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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Dimensional Control over Metal Halide Perovskite Crystallization Guided by Active Learning

Metal halide perovskite (MHP) derivatives, a promising class of optoelectronic materials, have been synthesized with a range of dimensionalities that govern their optoelectronic properties and determine their applications. We demonstrate a data-driven approach combining active learning and high-throughput experimentation to discover, control, and understand the formation of phases with different dimensionalities in the morpholinium (morph) lead iodide system. Using a robot-assisted workflow, we synthesized and characterized two novel MHP derivatives that have distinct optical properties: a one-dimensional (1D) morphPbI 3 phase ([C 4 H 10 NO][PbI 3 ]) and a two-dimensional (2D) (morph) 2 PbI 4 phase ([C 4 H 10 NO] 2 [PbI 4 ]). To efficiently acquire the data needed to construct a machine learning (ML) model of the reaction conditions where the 1D and 2D phases are formed, data acquisition was guided by a diverse-mini-batch-sampling active learning algorithm, using prediction confidence as a stopping criterion. Querying the ML model uncovered the reaction parameters that have the most significant effects on dimensionality control. Based on these insights, we discuss possible reaction schemes that may selectively promote the formation of morph-Pb-I phases with different dimensionalities. The data-driven approach presented here, including the use of additives to manipulate dimensionality, will be valuable for controlling the crystallization of a range of materials over large reaction-composition spaces.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Evaluating inkjet dispenser/liquid vortex capture-mass spectrometry for single-cell metabolomics in Hep G2 steatosis caused by tamoxifen

Single-cell mass spectrometry (MS) is advancing our understanding of metabolic pathways in heterogeneous cell populations; however, many techniques are slow or require disruptive sample preparations. This study evaluated coupling a modified HP D100 single-cell inkjet dispenser with liquid vortex capture-mass spectrometry (D100/LVC-MS). The D100 is a single-cell inkjet dispenser capable of titrating solutions and isolating single cells via disposable cassettes equipped with microfluidic channels and an impedance sensor. The LVC-MS enables high-throughput capture, lysis, and ionization of analytes for mass spectrometric analysis. The D100/LVC-MS system was characterized through titration and single-cell experiments. Propranolol titration demonstrated linearity across a broad concentration range using the D100/LVC-MS system. Additionally, Hep G2 hepatocarcinoma cells and Chlamydomonas reinhardtii algae were used to showcase the D100’s high-throughput or low-buffer-volume single-cell dispensing strategies. The D100/LVC-MS system’s performance was validated by evaluating tamoxifen-induced steatosis in Hep G2 cells. Tamoxifen, associated with nonalcoholic fatty liver disease in breast cancer patients following long-term use, was tested in Hep G2 cells at 20 µM for 72 h against DMSO-treated controls. High-throughput analysis of 500 cells per condition, completed in 25 min per run, demonstrated the system’s efficiency. The D100/LVC-MS system simultaneously quantified tamoxifen and measured triglycerides and phosphatidylcholines. Triglycerides were upregulated in the tamoxifen-treated cells and the results indicated two distinct cell populations, differing in tamoxifen and phosphatidylcholines levels, suggesting heterogeneity within the treated population. In conclusion, these findings highlight the D100/LVC-MS system as a cost-effective, high-throughput platform for single-cell metabolomics and lipidomics, with significant potential for evaluating metabolic alterations.

Chromatography↗
DOE OSTI2022

Silver Nanowire-Indium Zinc Oxide Composite Flexible Transparent Conducting Electrodes Made by Spin- coating and Photonic Curing

