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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Quenching-Induced Defects Liberate the Latent Reversible Capacity of Lithium Titanate Anode

Interest in defect engineering for lithium-ion battery (LIB) materials is sparked by its ability to tailor electrical conductivity and introduce extra active sites for electrochemical reactions. However, harvesting excessive intrinsic defects in the bulk of the electrodes rather than near their surface remains a long-standing challenge. Here, a versatile strategy of quenching is demonstrated, which is exercised in lithium titanate (Li 4 Ti 5 O 12 , LTO), a renowned anode for LIBs, to achieve off-stoichiometry in the interior region. In situ synchrotron analysis and atomic-resolution microscopy reveal the enriched oxygen vacancies and cation redistribution after ice-water quenching, which can facilitate the native unextractable Li ions to participate in reversible cycling. Further, the fabricated LTO anode delivers a sustained capacity of 202 mAh g -1 in the 1.0–2.5 V range with excellent rate capability and overcomes the poor cycling stability seen in conventional defective electrodes. The feasibility of tuning the degree of structural defectiveness via quenching agents is also proven, which can open up an intriguing avenue of research to harness the intrinsic defects for improving the energy density of rechargeable batteries.

25 ENERGY STORAGE↗
DOE OSTI2023

Mass spectrometry and spectroscopic characterization of a tetrameric photosystem I supercomplex from Leptolyngbya ohadii , a desiccation-tolerant cyanobacterium

Cyanobacteria inhabiting desert biological soil crusts face the harsh conditions of the desert. They evolved a suite of strategies toward desiccation-hydration cycles mixed with high light irradiations, etc. In this study we purified and characterized the structure and function of Photosystem I (PSI) from Leptolyngbya ohadii, a desiccation-tolerant desert cyanobacterium. We discovered that PSI forms tetrameric (PSI-Tet) aggregate. We investigated it by using sucrose density gradient centrifugation, clear native PAGE, high performance liquid chromatography, mass spectrometry (MS), time-resolved fluorescence (TRF) and time-resolved transient absorption (TA) spectroscopy. MS analysis identified the presence of two PsaB and two PsaL proteins in PSI-Tet and uniquely revealed that PsaLs are N-terminally acetylated in contrast to non-modified PsaL in the trimeric PSI from Synechocystis sp. PCC 6803. Chlorophyll (Chl) a fluorescence decay profiles of the PSI-Tet performed at 77 K revealed two emission bands at ∼690 nm and 725 nm with the former appearing only at early delay time. The main fluorescence emission peak, associated with emission from the low energy Chls a, decays within a few nanoseconds. TA studies demonstrated that the 725 nm emission band is associated with low energy Chls a with absorption band clearly resolved at ∼710 nm at 77 K. As a result, our work suggests that the heterogenous composition of PsaBs and PsaL in PSI-Tet is related with the adaptation mechanisms needed to cope with stressful conditions under which this bacterium naturally grows.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2018

Portable Electron Microscopy for ISS and Beyond

Advances in space exploration have evolved in lockstep with key technology advances in diverse fields such as materials science, biological science, and engineering risk management. Research in these areas, where structure and physical processes come together, can proceed rapidly in part due to sophisticated ground-based analytical tools that help re-searchers develop technologies and engineering processes that push frontiers of human space exploration. Electron microscopes (EM) are an example of such a workhorse tool, lending a unique blend of strong optical scattering, high native resolution, large depth of focus, and spectroscopy via characteristic X-ray emission, providing exquisite high-magnification structural imaging and chemical analysis. Ground-based EM’s have been essential in NASA research for many years. In particular, in mineralogy and petrology, EM is used to understand the origin and evolution of the solar system, particularly rocky bodies. In microbiology, EM has helped visualize the architecture of tissues and cells. In engineering/materials science, EM has been used to characterize particulate debris in air and water samples, determine pore sizes in ceramics/catalysts, understand the nature of fibers, determine composition and morphology of new and existing materials, and characterize micro-textures of vapor deposited films. EM is highly effective at investigating a wide variety of nanoscale materials/biomaterials at the core of many of NASA’s inquiries. Despite exquisite optical performance and versatility, EM’s are traditionally large, heavy, and have high power consumption. They are also expensive so they tend to be housed at universities and large research institutions, or at major industrial laboratory sites with support staff, supplies, and skilled operators. Since most organizations cannot support their own EM, samples are often sent to these large institutions and service centers to be imaged, at great expense and of-ten with delay of weeks to months for complex analyses. Complexity, high cost, and maintenance associated with collecting EM image data has until now severely limited fields in which EM is used. Making EM accessible outside constrained terrestrial laboratory environments will bring EM’s performance and versatility to a much broader range of scientific and engineering endeavors, including in space.

