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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 1,621 records · Page 90
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Structure of a lipid-bound viral membrane assembly protein reveals a modality for enclosing the lipid bilayer

Cellular membranes are maintained as closed compartments, broken up only transiently during membrane reorganization or lipid transportation. However, open-ended membranes, likely derived from scissions of the endoplasmic reticulum, persist in vaccinia virus-infected cells during the assembly of the viral envelope. A group of viral membrane assembly proteins (VMAPs) were identified as essential for this process. To understand the mechanism of VMAPs, we determined the 2.2-Å crystal structure of the largest member, named A6, which is a soluble protein with two distinct domains. The structure of A6 displays a novel protein fold composed mainly of alpha helices. The larger C-terminal domain forms a unique cage that encloses multiple glycerophospholipids with a lipid bilayer-like configuration. The smaller N-terminal domain does not bind lipid but negatively affects lipid binding by A6. Mutations of key hydrophobic residues lining the lipid-binding cage disrupt lipid binding and abolish viral replication. Furthermore, our results reveal a protein modality for enclosing the lipid bilayer and provide molecular insight into a viral machinery involved in generating and/or stabilizing open-ended membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

High aspect ratio nanotubes assembled from macrocyclic iminium salts

One-dimensional nanostructures such as carbon nanotubes and actin filaments rely on strong and directional interactions to stabilize their high aspect ratio shapes. This requirement has precluded making isolated, long, thin organic nanotubes by stacking molecular macrocycles, as their noncovalent stacking interactions are generally too weak. Here we report high aspect ratio (>10 3 ), lyotropic nanotubes of stacked, macrocyclic, iminium salts, which are formed by protonation of the corresponding imine-linked macrocycles. Iminium ion formation establishes cohesive interactions that, in organic solvent (tetrahydrofuran), are two orders of magnitude stronger than the neutral macrocycles, as explained by physical arguments and demonstrated by molecular dynamics simulations. Furthermore, nanotube formation stabilizes the iminium ions, which otherwise rapidly hydrolyze, and is reversed and restored upon addition of bases and acids. Acids generated by irradiating a photoacid generator or sonicating chlorinated solvents also induced nanotube assembly, allowing these nanostructures to be coupled to diverse stimuli, and, once assembled, they can be fixed permanently by cross-linking their pendant alkenes. As large macrocyclic chromonic liquid crystals, these iminium salts are easily accessible through a modular design and provide a means to rationally synthesize structures that mimic the morphology and rheology of carbon nanotubes and biological tubules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows

Mitochondrial ATP synthases form dimers, which assemble into long ribbons at the rims of the inner membrane cristae. We reconstituted detergent-purified mitochondrial ATP synthase dimers from the green algae Polytomella sp. and the yeast Yarrowia lipolytica into liposomes and examined them by electron cryotomography. Tomographic volumes revealed that ATP synthase dimers from both species self-assemble into rows and bend the lipid bilayer locally. The dimer rows and the induced degree of membrane curvature closely resemble those in the inner membrane cristae. Monomers of mitochondrial ATP synthase reconstituted into liposomes do not bend membrane visibly and do not form rows. No specific lipids or proteins other than ATP synthase dimers are required for row formation and membrane remodelling. Long rows of ATP synthase dimers are a conserved feature of mitochondrial inner membranes. They are required for cristae formation and a main factor in mitochondrial morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The cbb 3 -type cytochrome oxidase assembly factor CcoG is a widely distributed cupric reductase

Copper (Cu)-containing proteins execute essential functions in prokaryotic and eukaryotic cells, but their biogenesis is challenged by high Cu toxicity and the preferential presence of Cu(II) under aerobic conditions, while Cu(I) is the preferred substrate for Cu chaperones and Cu-transport proteins. These proteins form a coordinated network that prevents Cu accumulation, which would lead to toxic effects such as Fenton-like reactions and mismetalation of other metalloproteins. Simultaneously, Cu-transport proteins and Cu chaperones sustain Cu(I) supply for cuproprotein biogenesis and are therefore essential for the biogenesis of Cu-containing proteins. In eukaryotes, Cu(I) is supplied for import and trafficking by cell-surface exposed metalloreductases, but specific cupric reductases have not been identified in bacteria. It was generally assumed that the reducing environment of the bacterial cytoplasm would suffice to provide sufficient Cu(I) for detoxification and cuproprotein synthesis. Here, we identify the proposed cbb 3 -type cytochrome c oxidase ( cbb 3 -Cox) assembly factor CcoG as a cupric reductase that binds Cu via conserved cysteine motifs and contains 2 low-potential [4Fe-4S] clusters required for Cu(II) reduction. Deletion of ccoG or mutation of the cysteine residues results in defective cbb 3 -Cox assembly and Cu sensitivity. Furthermore, anaerobically purified CcoG catalyzes Cu(II) but not Fe(III) reduction in vitro using an artificial electron donor. Thus, CcoG is a bacterial cupric reductase and a founding member of a widespread class of enzymes that generate Cu(I) in the bacterial cytosol by using [4Fe-4S] clusters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2019

