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At least 253 records · Page 14

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2–3 × 10 −4 (Δ E / E ). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (Δ E / E = 3 × 10 −3 ) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction.

59 BASIC BIOLOGICAL SCIENCES↗

VitroJet: new features and case studies

Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before being able to inspect a biological sample in an electron microscope, it needs to be deposited in a thin layer on a grid and rapidly frozen. The VitroJet was designed with this aim, as well as avoiding the delicate manual handling and transfer steps that occur during the conventional grid-preparation process. Since its creation, numerous technical developments have resulted in a device that is now widely utilized in multiple laboratories worldwide. It features plasma treatment, low-volume sample deposition through pin printing, optical ice-thickness measurement and cryofixation of pre-clipped Autogrids through jet vitrification. This paper presents recent technical improvements to the VitroJet and the benefits that it brings to the cryo-EM workflow. A wide variety of applications are shown: membrane proteins, nucleosomes, fatty-acid synthase, Tobacco mosaic virus, lipid nanoparticles, tick-borne encephalitis viruses and bacteriophages. These case studies illustrate the advancement of the VitroJet into an instrument that enables accurate control and reproducibility, demonstrating its suitability for time-efficient cryo-EM structure determination.

59 BASIC BIOLOGICAL SCIENCES↗

Aridity and forest age mediate landscape scale patterns of tropical forest resistance to cyclonic storms

Abstract Cyclonic storms, or hurricanes, are expected to intensify as ocean heat energy rises due to climate change. Ecological theory suggests that tropical forest resistance to hurricanes should increase with forest age and wood density. However, most data on hurricane effects on tropical forests come from a limited number of well‐studied long‐term monitoring sites, restricting our capacity to evaluate the resistance of tropical forests to hurricanes across broad environmental gradients. In this study, we assessed whether forest age and aridity mediate the effects of hurricanes Irma and Maria in Puerto Rico, Vieques and Culebra islands. We leveraged functional trait data for 410 tree species, remotely sensed measurements of canopy height and cover, along with data on forest stand characteristics of 180 of 338 forest monitoring plots, each covering an area of 0.067 ha. The plots represent a broad mean annual precipitation (MAP) gradient from 701 to 4598 mm and a complex mosaic of forest age from 5 to around 85 years since deforestation. Hurricanes resulted in a 25% increase in basal area mortality rates, a 45% decrease in canopy height and a 21% reduction in canopy cover. These effects intensified with forest age, even after considering proximity to the hurricane path. The links between forest age and hurricane disturbances were likely due the prevalence of tall canopies. Tall forest canopies were strongly linked with low community‐weighted wood density (WD). These characteristics were on average more common in moist and wet forests (MAP >1250 mm). Conversely, dry forests were dominated by short species with high wood density (WD > 0.6 g cm −3 ) and did not show significant increases in basal area mortality rates after the hurricanes. Synthesis . Our findings show that selection towards drought‐tolerant traits across aridity gradients, such as short stature and dense wood, enhances resistance to hurricanes. However, forest age modulated responses to hurricanes, with older forests being less resistant across the islands. This evidence highlights the importance of considering the intricate links between ecological succession and plant function when forecasting tropical forests’ responses to increasingly strong hurricanes.

Vargas G., German↗

Climate lags and genetics determine phenology in quaking aspen ( Populus tremuloides )

Spatiotemporal patterns of phenology may be affected by mosaics of environmental and genetic variation. Environmental drivers may have temporally lagged impacts, but patterns and mechanisms remain poorly known. Here, we combine multiple genomic, remotely sensed, and physically modeled datasets to determine the spatiotemporal patterns and drivers of canopy phenology in quaking aspen, a widespread clonal dioecious tree species with diploid and triploid cytotypes. We show that over 391 km 2 of southwestern Colorado: greenup date, greendown date, and growing season length vary by weeks and differ across sexes, cytotypes, and genotypes; phenology has high phenotypic plasticity and heritabilities of 31–61% (interquartile range); and snowmelt date, soil moisture, and air temperature predict phenology, at temporal lags of up to 3 yr. Our study shows that lagged environmental effects are needed to explain phenological variation and that the effect of cytotype on phenology is obscured by its correlation with topography. Phenological patterns are consistent with responses to multiyear accumulation of carbon deficit or hydraulic damage.

carbon allocation↗

Viral‐mediated delivery of morphogenic regulators enables leaf transformation in Sorghum bicolor (L.)

