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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Controlling swelling in mixed transport polymers through alkyl side-chain physical cross-linking

Semiconducting conjugated polymers bearing glycol side chains can simultaneously transport both electronic and ionic charges with high charge mobilities, making them ideal electrode materials for a range of bioelectronic devices. However, heavily glycolated conjugated polymer films have been observed to swell irreversibly when subjected to an electrochemical bias in an aqueous electrolyte. The excessive swelling can lead to the degradation of their microstructure, and subsequently reduced device performance. An effective strategy to control polymer film swelling is to copolymerize glycolated repeat units with a fraction of monomers bearing alkyl side chains, although the microscopic mechanism that constrains swelling is unknown. Here we investigate, experimentally and computationally, a series of archetypal mixed transporting copolymers with varying ratios of glycolated and alkylated repeat units. Experimentally we observe that exchanging 10% of the glycol side chains for alkyl leads to significantly reduced film swelling and an increase in electrochemical stability. Through molecular dynamics simulation of the amorphous phase of the materials, we observe the formation of polymer networks mediated by alkyl side-chain interactions. When in the presence of water, the network becomes increasingly connected, counteracting the volumetric expansion of the polymer film.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts

Many remarkable phenotypes have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times, many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits. To understand the general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic traits and gene count in 14,785 gene families from 993 Saccharomycotina yeasts. Using a recently developed phylogenetic approach that reduces spurious correlations, we found that gene family expansion and contraction were significantly linked to trait gain and loss in 45/56 (80%) traits. While 595/739 (81%) significant gene families were associated with only one trait, we also identified several “keystone” gene families that were significantly associated with up to 13/56 (23%) of all traits. Strikingly, most of these families are known to encode metabolic enzymes and transporters, including all members of the industrially relevant MAL tose fermentation loci in the baker’s yeast Saccharomyces cerevisiae. These results indicate that convergent evolution on the gene family level may be more widespread across deeper timescales than previously believed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dependence of thick filament structure in relaxed mammalian skeletal muscle on temperature and interfilament spacing

Contraction of skeletal muscle is regulated by structural changes in both actin-containing thin filaments and myosin-containing thick filaments, but myosin-based regulation is unlikely to be preserved after thick filament isolation, and its structural basis remains poorly characterized. Here, we describe the periodic features of the thick filament structure in situ by high-resolution small-angle x-ray diffraction and interference. We used both relaxed demembranated fibers and resting intact muscle preparations to assess whether thick filament regulation is preserved in demembranated fibers, which have been widely used for previous studies. We show that the thick filaments in both preparations exhibit two closely spaced axial periodicities, 43.1 nm and 45.5 nm, at near-physiological temperature. The shorter periodicity matches that of the myosin helix, and x-ray interference between the two arrays of myosin in the bipolar filament shows that all zones of the filament follow this periodicity. The 45.5-nm repeat has no helical component and originates from myosin layers closer to the filament midpoint associated with the titin super-repeat in that region. Cooling relaxed or resting muscle, which partially mimics the effects of calcium activation on thick filament structure, disrupts the helical order of the myosin motors, and they move out from the filament backbone. Compression of the filament lattice of demembranated fibers by 5% Dextran, which restores interfilament spacing to that in intact muscle, stabilizes the higher-temperature structure. The axial periodicity of the filament backbone increases on cooling, but in lattice-compressed fibers the periodicity of the myosin heads does not follow the extension of the backbone. Thick filament structure in lattice-compressed demembranated fibers at near-physiological temperature is similar to that in intact resting muscle, suggesting that the native structure of the thick filament is largely preserved after demembranation in these conditions, although not in the conditions used for most previous studies with this preparation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Fast physics-based launcher optimization for electron cyclotron current drive

