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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Precursor-Dependent Routing of Aromatic Amino Acids Determines Lignin Structure in Grasses by Sensitivity-Enhanced Solid-State NMR

Lignin biosynthesis in grasses exhibits unique metabolic flexibility, yet the precursor-specific routing of carbon into lignin polymers remains poorly resolved in planta. Here, we combine 13 C-isotope labeling with solid-state NMR under sensitivity-enhancement by dynamic nuclear polarization (DNP), to directly track phenylalanine- and tyrosine-derived carbon incorporation into the lignin polymer in Brachypodium distachyon. Precursor-specific 13 C labeling reveals that phenylalanine is the dominant contributor to canonical guaiacyl and syringyl lignins, whereas tyrosine preferentially enriches hydroxyphenyl lignin and hydroxycinnamates, including ferulates characteristic of grass cell walls. Two-dimensional 13 C− 13 C correlation NMR resolves distinct lignin moieties arising from each precursor. Disruption of pcoumarate 3-hydroxylase (C3H) selectively impairs phenylalanine-derived lignification, while tyrosine-derived lignin remains comparatively unchanged, maintaining polymer assembly through alternative metabolic routes. These findings show precursordependent control of lignin composition and reveal tyrosine-mediated lignification as a compensatory pathway in grasses. This work also establishes precursor-resolved solid-state NMR and DNP as a powerful framework for dissecting lignin biosynthesis and metabolic plasticity in plant cell walls.

Biopolymers↗
DOE OSTI2024

Narrowing lab–to–market gaps: Device innovations in fuel generation, solar–cell, and photodetection

Academic translational research efforts to industry are often an underlying sought–after goal among various researchers. Through the interchanges of research endeavors between academia–industry, great innovations can/has been achieved that cater to the real–world application by bridging “industrially relevant” problem solving with pursuing fundamental studies. It is pertinent that most of the studies from university–level research works may not translate into demonstrable market products due to various reasons. Funding support, individual researcher goals, socioeconomic factors, and most importantly the technical know–how of generating revenue strategies for startups, are a few of the factors that have slowed the pace of collaborative efforts. However, we believe that the most crucial component is the identification of the critical parameters that solve long–standing problems that hinder the scale–up of the lab scale research into marketable products considering the techno–economic analysis. Here, to illustrate this, we take the three most relevant examples of devices for fuel generation, devices to utilize solar radiation, and devices for detection and other related applications. In this perspective, we provide an in–depth case study of each of these critical parameters to comment on the direction of research avenues that can serve as step–stones for the commercialization of university–level lab research studies.

42 ENGINEERING↗
DOE OSTI2023

Solvent-Mediated Formation of Quasi-2D Dion-Jacobson Phases on 3D Perovskites for Inverted Solar Cells Over 23% Efficiency

2D-on-3D (2D/3D) perovskite heterostructures present a promising strategy to realize efficient and stable photovoltaics. However, their applicability in inverted solar cells is limited due to the quantum confinement of the 2D-layer and solvent incompatibilities that disrupt the underlying 3D layer, hampering electron transport at the 2D/3D interface. Herein, solvent-dependent formation dynamics and structural evolution of 2D/3D heterostructures are investigated via in situ X-ray scattering. In this study, it is revealed that solvent interaction with the 3D surface determines the formation sequence and spatial distribution of quasi-2D phases with n = 2–4. Isopropanol (IPA) reconstructs the perovskite into a PbI 2 -rich surface, forming a strata with smaller n first, followed by a thinner substratum of larger n. In contrast, 2,2,2-Trifluoroethanol (TFE) preserves the 3D surface, promoting the formation of uniformly distributed larger n domains first, and smaller n last. Leveraging these insights, Dion–Jacobson perovskites are used with superior charge transport properties and structural robustness to fabricate 2D/3D heterostructures dominated by n ≥ 3 and engineer a favorable energy landscape for electron tunneling. Inverted solar cells based on 3-Aminomethylpyridine and TFE achieve a champion efficiency of 23.60%, with V oc and FF of 1.19 V and 84.5%, respectively, and superior stabilities with t 94 of 960 h under thermal stress.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Altered post-fracture systemic bone loss in a mouse model of osteocyte dysfunction