Own, C. S.↗
DOE OSTI2024

Bias Corrected NOAA HRRR Wind Resource Data for Grid Integration Applications

To address the need for regularly updated wind resource data, NREL has processed the High-Resolution Rapid Refresh (HRRR) outputs for use in grid integration modeling. The HRRR is an hourly-updated operational forecast product produced by the National Oceanic and Atmospheric Administration (NOAA) (Dowell et al., 2022). Several barriers have prevented the HRRR's widespread proliferation in the wind energy industry: missing timesteps (prior to 2019), challenging file format for wind energy analysis, limited vertical height resolution, and negative bias versus legacy WIND Toolkit data (2007-2013). NREL has applied re-gridding, interpolation, and bias-correction to the native HRRR data to overcome these limitations. This results in the now-publicly-available bias corrected and interpolated HRRR (BC-HRRR) dataset for weather years 2015 to 2023. Bias correction is necessary for wind resource consistency across weather years to be used simultaneously in planning-focused grid integration studies alongside the original WIND Toolkit data. We show that quantile mapping with the WIND Toolkit as a historical baseline is an effective method for bias correcting the interpolated HRRR data: the BC-HRRR has reduced mean bias versus comparable gridded wind resource datasets (+0.12 m/s versus Vortex) and has very low mean bias versus ground measurement stations (+0.01 m/s) (Buster et al., 2024). BC-HRRR's consistency with the legacy WIND Toolkit allows NREL to extend grid integration analysis to 15+ weather years of wind data with low-overhead extensibility to future years as they are made available by NOAA. As with historical datasets like the WIND Toolkit, BC-HRRR is intended for use in grid integration modeling (e.g., capacity expansion, production cost, and resource adequacy modeling) both independently and alongside the legacy WIND Toolkit.

Array↗
NASA NTRS2008

Modern Era Retrospective Restrospective-Analysis for Research and Applications (MERRA) Data and Services at the GES DISC

The Modern Era Retrospective-analysis for Research and Applications (MERRA) dataset is a NASA satellite era, 30 year (1979 - present), reanalysis using the Goddard Earth Observing System Data Assimilation System, Version 5 (GEOS-5). The project, run out of NASA's Global Modeling and Assimilation Office at Goddard Space Flight Center, provides the science and application communities with a state-of-the-art global analysis with emphasis on improved estimates of the hydrological cycle over a broad range of weather and climate time scales. MERRA products are generated as a long-term synthesis that places the NASA EOS suite of observations in a climate context. The MERRA analysis is performed at a horizontal resolution of 2/3 longitude x 1/2 latitude (540x361 global gridpoints) with observational analyses every 6 hours. The MERRA output data will include 3 dimensional state fields for every 6 hourly analysis cycle on 42 pressure levels (or 72 terrain following model coordinate levels) from the surface through the stratosphere. Several data products are specifically designed to support chemistry and stratosphere transport modeling. The 2 dimensional surface and atmospheric diagnostics (numbering 259) are being stored on the native grid at 1 hourly intervals. These include radiation and vertical integrals of the atmosphere for water and energy budget studies and also surface diagnostics where the diurnal cycle is important. The one hourly surface and near surface data product will also facilitate research on the integrated analysis of Earth system observations in the land, ocean and cryosphere. The MERRA products are archived and distributed by the Goddard Earth Sciences Data and Information Services Center (GES DISC) through its Modeling DISC Web (MDISC) portal. Multiple data access methods and services are available for MERRA data through MDISC: (1) Mirador offers a quick, comprehensive search of MERRA and all GES DISC archived data holdings, allowing searches on keywords, location names or latitude/longitude box, and date/time, with responses within a few seconds. (2) Giovanni is a GES DISC developed Web application that provides data visualization and analysis online. Giovanni features popular visualizations such as latitude-longitude maps, animations, cross sections, profiles, time series, etc. and some basic statistical analysis functions such as scatter plots and correlation coefficient maps. Users are able to download results in several different formats, including Google Earth. (3) On-the-fly parameter subsetting of data within a spatial/temporal window is provided through a simple select and click Web page. (4) MERRA data are also available via OPeNDAP, GrADS Data Server (GDS) and can be converted to netCDF on the fly.

