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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Abstract Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12 family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cell wall biology of the moss Physcomitrium patens

Abstract The moss Physcomitrium (previously Physcomitrella) patens is a non-vascular plant belonging to the bryophytes that has been used as a model species to study the evolution of plant cell wall structure and biosynthesis. Here, we present an updated review of the cell wall biology of P. patens. Immunocytochemical and structural studies have shown that the cell walls of P. patens mainly contain cellulose, hemicelluloses (xyloglucan, xylan, glucomannan, and arabinoglucan), pectin, and glycoproteins, and their abundance varies among different cell types and at different plant developmental stages. Genetic and biochemical analyses have revealed that a number of genes involved in cell wall biosynthesis are functionally conserved between P. patens and vascular plants, indicating that the common ancestor of mosses and vascular plants had already acquired most of the biosynthetic machinery to make various cell wall polymers. Although P. patens does not synthesize lignin, homologs of the phenylpropanoid biosynthetic pathway genes exist in P. patens and they play an essential role in the production of caffeate derivatives for cuticle formation. Further genetic and biochemical dissection of cell wall biosynthetic genes in P. patens promises to provide additional insights into the evolutionary history of plant cell wall structure and biosynthesis.

Plant Sciences↗
DOE OSTI2022

On the synthesis of heavy nuclei in protomagnetar outflows and implications for ultra-high energy cosmic rays

ABSTRACT It has been suggested that strongly magnetized and rapidly rotating protoneutron stars (PNSs) may produce long duration gamma-ray bursts (GRBs) originating from stellar core collapse. We explore the steady-state properties and heavy element nucleosynthesis in neutrino-driven winds from such PNSs whose magnetic axis is generally misaligned with the axis of rotation. We consider a wide variety of central engine properties such as surface dipole field strength, initial rotation period, and magnetic obliquity to show that heavy element nuclei can be synthesized in the radially expanding wind. This process is facilitated provided the outflow is Poynting-flux dominated such that its low entropy and fast expansion time-scale enables heavy nuclei to form in a more efficient manner as compared to the equivalent thermal GRB outflows. We also examine the acceleration and survival of these heavy nuclei and show that they can reach sufficiently high energies ≳ 1020 eV within the same physical regions that are also responsible for powering gamma-ray emission, primarily through magnetic dissipation processes. Although these magnetized outflows generally fail to achieve the production of elements heavier than lanthanides for our explored electron fraction range 0.4–0.6, we show that they are more than capable of synthesizing nuclei near and beyond iron peak elements.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Systematic exploration of heavy element nucleosynthesis in protomagnetar outflows

ABSTRACT We study the nucleosynthesis products in neutrino-driven winds from rapidly rotating, highly magnetized and misaligned protomagnetars using the nuclear reaction network SkyNet. We adopt a semi-analytic parametrized model for the protomagnetar and systematically study the capabilities of its neutrino-driven wind for synthesizing nuclei and eventually producing ultra-high energy cosmic rays (UHECRs). We find that for neutron-rich outflows (Ye < 0.5), synthesis of heavy elements ($\overline{A}\sim 20-65$) is possible during the first $\sim 10\, {\rm s}$ of the outflow, but these nuclei are subjected to composition-altering photodisintegration during the epoch of particle acceleration at the dissipation radii. However, after the first $\sim 10\, {\rm s}$ of the outflow, nucleosynthesis reaches lighter elements ($\overline{A}\sim 10-50$) that are not subjected to subsequent photodisintegration. For proton-rich (Ye ≥ 0.5) outflows, synthesis is more limited ($\overline{A}\sim 4-15$). These suggest that while protomagnetars typically do not synthesize nuclei heavier than second r-process peak elements, they are intriguing sources of intermediate/heavy mass UHECRs. For all configurations, the most rapidly rotating protomagnetars are more conducive for nucleosynthesis with a weaker dependence on the magnetic field strength.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

A family of α/β hydrolases removes phytol from chlorophyll metabolites for tocopherol biosynthesis in Arabidopsis