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom (Bbm), Wuschel2 (Wus2), Wuschel-like homeobox protein 2a (Wox2a) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

59 BASIC BIOLOGICAL SCIENCES↗

A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure

Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo–electron microscopy (cryo-EM), we visualized the structure of the mysterious viral transfer RNA (tRNA)–like structure (TLS) from the brome mosaic virus, which affects replication, translation, and genome encapsidation. Structures in isolation and those bound to tyrosyl-tRNA synthetase (TyrRS) show that this ~55-kilodalton purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs substantially from that of tRNA. Our study reveals how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions, and we highlight the utility of cryo-EM for visualizing small, conformationally dynamic structured RNAs.

Science & Technology - Other Topics↗

DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture

Investigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid C. acetobutylicum / C. ljungdahlii cells displaying hybrid DNA-methylation patterns.

59 BASIC BIOLOGICAL SCIENCES↗

Formation of wide-blocky calcite veins by extreme growth competition

Liassic limestones on the coast of Somerset in the UK contain dense arrays of calcite microveins with a common, but poorly understood microstructure, characterized by laterally wide crystals that form bridges across the vein. We investigated the mechanisms of formation and evolution of these ‘wide-blocky’ vein microstructures using a combination of high-resolution analytical methods, including virtual petrography, optical cathodoluminescence and scanning electron microscopy techniques (e.g. energy-dispersive X-ray spectrometry, back-scattered electron imaging, cathodoluminescence and electron back-scattered diffraction), laboratory experiments and multiphase field modelling. Our results indicate that the studied veins formed in open, fluid-filled fractures, each in a single opening and sealing episode. As shown by the optical and electron back-scattered diffraction images, the vein crystals grew epitaxially on grains of the wall rock and we hypothesize that their growth rates differed depending on whether the crystals were on a wall rock grain substrate that fractured intergranularly (slow growth rates) or transgranularly (rapid growth rates). Our multiphase field models support this hypothesis, showing that wide, blocky crystals only form where there are significant differences in the growth rate and are dependent on the type of seed grain. These results provide strong evidence for extreme growth competition, a process that we propose controls vein-filling in many micritic carbonate reservoirs, as well as demonstrate that the characteristics of the fracture wall can affect the filling processes in syntaxial veins. Supplementary material: The description and images of the studied thin sections are available at https://doi.org/10.6084/m9.figshare.c.5172371 . High-resolution optical microscopy mosaics (under plane-polarized- and crossed polarized light) of the thin section collection in PetroScan file format are available on request from the authors.

Geology↗

Berkeley eXtensible Environment (BXE) v3

The Berkeley eXtensible Environment (BXE) provides a cloud environment for hardware designers and computer architects to design, build, and simulate their custom architectures on an on-premises FPGA cluster. Utilizing the Chipyard, MoSAIC, and FireSim frameworks, users are provided an environment where they can assemble SoC designs from an existing library of components or import their own source code. Once their designs are ready, they can utilize the FireSim framework provided by BXE to deploy and simulate their designs on the FPGA. Users aren't limited to a single FPGA; they can deploy multiple instances across multiple FPGAs, acting like a rack of servers, or partition their large design across multiple FPGAs, ganging multiple FPGAs into a single simulated system.

Fatollahi-Fard, Farzin↗

Frozen Hydrometeor Terminal Fall Velocity Dependence on Particle Habit and Riming as Observed by Vertically Pointing Radars

Vertically pointing Ka-band radar measurements are used to derive fall velocity–reflectivity factor ($V$ t = $aZ$$^{b}_{e}$) relations for frozen hydrometeor populations of different habits during snowfall events observed at Oliktok Point, Alaska, and at the Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC). Case study events range from snowfall with highly rimed particles observed during periods with large amounts of supercooled liquid water path (LWP > 320 g m –2 ) to unrimed snowflakes including instances when pristine planar crystals were the dominant frozen hydrometeor habit. The prefactor a and the exponent b in the observed $V$ t –$Z$ e relations scaled to the sea level vary in the approximate ranges 0.5–1.4 and 0.03–0.13, respectively (reflectivities are in mm 6 m –3 and velocities are in m s –1 ). The coefficient a values are the smallest for planar crystals (a ~ 0.5) and the largest (a > 1.2) for particles under severe riming conditions with high LWP. There is no clear distinction between b values for high and low LWP conditions. The range of the observed $V$ t –$Z$ e relation coefficients is in general agreement with results of modeling using fall velocity–size (υ t = αD β ) relations for individual particles found in literature for hydrometeors of different habits, though there is significant variability in α and β coefficients from different studies even for a same particle habit. Correspondences among coefficients in the $V$ t –$Z$ e relations for particle populations and in the individual particle υ t –$D$ relations are analyzed. Furthermore, these correspondences and the observed $V$ t –$Z$ e relations can be used for evaluating different frozen hydrometeor fall velocity parameterizations in models.