Berrick, Stephen W.↗
DOE OSTI2023

Techno-Economic Analysis of a Microgrid System for Rural Communities in the United States

Access to running water has been a pressing issue in many developing countries across the globe, and also continues to be a problem in some rural areas in the United States. Today, more than two million Americans living in rural areas lack access to basic water supply and infrastructure. Rural communities tend to be located in environmentally fragile areas with poor economic conditions, making access to appropriate, low-cost technology for clean water supply and sanitation more challenging. In addition, many of the water resources located in these areas are being jeopardized by climate change in recent years. This research proposes a photovoltaic (PV)-battery microgrid system for powering water pumps in off-grid areas in an effort to identify economically and technologically feasible solution to the problems. Utilizing the HOMER Pro software, developed by the U.S. National Renewable Energy Laboratory (NREL), the case of the Navajo Nation is examined by analyzing the effects of this region's air temperature on the life and performance of battery storage and the economics of the proposed microgrid system.

battery↗
DOE OSTI2024

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

36 MATERIALS SCIENCE↗
DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Characterization of the Mechanical Trash Compactor Bag Removal Force

Managing trash accumulation is a critical challenge in human space explorations since the trash volume and mass can significantly influence launch cost and operational efficiency. This study aids the development of a Mechanical Trash Compactor (Mpactor) by testing the removal force required to remove a “trash bag” from the Mpactor. To do this, a Pneumatic Pressure Mandrel System was designed to simulate the normal force trash would exerts on the trash bag and subsequently the sidewalls of the Mpactor. For various levels of sidewall normal force, the removal force required to remove the simulated trash bag from the Mpactor compaction chamber was measured. This testing is used to identify optimal bag materials. Additionally, testing was done on both the native stainless steel walls of the compaction chamber as well as the walls after being Teflon lined. Split-plot ANOVA, simple main effects analysis, Holm’s post hoc comparisons for interaction, and sensitivity analyses were conducted to assess the influence of trash bag and sidewall materials on the required removal force. It was found that Teflon reduced the force required to remove the trash bag as well as reduced material-dependent variation in removal force. Testing showed that Teflon reduced the required removal force with a Polyvinylidene Fluoride , an unidentified Ethylene acrylate - Low Density Polyethylene copolymer, and a Polyvinyl Chloride all requiring significantly less removal force than the other materials tested.

pressure mandrel↗
DOE OSTI2021

X-composer: enabling cross-environments in-situ workflows between HPC and cloud

As large-scale scientific simulations and big data analyses become more popular, it is increasingly more expensive to store huge amounts of raw simulation results to perform post-analysis. To minimize the expensive data I/O, "in-situ" analysis is a promising approach, where data analysis applications analyze the simulation generated data on the fly without storing it first. However, it is challenging to organize, transform, and transport data at scales between two semantically different ecosystems due to the distinct software and hardware difference. To tackle these challenges, we design and implement the X-Composer framework. X-Composer connects cross-ecosystem applications to form an "in-situ" scientific workflow, and provides a unified approach and recipe for supporting such hybrid in-situ workflows on distributed heterogeneous resources. X-Composer reorganizes simulation data as continuous data streams and feeds them seamlessly into the Cloud-based stream processing services to minimize I/O overheads. For evaluation, we use X-Composer to set up and execute a cross-ecosystem workflow, which consists of a parallel Computational Fluid Dynamics simulation running on HPC, and a distributed Dynamic Mode Decomposition analysis application running on Cloud. Our experimental results show that X-Composer can seamlessly couple HPC and Big Data jobs in their own native environments, achieve good scalability, and provide high-fidelity analytics for ongoing simulations in real-time.

Wang, Dali↗
DOE OSTI2023

GPU-resident sparse direct linear solvers for alternating current optimal power flow analysis

Integrating renewable resources within the transmission grid at a wide scale poses significant challenges for economic dispatch as it requires analysis with more optimization parameters, constraints, and sources of uncertainty. This motivates the investigation of more efficient computational methods, especially those for solving the underlying linear systems, which typically take more than half of the overall computation time. In this paper, we present our work on sparse linear solvers that take advantage of hardware accelerators, such as graphical processing units (GPUs), and improve the overall performance when used within economic dispatch computations. We treat the problems as sparse, which allows for faster execution but also makes the implementation of numerical methods more challenging. We present the first GPU-native sparse direct solver that can execute on both AMD and NVIDIA GPUs. We demonstrate significant performance improvements when using high-performance linear solvers within alternating current optimal power flow (ACOPF) analysis. Furthermore, we demonstrate the feasibility of getting significant performance improvements by executing the entire computation on GPU-based hardware. Finally, we identify outstanding research issues and opportunities for even better utilization of heterogeneous systems, including those equipped with GPUs.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Cytochrome P450–catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass ( Panicum virgatum L.)