With the increased urgency to design fusion pilot plants, fast optimization of electron cyclotron current drive (ECCD) launchers is paramount. Traditionally, this is done by coarsely sampling the 4D parameter space of possible launch conditions consisting of (1) the launch location (constrained to lie along the reactor vessel), (2) the launch frequency, (3) the toroidal launch angle, and (4) the poloidal launch angle. For each initial condition, a ray-tracing simulation is performed to evaluate the ECCD efficiency. Unfortunately, this approach often requires a large number of simulations (sometimes millions in extreme cases) to build up a dataset that adequately covers the plasma volume, which must then be repeated every time the design point changes. Here we adopt a different approach. Rather than launching rays from the plasma periphery and hoping for the best, we instead directly reconstruct the optimal ray for driving current at a given flux surface using a reduced physics model coupled with a commercial ray-tracing code. Repeating this throughout the plasma volume requires only hundreds of simulations, constituting a significant speedup. The new method is validated on two separate example tokamak profiles, and is shown to reliably drive localized current at the specified flux surface with the same optimal efficiency as obtained from the traditional approach.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Curvature perturbations from stochastic particle production during inflation

We calculate the curvature power spectrum sourced by spectator fields that are excited repeatedly and non-adiabatically during inflation. In the absence of detailed information of the nature of spectator field interactions, we consider an ensemble of models with intervals between the repeated interactions and interaction strengths drawn from simple probabilistic distributions. We show that the curvature power spectra of each member of the ensemble shows rich structure with many features, and there is a large variability between different realizations of the same ensemble. Such features can be probed by the cosmic microwave background (CMB) and large scale structure observations. They can also have implications for primordial black hole formation and CMB spectral distortions. The geometric random walk behavior of the spectator field allows us to calculate the ensembleaveraged power spectrum of curvature perturbations semi-analytically. For sufficiently large stochastic sourcing, the ensemble averaged power spectrum shows a scale dependence arising from the time spent by modes outside the horizon during the period of particle production, in spite of there being no preferred scale in the underlying model. We find that the magnitude of the ensemble-averaged power spectrum overestimates the typical power spectra in the ensemble because the ensemble distribution of the power spectra is highly non-Gaussian with fat tails.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

3D radiation, density, and MHD structures following neon shattered pellet injection into stable DIII-D Super H-mode discharges

Six nominally repeat neon shattered pellet injection (SPI) shutdowns of stable DIII-D Super H-modes are studied to understand the 3D properties of the radiation and impurity transport. The radiation efficiency and radiation peaking determine whether first wall melting is expected following disruption mitigation in ITER. Previous studies make use of axisymmetric approximations to infer radiation efficiencies, but validating the high efficiency required by ITER necessitates improved accuracy, and this work contributes by exploring the 3D radiation and density structures that will inform forward modeling. When the neon shatter plume produced by the SPI reaches the plasma edge, m/n = 3/1 and 2/1 island O-points are observed to align with the injection trajectory in five out of six cases, suggesting that the injected material seeds the island O-points. Field aligned neon structures emitting Ne-I line radiation drift at 1 km/s in the ion diamagnetic drift direction during the pre-TQ, tracking the motion of the m/n = 2/1 island O-point. Neon fragments penetrate to the q = 2 surface by the time of the TQ. Techniques to constrain the 3D emissivity are explored, and one method constrains a 3D flux tube that is consistent with the radiation data, and when mapped to the interferometers, intersects the lasers that measure the highest density. The resulting structure derived from the radiation measurements exists near the 2/1 island X-point. In five repeatable discharges, the peak of the radiation in the toroidal direction exists in a 120° toroidal sector where the injection occurs, in contrast with the outlier discharge where the toroidal peak exists in the complementary 240° toroidal sector far from the injector, and where a 50% lower density rise is observed. In conclusion, the n = 1 phase behavior is markedly different in the outlier discharge, suggesting a possible dependence of the radiation structure and the assimilation efficiency on MHD.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Conceptual study on using Doppler backscattering to measure magnetic pitch angle in tokamak plasmas