Femur fracture leads to loss of bone at uninjured skeletal sites, which may increase risk of subsequent fracture. Osteocytes, the most abundant bone cells, can directly resorb bone matrix and regulate osteoclast and osteoblast activity, but their role in systemic bone loss after fracture remains poorly understood. In this study we used a transgenic (TG+) mouse model that overexpresses human B-cell lymphoma 2 (BCL-2) in osteoblasts and osteocytes. This causes enhanced osteoblast proliferation, followed by disruption in lacunar-canalicular connectivity and massive osteocyte death by 10 wk of age. We hypothesized that reduced viable osteocyte density would decrease the magnitude of systemic bone loss after femur fracture, reduce perilacunar remodeling, and alter callus formation. Bone remodeling was assessed using serum biomarkers of bone formation and resorption at 5 d post-fracture. We used micro-computed tomography, high resolution x-ray microscopy, mechanical testing, and Raman spectroscopy to quantify the magnitude of systemic bone loss, as well as changes in osteocyte lacunar volume, bone strength, and bone composition 2 wk post-fracture. Fracture was associated with a reduction in circulating markers of bone resorption in non-transgenic (TG-) animals. TG+ mice exhibited high bone mass in the limbs, greater cortical elastic modulus and reduced post-yield displacement. After fracture, TG+ mice lost less trabecular bone than TG- mice, but conversely TG+ mice exhibited trends toward a lower yield point and reduced femoral cortical thickness after fracture, though these were not statistically significant. Lacunar density was greater in TG+ mice, but fracture did not alter lacunar volume in TG+ or TG- mice. These findings suggest that osteocytes potentially play a significant role in the post-traumatic systemic response to fracture, though the effects differ between trabecular and cortical bone.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Structure-Based Design and Antigenic Validation of Respiratory Syncytial Virus G Immunogens

Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease of children, the elderly, and immunocompromised individuals. Currently, there are no FDA-approved RSV vaccines. The RSV G glycoprotein is used for viral attachment to host cells and impairment of host immunity by interacting with the human chemokine receptor CX3CR1. Antibodies that disrupt this interaction are protective against infection and disease. Nevertheless, development of an RSV G vaccine antigen has been hindered by its low immunogenicity and safety concerns. A previous study described three engineered RSV G proteins containing single-point mutations that induce higher levels of IgG antibodies and have improved safety profiles compared to wild-type RSV G. However, it is unclear if the mutations affect RSV G protein folding and display of its conformational epitopes. In this study, we show that the RSV G S177Q protein retains high-affinity binding to protective human and mouse monoclonal antibodies and has equal reactivity as wild-type RSV G protein to human reference immunoglobulin to RSV. Additionally, we determined the high-resolution crystal structure of RSV G S177Q protein in complex with the anti-RSV G antibody 3G12, further validating its antigenic structure. These studies show for the first time that an engineered RSV G protein with increased immunogenicity and safety retains conformational epitopes to high-affinity protective antibodies, supporting its further development as an RSV vaccine immunogen. Respiratory syncytial virus (RSV) causes severe lower respiratory diseases of children, the elderly, and immunocompromised populations. There currently are no FDA-approved RSV vaccines. Most vaccine development efforts have focused on the RSV F protein, and the field has generally overlooked the receptor-binding antigen RSV G due to its poor immunogenicity and safety concerns. However, single-point mutant RSV G proteins have been previously identified that have increased immunogenicity and safety. In this study, we investigate the antibody reactivities of three known RSV G mutant proteins. We show that one mutant RSV G protein retains high-affinity binding to protective monoclonal antibodies, is equally recognized by anti-RSV antibodies in human sera, and forms the same three-dimensional structure as the wild-type RSV G protein. Our study validates the structure-guided design of the RSV G protein as an RSV vaccine antigen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Optimized purification methods for metallic contaminant removal from directly recycled Li-ion battery cathodes

