolation capabilities across plant sizes, accurately reproducing both steady-state and transient responses with very low errors. Regarding the techno-economic analysis, plant performance results were integrated with cost models for hybrid geothermal systems, and the levelized cost of electricity (LCOE) was used as the main economic metric to evaluate system performance across a range of system capacities, solar shares, solar multiples, and storage durations. Results indicate that economies of scale significantly reduce geothermal LCOE as plant capacity increases, with large-scale systems (25-100 MW) achieving substantially lower costs than small plants. Hybridization with solar thermal energy and storage further improves economic performance by increasing capacity utilization and enabling flexible dispatch. In addition, thermal storage plays a critical role in reducing LCOE by maximizing geothermal, solar, and stored energy resources. In summary, the results from this project demonstrate that geothermal hybrid systems represent a promising alternative for increasing the energy conversion efficiency of geothermal technologies, contributing to the preservation of geothermal resources, and supporting the transition of geothermal plants from traditional baseload resources into flexible, resilient, and cost-competitive energy conversion technologies.

15 GEOTHERMAL ENERGY↗

NASA NTRS1979

Circuit for automatic load sharing in parallel converter modules

A nondissipative circuit for automatic load sharing in parallel converter modules having push-pull power transistors is presented. Each transistor has a separate current-sensing transformer and an impedance-adjusting transformer in series with its collector. The impedance-adjusting transformer functions as a current-controlled variable impedance that is responsive to the difference between the peak collector current of the transistor and the average peak current of all collector currents of power transistors in all modules, thereby to control the collector currents of all power transistors with reference to the average peak collector current.

Nagano, S.↗

DOE OSTI2017

Community Solar Value Project

The Community Solar Value Project (CSVP) is designed to assist electric utilities in designing better community solar programs. Better programs seek new sources of value to promote “win-win” solutions between utilities and their customers. The CSVP focused on five “challenge areas” in identifying new sources of value: - Strategic solar design for community solar projects (including technology choices, siting, orientation, and related issues) - Market research and targeted marketing approaches (for program design and for customer recruitment) - Procurement and financing (for establishing best practices that can bring economies of scale and economies of expertise) - Integration of “companion measures” (such as storage and demand-response options that can benefit customer and utility net load shapes) - Pricing in program design (including best practices for integration of identified value in program prices or credits) The CSVP directly engaged the Sacramento Municipal Utility District (SMUD), the Public Service Company of New Mexico (PNM), and more than a dozen other utilities to develop improved community solar program designs. The outcomes include a plan at SMUD for over 100 MW or more of community and shared solar and support for new or expanded programs at 15 other utilities so far. Resulting best-practice solutions have not only informed program applications, but also have generated discussion among experts and industry associations about the new opportunities and challenges CSVP has brought forth. In these ways, the CSVP has impacted community solar programs and DER plans, competitive innovations and policies nationwide. The CSVP team has been led by Extensible Energy under John Powers, President and CEO. Jill Cliburn, of Santa Fe, NM-based Cliburn and Associates, has served as Principal Investigator. The team also benefitted from expertise from Navigant, Olivine Inc. and Millennium Energy, LLC, in addition to the collaborative and cost-sharing contributions of its utility partners. The CSVP team participated fully in the Solar Market Pathways Program, which was initiated under the U.S. Department of Energy SunShot program and reports to the U.S. Department of Energy Solar Energy Technologies Office. This report summarizes a multi-disciplinary project that took place over 33 months from January, 2015 through September, 2017.

