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At least 1,135 records · Page 63

Conservation of endo -glucanase 16 (EG16) activity across highly divergent plant lineages

Plant cell walls are highly dynamic structures that are composed predominately of polysaccharides. As such, endogenous carbohydrate active enzymes (CAZymes) are central to the synthesis and subsequent modification of plant cells during morphogenesis. The endo-glucanase 16 (EG16) members constitute a distinct group of plant CAZymes, angiosperm orthologs of which were recently shown to have dual β-glucan/xyloglucan hydrolase activity. Molecular phylogeny indicates that EG16 members comprise a sister clade with a deep evolutionary relationship to the widely studied apoplastic xyloglucan endo-transglycosylases/hydrolases (XTH). A cross-genome survey indicated that EG16 members occur as a single ortholog across species and are widespread in early diverging plants, including the non-vascular bryophytes, for which functional data were previously lacking. Remarkably, enzymological characterization of an EG16 ortholog from the model moss Physcomitrella patens (PpEG16) revealed that EG16 activity and sequence/structure are highly conserved across 500 million years of plant evolution, vis-à-vis orthologs from grapevine and poplar. Ex vivo biomechanical assays demonstrated that the application of EG16 gene products caused abrupt breakage of etiolated hypocotyls rather than slow extension, thereby indicating a mode-of-action distinct from endogenous expansins and microbial endo-glucanases. As a result, the biochemical data presented here will inform future genomic, genetic, and physiological studies of EG16 enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Radiation-induced vacancy injection in heterogeneous multiphase materials

Understanding the synergy between corrosion and defect dynamics is a key consideration in the development of advanced materials for extreme environments. Here, we reveal a surprising phenomenon for the transport of point defects induced by irradiation in a heterogeneous multiphase structure of a metal and an oxide, similar to that formed under metal corrosion that takes place in most environments. Despite the confinement of the produced damage within the oxide, vacancies were injected into the unirradiated metal and coarsened with dose. Furthermore, the results show that the nature of the oxide layer dictates the defect evolution in the metal layer. This work reveals an interesting mechanism for point defect interactions in multiphase materials, with broad implications in many fields, while also emphasizing the complex coupling between corrosion and irradiation. Corrosion leads to the formation of multiphase materials, while irradiation enhances diffusion within the heterogeneous phases, which can impact corrosion rates.

36 MATERIALS SCIENCE↗

Understanding Metal–Organic Framework Nucleation from a Solution with Evolving Graphs

A mechanistic understanding of metal–organic framework (MOF) synthesis and scale-up remains underexplored due to the complex nature of the interactions of their building blocks. In this work, we investigate the collective assembly of building units at the early stages of MOF nucleation, using MIL-101(Cr) as a prototypical example. Using large-scale molecular dynamics simulations, we observe that the choice of solvent (water and N,N-dimethylformamide), the introduction of ions (Na+ and F–) and the relative populations of MIL-101(Cr) half-secondary building unit (half-SBU) isomers have a strong influence on the cluster formation process. Additionally, the shape, size, nucleation and growth rates, crystallinity, and short and long-range order largely vary depending on the synthesis conditions. We evaluate these properties as they naturally emerge when interpreting the self-assembly of MOF nuclei as the time evolution of an undirected graph. Solution-induced conformational complexity and ionic concentration have a dramatic effect on the morphology of clusters emerging during assembly. While pure solvents lead to the rapid formation of a small number of large clusters, the presence of ions in aqueous solutions results in smaller clusters and slower nucleation. This diversity is captured by the key features of the graph representation. Principle component analysis on graph properties reveals that only a small number of molecular descriptors is needed to deconvolute MOF self-assembly. Furthermore, descriptors such as the average coordination number between half-SBUs and fractal dimension are of particular interest as they can be can be followed experimentally by techniques like by time-resolved spectroscopy. Ultimately, graph theory emerges as an approach that can be used to understand complex processes revealing molecular descriptors accessible by both simulation and experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Binding of Formic Acid on Anatase TiO2(101)

