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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion

Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a "biofilm-in-capillary" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Century-long timelines of herbarium genomes predict plant stomatal response to climate change

Abstract Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants’ pores for gas exchange, are expected to decrease in density following increased CO 2 concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.

Environmental Sciences & Ecology↗
DOE OSTI2022

Revealing the short-range structure of the mirror nuclei 3 H and 3 He

When protons and neutrons (nucleons) are bound into atomic nuclei, they are close enough to feel significant attraction, or repulsion, from the strong, short-distance part of the nucleon-nucleon interaction. These strong interactions lead to hard collisions between nucleons, generating pairs of highly energetic nucleons referred to as short-range correlations (SRCs). SRCs are an important but relatively poorly understood part of nuclear structure, and mapping out the strength and the isospin structure (neutron-proton (np) versus proton-proton (pp) pairs) of these virtual excitations is thus critical input for modelling a range of nuclear, particle and astrophysics measurements. Two-nucleon knockout or 'triple coincidence' reactions have been used to measure the relative contribution of np-SRCs and pp-SRCs by knocking out a proton from the SRC and detecting its partner nucleon (proton or neutron). These measurements have shown that SRCs are almost exclusively np pairs, but they had limited statistics and required large model-dependent final-state interaction corrections. Here we report on measurements using inclusive scattering from the mirror nuclei hydrogen-3 and helium-3 to extract the np/pp ratio of SRCs in systems with a mass number of three. In this work we obtain a measure of the np/pp SRC ratio that is an order of magnitude more precise than previous experiments, and find a marked deviation from the near-total np dominance observed in heavy nuclei. This result implies an unexpected structure in the high-momentum wavefunction for hydrogen-3 and helium-3. Understanding these results will improve our understanding of the short-range part of the nucleon-nucleon interaction.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

A microbial supply chain for production of the anti-cancer drug vinblastine

Monoterpene indole alkaloids (MIAs) are a diverse family of complex plant secondary metabolites with many medicinal properties, including the essential anti-cancer therapeutics vinblastine and vincristine. As MIAs are difficult to chemically synthesize, the world’s supply chain for vinblastine relies on low-yielding extraction and purification of the precursors vindoline and catharanthine from the plant Catharanthus roseus, which is then followed by simple in vitro chemical coupling and reduction to form vinblastine at an industrial scale. Here, we demonstrate the de novo microbial biosynthesis of vindoline and catharanthine using a highly engineered yeast, and in vitro chemical coupling to vinblastine. The study showcases a very long biosynthetic pathway refactored into a microbial cell factory, including 30 enzymatic steps beyond the yeast native metabolites geranyl pyrophosphate and tryptophan to catharanthine and vindoline. In total, 56 genetic edits were performed, including expression of 34 heterologous genes from plants, as well as deletions, knock-downs and overexpression of ten yeast genes to improve precursor supplies towards de novo production of catharanthine and vindoline, from which semisynthesis to vinblastine occurs. As the vinblastine pathway is one of the longest MIA biosynthetic pathways, this study positions yeast as a scalable platform to produce more than 3,000 natural MIAs and a virtually infinite number of new-to-nature analogues.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Range extender mediates long-distance enhancer activity

Although most mammalian transcriptional enhancers regulate their cognate promoters over distances of tens of kilobases, some enhancers act over distances in the megabase range1. The sequence features that enable such long-distance enhancer–promoter interactions remain unclear. Here we used in vivo enhancer-replacement experiments at the mouse Shh locus to show that short- and medium-range limb enhancers cannot initiate gene expression at long-distance range. We identify a cis-acting element, range extender (REX), that confers long-distance regulatory activity and is located next to a long-range limb enhancer of Sall1. The REX element has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range limb enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of REX increased the range of an enhancer by an order of magnitude from its native 73 kb to 848 kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs that are critical for its activity. These motifs are enriched in long-range limb enhancers genome-wide, including the ZRS (zone of polarizing activity (ZPA) regulatory sequence), a benchmark long-range limb enhancer of Shh2. The ZRS enhancer with mutated [C/T]AATTA motifs maintains limb activity at short range, but loses its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature associated with long-range enhancer–promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer long-distance activation by remote enhancers.

