Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories.

The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.

Giant Modulation of Refractive Index from Picoscale Atomic Displacements.

It is shown that structural disorder-in the form of anisotropic, picoscale atomic displacements-modulates the refractive index tensor and results in the giant optical anisotropy observed in BaTiS3, a quasi-1D hexagonal chalcogenide. Single-crystal X-ray diffraction studies reveal the presence of antipolar displacements of Ti atoms within adjacent TiS6 chains along the c-axis, and threefold degenerate Ti displacements in the a-b plane. 47/49Ti solid-state NMR provides additional evidence for those Ti displacements in the form of a three-horned NMR lineshape resulting from a low symmetry local environment around Ti atoms. Scanning transmission electron microscopy is used to directly observe the globally disordered Ti a-b plane displacements and find them to be ordered locally over a few unit cells. First-principles calculations show that the Ti a-b plane displacements selectively reduce the refractive index along the ab-plane, while having minimal impact on the refractive index along the chain direction, thus resulting in a giant enhancement in the optical anisotropy. By showing a strong connection between structural disorder with picoscale displacements and the optical response in BaTiS3, this study opens a pathway for designing optical materials with high refractive index and functionalities such as large optical anisotropy and nonlinearity.

The Hydrogen Evolution Activity of BaZrS3, BaTiS3, and BaVS3 Chalcogenide Perovskites.

Chalcogenide perovskites are a class of materials with electronic and optoelectronic properties desirable for solar cells, infrared optics, and computing. The oxide counterparts of these chalcogenides have been studied extensively for their electrocatalytic and photoelectrochemical properties. As chalcogenide perovskites are more covalent, conductive, and stable, we hypothesize that they are more viable as electrocatalysts than oxide perovskites. The goal of this synthetic, experimental, and computational study is to examine the hydrogen evolution reaction (HER) activity of three Barium-based chalcogenides in perovskite and related structures: BaZrS3, BaTiS3, and BaVS3. Potential energy surfaces for hydrogen adsorption on surfaces of these materials are calculated using density functional theory and the computational hydrogen electrode model is used to contrast overpotentials with experiment. Although both experiments and computations agree that BaVS3 is the most active of the three materials, high overpotentials of these materials make them less viable than platinum for HER. Our work establishes a framework for future studies in the chemical and electrochemical properties of chalcogenide perovksites.

Antiviral fibrils of self-assembled peptides with tunable compositions.

The lasting threat of viral pandemics necessitates the development of tailorable first-response antivirals with specific but adaptive architectures for treatment of novel viral infections. Here, such an antiviral platform has been developed based on a mixture of hetero-peptides self-assembled into functionalized ß-sheets capable of specific multivalent binding to viral protein complexes. One domain of each hetero-peptide is designed to specifically bind to certain viral proteins, while another domain self-assembles into fibrils with epitope binding characteristics determined by the types of peptides and their molar fractions. The self-assembled fibrils maintain enhanced binding to viral protein complexes and retain high resilience to viral mutations. This method is experimentally and computationally tested using short peptides that specifically bind to Spike proteins of SARS-CoV-2. This platform is efficacious, inexpensive, and stable with excellent tolerability.

MAG-Res2Net: a novel deep learning network for human activity recognition.

Objective.Human activity recognition (HAR) has become increasingly important in healthcare, sports, and fitness domains due to its wide range of applications. However, existing deep learning based HAR methods often overlook the challenges posed by the diversity of human activities and data quality, which can make feature extraction difficult. To address these issues, we propose a new neural network model called MAG-Res2Net, which incorporates the Borderline-SMOTE data upsampling algorithm, a loss function combination algorithm based on metric learning, and the Lion optimization algorithm.Approach.We evaluated the proposed method on two commonly utilized public datasets, UCI-HAR and WISDM, and leveraged the CSL-SHARE multimodal human activity recognition dataset for comparison with state-of-the-art models.Main results.On the UCI-HAR dataset, our model achieved accuracy, F1-macro, and F1-weighted scores of 94.44%, 94.38%, and 94.26%, respectively. On the WISDM dataset, the corresponding scores were 98.32%, 97.26%, and 98.42%, respectively.Significance.The proposed MAG-Res2Net model demonstrates robust multimodal performance, with each module successfully enhancing model capabilities. Additionally, our model surpasses current human activity recognition neural networks on both evaluation metrics and training efficiency. Source code of this work is available at:https://github.com/LHY1007/MAG-Res2Net.

Charge Density Wave Order and Electronic Phase Transitions in a Dilute d-Band Semiconductor.