The adsorption of formic acid (FA) and the formation of formate species on metal oxide surfaces are of great interest in catalysis. Formic acid is used to probe the adsorption properties of surface sites and formates are common intermediates in many catalytic reactions. Here we focus on the interaction of FA with a prototypical anatase TiO2(101) surface by using a combination of scanning tunneling microscopy (STM), infrared reflection absorption spectroscopy (IRAS), electron stimulated desorption (ESD), and density functional theory (DFT) to assess the coverage dependent evolution of different FA-derived surface species at low temperatures (80–240 K). We find that isolated FA adsorbs at 80 K in both monodentate (MD) and bidentate (BD) configurations on top of undercoordinated Ti sites (Ti5c). The MD form is likely deprotonated and readily converts upon annealing to bridging BD on two neighboring Ti5c sites. DFT calculations show that molecularly-bound MD FA is metastable and readily converts into a deprotonated state in the proximity of subsurface oxygen vacancy. The stability of the MD species increases as the availability of the paired Ti5c sites for BD formation diminishes at high coverages. Upon surface saturation, a mixed configuration of alternating bidentate and monodentate species with coverage of 2/3 FA/Ti5c represents the most favorable configuration. This is in contrast with the adsorption of FA on rutile TiO2(110) and many other oxides, where bidentate formate species dominate. Y.W., A.D., G.A.K., R.R., N.G.P., and Z.D. were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences (CSGB) under FWP 47319. B.W. and A.S. acknowledge the support of DOE BES, CSGB Division under Award DESC0007347. The experimental studies were performed in EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated for DOE by Battelle. The authors also acknowledge computational resources from the TIGRESS high-performance computer center at Princeton University.

Wang, Yang↗

Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism

Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.

59 BASIC BIOLOGICAL SCIENCES↗

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗

Gas phase formation of phenalene via 10π-aromatic, resonantly stabilized free radical intermediates

For the last few decades, the Hydrogen-Abstraction/aCetylene-Addition (HACA) mechanism has been fundamental in aiding our understanding of the source of polycyclic aromatic hydrocarbons (PAHs) in combustion processes and in circumstellar envelopes of carbon rich stars. However, the reaction mechanisms driving high temperature molecular mass growth beyond triphenylene (C 18 H 12 ) along with the link between PAHs and graphene-type nanostructures as identified in carbonaceous meteorites such as in Murchison and Allende has remained elusive. By exploring the reaction of the 1-naphthyl radical (C 10 H 7 ˙) with methylacetylene (CH 3 CCH) and allene (H 2 CCCH 2 ) under conditions prevalent in carbon-rich circumstellar environments and combustion systems, we provide compelling evidence on a facile formation of 1H-phenalene (C 13 H 10 ) – the central molecular building block of graphene-type nanostructures. Beyond PAHs, molecular mass growth processes from 1H-phenalene via ring-annulation through C3 molecular building blocks may ultimately lead to two-dimensional structures such as graphene nano flakes and after condensation of multiple layers to graphitized carbon. Furthermore, these fundamental reaction mechanisms are of crucial significance to facilitate an understanding of the origin and chemical evolution of carbon in our Galaxy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Centrifugally driven winds from protostellar disks. I - Wind model and thermal structure

The thermal structure of a wind that is centrifugally driven from the surface of a protostellar disk is studied. A generalized version of the Blandford and Payne self-similar wind model is introduced, and the temperature and ionization distributions in the outflow are investigated. For the evolution of atomic winds, the heat equation and the rate equations that describe the ionization and excitation state of hydrogen are solved self-consistently. Ambipolar diffusion is found to be a robust mechanism for heating the gas. In the more powerful outflows, molecular hydrogen is collisionally dissociated close to the disk surface, and hydrogen is mainly atomic within a few astronomical units from the central source. It is also demonstrated that these outflows have enough momentum to lift dust grains from the disk surface.