Bower, Grace↗
DOE OSTI2024

Molecular dynamics simulations of displacement cascades in LiAlO2 and LiAl5O8 ceramics

Abstract Molecular dynamics was employed to investigate the radiation damage due to collision cascades in LiAlO 2 and LiAl 5 O 8 , the latter being a secondary phase formed in the former during irradiation. Atomic displacement cascades were simulated by initiating primary knock-on atoms (PKA) with energy values = 5, 10 and 15 keV and the damage was quantified by the number of Frenkel pairs formed for each species: Li, Al and O. The primary challenges of modeling an ionic system with and without a core–shell model for oxygen atoms were addressed and new findings on the radiation resistance of these ceramics are presented. The working of a variable timestep function and the kinetics in the background of the simulations have been elaborated to highlight the novelty of the simulation approach. More importantly, the key results indicated that LiAlO 2 experiences much more radiation damage than LiAl 5 O 8 , where the number of Li Frenkel pairs in LiAlO 2 was 3–5 times higher than in LiAl 5 O 8 while the number of Frenkel pairs for Al and O in LiAlO 2 are ~ 2 times higher than in LiAl 5 O 8 . The primary reason is high displacement threshold energies (E d ) in LiAl 5 O 8 for Li cations. The greater E d for Li imparts higher resistance to damage during the collision cascade and thus inhibits amorphization in LiAl 5 O 8 . The presented results suggest that LiAl 5 O 8 is likely to maintain structural integrity better than LiAlO 2 in the irradiation conditions studied in this work.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Nucleoporin downregulation modulates progenitor differentiation independent of nuclear pore numbers

Nucleoporins (NUPs) comprise nuclear pore complexes, gateways for nucleocytoplasmic transport. As primary human keratinocytes switch from the progenitor state towards differentiation, most NUPs are strongly downregulated, with NUP93 being the most downregulated NUP in this process. To determine if this NUP downregulation is accompanied by a reduction in nuclear pore numbers, we leveraged Stochastic Optical Reconstruction Microscopy. No significant changes in nuclear pore numbers were detected using three independent NUP antibodies; however, NUP reduction in other subcellular compartments such as the cytoplasm was identified. To investigate how NUP reduction influences keratinocyte differentiation, we knocked down NUP93 in keratinocytes in the progenitor-state culture condition. NUP93 knockdown diminished keratinocytes’ clonogenicity and epidermal regenerative capacity, without drastically affecting nuclear pore numbers or permeability. Using transcriptome profiling, we identified that NUP93 knockdown induces differentiation genes related to both mechanical and immune barrier functions, including the activation of known NF-κB target genes. Consistently, keratinocytes with NUP93 knockdown exhibited increased nuclear localization of the NF-κB p65/p50 transcription factors, and increased NF-κB reporter activity. Taken together, these findings highlight the gene regulatory roles contributed by differential NUP expression levels in keratinocyte differentiation, independent of nuclear pore numbers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Small, solubilized platinum nanocrystals consist of an ordered core surrounded by mobile surface atoms

In situ structures of Platinum (Pt) nanoparticles (NPs) can be determined with graphene liquid cell transmission electron microscopy. Atomic-scale three-dimensional structural information about their physiochemical properties in solution is critical for understanding their chemical function. We here analyze eight atomic-resolution maps of small (<3 nm) colloidal Pt NPs. Their structures are composed of an ordered crystalline core surrounded by surface atoms with comparatively high mobility. 3D reconstructions calculated from cumulative doses of 8500 and 17,000 electrons/pixel, respectively, are characterized in terms of loss of atomic densities and atomic displacements. Less than 5% of the total number of atoms are lost due to dissolution or knock-on damage in five of the structures analyzed, whereas 10–16% are lost in the remaining three. Less than 5% of the atomic positions are displaced due to the increased electron irradiation in all structures. The surface dynamics will play a critical role in the diverse catalytic function of Pt NPs and must be considered in efforts to model Pt NP function computationally.