Dynamic structure of the full-length scaffolding protein NHERF1 influences signaling complex assembly

The Na+/H+ exchange regulatory cofactor 1 (NHERF1) protein modulates the assembly and intracellular trafficking of several transmembrane G protein–coupled receptors (GPCRs) and ion transport proteins with the membrane–cytoskeleton adapter protein ezrin. We applied in this report solution NMR and small-angle neutron scattering (SANS) to structurally characterize full-length NHERF1 and disease-associated variants that are implicated in impaired phosphate homeostasis. Using NMR, we mapped the modular architecture of NHERF1, which is composed of two structurally-independent PDZ domains that are connected by a flexible, disordered linker. We observed that the ultra-long and disordered C-terminal tail of NHERF1 has a type 1 PDZ-binding motif that interacts weakly with the proximal, second PDZ domain to form a dynamically autoinhibited structure. Using ensemble-optimized analysis of SANS data, we extracted the molecular size distribution of structures from the extensive conformational space sampled by the flexible chain. Our results revealed that NHERF1 is a diffuse ensemble of variable PDZ domain configurations and a disordered C-terminal tail. The joint NMR/SANS data analyses of three disease variants (L110V, R153Q, and E225K) revealed significant differences in the local PDZ domain structures and in the global conformations compared with the WT protein. Furthermore, we show that the substitutions affect the affinity and kinetics of NHERF1 binding to ezrin and to a C-terminal peptide from G protein–coupled receptor kinase 6A (GRK6A). Significant insight into the modulation of the intrinsic flexibility of NHERF1 by disease-associated point mutations that alter the dynamic assembly of signaling complexes are provided in this work.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Thermohydraulic Design Analysis of the Target Assembly in the Material Plasma Exposure Experiment Facility

The Material Plasma Exposure eXperiment (MPEX) project seeks to design a steady-state linear plasma facility at Oak Ridge National Laboratory that will be used to study plasma-material interactions (PMIs) at fusion prototypic levels, supporting the evaluation and development of materials for the next generation of fusion devices. This study is focused on PMI exposure of small-size neutron-irradiated specimens, which are clamped onto an actively cooled component. A thermohydraulic evaluation of a new MPEX target assembly design to assess the appropriate operation during MPEX operation is presented. To further guide the design and assess the structural integrity of the components under expected loads, preliminary thermomechanical stress analyses were also conducted. To ensure good thermal contact between the components, thermal interface materials, such as silver flexible graphite, were used in the assembly. It was found that the maximum target temperatures of 1572, 1463, and 1315 K were obtained for Grafoil thicknesses of 0.61, 0.38, and 0.25 mm, respectively. The distribution of the axial deformation at high heat fluxes showed that there are no gaps between components, indicating good contact at material interfaces. Moreover, the contact pressure between the target and other components indicated that very good contact was established at these interfaces. Furthermore, the stress-strain conditions for the target will be further used to assess the appropriate operation during MPEX experiments and gain insight into materials science phenomena during PMI experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Layer-by-layer assembly of metal-organic framework nanosheets with polymer

Metal-organic framework (MOF) nanosheets are gaining more and more attention due to their tunable porous structure and two-dimensional shape. Adding MOF nanosheets into polymers can lead to improved properties, but the level of enhancement is usually thwarted by the difficulties in exfoliating and aligning these nanosheets within the polymer matrix. In order to establish a strategy for making polymer/MOF nanosheets composites with improved exfoliation and alignment, we combined MOF nanosheets and polymer using layer-by-layer (LbL) assembly for the first time. MOF nanosheets (ZIF67-L, leaf-like zeolitic imidazolate framework nanosheets) used here were functionalized with positively charged polyethylenimine, which could replace the original surface ligands and impart a positive charge on the nanosheet surface. These positively charged MOF nanosheets were then combined with negatively charged poly(acrylic acid) through ionic-bonding-assisted LbL assembly, generating a polymer composite with fully exfoliated and highly aligned MOF nanosheets.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