Tocopherol synthesis requires phytyl diphosphate derived from phytol esterified to chlorophyll metabolites. The >600-member Arabidopsis thaliana α/β hydrolase (ABH) gene family contains 4 members that can release phytol from chlorophyll metabolites in vitro; however, only pheophytinase (PPH) affects tocopherol synthesis when mutated, reducing seed tocopherols by 5%. We report the biochemical analysis of 2 previously uncharacterized ABHs, chlorophyll dephytylase 2 (CLD2) and CLD3, and their respective mutants singly and in combinations with pph and cld1 alleles. While all CLDs localized to the thylakoid and could hydrolyze phytol from chlorophylls and Pheophytin a in vitro, CLD3 had the highest in vitro activity and the largest effect on tocopherol synthesis in vivo. The 3 CLDs acted cooperatively to provide phytol for 31% of tocopherols synthesized in light-grown leaf tissue. Dark-induced leaf senescence assays showed PPH is required for 18% of the tocopherols synthesized. Though the cld123 triple mutant had no impact on dark-induced tocopherol content, cld123 in the pph background reduced tocopherol levels by an additional 18%. In seeds, pph and cld123 each reduced tocopherol content by 5% and by 15% in the cld123pph quadruple mutant. VTE7 ( ViTamin E7 ) is an envelope-localized ABH that specifically affects chlorophyll biosynthetic intermediates in vivo and is required for 55% of seed tocopherol synthesis. The introduction of cld123pph into the vte7 background further reduced seed tocopherol levels to 23% of that of the wild type. Our findings demonstrate that phytol provision for tocopherol biosynthesis and homeostasis is a complex process involving the coordinated spatiotemporal expression of multiple ABH family members.

arabidopsis↗
DOE OSTI2022

H-lignin can be deposited independently of CINNAMYL ALCOHOL DEHYDROGENASE C and D in Arabidopsis

Abstract Lignin contributes substantially to the recalcitrance of biomass toward saccharification. To circumvent this problem, researchers have genetically altered lignin, although, in a number of cases, these efforts have resulted in an undesirable yield penalty. Recent findings have shown that by knocking out two subunits (MED5A and MED5B) of the transcriptional regulatory complex Mediator, the stunted growth phenotype of mutants in p-coumaroyl shikimate 3′-hydroxylase, reduced epidermal fluorescence 8-1 (ref8-1), can be alleviated. Furthermore, these plants synthesize a lignin polymer almost entirely derived from p-coumaryl alcohol. Plants deficient in cinnamyl alcohol dehydrogenase (CAD) are notable in that they primarily incorporate coniferaldehyde and sinapaldehyde into their lignin. We tested the hypothesis that by stacking mutations in the genes encoding for the CAD paralogs C and D on an Arabidopsis (Arabidopsis thaliana) med5a/5b ref8-1 genetic background, the biosynthesis of p-coumaryl alcohol would be blocked, making p-coumaraldehyde available for polymerization into a novel kind of lignin. The med5a/5b ref8-1 cadc cadd plants are viable, but lignin analysis demonstrated that they continue to synthesize p-hydroxyphenyl lignin despite being mutated for the CADs typically considered to be required for monolignol biosynthesis. In addition, enzyme activity tests showed that even in the absence of CADC and CADD, there is high CAD activity in stems. We tested the potential involvement of other CADs in p-coumaraldehyde biosynthesis in the quintuple mutant by mutating them using the CRISPR/Cas9 system. Lignin analysis demonstrated that the resulting hextuple mutant plants continue to deposit p-coumaryl alcohol-derived lignin, demonstrating a route for the synthesis of p-hydroxyphenyl lignin in Arabidopsis independent of four CAD isoforms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Restricting electron flow at cytochrome b6f when downstream electron acceptors are severely limited

Abstract Photosynthetic organisms frequently experience abiotic stress that restricts their growth and development. Under such circumstances, most absorbed solar energy cannot be used for CO2 fixation and can cause the photoproduction of reactive oxygen species (ROS) that can damage the photosynthetic reaction centers of PSI and PSII, resulting in a decline in primary productivity. This work describes a biological “switch” in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b6f (Cyt b6f) complex when the capacity for accepting electrons downstream of PSI is severely limited. We specifically show this restriction in STARCHLESS6 (sta6) mutant cells, which cannot synthesize starch when they are limited for nitrogen (growth inhibition) and subjected to a dark-to-light transition. This restriction represents a form of photosynthetic control that causes diminished electron flow to PSI and thereby prevents PSI photodamage but does not appear to rely on a ΔpH. Furthermore, when electron flow is restricted, the plastid alternative oxidase (PTOX) becomes active, functioning as an electron valve that dissipates some excitation energy absorbed by PSII and allows the formation of a proton motive force (PMF) that would drive some ATP production (potentially sustaining PSII repair and nonphotochemical quenching [NPQ]). The restriction at the Cyt b6f complex can be gradually relieved with continued illumination. This study provides insights into how PET responds to a marked reduction in availability of downstream electron acceptors and the protective mechanisms involved.