Safier, Pedro N.↗

Reverse Energy Cascade in Turbulent Weakly Ionized Plasmas

For systems far from equilibrium, the neglect of a role for viscous effects in turbulence may be generally inappropriate when the relaxation time for the molecular process approaches the local flow time (Orou et al. (1996)). Furthermore, for stationary collisional plasmas, the conventional Reynolds number is irrelevant under circumstances where the standard features of turbulence in ordinary gases are observed in the plasma (Johnson et al. (1987)). The current theoretical understanding of these turbulent phenomenon is particularly inadequate for turbulence associated with ionizing shock waves; generally speaking, thermodynamic, acoustic and pressure fluctuations are all seen as amplified across the shock wave followed by a dramatic decay (relaminarization) usually attributed to a lack of importance of viscosity in the turbulent regions. This decay would be accelerated when the flow speed is also reduced due to the importance usually given to the conventional Reynolds number (which is directly proportional to velocity) as a quality of turbulence index. However, evidence supporting this consensus is lacking. By contrast, recent evidence of vanishing triple correlations form De Silva et al. (1996) provides strong support for early theoretical speculation of inherently molecular effects in macroscopic turbulence in Tsuge (1974). This specifically suggests that the role of compressive effects ordinarily associated with the shock wave could be significantly muted by the existence of a strongly turbulent local environment. There is also more recent theoretical speculation (Frisch et al. (1984)) of an inherently and previously unsuspected non-dissipative nature to turbulence, with energy conservation being nurtured by reverse energy cascades in the turbulent fluctuation spectra. Furthermore, the role which might be played by fluctuations on quantum mechanical phenomena and variations in molecular parameters is completely unknown, especially of the sort which might be found in optical spectra. A determination of the role which changing turbulent parameters might play on optical signatures behind a reflected shock wave should therefore provide a useful tool for the evolution of theoretical models for turbulence.

Williams, Kyron↗

R-O-C(triple bond)N species produced by ion irradiation of ice mixtures: comparison with astronomical observations

We have investigated the effects induced by ion bombardment of mixtures containing nitrogen-bearing compounds at low temperatures. The results show the formation of a band at 2080 cm-1 in binary mixtures, NH3:CH4 and N2:CH4, which we attribute to HCN embedded in the organic residue formed by ion irradiation. In addition to this band, ternary mixtures containing an oxygen-bearing species (i.e., H2O) form a compound with a prominent absorption band at about 2165 cm-1 (4.62 microns). We ascribe this band to a nitrile compound containing O that is bonded to the organic residue. A detailed comparison of the laboratory results with astronomical data of the 4.62 microns absorption band in protostellar spectra shows good agreement in peak position and profile. Our experimental studies show that N2, which is a more likely interstellar ice component than NH3, can be the molecular progenitor of the carrier of the interstellar band. This is an alternative to the pathway by which UV photolysis of NH3-containing ices produces the 4.62 microns band and implies that ion bombardment may well play an important role in the evolution of interstellar ices. Here, we discuss the implications of our studies for the chemical route by which the carrier of the 4.62 microns band is formed in these laboratory experiments.

NASA Discipline Exobiology↗

Theoretical Developments in Understanding Massive Star Formation

Except under special circumstances massive stars in galactic disks will form through accretion. The gravitational collapse of a molecular cloud core will initially produce one or more low mass quasi-hydrostatic objects of a few Jupiter masses. Through subsequent accretion the masses of these cores grow as they simultaneously evolve toward hydrogen burning central densities and temperatures. We review the evolution of accreting (proto-)stars, including new results calculated with a publicly available stellar evolution code written by the authors.

stellar evolution↗

Concentric core-shell tracks and spectroscopic properties of SrTiO 3 under intense electronic excitation