We introduce a new approach to measure the magnetic pitch angle profile in tokamak plasmas with Doppler backscattering (DBS), a technique traditionally used for measuring flows and density fluctuations. The DBS signal is maximised when its probe beam's wavevector is perpendicular to the magnetic field at the cutoff location, independent of the density fluctuations [Hillesheim \emph{et al} 2022 \emph{Nucl. Fusion} \textbf{55} 073024]. Hence, if one could isolate this effect, DBS would then yield information about the magnetic pitch angle. By varying the toroidal launch angle, the DBS beam reaches cutoff with different angles with respect to the magnetic field, but with other properties remaining similar. Hence, the toroidal launch angle which gives maximum backscattered power is thus that which is matched to the pitch angle at the cutoff location, enabling inference of the magnetic pitch angle. We performed systematic scans of the DBS toroidal launch angle for repeated DIII-D tokamak discharges. Experimental DBS data from this scan were analysed and combined with Gaussian beam-tracing simulations using the Scotty code [Hall-Chen \emph{et al} 2022 \emph{Plasma Phys. Control. Fusion} \textbf{64} 095002]. The pitch-angle inferred from DBS is consistent with that from magnetics-only and motional-Stark-effect-constrained (MSE) equilibrium reconstruction in the edge. In the core, the pitch angles from DBS and magnetics-only reconstructions differ by one to two degrees, while simultaneous MSE measurements were not available. The uncertainty in these measurements was under a degree; we show that this uncertainty is primarily due to the error in toroidal steering, the number of toroidally separated measurements, and shot-to-shot repeatability. We find that the error of pitch-angle measurements can be reduced by optimising the poloidal launch angle and initial beam properties. Since DBS has high spatial and temporal resolutions, is non-perturbative, does not require neutral beams, and is likely robust to neutron damage of and debris on the first mirrors, using DBS to measure the pitch angle in future fusion energy systems is especially appealing.

beam tracing↗
DOE OSTI2021

The case for digital twins in metal additive manufacturing

The digital twin (DT) is a relatively new concept that is finding increased acceptance in industry. A DT is generally considered as comprising a physical entity, its virtual replica, and two-way digital data communications in-between. Its primary purpose is to leverage the process intelligence captured within digital models—or usually their faster-solving surrogates—towards generating increased value from the physical entities. The surrogate models are created using machine learning based on data obtained from the field, experiments and digital models, which may be physics-based or statistics-based. Anomaly detection and correction, and diagnostic closed-loop process control are examples of how a process DT can be deployed. In the manufacturing industry, its use can achieve improvements in product quality and process productivity. Metal additive manufacturing (AM) stands to gain tremendously from the use of DTs. This is because the AM process is inherently chaotic, resulting in poor repeatability. However, a DT acting in a supervisory role can inject certainty into the process by actively keeping it within bounds through real-time control commands. Closed-loop feedforward control is achieved by observing the process through sensors that monitor critical parameters and, if there are any deviations from their respective optimal ranges, suitable corrective actions are triggered. The type of corrective action (e.g. a change in laser power or a modification to the scanning speed) and its magnitude are determined by interrogating the surrogate models. Because of their artificial intelligence (AI)-endowed predictive capabilities, which allow them to foresee a future state of the physical twin (e.g. the AM process), DTs proactively take context-sensitive preventative steps, whereas traditional closed-loop feedback control is usually reactive. Apart from assisting a build process in real-time, a DT can help with planning the build of a part by pinpointing the optimum processing window relevant to the desired outcome. Again, the surrogate models are consulted to obtain the required information. In this article, we explain how the application of DTs to the metal AM process can significantly widen its application space by making the process more repeatable (through quality assurance) and cheaper (by getting builds right the first time).

36 MATERIALS SCIENCE↗
DOE OSTI2023

Finding simplicity: unsupervised discovery of features, patterns, and order parameters via shift-invariant variational autoencoders *