Realizing high-throughput, low-cost perovskite solar cell (PSC) manufacturing is highly sought-after in photovoltaic (PV) research in recent years. To fully achieve roll-to-roll (R2R) manufacturing of PSCs, it is important to consider the flexible transparent electrode (TE). PET/ITO is a commonly used substrate for making flexible PSCs. When optimizing transparent conducting materials, there is a tradeoff between sheet resistance (Rsh) and optical transparency. Because commercial PET/ITO substrates are made with slow (~1 m/min) vacuum deposition processes, they tend to be expensive. Therefore, it would be advantageous to develop a high-throughput, R2R compatible, solution-deposition approach for fabricating the TE on PET substrates. While various solution-deposition processes, such as blade coating or slot-die coating, can achieve the desired web speed of > 10 m/min, there is still a need to improve the post-deposition annealing step. One promising post-deposition processing technique is intense-pulsed-light processing, also known as photonic curing. Photonic curing delivers short (0.01 – 100 ms) pulses of broadband (200 – 1500 nm) light from a xenon flash lamp to the samples. Any materials in the sample stack that absorb light will convert the impinging light pulse into heat within the sample, which drives changes in the sample (calcination, phase change, crystallization, etc.). Photonic curing has three main advantages over thermal annealing: 1. Faster processing speed (milliseconds or seconds). 2. Compatibility with plastic substrates. 3. Smaller physical footprint and less wasted energy. Since the light pulses are on for a short time, the intensity can be high while the total energy delivered to the sample is low, minimizing damages to the plastic substrates. In this work, a hybrid TE material is fabricated on PET substrates using photonic curing. The hybrid TE material contains a layer of silver nanowires (AgNWs) and a layer of metal-oxide (InOx, ITO, IZO, etc.). The AgNWs increase the light absorbed by the film during the photonic curing process, which leads to higher processing temperatures, possibly improving the conversion of the metal-oxide layer. The AgNWs also enhance the electrical conductivity of the final TE layer after photonic curing. A AgNW and metal-oxide bilayer is formed by spin coating each solution onto the PET substrate sequentially followed by a single photonic curing process. We use average optical transmittance (Tavg) from 400 to 700 nm and average Rsh to evaluate the TE performance. The following photonic curing parameters are varied to optimize Tavg (maximize) and Rsh (minimize): Pulse voltage, pulse envelope, number of micro-pulses, duty cycle, number of pulses, and pulse repetition rate. Preliminarily, we also observe a significant impact on the TE properties by the volume of AgNW deposited during the spin coating deposition step. Using dispense volumes of 80 µL and 20 µL, we achieve samples with Tavg = 73%, Rsh = 19 Ω/sq, and roughness = 9 nm, and Tavg = 83%, Rsh = 58 Ω/sq, and roughness = 5.6 nm, respectively, after photonic curing.

14 SOLAR ENERGY↗
DOE OSTI2025

Discovery of an autoinhibited conformation in mesotrypsin reveals a strategy for selective serine protease inhibition

Selective inhibition of the more than 100 S1 family serine proteases is a long-standing challenge due to their active site similarity. Mesotrypsin, implicated in cancer progression, exemplifies these difficulties; no current inhibitors achieve selectivity over other human trypsins. We found an unexpected autoinhibited conformation of mesotrypsin via x-ray crystallography, revealing a cryptic pocket adjacent to the active site. Using high-throughput virtual screening targeting this cryptic pocket, we identified a conformationally selective small-molecule inhibitor that stabilizes the inactive state of mesotrypsin. This inhibitor demonstrates selectivity for mesotrypsin over other trypsins. Our findings challenge the accepted view of digestive trypsins as constitutively active enzymes lacking potential for allosteric regulation. Furthermore, analyses of other structures suggest that dynamic sampling of closed states with analogous allosteric cryptic pockets appears widespread among S1 serine proteases. These observations point to a potentially generalizable strategy to achieve selective inhibition, offering broad implications for drug development targeting serine proteases in cancer and other diseases.