A combined TEM and SAXS study of the growth and self-assembly of ultrathin Pt nanowires

Ultrathin Pt nanowires possess high activity for various electrocatalytic applications. However, little work has focused on understanding their growth mechanisms. Herein, we utilize a combination of time-dependent, ex situ transmission electron microscopy (TEM) and small angle x-ray scattering (SAXS) techniques to observe the growth process in addition to associated surfactant-based interactions. TEM images indicate that initially nanoparticles are formed within 30 s; these small 'seed' particles quickly elongate to form ultrathin nanowires after 2 min. These motifs remain relatively unchanged in size and shape up to 480 min of reaction. Complementary SAXS data suggests that the initial nanoparticles, which are coated by a surfactant bilayer, arrange into a bcc superlattice. With increasing reaction time, the bcc lattice disappears as the nanoparticles grow into nanowires, which then self-assemble into a columnar hexagonal structure in which the individual nanowires are covered by a CTAB monolayer. The hexagonal structure eventually degrades, thereby leading to the formation of lamellar stacking phases comprised of surfactant bilayers. To the best of our knowledge, this is the first time that SAXS has been used to monitor the growth and self-assembly of Pt nanowires. In conclusion, these insights can be used to better understand and rationally control the formation of anisotropic motifs of other metallic nanostructures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Construction and assembly of the wire planes for the MicroBooNE Time Projection Chamber

In this paper we describe how the readout planes for the MicroBooNE Time Projection Chamber were constructed, assembled and installed. We present the individual wire preparation using semi-automatic winding machines and the assembly of wire carrier boards. The details of the wire installation on the detector frame and the tensioning of the wires are given. A strict quality assurance plan ensured the integrity of the readout planes. The different tests performed at all stages of construction and installation provided crucial information to achieve the successful realization of the MicroBooNE wire planes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Abstract Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

Gomes-dos-Santos, André (ORCID:0000000199734861)↗
DOE OSTI2022

Chromosome-Level Genome Assembly of Mentha longifolia L. Reveals Gene Organization Underlying Disease Resistance and Essential Oil Traits

Mentha longifolia (L.) Huds., a wild, diploid mint species, has been developed as a model for mint genetic and genomic research to aid breeding efforts that target Verticillium wilt disease resistance and essential oil monoterpene composition. Here, we present a near-complete, chromosome-scale mint genome assembly for M. longifolia USDA accession CMEN 585. This new assembly is an update of a previously published genome draft, with dramatic improvements. A total of 42,107 protein-coding genes were annotated and placed on 12 chromosomal scaffolds. One hundred fifty-three genes contained conserved sequence domains consistent with nucleotide binding site-leucine-rich-repeat (NBS-LRR) plant disease resistance genes. Homologs of genes implicated in Verticillium wilt resistance in other plant species were also identified. Multiple paralogs of genes putatively involved in p-menthane monoterpenoid biosynthesis were identified and several cases of gene clustering documented. Heterologous expression of candidate genes, purification of recombinant target proteins, and subsequent enzyme assays allowed us to identify the genes underlying the pathway that leads to the most abundant monoterpenoid volatiles. Here, the bioinformatic and functional analyses presented here are laying the groundwork for using marker-assisted selection in improving disease resistance and essential oil traits in mints.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.

Cenococcum geophilum↗
DOE OSTI2020

Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance. We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs. Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Galactosylation of xyloglucan is essential for the stabilization of the actin cytoskeleton and endomembrane system through the proper assembly of cell walls

Abstract Xyloglucan, a major hemicellulose, interacts with cellulose and pectin to assemble primary cell walls in plants. Loss of the xyloglucan galactosyltransferase MURUS3 (MUR3) leads to the deficiency of galactosylated xyloglucan and perturbs plant growth. However, it is unclear whether defects in xyloglucan galactosylation influence the synthesis of other wall polysaccharides, cell wall integrity, cytoskeleton behaviour, and endomembrane homeostasis. Here, we found that in mur3-7 etiolated seedlings cellulose was reduced, CELLULOSE SYNTHASE (CESA) genes were down-regulated, the density and mobility of cellulose synthase complexes (CSCs) were decreased, and cellulose microfibrils become discontinuous. Pectin, rhamnogalacturonan II (RGII), and boron contents were reduced in mur3-7 plants, and B-RGII cross-linking was abnormal. Wall porosity and thickness were significantly increased in mur3-7 seedlings. Endomembrane aggregation was also apparent in the mur3-7 mutant. Furthermore, mutant seedlings and their actin filaments were more sensitive to Latrunculin A (LatA) treatment. However, all defects in mur3-7 mutants were substantially restored by exogenous boric acid application. Our study reveals the importance of MUR3-mediated xyloglucan galactosylation for cell wall structural assembly and homeostasis, which is required for the stabilization of the actin cytoskeleton and the endomembrane system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Diffstar: a fully parametric physical model for galaxy assembly history