Plant Sciences↗
DOE OSTI2024

From sensing to acclimation: The role of membrane lipid remodeling in plant responses to low temperatures

Abstract Low temperatures pose a dramatic challenge to plant viability. Chilling and freezing disrupt cellular processes, forcing metabolic adaptations reflected in alterations to membrane compositions. Understanding the mechanisms of plant cold tolerance is increasingly important due to anticipated increases in the frequency, severity, and duration of cold events. This review synthesizes current knowledge on the adaptive changes of membrane glycerolipids, sphingolipids, and phytosterols in response to cold stress. We delve into key mechanisms of low-temperature membrane remodeling, including acyl editing and headgroup exchange, lipase activity, and phytosterol abundance changes, focusing on their impact at the subcellular level. Furthermore, we tabulate and analyze current gycerolipidomic data from cold treatments of Arabidopsis, maize, and sorghum. This analysis highlights congruencies of lipid abundance changes in response to varying degrees of cold stress. Ultimately, this review aids in rationalizing observed lipid fluctuations and pinpoints key gaps in our current capacity to fully understand how plants orchestrate these membrane responses to cold stress.

Plant Sciences↗
DOE OSTI2025

Mechanism of shape symmetry breaking in surfactant-mediated crystal growth

We present a dynamical model of crystal growth, in which it is possible to reliably achieve asymmetric products, beginning from symmetric initial conditions and growing within an isotropic environment. The asymmetric growth is the result of a positive feedback mechanism that amplifies the effect of thermal fluctuations in the coverage of surfactants on the growing crystalline facets. Within our simple model, we are able to understand the kinetic and thermodynamic factors involved in both the onset of symmetry breaking and the persistence of anisotropic growth. We demonstrate that the mechanism is general by studying models with increasing complexity. We argue that this mechanism of symmetry breaking underpins observations of colloidal, seed-mediated syntheses of single crystalline metal nanorods capped with strongly interacting surfactants. The parameters within our model are related to experimental observables such as the concentration, hydrophobicity, and binding strength of the surfactants, which suggests a potential route to optimize the yield of asymmetric products in colloidal nanoparticle syntheses.

Oaks-Leaf, Sam↗
DOE OSTI2026

Local Structural Coherence and Interfacial Charge Transfer in Cu 2 ⁢S/Mo⁢S 2 Heterostructure

Precise control over electronic coupling at nanoscale interfaces is critical for designing materials with tunable charge-transfer behavior and catalytic function. Heterostructures with locally coherent interfaces provide a platform for interrogating interfacial charge redistribution in coupled material systems. Here, we report Cu 2 ⁢S/Mo⁢S 2 heterostructures exhibiting nanoscale crystallographic alignment, which are synthesized through a rapid thermal transformation pathway. We employed electrochemical reduction reactions to probe interfacial charge transfer, revealing shifts in product distribution attributable to modified interfacial energetics, even in the absence of optimized catalytic performance. The observed formate Faradaic efficiency suggests that interfacial electronic modulation in the heterostructure shifts product selectivity towards formate, highlighting how interface-driven electronic modulation can direct reaction pathways and influence product selectivity. Optimizing catalyst loading, architecture, and reactor configuration will be critical for future improvement. Structural and compositional integrity were confirmed through powder x-ray diffraction, x-ray photoelectron spectroscopy, and high-resolution transmission electron microscopy. Electron transfer between Cu 2 ⁢S and Mo⁢S 2 domains was further evaluated by electrochemical impedance spectroscopy, while selected-area electron diffraction revealed local crystallographic alignment consistent with a local epitaxial relationship at the Cu 2 S/Mo⁢S 2 heterointerface. To illustrate the broader applicability of this approach, a Zn⁢S/Mo⁢S 2 heterostructure was also synthesized using the same microwave strategy, confirming the generalizability of interfacial engineering principles across metal sulfide-Mo⁢S 2 systems. Collectively, these findings demonstrate that controlled local epitaxial alignment serves as an effective design principle for tuning interfacial energetics and catalytic reactivity in complex heterostructure materials.