Abstract Recent advances in scanning tunneling and transmission electron microscopies (STM and STEM) have allowed routine generation of large volumes of imaging data containing information on the structure and functionality of materials. The experimental data sets contain signatures of long-range phenomena such as physical order parameter fields, polarization, and strain gradients in STEM, or standing electronic waves and carrier-mediated exchange interactions in STM, all superimposed onto scanning system distortions and gradual changes of contrast due to drift and/or mis-tilt effects. Correspondingly, while the human eye can readily identify certain patterns in the images such as lattice periodicities, repeating structural elements, or microstructures, their automatic extraction and classification are highly non-trivial and universal pathways to accomplish such analyses are absent. We pose that the most distinctive elements of the patterns observed in STM and (S)TEM images are similarity and (almost-) periodicity, behaviors stemming directly from the parsimony of elementary atomic structures, superimposed on the gradual changes reflective of order parameter distributions. However, the discovery of these elements via global Fourier methods is non-trivial due to variability and lack of ideal discrete translation symmetry. To address this problem, we explore the shift-invariant variational autoencoders (shift-VAEs) that allow disentangling characteristic repeating features in the images, their variations, and shifts that inevitably occur when randomly sampling the image space. Shift-VAEs balance the uncertainty in the position of the object of interest with the uncertainty in shape reconstruction. This approach is illustrated for model 1D data, and further extended to synthetic and experimental STM and STEM 2D data. We further introduce an approach for training shift-VAEs that allows finding the latent variables that comport to known physical behavior. In this specific case, the condition is that the latent variable maps should be smooth on the length scale of the atomic lattice (as expected for physical order parameters), but other conditions can be imposed. The opportunities and limitations of the shift VAE analysis for pattern discovery are elucidated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function

ABSTRACT Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots.

Microbiology↗
DOE OSTI2023

Involvement of the Streptococcus mutans PgfE and GalE 4-epimerases in protein glycosylation, carbon metabolism, and cell division

Streptococcus mutans is a key pathogen associated with dental caries and is often implicated in infective endocarditis. This organism forms robust biofilms on tooth surfaces and can use collagen-binding proteins (CBPs) to efficiently colonize collagenous substrates, including dentin and heart valves. One of the best characterized CBPs of S. mutans is Cnm, which contributes to adhesion and invasion of oral epithelial and heart endothelial cells. These virulence properties were subsequently linked to post-translational modification (PTM) of the Cnm threonine-rich repeat region by the Pgf glycosylation machinery, which consists of 4 enzymes: PgfS, PgfM1, PgfE, and PgfM2. Inactivation of the S. mutans pgf genes leads to decreased collagen binding, reduced invasion of human coronary artery endothelial cells, and attenuated virulence in the Galleria mellonella invertebrate model. The present study aimed to better understand Cnm glycosylation and characterize the predicted 4-epimerase, PgfE. Using a truncated Cnm variant containing only 2 threonine-rich repeats, mass spectrometric analysis revealed extensive glycosylation with HexNAc2. Compositional analysis, complemented with lectin blotting, identified the HexNAc2 moieties as GlcNAc and GalNAc. Comparison of PgfE with the other S. mutans 4-epimerase GalE through structural modeling, nuclear magnetic resonance, and capillary electrophoresis demonstrated that GalE is a UDP-Glc-4-epimerase, while PgfE is a GlcNAc-4-epimerase. While PgfE exclusively participates in protein O-glycosylation, we found that GalE affects galactose metabolism and cell division. Furthermore, this study further emphasizes the importance of O-linked protein glycosylation and carbohydrate metabolism in S. mutans and identifies the PTM modifications of the key CBP, Cnm.

4-epimerases↗
DOE OSTI2020

Cross-correlating Planck with VST ATLAS LRGs: a new test for the ISW effect in the Southern hemisphere

ABSTRACT The integrated Sachs–Wolfe (ISW) effect probes the late-time expansion history of the Universe, offering direct constraints on dark energy. Here, we present our measurements of the ISW signal at redshifts of $\bar{z}=0.35$, 0.55, and 0.68, using the cross-correlation of the Planck cosmic microwave background temperature map with ∼0.5 million luminous red galaxies (LRGs) selected from the VST ATLAS survey. We then combine these with previous measurements based on WMAP and similar SDSS LRG samples, providing a total sample of ∼2.1 million LRGs covering ∼12 000 deg2 of sky. At $\bar{z}=0.35$ and $\bar{z}=0.55$, we detect the ISW signal at 1.2σ and 2.3σ (or 2.6σ combined), in agreement with the predictions of lambda cold dark matter (ΛCDM). We verify these results by repeating the measurements using the BOSS LOWZ and CMASS, spectroscopically confirmed LRG samples. We also detect the ISW effect in three magnitude limited ATLAS + SDSS galaxy samples extending to z ≈ 0.4 at ∼2σ per sample. However, we do not detect the ISW signal at $\bar{z}=0.68$ when combining the ATLAS and SDSS results. Further tests using spectroscopically confirmed eBOSS LRGs at this redshift remain inconclusive due to the current low sky coverage of the survey. If the ISW signal is shown to be redshift dependent in a manner inconsistent with the predictions of ΛCDM, it could open the door to alternative theories such as modified gravity. It is therefore important to repeat the high-redshift ISW measurement using the completed eBOSS sample, as well as deeper upcoming surveys such as DESI and LSST.