14 SOLAR ENERGY↗

DOE OSTI2017

Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel

Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have various degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons, while P. aeruginosa strain PAO1, a human pathogen, is less adapted and degrades jet fuel at a lower rate than does ATCC 33988. We investigated fuel-specific transcriptomic differences between these strains in order to ascertain the underlying mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat shock response, membrane proteins, efflux pumps, and several novel genes were upregulated in ATCC 33988. Overexpression of alk genes in PAO1 provided some improvement in growth, but it was not as robust as that of ATCC 33988, suggesting the role of other genes in adaptation. Expression of the function unknown gene PA5359 from ATCC 33988 in PAO1 increased the growth in fuel. Bioinformatic analysis revealed that PA5359 is a predicted lipoprotein with a conserved Yx(FWY)xxD motif, which is shared among bacterial adhesins. Overexpression of the putative resistance-nodulation-division (RND) efflux pump PA3521 to PA3523 increased the growth of the ATCC 33988 strain, suggesting a possible role in fuel tolerance. Interestingly, the PAO1 strain cannot utilize n -C 8 and n -C 10 . The expression of green fluorescent protein (GFP) under the control of alkB promoters confirmed that alk gene promoter polymorphism affects the expression of alk genes. Promoter fusion assays further confirmed that the regulation of alk genes was different in the two strains. Protein sequence analysis showed low amino acid differences for many of the upregulated genes, further supporting transcriptional control as the main mechanism for enhanced adaptation. Lastly, these results support that specific signal transduction, gene regulation, and coordination of multiple biological responses are required to improve the survival, growth, and metabolism of fuel in adapted strains. This study provides new insight into the mechanistic differences between strains and helpful information that may be applied in the improvement of bacterial strains for resistance to biotic and abiotic factors encountered during bioremediation and industrial biotechnological processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids

Abstract In planta, H2O2 is produced as a by-product of enzymatic reactions and during defense responses. Ascorbate peroxidase (APX) is a key enzyme involved in scavenging cytotoxic H2O2. Here, we report the crystal structure of cytosolic APX from sorghum (Sorghum bicolor) (Sobic.001G410200). While the overall structure of SbAPX was similar to that of other APXs, SbAPX uniquely displayed four bound ascorbates rather than one. In addition to the ɣ-heme pocket identified in other APXs, ascorbates were bound at the δ-meso and two solvent-exposed pockets. Consistent with the presence of multiple binding sites, our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Bound ascorbate at two surface sites established an intricate proton network with ascorbate at the ɣ-heme edge and δ-meso sites. Based on crystal structures, steady-state kinetics, and site-directed mutagenesis results, both ascorbate molecules at the ɣ-heme edge and the one at the surface are expected to participate in the oxidation reaction. We provide evidence that the H2O2-dependent oxidation of ascorbate by APX produces a C2-hydrated bicyclic hemiketal form of dehydroascorbic acid at the ɣ-heme edge, indicating two successive electron transfers from a single-bound ascorbate. In addition, the δ-meso site was shared with several organic compounds, including p-coumaric acid and other phenylpropanoids, for the potential radicalization reaction. Site-directed mutagenesis of the critical residue at the ɣ-heme edge (R172A) only partially reduced polymerization activity. Thus, APX removes stress-generated H2O2 with ascorbates, and also uses this same H2O2 to potentially fortify cell walls via oxidative polymerization of phenylpropanoids in response to stress.

Plant Sciences↗

DOE OSTI2011

Responses of soil cellulolytic fungal communities to elevated atmospheric CO2 are complex and variableacross five ecosystems

Elevated atmospheric CO(2) generally increases plant productivity and subsequently increases the availability of cellulose in soil to microbial decomposers. As key cellulose degraders, soil fungi are likely to be one of the most impacted and responsive microbial groups to elevated atmospheric CO(2) . To investigate the impacts of ecosystem type and elevated atmospheric CO(2) on cellulolytic fungal communities, we sequenced 10 677 cbhI gene fragments encoding the catalytic subunit of cellobiohydrolase I, across five distinct terrestrial ecosystem experiments after a decade of exposure to elevated CO(2) . The cbhI composition of each ecosystem was distinct, as supported by weighted Unifrac analyses (all P-values; < 0.001), with few operational taxonomic units (OTUs) being shared across ecosystems. Using a 114-member cbhI sequence database compiled from known fungi, less than 1% of the environmental sequences could be classified at the family level indicating that cellulolytic fungi in situ are likely dominated by novel fungi or known fungi that are not yet recognized as cellulose degraders. Shifts in fungal cbhI composition and richness that were correlated with elevated CO(2) exposure varied across the ecosystems. In aspen plantation and desert creosote bush soils, cbhI gene richness was significantly higher after exposure to elevated CO(2) (550 mol mol(-1) ) than under ambient CO(2) (360 mol mol(-1) CO(2) ). In contrast, while the richness was not altered, the relative abundance of dominant OTUs in desert soil crusts was significantly shifted. This suggests that responses are complex, vary across different ecosystems and, in at least one case, are OTU-specific. Collectively, our results document the complexity of cellulolytic fungal communities in multiple terrestrial ecosystems and the variability of their responses to long-term exposure to elevated atmospheric CO(2) .