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

Kinetic pathways of fast lithium transport in solid electrolyte interphases with discrete inorganic components

The transport of lithium ions in the solid electrolyte interphase (SEI) has been previously accepted to proceed in two steps: a fast pore diffusion through the outer, porous organic layer followed by a slow knock-off or vacancy diffusion in the inner, dense inorganic layer. The second step is believed to be the rate-limiting step during fast-charging. In this study, we have intentionally constructed a thicker SEI (SEI-rich) structure on the surface of monoclinic Nb 2 O 5 (H-Nb 2 O 5 ) by adding LiNO 3 into a conventional ethylene carbonate based electrolyte. The electrochemical performance of two electrodes, one SEI-rich and one with few SEI (SEI-lean), was found to be almost the same, including their fast-charging capability and cycling stability, despite the significant difference in their SEI structure. Importantly, analysis using cryogenic scanning/transmission electron microscopy showed the discrete decoration of individual inorganic particles (e.g., Li 2 O) and amorphous species (LiN x O y /organic components) over the surface of H-Nb 2 O 5 . These discrete inorganic particles are in contradiction to the formation of dense inner inorganic layer, which has been commonly postulated. Based on these findings, we propose a new mechanism for Li ion transport through the SEI: one-step pore diffusion, without the second step slow diffusion. This one-step pore diffusion process provides an extremely fast Li ion transport, and effectively removes the kinetic limitation of Li ion transport in the SEI for fast charging. Finally, these results strongly suggest that the influence of SEI structure on the transport kinetics of lithium ions is much less significant than previously accepted. These results offer a new understanding of possible lithium ion transport pathway within SEI and may have implications for the future designs of fast-charging battery materials.

25 ENERGY STORAGE↗
DOE OSTI2023

First bromine doped cryogenic implosion at the National Ignition Facility

We report on the first experiment dedicated to the study of nuclear reactions on dopants in a cryogenic capsule at the National Ignition Facility (NIF). This was accomplished using bromine doping in the inner layers of the CH ablator of a capsule identical to that used in the NIF shot N140520. The capsule was doped with 3 × 1016 bromine atoms. The doped capsule shot, N170730, resulted in a DT yield that was 2.6 times lower than the undoped equivalent. The Radiochemical Analysis of Gaseous Samples (RAGS) system was used to collect and detect 79Kr atoms resulting from energetic deuteron and proton ion reactions on 79Br. RAGS was also used to detect 13N produced dominantly by knock-on deuteron reactions on the 12C in the ablator. High-energy reaction-in-flight neutrons were detected via the 209Bi(n,4n)206Bi reaction, using bismuth activation foils located 50 cm outside of the target capsule. The robustness of the RAGS signals suggests that the use of nuclear reactions on dopants as diagnostics is quite feasible.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

The next-generation magnetic recoil spectrometer (MRSnext) on OMEGA and NIF for diagnosing ion temperature, yield, areal density, and alpha heating

The next-generation magnetic recoil spectrometer (MRSnext) is being designed to replace the current MRS at the National Ignition Facility and OMEGA for measurements of the neutron spectrum from an inertial confinement fusion implosion. The MRSnext will provide a far-superior performance and faster data turnaround than the current MRS systems, i.e., a 2× and 6× improvement in energy resolution at the NIF and OMEGA, respectively, and 20× improvement in data turnaround time. The substantially improved performance of the MRSnext is enabled by using electromagnets that provide a short focal plane (12–16 cm) and unprecedented flexibility for a wide range of applications. In addition to being able to measure neutron yield, apparent ion temperature, areal density, and plasma-flow velocity over a wide range of yields, the NIF MRSnext will be able to directly, uniquely assess the alpha heating of the fuel ions through measurements of the alpha knock-on tail in the neutron spectrum. The goal is to implement a radiation-hard electronic detection system capable of providing rapid data acquisition and analysis. The development of the MRSnext will also set the foundation for the more advanced, time-resolving MRSt and serve as a testbed for its implementation on the NIF.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Distortions in charged-particle images of laser direct-drive inertial confinement fusion implosions

Energetic charged particles generated by inertial confinement fusion (ICF) implosions encode information about the spatial morphology of the hotspot and dense fuel during the time of peak fusion reactions. The knock-on deuteron imager (KoDI) was developed at the Omega Laser Facility to image these particles in order to diagnose low-mode asymmetries in the hotspot and dense fuel layer of cryogenic deuterium–tritium ICF implosions. However, the images collected are distorted in several ways that prevent reconstruction of the deuteron source. In this paper, we describe these distortions and a series of attempts to mitigate or compensate for them. We present several potential mechanisms for the distortions, including a new model for scattering of charged particles in filamentary electric or magnetic fields surrounding the implosion. Particle-tracing is used to create synthetic KoDI data based on the filamentary field model that reproduces the main experimentally observed image distortions. We conclude that the filamentary scattering model best matches the observed image distortions. Finally, we discuss potential impacts of filamentary fields on other charged-particle diagnostics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Proton radiation effects in indium oxide using cascade molecular dynamics simulations