As one of the most fundamental physical phenomena, charge density wave (CDW) order predominantly occurs in metallic systems such as quasi-1D metals, doped cuprates, and transition metal dichalcogenides, where it is well understood in terms of Fermi surface nesting and electron-phonon coupling mechanisms. On the other hand, CDW phenomena in semiconducting systems, particularly at the low carrier concentration limit, are less common and feature intricate characteristics, which often necessitate the exploration of novel mechanisms, such as electron-hole coupling or Mott physics, to explain. In this study, an approach combining electrical transport, synchrotron X-ray diffraction, and density-functional theory calculations is used to investigate CDW order and a series of hysteretic phase transitions in a dilute d-band semiconductor, BaTiS3 . These experimental and theoretical findings suggest that the observed CDW order and phase transitions in BaTiS3 may be attributed to both electron-phonon coupling and non-negligible electron-electron interactions in the system. This work highlights BaTiS3 as a unique platform to explore CDW physics and novel electronic phases in the dilute filling limit and opens new opportunities for developing novel electronic devices.

Colossal Optical Anisotropy from Atomic-Scale Modulations.

Materials with large birefringence (Δn, where n is the refractive index) are sought after for polarization control (e.g., in wave plates, polarizing beam splitters, etc.), nonlinear optics, micromanipulation, and as a platform for unconventional light-matter coupling, such as hyperbolic phonon polaritons. Layered 2D materials can feature some of the largest optical anisotropy; however, their use in most optical systems is limited because their optical axis is out of the plane of the layers and the layers are weakly attached. This work demonstrates that a bulk crystal with subtle periodic modulations in its structure-Sr9/8 TiS3 -is transparent and positive-uniaxial, with extraordinary index ne = 4.5 and ordinary index no = 2.4 in the mid- to far-infrared. The excess Sr, compared to stoichiometric SrTiS3 , results in the formation of TiS6 trigonal-prismatic units that break the chains of face-sharing TiS6 octahedra in SrTiS3 into periodic blocks of five TiS6 octahedral units. The additional electrons introduced by the excess Sr form highly oriented electron clouds, which selectively boost the extraordinary index ne and result in record birefringence (Δn > 2.1 with low loss). The connection between subtle structural modulations and large changes in refractive index suggests new categories of anisotropic materials and also tunable optical materials with large refractive-index modulation.

Structure of Orthoreovirus RNA Chaperone σNS, a Component of Viral Replication Factories.

The reovirus σNS RNA-binding protein is required for formation of intracellular compartments during viral infection that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of an R6A mutant of σNS that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure of selenomethionine-substituted σNS-R6A reveals that the mutant protein forms a stable antiparallel dimer, with each subunit having a well-folded central core and a projecting N-terminal arm. The dimers interact with each other by inserting the N-terminal arms into a hydrophobic pocket of the neighboring dimers on either side to form a helical assembly that resembles filaments of WT σNS in complex with RNA observed using cryo-EM. The interior of the crystallographic helical assembly is positively charged and of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same hydrophobic pocket as the N-terminal arm, as demonstrated in the crystal structure of σNS-R6A in complex with bile acid, suggesting that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS. This idea is supported by the structure of σNS lacking the N-terminal arm. We discovered that σNS displays RNA helix destabilizing and annealing activities, likely essential for presenting mRNA to the viral RNA-dependent RNA polymerase for genome replication. The RNA chaperone activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.

Characteristics of the paravertebral muscle in adult degenerative scoliosis with PI-LL match or mismatch and risk factors for PI-LL mismatch.

Objective: Pelvic incidence (PI) minus the lumbar lordosis (LL) angle (PI-LL) correlates with function and disability. It is associated with paravertebral muscle (PVM) degeneration and is a valuable tool for surgical planning of adult degenerative scoliosis (ADS). This study aims to explore the characteristics of PVM in ADS with PI-LL match or mismatch and to identify the risk factors for PI-LL mismatch. Methods: A total of 67 patients with ADS were divided into PI-LL match and mismatch groups. The visual analog scale (VAS), symptom duration, and Oswestry disability index (ODI) were used to assess patients' clinical symptoms and quality of life. The percentage of fat infiltration area (FIA%) of the multifidus muscle at the L1-S1 disc level was measured by using MRI with Image-J software. Sagittal vertical axis, LL, pelvic tilt (PT), PI, sacral slope, and the asymmetric and average degeneration degree of the multifidus were recorded. Logistic regression analysis was done to identify the risk factors for PI-LL mismatch. Results: In the PI-LL match and mismatch groups, the average FIA% of the multifidus on the convex side was less than that on the concave side (P < 0.05). There was no statistical difference of asymmetric degeneration degree of the multifidus between the two groups (P > 0.05). In the PI-LL mismatch group, the average degeneration degree of the multifidus, VAS, symptom duration, and ODI were significantly higher than that in the PI-LL match group, respectively (32.22 ± 6.98 vs. 26.28 ± 6.23 (%), 4.33 ± 1.60 vs. 3.52 ± 1.46, 10.81 ± 4.83 vs. 6.58 ± 4.23 (month), 21.06 ± 12.58 vs. 12.97 ± 6.49, P < 0.05). The average degeneration degree of the multifidus muscle was positively correlated with the VAS, symptom duration, and ODI, respectively (r = 0.515, 0.614, and 0.548, P < 0.05). Sagittal plane balance, LL, PT, and the average degeneration degree of the multifidus were the risk factors for PI-LL mismatch (OR: 15.447, 95% CI: 1.274-187.269; OR: 0.001, 95% CI: 0.000-0.099; OR: 107.540, 95% CI: 5.195-2,225.975; OR: 52.531, 95% CI: 1.797-1,535.551, P < 0.05). Conclusion: The PVM on the concave side was larger than that on the convex side in ADS irrespective of whether PI-LL matched or not. PI-LL mismatch could aggravate this abnormal change, which is an important cause of pain and disability in ADS. Sagittal plane imbalance, decreased LL, higher PT, and larger average degeneration degree of the multifidus were independent risk factors for PI-LL mismatch.