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Constitutive and inducible oleoresin defenses share genetic architectures and mechanisms in Pinus taeda

The oleoresin defense system of loblolly pine (Pinus taeda) protects trees from insects and pathogens and is an important source of renewable biofuels and chemicals, but the genetic basis of oleoresin production is poorly understood. We characterized the genetic architecture of oleoresin flow, resin canal number, stem wood terpene content, and monoterpene composition in two clonal populations of P. taeda. We used quantitative genetic analyses, genome-wide association studies (GWASs), multiplex network learning, and gene expression profiling to elucidate shared gene networks underlying defense traits and to identify high-quality candidates for breeding and engineering loblolly pine. Genetic analyses revealed polygenic inheritance and trait-to-trait correlations provide strong evidence for shared genes regulating constitutive and induced oleoresin flow. We identified 236 single nucleotide polymorphisms associated with oleoresin flow, resin canal number, and terpene composition and highlight candidate genes likely involved in terpene biosynthesis, cambial meristem reprogramming, and pathogen perception and immune signaling. Fourteen GWAS candidates were methyl jasmonate-responsive in tissues where resin canals initiate and terpene production occurs. Integrating quantitative genetics, GWAS, gene expression, and multiplex network analyses enabled the prioritization of high-quality candidate genes. This work advances the development of more resilient loblolly pine optimized for ecological performance, renewable chemical, and biofuel production.

genome-wide association study↗

DOE OSTI2020

Understanding Interactive and Reproducible Computing With Jupyter Tools at Facilities

Increasingly Jupyter tools are being adopted and incorporated into High Performance Computing (HPC) and scientific user facilities. Adopting Jupyter tools enables more interactive and reproducible computational work at facilities across data life cycles. As the volume, variety, and scope of data grow, scientists need to be able to analyze and share results in user friendly ways. Human-centered research highlights design challenges around computational notebooks, and our qualitative user study shifts focus to better characterize how Jupyter tools are being used in HPC and science user facilities today. We conducted twenty-nine interviews, and obtained 103 survey responses from NERSC Jupyter users, to better understand the increasing role of interactive computing tools in DOE sponsored scientific work. We examine a range of issues that emerge using and supporting Jupyter in HPC ecosystems, including: how Jupyter is being used by scientists in HPC and user facility ecosystems; how facilities are purposefully supporting Jupyter in their ecosystems; feedback NERSC users have about the facility’s deployment, and, discuss features NERSC indicated would be helpful. We offer a variety of takeaways for staff supporting Jupyter at facilities, Project Jupyter and related open source communities, and funding agencies supporting interactive computing work.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Emulating the Android Boot Process

Critical vulnerabilities continue to be discovered in the boot process of Android smartphones used around the world. The entire device's security is compromised if boot security is compromised, so any weakness presents undue risk to users. Vulnerabilities persist, in part, because independent security analysts lack access and appropriate tools. In response to this gap, we implemented a procedure for emulating the early phase of the Android boot process. This work demonstrated feasibility and utility of emulation in this space. By using HALucinator, we derived execution context and data flow, as well as incorporated peripheral hardware behavior. While smartphones with shared processors have substantial code overlap regardless of vendor, generational changes can have a significant impact. By applying our approach to older and modern devices, we learned interesting characteristics about the system. Such capabilities introduce new levels of introspection and operation understanding not previously available to mobile researchers.

97 MATHEMATICS AND COMPUTING↗