Metal oxide (MO) semiconductors, characterized by their wide band gaps and notable charge transport properties, are promising candidates for electronic applications in extreme environments, including near-Earth space. However, atomistic simulations of radiation–matter interactions in MOs remain challenging due to the limitations of existing interatomic potentials, which often fail to capture both the short-range repulsive forces essential for radiation damage modeling and the long-range electrostatic effects governing defect evolution. In this work, we develop a customized interatomic potential tailored for radiation damage simulations in indium oxide (In 2 O 3 ) as a model system, a representative MO material. Our potential integrates the Ziegler-Biersack-Littmark potential to accurately describe short-range interactions with Buckingham and Coulombic potentials to account for long-range forces. We perform molecular dynamics simulations of low-energy proton irradiation using this custom potential. We employ the primary knock-on atom (PKA) cascade method to study atomic displacements and primary defect formation. Simulations were conducted for 1 keV proton irradiation in four randomly chosen directions, and PKA-driven defect analyses at 5, 10, and 15 keV to examine the effects of direction and energy level on damage generation. Our results provide insight into the impact of irradiation direction and energy level on the cascade evolution and defect formation mechanisms.

Atomistic simulations↗
DOE OSTI2025

A charged particle transport approximation for thick and thin plasmas

In this work, we will construct a simple method to be utilized in the interpretation of the properties of a thin plasma from a study of the transport of charged particles through it. We do so by first demonstrating how charged particle fluxes encode local plasma information in their spectra for sufficiently thick plasmas and then propose how to extend that analysis to the thin plasma limit where the extensive geometry cannot be neglected through arguments from scale separation. We provide a numerical treatment of the transport problem and demonstrate that it is in good agreement with the approximation we present. Finally, we utilize both the numerical solution and our novel approximation to study the impact of the extensive scale of the plasma on the yield and flux normalized high-energy neutron spectra resulting from the upscattering of charged fuel ions. Using this analysis, we show that (after controlling for fusion yield) for the same uniform densities and temperatures, larger plasmas have higher magnitude but softer reaction-in-flight (RIF) neutron spectra relative to smaller plasmas. This is because larger plasmas retain more knocked-on suprathermal ions within their bulk and can downscatter them to lower average energies, while smaller plasmas allow a larger fraction of high energy particles to “range out” of the system prior to substantial downscattering or inducing an RIF reaction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

A WRKY transcription factor confers broad-spectrum resistance to biotic stresses and yield stability in rice

Plants are subject to attack by diverse pests and pathogens. Few genes conferring broad-spectrum resistance to both insects and pathogens have been identified. Because of the growth–defense tradeoff, it is often challenging to balance biotic stress resistance and yield for crops. Here, we report thatOsWRKY36suppresses the resistance to insects and pathogens via transcriptional repression ofPhenylalanine Ammonia Lyases(PALs), a key enzyme in phenylpropanoid pathway in rice. Knocking outOsWRKY36causes elevated lignin biosynthesis and increased sclerenchyma thickness of leaf sheath, leading to enhanced resistance to multiple pests and pathogens. Additionally, loss ofOsWRKY36also derepresses the transcription ofIdeal Plant Architecture 1(IPA1) andMONOCULM2(MOC2), resulting in increased spikelet number per panicle and tiller number. These findings provide mechanistic insights into biotic stress tolerance in rice and offer a promising strategy to breed rice cultivars with broad-spectrum resistance to insects and pathogens while maintaining stable yield.