Specialized diterpenoid metabolites are important mediators of plant-environment interactions in monocot crops. To understand metabolite functions in plant environmental adaptation that ultimately can enable crop improvement strategies, a deeper knowledge of the underlying species-specific biosynthetic pathways is required. Furthermore, we report the genomics-enabled discovery of five cytochrome P450 monooxygenases (CYP71Z25-CYP71Z29) that form previously unknown furanoditerpenoids in the monocot bioenergy crop Panicum virgatum (switchgrass). Combinatorial pathway reconstruction showed that CYP71Z25-CYP71Z29 catalyze furan ring addition directly to primary diterpene alcohol intermediates derived from distinct class II diterpene synthase products. Transcriptional co-expression patterns and the presence of select diterpenoids in switchgrass roots support the occurrence of P450-derived furanoditerpenoids in planta. Integrating molecular dynamics, structural analysis and targeted mutagenesis identified active site determinants that contribute to the distinct catalytic specificities underlying the broad substrate promiscuity of CYP71Z25-CYP71Z29 for native and non-native diterpenoids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Comparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomass

Abstract Background Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals. Results The authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed. Conclusions This work demonstrates that different methods using chemical, thermal, and non-destructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.

09 BIOMASS FUELS↗
DOE OSTI2024

Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire

The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.

Microbiology↗
NASA NTRS1990

Use of high-dimensional spectral data to evaluate organic matter, reflectance relationships in soils

Recent breakthroughs in remote sensing technology have led to the development of a spaceborne high spectral resolution imaging sensor, HIRIS, to be launched in the mid-1990s for observation of earth surface features. The effects of organic carbon content on soil reflectance over the spectral range of HIRIS, and to examine the contributions of humic and fulvic acid fractions to soil reflectance was evaluated. Organic matter from four Indiana agricultural soils was extracted, fractionated, and purified, and six individual components of each soil were isolated and prepared for spectral analysis. The four soils, ranging in organic carbon content from 0.99 percent, represented various combinations of genetic parameters such as parent material, age, drainage, and native vegetation. An experimental procedure was developed to measure reflectance of very small soil and organic component samples in the laboratory, simulating the spectral coverage and resolution of the HIRIS sensor. Reflectance in 210 narrow (10 nm) bands was measured using the CARY 17D spectrophotometer over the 400 to 2500 nm wavelength range. Reflectance data were analyzed statistically to determine the regions of the reflective spectrum which provided useful information about soil organic matter content and composition. Wavebands providing significant information about soil organic carbon content were located in all three major regions of the reflective spectrum: visible, near infrared, and middle infrared. The purified humic acid fractions of the four soils were separable in six bands in the 1600 to 2400 nm range, suggesting that longwave middle infrared reflectance may be useful as a non-destructive laboratory technique for humic acid characterization.

Henderson, T. L.↗
NASA NTRS2020

Near 40 Years MERRA-2 Data at NASA GES DISC -Opportunity and Challenge to Support Extremes Study

To the end of 2019, 40 years NASA climate reanalysis data sets from the Modern Era Retrospective-analysis for Research and Applications, Version 2 (MERRA-2) will be available at NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). MERRA-2 consists atmosphere, land, and ocean data, which may be used for the studies ranging from the short scale weather events to the large scale decadal vulnerabilities. The hourly products, such as precipitation, soil moisture, temperature, and aerosols etc., have been used widely to study extreme events.In supporting users from broad communities, GES DISC have developed various data access services, including subsetter for downloading only data of interest with preferred format; OPeNDAP - for machine-to-machine data access; and Giovanni- for online visualization and analysis, etc. A big challenge for extreme study is to downloading and processing long-term hourly or daily data. The data downloading performance is not very satisfied by many users with current services and the native archived data structure. Late June 2019, many people in Europe had experienced extreme heat waves. The temperatures in several countries exceeded 40°C (104°F). For example, MERRA-2 shows that the near surface daily maximum temperature of June 28 2019 over Marseille, a city in southern France, reached 41.1 °C (106°F), which is the record breaking temperature in the last 40 years. GES DISC is working together with domain science experts to improve the performance of long time series access, making analysis ready data sets in supporting application researches, such as extreme study. In this presentation, using Europe heat wave as an example, we will show prototype of the in developing service for finding extremes from near 40 years MERRA-2 data at a given location. MERRA-2 data can be accessed from NASA GES DISC(https://disc.gsfc.nasa.gov/ ) by search keyword "MERRA-2".

Shen, Suhung↗
DOE OSTI2022

A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanism-guided engineering of a minimal biological particle for genome editing

The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered virally derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication proteins in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here, we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs and demonstrated increased editing in cell lines and therapeutically relevant primary human T cells. These results show that virally derived particles can be streamlined to create efficacious genome editing delivery vehicles with simpler production and manufacturing.

59 BASIC BIOLOGICAL SCIENCES↗