Coban, Matt↗
DOE OSTI2024

Rapid and high-throughput determination of sorghum ( Sorghum bicolor ) biomass composition using near infrared spectroscopy and chemometrics

Compositional characterization of biomass is vital for the biofuel industry. Traditional wet chemistry-based methods for analyzing biomass composition are laborious, time-consuming, and require extensive use of chemical reagents as well as highly skilled personnel. In this study, near-infrared (NIR) spectroscopy was used to quickly assess the composition of above-ground vegetative biomass from 113 diverse, photoperiod-sensitive, biomass-type sorghum (Sorghum bicolor) accessions cultivated under field conditions in Central Illinois. Biomass samples were analyzed using NIR spectra collected in the spectral range of 867–2536 nm, with their chemical compositions determined following the National Renewable Energy Laboratory (NREL) protocol. Advanced spectral pre-treatment and band selection techniques were utilized to develop calibration models using partial least squares regression (PLSR). The models’ effectiveness was assessed through cross-validation and independent data tests. The predictions for moisture, ash, extractives, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin were accurate and reliable, demonstrating the capability of NIR spectroscopy to provide rapid and precise characterization of sorghum biomass. The results demonstrated that NIR spectroscopy is an efficient tool for rapidly characterizing sorghum biomass, making it a sustainable option for screening desirable feedstock for biofuel or bioproduct production.

09 BIOMASS FUELS↗
DOE OSTI2020

Site 300 B-851 Permit: Radiological Assumptions and Source Term - Air Dispersion Modeling for Radiological Dose Assessment

The following modeling assumptions and source term that is provided in the attachments to this document are meant to serve as a guide to the presentation delivered on April 23rd, 2020, to the San Joaquin Air District Permit Services slides. This analysis is in response to the District’s “Project Incompleteness Letter” (Facility Number: N-472 and Project Number: N-1173492) regarding the potential for depleted uranium (DU) to be resuspended from areas of contaminated soil at Site 300 as a result of high explosive (HE) experiments increased to a requested permitted maximum of 1,000 pound detonations with an annual HE throughput not to exceed 7,500 pounds per year. LLNL has taken every step in the radiological health risk concerns in the modeling assumptions and final source term to be at a level of maximum conservativeness. As an example, forty soil samples were taken in the B-851 area (LLNL-AR-738708 – 2018) and assayed for uranium-234, uranium-235, and uranium-238 concentrations. The maximum uranium soil concentrations were used in the assumptions (potential for resuspended dust occurring from detonation experiments) and not the use of median uranium soil concentrations – a more realistic outcome. Additionally, these uranium soil concentrations were considered to be at 100% uptake in the vegetation for prescribed burns; vegetation uptake factors were not used as that would lower the final source term. This level of conservativeness was maintained throughout the modeling assumptions.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2020

Development of Mischmetal–Fe–Co–B Permanent Magnet Alloys via High-Throughput Methods

Additive manufacturing synthesis using laser engineered net shaping (LENS) is utilized in this work to rapidly print libraries of mischmetal (MM = La, Ce, Nd, and Pr) containing R 2 TM 14 B alloys (R = MM + separated Nd and TM = Fe and Co) enabling robust evaluation of physical properties over a wide composition range. High-throughput characterization of the magnetic and thermal properties are used to identify compositions for potential high-temperature, high-performance permanent magnets with reduced critical rare-earth elements. Improved Curie temperature ( T c ~ 450 °C) is obtained with substitution of Fe by Co in pseudoternary R 2 TM 14 B alloys. Furthermore, a 4-fold decrease in the Nd content can be achieved through substitution with less critical Ce- and La-rich MM, while retaining high T c . Guided by the properties of the LENS printed samples, selected compositions with and without TiC additions are synthesized via melt-spinning techniques to produce nanostructured ribbons. The maximum room temperature coercivity ( H c ) and energy product ((BH) max ) without TiC are found to be 5.8 kOe, 8.5 MGOe, respectively, while TiC additions as a grain refiner gave H c and (BH) max of 4.9 kOe, 9.8 MGOe, respectively. Structural characterization of the melt-spun ribbons shows homogeneous grain refinement with TiC additions, which leads to an increase in the energy product.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Acoustic mapping by picosecond ultrasonics for elastic property measurement: Experimental demonstration on a TRISO fuel compact