A deeper understanding of the intrinsic link between the irradiation-induced microstructures and the corresponding spectroscopic properties is becoming increasingly attractive for the research fields of materials science, physics, and information technology. In this work, the structural damage response, spectroscopic features, and associated physical mechanisms of SrTiO 3 single crystals under swift heavy ion irradiation were comparatively analyzed using a combination of experimental and theoretical approaches. Corresponding to 0.11–5.00 MeV/u ion irradiation with electronic energy loss ranging from 4.0 to 29.3 keV/nm, the inelastic thermal spike calculations combined with molecular dynamics simulations are compared with the experimental observations, revealing the track fine structures (individual spherical defects with a disordered region, and discontinuous and continuous tracks consisting of an amorphous core and a disordered outer shell) and demonstrating the dominant effects of the deposition energy and lattice temperature on track damage formation and evolution; thus, two essential thresholds for defect formation of ~0.60 eV/atom and amorphous region formation of ~1.81 eV/atom were identified to better describe the concentric core-shell track structure. The enhanced nanohillock formation in the surface region is attributed to the combined action of kinetic and potential energy depositions, and the fluence dependence in regulating the hillock dimensions is also presented. The measured refractive index profiles along different crystal axes further indicate the anisotropy of irradiation-induced lattice expansion. With increasing ion fluence and damage level, the intrinsic bandgap gradually decreased, and the concentration of additional radiative recombination centers (1.81 eV, 2.31 eV, and 2.42 eV) accordingly increased in the SrTiO 3 crystal, providing the possibility of regulating related defects to achieve tunable/selective photon emission for more critical technological applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The Evolution of Interstellar Gas: Massive Stars and the Dispersal of Neutral Material

We studied the effects of newly formed O and B stars on their surrounding interstellar material through a combination of observations and theoretical modeling. The observational data came from measurements of absorption seen in the spectra of background, newly formed stars. Particular attention was given to stellar radiation which converts molecular to atomic material. Laboratory data on absorption cross sections relevant to the analysis and interpretation of carbon monoxide formed part of the effort. The grant supported Postdoctoral Fellows, Drs. Min Yan and Yaron Sheffer, and a laboratory technician. Though the students themselves were not supported. one M.S. Thesis and two Ph.D. dissertations from the University of Toledo were based on the research done under the grant. The research accomplished under this grant led directly to other funded programs. An observing proposal to study the chemistry of diffuse molecular clouds in the Large and Small Magellanic Clouds with ESO s Very Large Telescope was another example of a successful outcome of my LTSA program.

Federman, Steven R.↗

Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ

Translesion synthesis (TLS) DNA polymerase Polζ is crucial for the bypass replication over sites of DNA damage. The Rev7 subunit of Polζ is a HORMA (Hop1, Rev7, Mad2) protein that facilitates recruitment of Polζ to the replication fork via interactions with the catalytic subunit Rev3 and the translesion synthesis scaffold protein Rev1. Human Rev7 (hRev7) interacts with two Rev7-binding motifs (RBMs) of hRev3 by a mechanism conserved among HORMA proteins whereby the safety-belt loop of hRev7 closes on the top of the ligand. The two copies of hRev7 tethered by the two hRev3-RBMs form a symmetric head-to-head dimer through the canonical HORMA dimerization interface. Recent cryo-EM structures reveal that Saccharomyces cerevisiae Polζ (scPolζ) also includes two copies of scRev7 bound to distinct regions of scRev3. Surprisingly, the HORMA dimerization interface is not conserved in scRev7, with the two scRev7 protomers forming an asymmetric head-to-tail dimer with a much smaller interface than the hRev7 dimer. Here, we validated the two adjacent RBM motifs in scRev3, which bind scRev7 with affinities that differ by two orders of magnitude and confirmed the 2:1 stoichiometry of the scRev7:Rev3 complex in solution. However, our biophysical studies reveal that scRev7 does not form dimers in solution either on its own accord or when tethered by the two RBMs in scRev3. These findings imply that the scRev7 dimer observed in the cryo-EM structures is induced by scRev7 interactions with other Polζ subunits and that Rev7 homodimerization via the HORMA interface is a mechanism that emerged later in evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adapting enzymes to improve their functionality in plants: why and how

Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context (‘plantized’) even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can — or cannot — be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.