We present Diffstar, a smooth parametric model for the in situ star formation history (SFH) of galaxies. The Diffstar model is distinct from traditional SFH models because it is parametrized directly in terms of basic features of galaxy formation physics. Diffstar includes ingredients for: the halo mass assembly history; the accretion of gas into the dark matter halo; the fraction of gas that is eventually transformed into stars, ϵ ms ; the time-scale over which this transformation occurs, τ cons ; and the possibility that some galaxies will experience a quenching event at time t q , and may subsequently experience rejuvenated star formation. We show that our model is sufficiently flexible to describe the average stellar mass histories of galaxies in both the IllustrisTNG (TNG) and UniverseMachine (UM) simulations with an accuracy of ~0.1 dex across most of cosmic time. We use Diffstar to compare TNG to UM in common physical terms, finding that: (i) star formation in UM is less efficient and burstier relative to TNG; (ii) UM galaxies have longer gas consumption time-scales, relative to TNG; (iii) rejuvenated star formation is ubiquitous in UM, whereas quenched TNG galaxies rarely experience sustained rejuvenation; and (iv) in both simulations, the distributions of ϵ ms , τ cons , and t q share a common characteristic dependence upon halo mass, and present significant correlations with halo assembly history. Finally, we conclude with a discussion of how Diffstar can be used in future applications to fit the SEDs of individual observed galaxies, as well as in forward-modelling applications that populate cosmological simulations with synthetic galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Probing Galaxy assembly bias in BOSS galaxies using void probabilities

ABSTRACT We measure the void probability function (VPF) of galaxies in the Baryon Oscillation Spectroscopic Survey (BOSS). The VPF provides complementary information to standard two-point statistics in that it is sensitive to galaxy bias in the most extreme underdensities in the cosmic web. Thus, the VPF is ideal for testing whether halo occupation of galaxies depends on large-scale density, an effect known as galaxy assembly bias. We find that standard HOD model – one parameterized by halo mass only – fit only to the two-point function, accurately predicts the VPF. Additionally, for HOD models where density dependence is explicitly incorporated, the best-fitting models fit to the combination of the correlation function and the VPF have zero density dependence. Thus, galaxy assembly bias is not a strong source of systematic uncertainty when modelling the clustering of massive galaxies.

Walsh, Kilian↗
DOE OSTI2017

Wnt5a promotes Frizzled-4 signalosome assembly by stabilizing cysteine-rich domain dimerization

Wnt/β-catenin signaling is activated when extracellular Wnt ligands bind Frizzled (FZD) receptors at the cell membrane. Wnts bind FZD cysteine-rich domains (CRDs) with high affinity through a palmitoylated N-terminal “thumb” and a disulfide-stabilized C-terminal “index finger,” yet how these binding events trigger receptor activation and intracellular signaling remains unclear. In this work, we report the crystal structure of the Frizzled-4 (FZD 4 ) CRD in complex with palmitoleic acid, which reveals a CRD tetramer consisting of two cross-braced CRD dimers. Each dimer is stabilized by interactions of one hydrophobic palmitoleic acid tail with two CRD palmitoleoyl-binding grooves oriented end to end, suggesting that the Wnt palmitoleoyl group stimulates CRD–CRD interaction. Using bioluminescence resonance energy transfer (BRET) in live cells, we show that WNT5A stimulates dimerization of membrane-anchored FZD 4 CRDs and oligomerization of full-length FZD 4 , which requires the integrity of CRD palmitoleoyl-binding residues. These results suggest that FZD receptors may form signalosomes in response to Wnt binding through the CRDs and that the Wnt palmitoleoyl group is important in promoting these interactions. These results complement our understanding of lipoprotein receptor-related proteins 5 and 6 (LRP5/6), Dishevelled, and Axin signalosome assembly and provide a more complete model for Wnt signalosome assembly both intracellularly and at the membrane.

59 BASIC BIOLOGICAL SCIENCES↗