54 ENVIRONMENTAL SCIENCES↗

Urbanization-induced land and aerosol impacts on storm propagation and hail characteristics

Changes in land surface and aerosol characteristics from urbanization can affect dynamic and microphysical properties of severe storms, thus affecting hazardous weather events resulting from such storms such as hail and tornado. We examine the joint and individual effects of urban land and anthropogenic aerosols of Kansas City on a severe convective storm observed during the 2015 Plains Elevated Convection At Night (PECAN) field campaign, focusing on storm evolution, convective intensity, and hail characteristics. The simulations are carried out at the cloud-resolving scale (1 km) using a version of WRF-Chem in which the spectral-bin microphysics (SBM) is coupled with the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC). It is found that the urban land effect of Kansas City initiated a much stronger convective cell and the storm got further intensified when interacting with stronger turbulence induced by the urban land. The urban land effect also changed the storm path by diverting the storm toward the city mainly resulting from enhanced urban land-induced convergence in the urban area and around the urban-rural boundaries. The joint effect of urban land and anthropogenic aerosols enhances occurrences of both severe hail and significant severe hail by ~ 20% by enhancing hail formation and growth from riming. Overall the urban land effect on convective intensity and hail is relatively larger than the anthropogenic aerosol effect, but the joint effect is much notable than either of the individual effects, emphasizing the importance to consider both effects in evaluating urbanization effects.

Lin, Yun↗

A Machine Learning Correction Model of the Winter Clear-Sky Temperature Bias over the Arctic Sea Ice in Atmospheric Reanalyses

Atmospheric reanalyses are widely used to estimate the past atmospheric near-surface state over sea ice. They provide boundary conditions for sea ice and ocean numerical simulations and relevant information for studying polar variability and anthropogenic climate change. Previous research revealed the existence of large near-surface temperature biases (mostly warm) over the Arctic sea ice in the current generation of atmospheric reanalyses, which is linked to a poor representation of the snow over the sea ice and the stably stratified boundary layer in the forecast models used to produce the reanalyses. These errors can compromise the employment of reanalysis products in support of polar research. Here, we train a fully connected neural network that learns from remote sensing infrared temperature observations to correct the existing generation of uncoupled atmospheric reanalyses (ERA5, JRA-55) based on a set of sea ice and atmospheric predictors, which are themselves reanalysis products. The advantages of the proposed correction scheme over previous calibration attempts are the consideration of the synoptic weather and cloud state, compatibility of the predictors with the mechanism responsible for the bias, and a self-emerging seasonality and multidecadal trend consistent with the declining sea ice state in the Arctic. The correction leads on average to a 27% temperature bias reduction for ERA5 and 7% for JRA-55 if compared to independent in situ observations from the MOSAiC campaign (respectively, 32% and 10% under clear-sky conditions). These improvements can be beneficial for forced sea ice and ocean simulations, which rely on reanalyses surface fields as boundary conditions.

54 ENVIRONMENTAL SCIENCES↗

BSMV-mediated genome editing exhibits host-specific heritability: germline transmission in barley and somatic edits in Nicotiana benthamiana

Plant RNA virus–mediated guide RNA (gRNA) delivery represents a transformative advance in genome editing technologies. Unlike conventional transformation methods that rely on labor-intensive tissue culture and regeneration for each individual gRNA delivery, viral vectors can rapidly and systemically transmit gRNAs into pre-established Cas-expressing plants, providing an accelerated route for functional genomics and trait discovery directly in planta . However, key design parameters, including subgenomic promoter choice, transcript architecture, and their effects on viral fitness and editing outcomes, remain to be elucidated for most viral platforms. We developed five Barley stripe mosaic virus (BSMV) vectors, each with distinct subgenomic promoter elements to drive single gRNA expression. These were initially evaluated in Cas9-expressing transgenic Nicotiana benthamiana plants targeting the Phytoene desaturase ( PDS ) gene to compare their editing efficiencies. Single gRNAs expressed under the duplicated γb subgenomic promoter or when fused directly to the γb genome achieved the highest mutation frequencies (up to 90% at 60 days post-inoculation), whereas β1- and β2-driven sgRNAs produced delayed and reduced editing. Thus, promoter selection critically determines gRNA accumulation and the efficacy of BSMV-mediated genome editing. The top-performing design was then applied to Cas9-expressing barley ( Hordeum vulgare ) targeting HvCMF7 (conferring green-white variegation) and HvGW2.1 (impacts grain width and weight). BSMV spread systemically throughout barley, inducing somatic and heritable mutations at frequencies up to 100%, with virus-free edited progeny. In contrast, despite robust somatic editing in N. benthamiana, no heritable mutations were detected indicating species-dependent limitations in germline transmission. Our systematic comparison of subgenomic promoter architectures establishes clear design principles for optimizing viral vector–mediated delivery. Promoter choice and transcript structure critically shape editing efficiency and viral stability. The host-specific boundary for germline editing, defined by efficient heritable editing in barley but not N. benthamiana , highlights where BSMV offers advantages and where alternative vectors or hybrid strategies are required, guiding rational platform selection for diverse crop species and applications. Collectively, these findings establish BSMV as a promising next-generation vector for rapid, tissue culture–free, and transformation-independent genome editing in cereals and other recalcitrant monocots.

