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Clinical use of polymeric scaffolds for tissue engineering often suffers from their inability to promote strong cellular interactions. Functionalization with biomolecules may improve outcomes; however, current functionalization approaches using covalent chemistry or physical adsorption can lead to loss of biomolecule bioactivity. Here, we demonstrate a novel bottom-up approach for enhancing the bioactivity of poly(l-lactic acid) electrospun scaffolds though interfacial coassembly of protein payloads with silk fibroin into nanothin coatings. In our approach, protein payloads are first added into an aqueous solution with Bombyx mori-derived silk fibroin. Phosphate anions are then added to trigger coassembly of the payload and silk fibroin, as well as noncovalent formation of a payload-silk fibroin coating at poly(l-lactic) acid fiber surfaces. Importantly, the coassembly process results in homogeneous distribution of protein payloads, with the loading quantity depending on payload concentration in solution and coating time. This coassembly process yields greater loading capacity than physical adsorption methods, and the payloads can be released over time in physiologically relevant conditions. We also demonstrate that the coating coassembly process can incorporate nerve growth factor and that coassembled coatings lead to significantly more neurite extension than loading via adsorption in a rat dorsal root ganglia explant culture model. 

We report striking Doppler velocity gradients observed during the well-observed 2017 September 10 solar flare, and argue that they are consistent with the presence of an above-the-looptop termination shock beneath the flare current sheet. Observations from the Hinode Extreme-ultraviolet Imaging Spectrometer measure plasma sheet Doppler shifts up to 35 km s−1 during the late-phase of the event. By comparing these line-of-sight flows with plane-of-sky (POS) measurements, we calculate total velocity downflows of 200+ km s−1, orientated ≈6–10° out of the POS. The observed velocities drop rapidly at the base of the hot plasma sheet seen in extreme ultraviolet, consistent with simulated velocity profiles predicted by our 2.5D magnetohydrodynamics model that features a termination shock at the same location. Finally, the striking velocity deceleration aligns spatially with the suppression of Fe xxiv non-thermal velocities, and a 35–50 keV hard X-ray looptop source observed by the Reuven Ramaty High Energy Solar Spectroscopic Imager. Together, these observations are consistent with the presence of a possible termination shock within the X8.2-class solar flare.

 

Perovskite oxides (ternary chemical formula ABO₃) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent (chemical formula$${A}_{x}{A}_{1-x}^{\text{'}}{B}_{y}{B}_{1-y}^{\text{'}}{O}_{3}$$$A_x{A}_{1-x}^{\text{'}}{B}_y{B}_{1-y}^{\text{'}}{O}_3$) chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed$${A}_{x}{A}_{1-x}^{{\prime} }{B}_{y}{B}_{1-y}^{{\prime} }{O}_{3}$$$A_x{A}_{1-x}^{\prime }{B}_y{B}_{1-y}^{\prime }{O}_3$compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, 69,407$${A}_{0.5}{A}_{0.5}^{{\prime} }{B}_{0.5}{B}_{0.5}^{{\prime} }{O}_{3}$$$A_{0.5}{A}_{0.5}^{\prime }{B}_{0.5}{B}_{0.5}^{\prime }{O}_3$compositions were generated in thea⁻b⁺a⁻Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with density functional theory (DFT) using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔH_f) and decomposition enthalpies (ΔH_d) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated$${A}_{0.5}{A}_{0.5}^{{\prime} }{B}_{0.5}{B}_{0.5}^{{\prime} }{O}_{3}$$$A_{0.5}{A}_{0.5}^{\prime }{B}_{0.5}{B}_{0.5}^{\prime }{O}_3$perovskite structures using MP-compatible DFT calculations.

 

Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well described by a stable three-dimensional structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means that IDRs are largely absent from the Protein Data Bank, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations and deep learning to develop ALBATROSS, a deep-learning model for predicting ensemble dimensions of IDRs, including the radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences at a proteome-wide scale. ALBATROSS is lightweight, easy to use and accessible as both a locally installable software package and a point-and-click-style interface via Google Colab notebooks. We first demonstrate the applicability of our predictors by examining the generalizability of sequence–ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize the sequence-specific biophysical behavior of IDRs within and between proteomes.