Picosecond ultrasonics has been demonstrated on a tristructural isotropic (TRISO) fuel compact to measure the elastic properties of each compact layer. This technique utilizes an ultrashort pump laser pulse to excite vibrations in a gold transducer film covering the surface of each component and a second probe laser pulse to record the resulting acoustic strain induced change in optical reflectance. From the damping of this film vibration, the acoustic reflection coefficient, which couples the elastic properties of the transducer film and the sample, can be obtained, enabling a calculation of the sample’s acoustic velocity and elastic modulus. Overall, results obtained from this method are consistent with known values of elastic moduli, namely that the SiC coating is the stiffest component of the compact while the carbonaceous matrix is the most compliant. Nanoindentation was conducted as a benchmark technique on the same sample and shows satisfactory agreement with the results of picosecond ultrasonics. Compared to other methods like nanoindentation, picosecond ultrasonics is multimodal with a capability of measuring several key properties simultaneously and has potentials to be coupled into optical fibers for remote sensing. Thus, these demonstration measurements reveal the methodology to be a promising candidate for in-situ and high-throughput optical characterizations of nuclear materials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS2001

Ion Propulsion Technology Programs at NASA Glenn Research Center

As lead center for the agency in electric and ion propulsion, the NASA Glenn Research Center (GRC) is pursuing technology development in ion propulsion for a range of mission applications. The program goal is to develop key technologies for advanced NSTAR-derivative high-power ion propulsion, lightweight low power high-performance ion propulsion, 'micro' ion propulsion, and engine and component technologies for high-power electric propulsion for very ambitious missions. Products include: (1) a 5 kW, 400 kg throughput ion thruster and power processing technology; (2) extremely-lightweight high-efficiency sub-kilowatt ion thruster and power processor; (3) a 1-25 W high-specific impulse ion engine; and (4) engine and component technologies for high-power (30 kW class) ion and Hall engines. Identified applications include outer planetary science missions such as Europa orbiter/lander, Comet Nucleus Sample Return mission, Titan Explorer, Neptune/Triton, Pluto-Kuiper Belt Objects Mission, various second generation interplanetary Micro spacecraft, and the Interstellar Probe Mission. Additional information is contained in the original extended abstract.

Patterson, M. J.↗
NASA NTRSDate not supplied

Space Flown Rodent Liver RNA Sequencing Data for Machine Learning in Space Biology Research

High-throughput nucleic acid sequencing (DNA-seq, RNA-seq) has become widespread in biomedical research due to the growing availability and affordability of these assays. Data analysis has been accelerated in recent years by the adoption of artificial intelligence (AI) and machine learning (ML) techniques by biomedical researchers. In space biology research, RNAseq datasets from space-flown experimental samples are critical for characterizing the gene expression aberrations associated with exposure to spaceflight stressors. However, space biological experiments tend to be very low sample size, so identifying proper AI/ML algorithms for sequencing data analysis is an ongoing challenge since these algorithms typically require large sample size. The NASA Science Mission Directorate (SMD) has started the “Benchmark Initiative for AI/ML”, focused on creating datasets meant for three main applications: 1) scientific benchmarking, which finds the best algorithm for a specific problem; 2) application benchmarking, which measures algorithm performance against a set of parameters; and 3) system benchmarking, which evaluates performance of hardware and software architecture. These scientific benchmarks consist of an AI-ready dataset and a reference implementation on a specific scientific question. In this work, we focused on generating standardized datasets to allow the scientific community to benchmark AI/ML algorithms in the domain of space biology. We present here a standardized, AI-ready, publicly available benchmark dataset for space biology RNA-seq data as a collaboration between the NASA AI4LS (Artificial Intelligence for Life Sciences) working group. and NASA’s SMD. This dataset consists of space-flown and ground control mouse liver found in the NASA GeneLab omics database. However, to amplify the small sample number (n=112 samples) for ML purposes, we employ Gaussian noise and a generative adversarial network to extend this dataset to 6,000 synthetic samples, matching the original gene expression characteristics.