Metallic contaminants pose a significant challenge to the viability of directly recycling Li-ion batteries. To date, few strategies exist to selectively remove metallic impurities from mixtures of shredded end-of-life material (black mass; BM) without concurrently damaging the structure and electrochemical performance of the target active material. We herein present tailored methods to selectively ionize two major contaminants—Al and Cu—while retaining a representative cathode (LiNi 0.33 Mn 0.33 Co 0.33 O 2 ; NMC-111) intact. This BM purification process is conducted at moderate temperatures in a KOH-based solution matrix. We rationally evaluate approaches to increase both the kinetic corrosion rate and the thermodynamic solubility of Al 0 and Cu 0 , and evaluate the impact of these treatment conditions on the structure, chemistry, and electrochemical performance of NMC. Specifically, we explore the impacts of chloride-based salts, a strong chelating agent, elevated temperature, and sonication on the rate and extent of contaminant corrosion, while concurrently evaluating the effects on NMC. The reported BM purification process is then demonstrated on samples of “simulated BM” containing a practically relevant 1 wt% concentration of Al or Cu. Increasing the kinetic energy of the purifying solution matrix through elevated temperature and sonication accelerates the corrosion of metallic Al and Cu, such that ∼100% corrosion of 75 μm Al and Cu particles is achieved within 2.5 hr. Further, we determine that effective mass transport of ionized species critically impacts the efficacy of Cu corrosion, and that saturated Cl – hinders rather than accelerates Cu corrosion by increasing solution viscosity and introducing competitive pathways for Cu surface passivation. The purification conditions do not induce bulk structural damage to NMC, and electrochemical capacity is maintained in half-cell format. Testing in full cells suggests that a limited quantity of residual surface species are present after treatment, which initially disrupt electrochemical behavior at the graphite anode but are subsequently consumed. Process demonstration on simulated BM suggests that contaminated samples—which prior to treatment show catastrophic electrochemical performance—can be recovered to pristine electrochemical capacity. The reported BM purification method offers a compelling and commercially viable solution to address contamination, particularly in the “fine” fraction of BM where contaminant sizes are on the same order of magnitude as NMC and where traditional separation approaches are unfeasible. Thus, this optimized BM purification technique offers a pathway towards viable direct recycling of BM feedstocks that would otherwise be unusable.

25 ENERGY STORAGE↗
DOE OSTI2022

Chapter 1.18 - The Promise of Perovskite Solar Cells

Perovskite solar cells (PSCs) based on a new class of semiconductors - organic and inorganic hybrid halide perovskites - have emerged as a disruptive photovoltaic (PV) technology that is potentially cost-effective, scalable, and highly efficient, with an expectation for future deployment at terawatt scale. This new PV technology has drawn significant R&D attention from academics and industries as an alternate to compete with traditional PV technologies to help mitigate challenges associated with global energy demand. The synthesis of the hybrid halide perovskites was reported in the 1970s. The structural knowledge, solution processing and optoelectronic characteristics of this hybrid material family were further studied in the 1990s. It is until 2009-2012 when the use of methylammonium lead triiodide (MAPbI3) was first demonstrated in PV cells worldwide researchers have started to show a general interest in using hybrid halide perovskites for PV and other optoelectronic applications.

perovskite↗
DOE OSTI2025

Mechanical Roles of Polysaccharide Assembly and Interactions in Plant Cell Walls

Plants synthesize polysaccharide-based primary cell walls that possess unique microstructures and mechanical properties to accommodate plant growth and provide protection. Here, it remains challenging to assess the role of polysaccharide organization and interactions in the mechanical behavior of primary cell walls owing to their complex microstructure and highly nonlinear mechanical responses. Employing a coarse-grained molecular dynamics model developed for onion epidermal walls, this work explores the conditions under which polysaccharide assembly and interactions might play a significant role in primary cell wall mechanics. Cellulose–cellulose adhesion plays a dominant role in the wall load-bearing capacity, but when cellulose–cellulose adhesion was disrupted computationally, cellulose–xyloglucan adhesion could influence the wall load-bearing capacity. Contrary to the common concept that xyloglucans mechanically tether well-separated cellulose microfibrils, xyloglucans functioned in this case as interfibrillar adhesives capable of transmitting tensile forces between cellulose microfibrils. Our findings may inform design criteria of new materials inspired by plant cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance

The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability to physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. Analysis of EGRIN 2.0 shows how modulation of the MtrAB two-component signaling system tunes Mtb growth in response to related host microenvironmental cues. Disruption of MtrAB by tunable CRISPR interference confirms that the signaling system regulates multiple peptidoglycan hydrolases, among other targets, that are important for cell division. Further, MtrA decreases the effectiveness of antibiotics by mechanisms of both intrinsic resistance and drug tolerance. Together, the model-enabled dissection of complex MtrA regulation highlights its importance as a drug target and illustrates how EGRIN 2.0 facilitates discovery and mechanistic characterization of Mtb adaptation to specific host microenvironments within the host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Swine Host Protein Coiled-Coil Domain-Containing 115 (CCDC115) Interacts with Classical Swine Fever Virus Structural Glycoprotein E2 during Virus Replication

Interactions between the major structural glycoprotein E2 of classical swine fever virus (CSFV) with host proteins have been identified as important factors affecting virus replication and virulence. Previously, using the yeast two-hybrid system, we identified swine host proteins specifically interacting with CSFV E2. In this report, we use a proximity ligation assay to demonstrate that swine host protein CCDC115 interacts with E2 in CSFV-infected swine cells. Using a randomly mutated E2 library in the context of a yeast two-hybrid methodology, specific amino acid mutations in the CSFV E2 protein responsible for disrupting the interaction with CCDC115 were identified. A recombinant CSFV mutant (E2ΔCCDC115v) harboring amino acid changes disrupting the E2 protein interaction with CCDC115 was produced and used as a tool to assess the role of the E2–CCDC115 interaction in viral replication and virulence in swine. CSFV E2ΔCCDC115v showed a slightly decreased ability to replicate in the SK6 swine cell line and a greater replication defect in primary swine macrophage cultures. A decreased E2–CCDC115 interaction detected by PLA is observed in cells infected with E2ΔCCDC115v. Importantly, animals intranasally infected with 105 TCID50 of E2ΔCCDC115v experienced a significantly longer survival period when compared with those infected with the parental Brescia strain. This result would indicate that the ability of CSFV E2 to bind host CCDC115 protein during infection plays an important role in virus replication in swine macrophages and in virus virulence during the infection in domestic swine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Indium segregation in Gd 5 (Si, Ge) 4 magnetocaloric materials

Chemical substitution is one of the most efficient tools to tune and optimize magnetic and magnetocaloric properties of the giant magnetocaloric materials. In particular, Indium substitutions could be useful both for tuning properties of these interesting intermetallic materials and to unveil their local-scale behavior across the magnetostructural transition via hyperfine techniques. Hence, in order to investigate the effect of Indium additions on the crystal structure, micro-structure, magnetic and magnetocaloric properties, a series of In-containing samples derived from the base Gd 5 Si 1.2 Ge 2.8 stoichiometry were prepared. Here, the major findings are that while In is insoluble in the 5:4 phase, it will instead promote the emergence of the impurity 5:3 phase and segregates into this phase. Hence, In leads to major crystallographic changes, which enhance atomic disorder and disrupt the Si to Ge ratio in the 5:4 phase. Subsequently, a higher 5:4 unit cell volume and a lower magnetic ordering temperature are found in the In-substituted samples. Finally, the magnetocaloric properties of the In-substituted samples reveal a detrimental effect on the maximum magnetic entropy change.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗
DOE OSTI2023

Chemical contributions to silicon anode calendar aging are dominant over mechanical contributions

Silicon (Si) anodes are a promising candidate for increasing the energy density of lithium (Li)-ion batteries for electric vehicles. However, they have recently been identified as having poor calendar life that is insufficient for commercial needs, in addition to the well-known issue of their poor cycle life resulting from large volume expansion. Here, a specially designed protocol with variable rest periods between intermittent cycling is used to evaluate the impact of the mechanical disruption of Si and solid electrolyte interphase (SEI) from cycling on calendar aging measurements. Si was found to undergo more mechanical degradation during calendar aging with intermittent cycling than graphite. However, Si anode capacity fade was still dominated by time, especially for rest periods greater than or equal to 1 month between cycling. Postmortem dQ/dV half-cell analysis indicated this was mainly due to Li inventory loss and an increase in electrode resistance. Isothermal microcalorimetry further demonstrated that Si passivation is more disrupted than graphite passivation with intermittent cycling and suggested that there may be a chemical buildup of a detrimental species in the electrolyte, leading to a large spike in heat after the Si and SEI are disrupted by cycling.