 

Since the early 2010s, anthropogenic aerosols have started decreasing in East Asia (EA) while have continued to increase in South Asia (SA). Yet the climate impacts of this Asian aerosol dipole (AAD) pattern remain largely unknown. Using a state-of-the-art climate model, we demonstrate that the climate response is distinctly different between the SA aerosol increases and EA aerosol decreases. The SA aerosol increases lead to ~2.7 times stronger land summer precipitation change within the forced regions than the EA aerosol decreases. Contrastingly, the SA aerosol increases, within the tropical monsoon regime, produce weak and tropically confined responses, while the EA aerosol decreases yield a pronounced northern hemisphere warming aided by extratropical mean westerly and positive air-sea feedbacks over the western North Pacific. By scaling the observed instantaneous shortwave radiative forcing, we reveal that the recent AAD induces a pronounced northern hemisphere extratropical (beyond 30°N) warming (0.024 ± 0.010 °C decade⁻¹), particularly over Europe (0.049 ± 0.009 °C decade⁻¹). These findings highlight the importance of the pattern effect of forcings in driving global climate and have important implications for decadal prediction.

 

CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the pathogenic (A2G3)n and nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.

 

Methylphosphate Capping Enzyme (MePCE) monomethylates the gamma phosphate at the 5′ end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MePCE in vitro, little is known about its functions in vivo, or what roles—if any—there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MePCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MePCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MePCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some—but not all—bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.

 

Recent coarse-grained (CG) models have often supplemented conventional pair potentials with potentials that depend upon the local density around each particle. In this work, we investigate the temperature-dependence of these local density (LD) potentials. Specifically, we employ the multiscale coarse-graining (MS-CG) force-matching variational principle to parameterize pair and LD potentials for one-site CG models of molecular liquids at ambient pressure. The accuracy of these MS-CG LD potentials quite sensitively depends upon the length-scale, rc, that is employed to define the local density. When the local density is defined by the optimal length-scale, rc*, the MS-CG potential often accurately describes the reference state point and can provide reasonable transferability across a rather wide range of temperatures. At ambient pressure, the optimal LD length-scale varies linearly with temperature over a very wide range of temperatures. Moreover, if one adopts this temperature-dependent LD length-scale, then the MS-CG LD potential appears independent of temperature, while the MS-CG pair potential varies linearly across this temperature range. This provides a simple means for predicting pair and LD potentials that accurately model new state points without performing additional atomistic simulations. Surprisingly, at certain state points, the predicted potentials provide greater accuracy than MS-CG potentials that were optimized for the state point. 

Abstract Background Many snakes are low-energy predators that use crypsis to ambush their prey. Most of these species feed very infrequently, are sensitive to the presence of larger vertebrates, such as humans, and spend large portions of their lifetime hidden. This makes direct observation of feeding behaviour challenging, and previous methodologies developed for documenting predation behaviours of free-ranging snakes have critical limitations. Animal-borne accelerometers have been increasingly used by ecologists to quantify activity and moment-to-moment behaviour of free ranging animals, but their application in snakes has been limited to documenting basic behavioural states (e.g., active vs. non-active). High-frequency accelerometry can provide new insight into the behaviour of this important group of predators, and here we propose a new method to quantify key aspects of the feeding behaviour of three species of viperid snakes ( Crotalus spp.) and assess the transferability of classification models across those species. Results We used open-source software to create species-specific models that classified locomotion, stillness, predatory striking, and prey swallowing with high precision, accuracy, and recall. In addition, we identified a low cost, reliable, non-invasive attachment method for accelerometry devices to be placed anteriorly on snakes, as is likely necessary for accurately classifying distinct behaviours in these species. However, species-specific models had low transferability in our cross-species comparison. Conclusions Overall, our study demonstrates the strong potential for using accelerometry to document critical feeding behaviours in snakes that are difficult to observe directly. Furthermore, we provide an ‘end-to-end’ template for identifying important behaviours involved in the foraging ecology of viperids using high-frequency accelerometry. We highlight a method of attachment of accelerometers, a technique to simulate feeding events in captivity, and a model selection procedure using biologically relevant window sizes in an open-access software for analyzing acceleration data (AcceleRater). Although we were unable to obtain a generalized model across species, if more data are incorporated from snakes across different body sizes and different contexts (i.e., moving through natural habitat), general models could potentially be developed that have higher transferability.