James Casaletto↗
DOE OSTI2025

A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this “Fast-Pass” DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ~40 s per sample. This Fast-Pass strategy was implemented in the analysis of genetically edited Escherichia coli strains that have been engineered to produce various free-fatty acids (FFAs) for applications relevant to biofuels. Due to the untargeted nature of DESI-MSI, the investigation of these strains yielded molecular information for both global metabolites and targeted detection of accumulated bioproducts, allowing simultaneous readouts of strain-specific chemical profiles and comparative measurements of FFA production levels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A novel statistical methodology for quantifying the spatial arrangements of axons in peripheral nerves

A thorough understanding of the neuroanatomy of peripheral nerves is required for a better insight into their function and the development of neuromodulation tools and strategies. In biophysical modeling, it is commonly assumed that the complex spatial arrangement of myelinated and unmyelinated axons in peripheral nerves is random, however, in reality the axonal organization is inhomogeneous and anisotropic. Present quantitative neuroanatomy methods analyze peripheral nerves in terms of the number of axons and the morphometric characteristics of the axons, such as area and diameter. In this study, we employed spatial statistics and point process models to describe the spatial arrangement of axons and Sinkhorn distances to compute the similarities between these arrangements (in terms of first- and second-order statistics) in various vagus and pelvic nerve cross-sections. We utilized high-resolution transmission electron microscopy (TEM) images that have been segmented using a custom-built high-throughput deep learning system based on a highly modified U-Net architecture. Our findings show a novel and innovative approach to quantifying similarities between spatial point patterns using metrics derived from the solution to the optimal transport problem. We also present a generalizable pipeline for quantitative analysis of peripheral nerve architecture. Our data demonstrate differences between male- and female-originating samples and similarities between the pelvic and abdominal vagus nerves.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

A Formal Messaging Notation for Alaskan Aviation Data

Data exchange is an increasingly important aspect of the National Airspace System. While many data communication channels have become more capable of sending and receiving data at higher throughput rates, there is still a need to use communication channels efficiently with limited throughput. The limitation can be based on technological issues, financial considerations, or both. This paper provides a complete description of several important aviation weather data in Abstract Syntax Notation format. By doing so, data providers can take advantage of Abstract Syntax Notation's ability to encode data in a highly compressed format. When data such as pilot weather reports, surface weather observations, and various weather predictions are compressed in such a manner, it allows for the efficient use of throughput-limited communication channels. This paper provides details on the Abstract Syntax Notation One (ASN.1) implementation for Alaskan aviation data, and demonstrates its use on real-world aviation weather data samples as Alaska has sparse terrestrial data infrastructure and data are often sent via relatively costly satellite channels.

communications↗
NASA NTRS2008

Informatics and High Throughput Screening of Thermophysical Properties

The combination of computer-aided experiments with computational modeling enables a new class of powerful tools for materials research. A non-contact method for measuring density, thermal expansion, and creep of undercooled and high-temperature materials has been developed, using electrostatic levitation and optical diagnostics, including digital video. These experiments were designed to take advantage of the large volume of data (many gigabytes/experiment, terabytes/campaign) to gain additional information about the samples. For example, using sub-pixel interpolation to measure about 1000 vectors per image of the sample's surface allows the density of an axisymmetric sample to be determined to an accuracy of about 200 ppm (0.02%). A similar analysis applied to the surface shape of a rapidly rotating sample is combined with finite element modeling to determine the stress-dependence of creep in the sample in a single test. Details of the methods for both the computer-aided experiments and computational models will be discussed.

Hyers, Robert W.↗
DOE OSTI2025

An In Situ , Automated High-Explosives Aging Method Utilizing Two-Dimensional Gas Chromatography–Mass Spectrometry

Understanding chemical changes that occur in high explosives as they age is of great importance to the safe employment and storage of these compounds. Traditional methods of aging high explosives even under accelerated aging conditions are time intensive with durations on the order of months to years. The nature of traditional aging analyses reduces each sample to a snapshot data point often separated widely in time, requiring many assumptions as to how the degradation products develop. Further complicating matters, several analytical techniques are typically employed for each sample analysis in order to ascertain an entire picture of the decomposition pathways. To address these shortcomings with existing methods, a new method of accelerated aging of high explosives utilizing comprehensive two-dimensional gas chromatography coupled to high-resolution mass spectrometry (GC × GC-HRMS) was developed using 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) as a model compound for method development. This in situ automated method reduces the time scale of aging to a matter of hours using the inlet of the GC × GC as the aging vessel. GC × GC in combination with HRMS allowed for the collection of both evolved gases and other decomposition products produced during the entire aging process in real time with HRMS providing far greater certainty in identification of explosives aging products. Additionally, this method allowed for a higher throughput of samples with greatly simplified sample preparation. Chemometric analysis of the GC × GC-HRMS data set via the alteration analysis (ALA) enabled discovery of statistically significant chemical changes providing insight into the variation of decomposition pathways with varying aging temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