25 ENERGY STORAGE↗
DOE OSTI2021

NF-κB and neutrophil extracellular traps cooperate to promote breast cancer progression and metastasis

Highlights: • Cancer cells–derived factors, such as IL-8 and G-CSF, induce NETs formation via PAD4 and NF-κB. • NETs increase the interaction of NEMO with IKKα/β and enhance NF-κB activation. • Blockade of NETs using PAD4 inhibitor decreases NF-κB and tumor metastasis. • Selective inhibition of NF-κB reduces NETs formation and tumor growth and metastasis. Aberrant NF-κB activation and neutrophil extracellular traps (NETs) are associated with breast cancer progression. How NF-κB and NETs modulate each other in breast cancer development remains unclear. Here, we found that NETs induced by phorbol 12-myristate 13-acetate promote breast cancer cell progression. In turn, cancer cells–derived factors, such as IL-8 and granulocyte colony-stimulating factor, stimulate neutrophils to form NETs. Mechanistically, NETs increased the interaction of NF-κB essential modifier (NEMO) with IκB kinase (IKK)α/β and enhanced NF-κB activation. We then employed a cell-permeable peptide corresponding to the NEMO-binding domain (NBD) of IKKα/β, termed NBD peptide, which disrupts NETs-mediated NEMO interaction with IKKα/β and abolished NF-κB activation in vitro. NBD peptide also reduced IL-8 level and NETs formation, and suppressed primary tumor growth and/or lung metastasis in human breast cancer mouse xenograft models and mouse spontaneous breast cancer model. Blockade of NET formation using a peptidylarginine deiminase 4 (PAD4) pharmacologic inhibitor decreased NF-κB activation and tumor metastasis. Collectively, these data suggest that NF-κB associates with NETs to form a positive loop facilitating breast tumor progression and metastasis, and that selective inhibition of NF-κB and PAD4-dependent NETs provides an effective therapeutic approach for treating breast cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

PET-FBA: A lightweight enzyme allocation and thermodynamics-constrained flux analysis approach to explore Escherichia coli metabolic adaptation to intracellular acidification

Escherichia coli employs diverse strategies to adapt to acidic environments that disrupt enzyme activity and the thermodynamic feasibility of essential reactions. To understand the impact of pH stress on cell metabolism, we present the PET-FBA (pH-, Enzyme protein allocation-, and Thermodynamics-constrained Flux Balance Analysis) framework. PET-FBA extends genome-scale modeling by integrating enzyme protein costs and reaction Gibbs free energy changes. Additionally, by incorporating pH-dependent enzyme kinetics in response to intracellular acidification, this framework enables the simulation of E. coli's metabolic adjustments across varying external pH levels. The model's accuracy is validated by comparing in silico growth simulations with experimental measurements under both anaerobic and aerobic conditions, as well as in silico gene knockouts of essential genes. By explicitly incorporating pH effects, our model accurately replicates the metabolic shift towards lactate production as the primary fermentation product at low pH in anaerobic conditions. This shift is only predicted when enzyme kinetics are dynamically adjusted as a function of pH. Further analysis revealed that this shift can be attributed to the reduced protein efficiency of the acetyl-CoA branch compared to lactate dehydrogenase under acidic stress, which then becomes crucial for maintaining NAD regeneration and cell growth at low pH. Furthermore, we identified strategies for enhancing cell growth under acidic anaerobic conditions by improving the enzyme activity of lactate dehydrogenase and pyruvate formate lyase, which increases NAD production efficiency and reduces enzyme protein allocation costs. Designed as a lightweight yet versatile framework, PET-FBA enables efficient genome-scale metabolic analysis. Using E. coli as a model system, our framework provides a systematic approach to understanding metabolic responses to environmental stress, pinpointing key metabolic bottlenecks, and identifying potential targets for strain optimization.