Biochemistry & Molecular Biology↗

Optical readout of singlet fission biexcitons in a heteroacene with photoluminescence detected magnetic resonance

Molecular spin systems based on photoexcited triplet pairs formed via singlet fission (SF) are attractive as carriers of quantum information because of their potentially pure and controllable spin polarization, but developing systems that offer optical routes to readout as well as initialization is challenging. Herein, we characterize the electron spin magnetic resonance change in the photoluminescence intensity for a tailored organic molecular crystal while sweeping a microwave drive up to 10 GHz in a broadband loop structure. We observe resonant transitions for both triplet and quintet spin sublevel populations showing their optical sensitivity and revealing the zero-field parameters for each. We map the evolution of these spectra in both microwave frequency and magnetic field, producing a pattern of optically detected magnetic resonance (ODMR) peaks. Fits to these data using a suitable model suggest significant spin polarization in this system with orientation selectivity. Unusual excitation intensity dependence is also observed, which inverts the sign of the ODMR signal for the triplet features, but not for the quintet. These observations demonstrate optical detection of the spin sublevel population dictated by SF and intermolecular geometry, and highlight anisotropic and multi-scale dynamics of triplet pairs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Theoretical, observational, and isotopic estimates of the lifetime of the solar nebula

There are a variety of isotopic data for meteorites which suggest that the protostellar nebula existed and was involved in making planetary materials for some 10(exp 7) yr or more. Many cosmochemists, however, advocate alternative interpretations of such data in order to comply with a perceived constraint, from theoretical considerations, that the nebula existed only for a much shorter time, usually stated as less than or = 10(exp 6) yr. In this paper, we review evidence relevant to solar nebula duration which is available through three different disciplines: theoretical modelling of star formation, isotopic data from meteorites, and astronomical observations of T Tauri stars. Theoretical models based on observations of present star-forming regions indicate that stars like the Sun form by dynamical gravitational collapse of dense cores of cold molecular clouds in the interstellar medium. The collapse to a star and disk occurs rapidly on a time scale of the order 10(exp 5) yr. Disks evolve by dissipating energy while redistributing angular momentum, but it is difficult to predict the rate of evolution, particularly for low mass (compared to the star) disks which nonetheless still contain enough material to account for the observed planetary system. There is no compelling evidence, from available theories of disk structure and evolution, that the solar nebula must have evolved rapidly and could not have persisted for more than 1 Ma. In considering chronologically relevant isotopic data for meteorites, we focus on three methodologies: absolute ages by U-Pb/Pb-Pb, and relative ages by short-lived radionuclides (especially Al-26) and by evolution of Sr-87/Sr-86. Two kinds of meteoritic materials-refractory inclusions such as CAIs and differentiated meteorites (eucrites and angrites) - appear to have experience potentially dateable nebular events. In both case, the most straightforward interpretations of the available data indicate nebular events spanning several Ma. We also consider alternative interpretations, particularly the hypothesis of radically heterogeneous distribution of Al-26, which would avoid these chronological interpretations. The principal impetus for such alternative interpretations seems to be precisely the obviation of the chronological interpretation (i.e., the presumption rather than the inference of a short (less than or = Ma) lifetime of the nebula). Astronomical observations of T Tauri stars indicate that the presence of dusty disks is a common if not universal feature, that the disks are massive enough to accomodate a planetary system such as ours, and that at least some persist for 10(exp 7) yr or more. The results are consistent with the time scales inferred from the meteorite isotopic data. They cannot be considered conclusive with regard to solar nebula time scales, however,in part because it is difficult to relate disk observations to processes that affect meteorites, and in part because the ages assigned for these stars could be wrong by a factor of several in either direction. We conclude that the balance of available evidence favors the view that the nebula existed and was active for at least several Ma. However, because the evidence is not definitive, it is important that the issue be perceived to be an open question, whose answer should be sought rather than presumed.

Podosek, Frank A.↗