High-throughput characterization, correlation, and mapping of leaf photosynthetic and functional traits in the soybean ( Glycine max ) nested association mapping population

We report photosynthesis is a key target to improve crop production in many species including soybean [Glycine max (L.) Merr.]. A challenge is that phenotyping photosynthetic traits by traditional approaches is slow and destructive. There is proof-of-concept for leaf hyperspectral reflectance as a rapid method to model photosynthetic traits. However, the crucial step of demonstrating that hyperspectral approaches can be used to advance understanding of the genetic architecture of photosynthetic traits is untested. To address this challenge, we used full-range (500–2,400 nm) leaf reflectance spectroscopy to build partial least squares regression models to estimate leaf traits, including the rate-limiting processes of photosynthesis, maximum Rubisco carboxylation rate, and maximum electron transport. In total, 11 models were produced from a diverse population of soybean sampled over multiple field seasons to estimate photosynthetic parameters, chlorophyll content, leaf carbon and leaf nitrogen percentage, and specific leaf area (with R 2 from 0.56 to 0.96 and root mean square error approximately <10% of the range of calibration data). We explore the utility of these models by applying them to the soybean nested association mapping population, which showed variability in photosynthetic and leaf traits. Genetic mapping provided insights into the underlying genetic architecture of photosynthetic traits and potential improvement in soybean. Notably, the maximum Rubisco carboxylation rate mapped to a region of chromosome 19 containing genes encoding multiple small subunits of Rubisco. We also mapped the maximum electron transport rate to a region of chromosome 10 containing a fructose 1,6-bisphosphatase gene, encoding an important enzyme in the regeneration of ribulose 1,5-bisphosphate and the sucrose biosynthetic pathway. The estimated rate-limiting steps of photosynthesis were low or negatively correlated with yield suggesting that these traits are not influenced by the same genetic mechanisms and are not limiting yield in the soybean NAM population. Leaf carbon percentage, leaf nitrogen percentage, and specific leaf area showed strong correlations with yield and may be of interest in breeding programs as a proxy for yield. This work is among the first to use hyperspectral reflectance to model and map the genetic architecture of the rate-limiting steps of photosynthesis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Enzymatic cleavage of model lignin dimers depends on pH, enzyme, and bond type

Lignin is composed of phenylpropanoid monomers linked by ether and carbon-carbon bonds to form a complex heterogeneous structure. Bond-specific studies of lignin-modifying enzymes (LMEs; e.g., laccases and peroxidases) are limited by the polymerization of model lignin substrates and repolymerization of cleavage products. Here we present a high throughput platform to screen LME activities on four tagged model lignin compounds that represent the β-O-4’, β-β’, 5–5’, and 4-O-5’ linkages in lignin. We utilized nanostructure-initiator mass spectrometry (NIMS) and model lignin compounds with tags containing perfluorinated and cationic moieties, which effectively limit polymerization and condensation of the substrates and their degrading products. Sub-microliter sample droplets were printed on the NIMS chip with a novel robotics method. This rapid platform enabled characterization of LMEs across a range of pH 3–10 and relative quantification of modified (typically oxidized), cleaved, and polymerized products. All tested enzymes oxidized the four substrates and cleaved the β-O-4’ and β-β’ substrates to monomeric products. We discovered that the active pH range depended on both the substrate and the enzyme type. This has important applications for biomass conversion to biofuels and bioproducts, where the relative percentages of different bond types in lignin varies depending on feedstock and chemical pretreatment methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Abstract Background Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Results Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Conclusions Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.

54 ENVIRONMENTAL SCIENCES↗