Ansarinejad, Behzad↗
DOE OSTI2022

The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes

Abstract G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3′-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5′-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes

Abstract Poly(UG) or ‘pUG’ dinucleotide repeats are highly abundant sequences in eukaryotic RNAs. In Caenorhabditis elegans, pUGs are added to RNA 3′ ends to direct gene silencing within Mutator foci, a germ granule condensate. Here, we show that pUG RNAs efficiently self-assemble into gel condensates through quadruplex (G4) interactions. Short pUG sequences form right-handed intermolecular G4s (pUG G4s), while longer pUGs form left-handed intramolecular G4s (pUG folds). We determined a 1.05 Å crystal structure of an intermolecular pUG G4, which reveals an eight stranded G4 dimer involving 48 nucleotides, 7 different G and U quartet conformations, 7 coordinated potassium ions, 8 sodium ions and a buried water molecule. A comparison of the intermolecular pUG G4 and intramolecular pUG fold structures provides insights into the molecular basis for G4 handedness and illustrates how a simple dinucleotide repeat sequence can form complex structures with diverse topologies.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Interannual consistency of migration phenology is season- and breeding region-specific in North American Golden Eagles

Abstract Interannual consistency (an indicator of the strength of adjustments) in migration phenology of Golden Eagles (Aquila chrysaetos) in North America is most strongly associated with the breeding region, the season, and with late-season temperature on breeding and wintering grounds. Consistency was greatest in boreal spring migration and the breeding regions of eastern Canada. Using multi-year GPS tracks of 83 adults breeding in 3 spatially distant regions (Alaska, northeast Canada, and southeast Canada), we quantified the interannual consistency of migration phenology and wintering latitude within and among individuals tracked across multiple years and the repeatability (r) by breeding regions and seasons. By comparing regions and seasons, we found that consistency was highest (r > 0.85) for boreal spring migration in eastern Canada while Alaska had the lowest value (r < 0.15). Because seasonal consistency of migration phenology was only detected in eastern Canada, we conclude that seasonal features are not a primary constraint. While regional differences in consistency were not related to differences in migratory distances, they could be the result of genetic or habitat differences. We also found that temperatures warmer than the decadal average at the region of departure delayed the start of boreal spring migration by ~10 days and advanced boreal autumn migration by ~20 days. These results suggest that warmer temperatures would reduce residence time on breeding grounds, contrary to expectations and trends found in other studies. Wide variations in migratory strategies across a species distribution can add to the list of challenges for conservation but may give migrants the capacity to acclimate to environmental changes.