Science & Technology - Other Topics↗
DOE OSTI2025

SHP2 genetic variants in NSML-associated RASopathies disrupt the PZR–IRX transcription factor signaling axis

Noonan syndrome with multiple lentigines (NSML) is a rare autosomal dominant disorder caused by mutations inPTPN11(protein tyrosine phosphatase nonreceptor type 11) which encodes for the protein tyrosine phosphatase, SHP2. Approximately 85% of NSML patients develop hypertrophic cardiomyopathy (HCM). Here, we show that SHP2 is recruited to tyrosyl phosphorylated protein-zero related (PZR) in NSML mice. This recruitment is required for the Iroquois homeobox (IRX) transcription factors 3 and 5 to suppress BMP10 which negatively regulates postnatal cardiac growth. The protein expression of IRX3 and IRX5 was elevated in hypertrophied NSML hearts. IRX3 and IRX5 upregulation was rescued in NSML mice harboring a knock-in mutation of PZR that fails to become tyrosyl phosphorylated and recruit SHP2. NSML mice treated with low-dose dasatinib also exhibited normalized IRX3 and IRX5 expression levels. Consistent with this, BMP10 expression levels were reduced in NSML mice and rescued in PZR tyrosyl phosphorylation-deficient and low-dose dasatinib-treated NSML mice. A crystal structure of the tandem SH2 domains of SHP2 bound to tyrosyl phosphorylated PZR reveals that recruitment constrains the open SHP2 conformation to facilitate cellular-Src (c-Src) binding. Disruption of c-Src binding to SHP2 abolished IRX activation and failure to suppress BMP10. Hence, NSML-associated SHP2 genetic variants disrupt IRX transcription factor signaling to BMP10, implicating this axis as a target for RASopathy-associated HCM.

Science & Technology - Other Topics↗
DOE OSTI2026

Rewinding evolution in planta: A Rubisco-null platform validates high-performance ancestral enzymes

Improving the photosynthetic enzyme Rubisco is a key target for enhancing C3 crop productivity, but progress has been hampered by the difficulty of evaluating engineered variants in planta without interference from the native enzyme. Here, we report the creation of a Rubisco-null Nicotiana tabacum platform by using CRISPR-Cas9 to knock out all 11 nuclear-encoded small subunit (rbcS) genes. Knockout was achieved in a line expressing cyanobacterial Rubisco from the plastid genome, allowing the recovery of viable plants. We then developed a chloroplast expression system for coexpressing both large and small subunits from the plastid genome. We expressed two resurrected ancestral Rubiscos from the Solanaceae family. The resulting transgenic plants were phenotypically normal and accumulated Rubisco to wild-type levels. Importantly, kinetic analyses of the purified ancestral enzymes revealed they possessed a 16 to 20% higher catalytic efficiency (k cat,air /K c,air ) under ambient conditions, driven by a significantly faster turnover rate (k cat,air ). We have demonstrated that our system allows robust in vivo assessment of novel Rubiscos and that ancestral reconstruction is a powerful strategy for identifying superior enzymes to improve photosynthesis in C3 crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure and Function of REP34 Implicates Carboxypeptidase Activity in Francisella tularensis Host Cell Invasion

Francisella tularensis is the etiological agent of tularemia, or rabbit fever. Although F. tularensis is a recognized biothreat agent with broad and expanding geographical range, its mechanism of infection and environmental persistence remain poorly understood. Previously, we identified seven F. tularensis proteins that induce a rapid encystment phenotype (REP) in the free-living amoeba, Acanthamoeba castellanii. Encystment is essential to the pathogen's long term intracellular survival in the amoeba. Here, we characterize the cellular and molecular function of REP34, a REP protein with a mass of 34 kDa. A REP34 knock-out strain of F. tularensis has a reduced ability to both induce encystment in A. castellanii and invade human macrophages. We determined the crystal structure of REP34 to 2.05-Å resolution and demonstrate robust carboxypeptidase B-like activity for the enzyme. REP34 is a zinc-containing monomeric protein with close structural homology to the metallocarboxypeptidase family of peptidases. REP34 possesses a novel topology and substrate binding pocket that deviates from the canonical funnelin structure of carboxypeptidases, putatively resulting in a catalytic role for a conserved tyrosine and distinct S1' recognition site. Taken together, these results identify REP34 as an active carboxypeptidase, implicate the enzyme as a potential key F. tularensis effector protein, and may help elucidate a mechanistic understanding of F. tularensis infection of phagocytic cells.

59 BASIC BIOLOGICAL SCIENCES↗