carbon capture & utilization↗
DOE OSTI2025

Synthesis of single-qutrit circuits from Clifford+𝑅 gates

Here, we present two deterministic compilation algorithms for single-qutrit unitaries with O ( log 1 / ɛ ) gate depth. Each algorithm selects a nearby approximation to the target unitary and then exactly synthesizes the approximation over the Clifford + R basis. The first algorithm exhaustively searches over the group; while the second algorithm searches only for Householder reflections. The exhaustive search algorithm yields an average R count of 2.193 ( 11 ) + 8.621 ( 7 ) log 10 ( 1 / ɛ ) , albeit with a time complexity of O ( ɛ − 4.4 ) . The Householder search algorithm results in a larger average R count of 3.20 ( 13 ) + 10.77 ( 3 ) log 10 ( 1 / ɛ ) at a reduced time complexity of O ( ɛ − 0.42 ) , greatly extending the reach in ɛ . These costs correspond asymptotically to 35% and 69% more non-Clifford gates compared with synthesizing the same unitary with two qubits. Such initial results are encouraging for using the R gate as the nontransversal gate for qutrit-based computation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Gamma-ray signatures of 𝑟-process radioactivity from the collapse of magnetized white dwarfs

We predict the gamma-ray line emission from 𝑟-process nuclei synthesized in the ejecta of the accretion-induced collapse (AIC) of a magnetized, rapidly rotating white dwarf. Using ejecta from a two-dimensional general-relativistic neutrino-magnetohydrodynamic simulation, further evolved with a radiation-hydrodynamics code coupled to an in situ nuclear reaction network, we construct angle-dependent gamma-ray spectra in the 0.01–10 MeV band via composition-dependent ray tracing through the ejecta. The emission between ∼1 and 10 d is dominated by 132 I (𝑡 1/2 = 2.3 h), continuously replenished by the decay of its parent 132 Te (𝑡 1/2 = 3.2 d), with additional contributions from 131 I, 133 Xe, and 132 Te . At 𝑡 ≳ 20 d, 56 Co (from 56 Ni decay) becomes the primary emitter. The simultaneous presence of 𝑟 process and iron-peak gamma-ray lines is distinctive of AIC ejecta and absent in binary neutron star mergers, where iron-peak nuclei are generally not synthesized. Comparing with the 3⁢𝜎 continuum sensitivities of planned MeV gamma-ray telescopes (COSI, AMEGO-X, e-ASTROGAM, GRAMS, GammaTPC), we find the brightest 𝑟-process lines detectable to ∼10 Mpc by GammaTPC and GRAMS, with the signal approaching their sensitivity threshold at 30 Mpc. As a result, the 𝑟-process spectral features survive time integration over ∼30 d exposures, demonstrating robustness against the long observation times required by gamma-ray detectors.

Nuclear reactions↗
DOE OSTI2020

Approximate quantum circuit synthesis using block encodings

One of the challenges in quantum computing is the synthesis of unitary operators into quantum circuits with polylogarithmic gate complexity. Exact synthesis of generic unitaries requires an exponential number of gates in general. We propose a novel approximate quantum circuit synthesis technique by relaxing the unitary constraints and interchanging them for ancilla qubits via block encodings. This approach combines smaller block encodings, which are easier to synthesize, into quantum circuits for larger operators. Due to the use of block encodings, our technique is not limited to unitary operators and can be applied for the synthesis of arbitrary operators. Overall, we show that operators which can be approximated by a canonical polyadic expression with a polylogarithmic number of terms can be synthesized with polylogarithmic gate complexity with respect to the matrix dimension.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Low-Pressure Electrochemical Synthesis of Complex High-Pressure Superconducting Superhydrides