Zoology↗
DOE OSTI2022

The relation between quasars’ optical spectra and variability

Abstract Brightness variation is an essential feature of quasars, but its mechanism and relationship to other physical quantities are not understood well. We aimed to find the relationship between the optical variability and spectral features to reveal the regularity behind the random variation. It is known that a quasar’s Fe ii/Hβ flux ratio and equivalent width of [O iii]5007 are negatively correlated; this is called Eigenvector 1. In this work, we visualized the relationship between the position on this Eigenvector 1 (EV1) plane and how the brightness of the quasars had changed after ∼10 yr. We conducted three analyses, using a different quasar sample in each. The first analysis showed the relation between the quasars’ distributions on the EV1 plane and how much they had changed brightness, using 13438 Sloan Digital Sky Survey quasars. This result shows how brightness changes later are clearly related to the position on the EV1 plane. In the second analysis, we plotted the sources reported as “changing-look quasars” (or “changing-state quasars”) on the EV1 plane. This result shows that the position on the EV1 plane corresponds to the activity level of each source, and the bright or dim states of them are distributed on the opposite sides divided by the typical quasar distribution. In the third analysis, we examined the transition vectors on the EV1 plane using sources with multiple-epoch spectra. This result shows that the brightening and dimming sources move on a similar path and they reach a position corresponding to the opposite activity level. We also found this trend is opposite to the empirical rule that $R_{\rm {Fe\, \small {II}}}$ positively correlated with the Eddington ratio, which has been proposed based on the trends of a large number of quasars. From all these analyses, it is indicated that quasars tend to oscillate between both sides of the distribution ridge on the EV1 plane; each of them corresponds to a dim state and a bright state. This trend in optical variation suggests that significant brightness changes, such as changing-look quasars, are expected to repeat.

Astronomy & Astrophysics↗
DOE OSTI2021

A Single Xyloglucan Xylosyltransferase Is Sufficient for Generation of the XXXG Xylosylation Pattern of Xyloglucan

ABSTRACT Xyloglucan is the most abundant hemicellulose in the primary cell walls of dicots. Dicot xyloglucan is the XXXG type consisting of repeating units of three consecutive xylosylated Glc residues followed by one unsubstituted Glc. Its xylosylation is catalyzed by xyloglucan 6-xylosyltransferases (XXTs) and there exist five XXTs (AtXXT1-5) in Arabidopsis. While AtXXT1 and AtXXT2 have been shown to add the first two Xyl residues in the XXXG repeat, which XXTs are responsible for the addition of the third Xyl residue remains elusive although AtXXT5 was a proposed candidate. In this report, we generated recombinant proteins of all five Arabidopsis XXTs and one rice XXT (OsXXT1) in the mammalian HEK293 cells and investigated their ability to sequentially xylosylate Glc residues to generate the XXXG xylosylation pattern. We found that like AtXXT1/2, AtXXT4 and OsXXT1 could efficiently xylosylate the cellohexaose (G6) acceptor to produce mono- and di-xylosylated G6, whereas AtXXT5 was only barely capable of adding one Xyl onto G6. When AtXXT1-catalyzed products were used as acceptors, AtXXT1/2/4 and OsXXT1, but not AtXXT5, were able to xylosylate additional Glc residues to generate tri- and tetra-xylosylated G6. Further characterization of the tri- and tetra-xylosylated G6 revealed that they had the sequence of GXXXGG and GXXXXG with three and four consecutive xylosylated Glc residues, respectively. In addition, we have found that although tri-xylosylation occurred on G6, cello-oligomers with a degree of polymerization of 3 to 5 could only be mono- and di-xylosylated. Together, these results indicate that each of AtXXT1/2/4 and OsXXT1 is capable of sequentially adding Xyl onto three contiguous Glc residues to generate the XXXG xylosylation pattern and these findings provide new insight into the biochemical mechanism underlying xyloglucan biosynthesis.

Cell Biology↗
DOE OSTI2021

Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites

The evolution of recognition specificities by the immune system depends on the generation of receptor diversity and on connecting the binding of new antigens with the initiation of downstream signaling. In plant immunity, the innate Nucleotide-Binding Leucine-Rich Repeat (NLR) receptor family enables antigen binding and immune signaling. In this study, we surveyed the NLR complements of 62 ecotypes of Arabidopsis thaliana and 54 lines of Brachypodium distachyon and identified a limited number of NLR subfamilies that show high allelic diversity. We show that the predicted specificity-determining residues cluster on the surfaces of Leucine-Rich Repeat domains, but the locations of the clusters vary among NLR subfamilies. By comparing NLR phylogeny, allelic diversity, and known functions of the Arabidopsis NLRs, we formulate a hypothesis for the emergence of direct and indirect pathogen-sensing receptors and of the autoimmune NLRs. These findings reveal the recurring patterns of evolution of innate immunity and can inform NLR engineering efforts.

59 BASIC BIOLOGICAL SCIENCES↗