42 ENGINEERING↗
DOE OSTI2026

Purpose, Design, and Analysis of the NSTX-U Centerstack Casing Lateral Support Shims

The National Spherical Torus Experiment Upgrade (NSTX-U) centerstack casing surrounds the central magnet core of NSTXU. It provides the inner vacuum boundary of the plasma chamber and supports the radially inboard plasma facing components lining the plasma chamber. The casing is supported like a cantilever, fixed at the lower flange by a connection to the TF Bundle through a G-10 ring. It is flexibly supported at the top by bellows, and insulated shims intended to react the largest part of the inventory of the disruption loads at the upper support, thereby protecting the upper and lower connections from excessive loads. A large part of the qualification of the casing and tiles requires addressing and quantifying disruption loads. These have been estimated based on extensions of the behavior of NSTX during its run period roughly 15 years ago. Structural qualification of the Upgrade used these estimates of the loading as input to calculations to demonstrate adequacy for a “most probable” disruption. The estimates are included in a requirements document to guide conservative design of all components loaded by disruptions. However, the changes made for the upgrade made the extrapolation of disruption behavior uncertain. Disruptions include axisymmetric loading from axisymmetric currents induced in the vessel shells. In addition, more complex currents called Halo currents are a result of plasma poloidal currents impinging on the casing. The halo currents add another layer of uncertain behavior and net lateral loading to the casing. As a result, NSTX-U is equipped with a number of instruments intended to assess the nature and severity of disruptions. The casing shims are required for lateral support of the casing, but these have also been converted to load cells to provide another measure of the magnitude of symmetric and asymmetric loading. Some of the logic in the development of the requirements document are presented. Electromagnetic analysis of axisymmetric and halo loading is described. Global simulations of the casing transient dynamic response, and local analysis and testing of the shim/load cell are included. The shim load cells and other instrumentation will be an important guide in planning NSTX-U experiments beyond its next run period expected in late 2026 or early 2027.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Disruption of p -coumaroyl-CoA:monolignol transferases in rice drastically alters lignin composition

Grasses are abundant feedstocks that can supply lignocellulosic biomass for production of cell-wall-derived chemicals. In grass cell walls, lignin is acylated with p-coumarate. These p-coumarate decorations arise from the incorporation of monolignol p-coumarate conjugates during lignification. A previous biochemical study identified a rice (Oryza sativa) BAHD acyltransferase (AT) with p-coumaroyl-CoA:monolignol transferase (PMT) activity in vitro. In this study, we determined that that enzyme, which we name OsPMT1 (also known as OsAT4), and the closely related OsPMT2 (OsAT3) harbor similar catalytic activity toward monolignols. We generated rice mutants deficient in either or both OsPMT1 and OsPMT2 by CRISPR/Cas9-mediated mutagenesis and subjected the mutants’ cell walls to analysis using chemical and nuclear magnetic resonance methods. Our results demonstrated that OsPMT1 and OsPMT2 both function in lignin p-coumaroylation in the major vegetative tissues of rice. Notably, lignin-bound p-coumarate units were undetectable in the ospmt1 ospmt2-2 double-knockout mutant. Further, in-depth structural analysis of purified lignins from the ospmt1 ospmt2-2 mutant compared with control lignins from wild-type rice revealed stark changes in polymer structures, including alterations in syringyl/guaiacyl aromatic unit ratios and inter-monomeric linkage patterns, and increased molecular weights. Furthermore, our results provide insights into lignin polymerization in grasses that will be useful for the optimization of bioengineering approaches for the effective use of biomass in biorefineries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multiomics and deep learning dissect regulatory syntax in human development

Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression1. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs or single modalities2. Here we present the Human Development Multiomic Atlas, a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and more than 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs that influence accessibility, including composite motifs exhibiting distinct syntactic constraints that are predicted to mediate transcription factor cooperativity. We identify ‘hard’ syntactic rules requiring precise motif spacing and orientation, ‘soft’ rules allowing flexible motif arrangements, and ubiquitous motifs inhibiting accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell-type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.

59 BASIC BIOLOGICAL SCIENCES↗