There is great current interest in multicomponent superhydrides due to their unique quantum properties under pressure. A remarkable example is the ternary superhydride Li 2 MgH 16 computationally identified to have an unprecedented high superconducting critical temperature T c of ~470 K at 250 GPa. However, the very high synthesis pressures required remains a significant hurdle for detailed study and potential applications. In this Letter, we evaluate the feasibility of synthesizing ternary Li-Mg superhydrides by the recently proposed pressure-potential (P 2 ) method that uniquely combines electrochemistry and applied pressure to control synthesis and stability. Furthermore, the results indicate that it is possible to synthesize Li-Mg superhydrides at modest pressures by applying suitable electrode potentials. Using pressure alone, no Li-Mg ternary hydrides are predicted to be thermodynamically stable, but in the presence of electrode potentials, both Li 2 MgH 16 and Li 4 MgH 24 can be stabilized at modest pressures. Three polymorphs are predicted as ground states of Li 2 MgH 16 below 300 GPa, with transitions at 33 and 160 GPa. The highest pressure phase is superconducting, while the two at lower pressures are not. Our findings point out the potentially important role of the P 2 method in controlling phase stability of complex multicomponent superhydrides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Potential for exciton condensation in a highly conductive amorphous polymer

An outstanding challenge in synthesis and theory is to develop molecular materials at ambient conditions that exhibit highly efficient energy transfer. Here, in this study, we demonstrate the potential of a recently synthesized, highly conductive amorphous material—a nickel tetrathiafulvalene-tetrathiolate (NiTTFtt) polymer—to become an exciton condensate—a Bose-Einstein condensate of particle-hole pairs, known as excitons, that supports dissipationless flow of excitation energy. While exciton condensates have recently been realized in ordered materials, we show by advanced electronic structure calculations that this highly correlated phenomenon can potentially be realized in molecularly tailored, amorphous materials. In contrast to the Bechgaard salts that support superconductivity at compressed geometries requiring high pressures, we show that the recently synthesized, amorphous NiTTFtt polymer exhibits the computational signature of exciton condensation at experimentally realizable geometries, occurring at ambient pressures. Results suggest that superfluidity in this system and related systems—including van der Waals structures, molecular metals with extended-TTF dithiolate ligands, and Bechgaard salts—may occur via a nontraditional excitonic mechanism tuneable according to system composition, geometry, size, and charge. This study prompts further experimental investigation of the rational design of molecularly scaled exciton condensates with potential applications to efficient transport in technologically relevant materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis

Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transglycosylation step, the glucosyl moiety is transferred to the nonreducing end of an acceptor to form a growing glucan polymer chain made up of glucose molecules. It has been proposed that both sucrose breakdown and glucan synthesis occur in the same active site of the catalytic domain, although the active site does not appear to be large enough to accommodate both functions. These three enzymes belong to glycoside hydrolase family 70 (GH70), which shows homology to glycoside hydrolase family 13 (GH13). GtfC synthesizes both soluble and insoluble glucans (α-1,3 and α-1,6 glycosidic linkages), while GtfB and GtfD synthesize only insoluble or soluble glucans, respectively. Here, crystal structures of the catalytic domains of GtfB and GtfD are reported. These structures are compared with previously determined structures of the catalytic domain of GtfC. With this work, apo structures and inhibitor-complex structures with acarbose are now available for the catalytic domains of GtfC and GtfB. The structure of GtfC with maltose allows further identification and comparison of active-site residues. A model of sucrose binding to GtfB is also included. The new structure of the catalytic domain of GtfD affords a structural comparison of the three S. mutans glycosyltransferases. Unfortunately, the catalytic domain of GtfD is not complete since crystallization resulted in the structure of a truncated protein lacking approximately 200 N-terminal residues of domain IV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Crystal structures and comparisons of huntite aluminum borates RE Al 3 (BO 3 ) 4 ( RE = Tb, Dy and Ho)

Three huntite-type aluminoborates of stoichiometry RE Al 3 (BO 3 ) 4 ( RE = Tb, Dy and Ho), namely, terbium/dysprosium/holmium trialuminium tetrakis(borate), were synthesized by slow cooling within a K 2 Mo 3 O 10 flux with spontaneous crystallization. The crystal structures were determined using single-crystal X-ray diffraction (SC-XRD) data. The synthesized borates are isostructural to the huntite [CaMg 3 (CO 3 ) 4 ] structure and crystallized within the trigonal R 32 space group. The structural parameters were compared to literature data of other huntite RE Al 3 (BO 3 ) 4 crystals within the R 32 space group. All three borates fit well into the trends calculated from the literature data. The unit-cell parameters and volumes increase linearly with larger RE cations whereas the densities decrease. All of the crystals studied were refined as inversion twins.

36 MATERIALS SCIENCE↗