barley↗

Characterizing post-fire delayed tree mortality with remote sensing: sizing up the elephant in the room

Abstract Background Despite recent advances in understanding the drivers of tree-level delayed mortality, we lack a method for mapping delayed mortality at landscape and regional scales. Consequently, the extent, magnitude, and effects of delayed mortality on post-fire landscape patterns of burn severity are unknown. We introduce a remote sensing approach for mapping delayed mortality based on post-fire decline in the normalized burn ratio (NBR). NBR decline is defined as the change in NBR between the first post-fire measurement and the minimum NBR value up to 5 years post-fire for each pixel. We validate the method with high-resolution aerial photography from six wildfires in California, Oregon, and Washington, USA, and then compare the extent, magnitude, and effects of delayed mortality on landscape patterns of burn severity among fires and forest types. Results NBR decline was significantly correlated with post-fire canopy mortality (r 2 = 0.50) and predicted the presence of delayed mortality with 83% accuracy based on a threshold of 105 NBR decline. Plots with NBR decline greater than 105 were 23 times more likely to experience delayed mortality than those below the threshold (p < 0.001). Delayed mortality occurred across 6–38% of fire perimeters not affected by stand-replacing fire, generally affecting more areas in cold (22–41%) and wet (30%) forest types than in dry (1.7–19%) types. The total area initially mapped as unburned/very low-severity declined an average of 38.1% and generally persisted in smaller, more fragmented patches when considering delayed mortality. The total area initially mapped as high-severity increased an average of 16.2% and shifted towards larger, more contiguous patches. Conclusions Differences between 1- and 5-year post-fire burn severity maps depict dynamic post-fire mosaics resulting from delayed mortality, with variability among fires reflecting a range of potential drivers. We demonstrate that tree-level delayed mortality scales up to alter higher-level landscape patterns of burn severity with important implications for forest resilience and a range of fire-driven ecological outcomes. Our method can complement existing tree-level studies on drivers of delayed mortality, refine mapping of fire refugia, inform estimates of habitat and carbon losses, and provide a more comprehensive assessment of landscape and regional scale fire effects and trends.

Environmental Sciences & Ecology↗

Data for Quantifying the Impact of Surfactants on Cloud Condensation Nuclei Activity Using a Particle-Resolved Model

This dataset contains simulation results from PartMC-MOSAIC and WRF-PartMC that used in the journal article: Quantifying the Impact of Surfactants on Cloud Condensation Nuclei Activity Using a Particle-Resolved Model. Two compressed folder are uploaded here, one is for the data that used in this article, the other folder is the python scripts to process the data. For more details of the uploaded files, please check the README file.

CCN↗

Data for "Viral-mediated Delivery of Morphogenic Regulators Enables Leaf Transformation in Sorghum bicolor (L.)"

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom ( Bbm ), Wuschel2 ( Wus2 ), Wuschel-like homeobox protein 2a ( Wox2a ) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

gene editing↗

Magnon Dispersion in CeIn3

This dataset contains measurements of the low-energetic magnetic excitations in the heavy-fermion material CeIn3. Neutron spectroscopy data were recorded on a single-crystal mosaic of around 2 g total mass at the spectrometer CNCS. In a first row of measurements with incident neutron energy 12 meV the excitations were mapped out in major parts of the first Brillouin zone. In a second row of measurements with 3.315 meV incident neutron energy, the gapless and relatively steep dispersion in the vicinity of the R-point, corresponding to (1/2,1/2,1/2) in reciprocal space, was investigated.

excitations↗

Time-of-flight inelastic neutron scattering data of the quantum spin-Peierls chain CuGeO3

Inelastic neutron scattering data of co-aligned CuGeO3 single crystals (5.21 g). The data were collected at SEQUOIA time-of-flight spectrometer. The samples were mounted with the (0KL) plane horizontal. Co-alignment was achieved with overall mosaicity of 1 degree. The data were collected at 5 K, 20 K, 50 K, 100 K, and 150 K with incident neutron energies Ei = 24 and 60 meV and the standard high-resolution chopper condition.

36 MATERIALS SCIENCE↗