Charge transport properties of SARS-CoV-2 Delta variant (B.1.617.2).

The B.1.617.2 (Delta) variant of concern is causing a new wave of infections in many countries. In order to better understand the changes of the SARS-CoV-2 mutation at the genetic level, we selected six mutations in the S region of the Delta variant compared with the native SARS-CoV-2 and get the conductance information of these six short RNA oligonucleotides groups by construct RNA: DNA hybrids. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. We found that conductance is very sensitive to small changes in virus sequence. Among the 6 mutations in the Delta S region, D950N shows the largest change in relative conductance, reaching a surprising 4104.75%. These results provide new insights into the Delta variant from the perspective of its electrical properties. This may be a new method to distinguish virus variation and possess great research prospects.

Starch-Binding Domain Modulates the Specificity of Maltopentaose Production at Moderate Temperatures.

Maltooligosaccharide-forming amylases (MFAs) hydrolyze starch into maltooligosaccharides with a defined degree of polymerization. However, the enzymatic mechanism underlying the product specificity remains partially understood. Here, we show that Saccharophagus degradans MFA (SdMFA) contains a noncatalytic starch-binding domain (SBD), which belongs to the carbohydrate-binding module family 20 and enables modulation of the product specificity. Removal of SBD from SdMFA resulted in a 3.5-fold lower production of the target maltopentaose. Conversely, appending SBD to another MFA from Bacillus megaterium improved the specificity for maltopentaose. SdMFA exhibited a higher level of exo-action and greater product specificity when reacting with amylopectin than with amylose. Our structural analysis and molecular dynamics simulation suggested that SBD could promote the recognition of nonreducing ends of substrates and delivery of the substrate chain to a groove end toward the active site in the catalytic domain. Furthermore, we demonstrate that a moderate temperature could mediate SBD to interact with the substrate with loose affinity, which facilitates the substrate to slide toward the active site. Together, our study reveals the structural and conditional bases for the specificity of MFAs, providing generalizable strategies to engineer MFAs and optimize the biosynthesis of maltooligosaccharides.

Time-resolved photoluminescence studies of perovskite chalcogenides.

Chalcogenides in the perovskite and related crystal structures ("chalcogenide perovskites" for brevity) may be useful for future optoelectronic and energy-conversion technologies inasmuch as they have good excited-state, ambipolar transport properties. In recent years, several studies have suggested that semiconductors in the Ba-Zr-S system have slow non-radiative recombination rates. Here, we present a time-resolved photoluminescence (TRPL) study of excited-state carrier mobility and recombination rates in the perovskite-structured material BaZrS3, and the related Ruddlesden-Popper phase Ba3Zr2S7. We measure state-of-the-art single crystal samples, to identify properties free from the influence of secondary phases and random grain boundaries. We model and fit the data using a semiconductor physics simulation, to enable more direct determination of key material parameters than is possible with empirical data modeling. We find that both materials have Shockley-Read-Hall recombination lifetimes on the order of 50 ns and excited-state diffusion lengths on the order of 5 µm at room temperature, which bodes well for ambipolar device performance in optoelectronic technologies including thin-film solar cells.

Prolonged drying trend coincident with the demise of Norse settlement in southern Greenland.

Declining temperature has been thought to explain the abandonment of Norse settlements, southern Greenland, in the early 15th century, although limited paleoclimate evidence is available from the inner settlement region itself. Here, we reconstruct the temperature and hydroclimate history from lake sediments at a site adjacent to a former Norse farm. We find no substantial temperature changes during the settlement period but rather that the region experienced a persistent drying trend, which peaked in the 16th century. Drier climate would have notably reduced grass production, which was essential for livestock overwintering, and this drying trend is concurrent with a Norse diet shift. We conclude that increasingly dry conditions played a more important role in undermining the viability of the Eastern Settlement than minor temperature changes.

A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments.

A genetic knockout can be lethal to one human cell type while increasing growth rate in another. This context specificity confounds genetic analysis and prevents reproducible genome engineering. Genome-wide CRISPR compendia across most common human cell lines offer the largest opportunity to understand the biology of cell specificity. The prevailing viewpoint, synthetic lethality, occurs when a genetic alteration creates a unique CRISPR dependency. Here, we use machine learning for an unbiased investigation of cell type specificity. Quantifying model accuracy, we find that most cell type specific phenotypes are predicted by the function of related genes of wild-type sequence, not synthetic lethal relationships. These models then identify unexpected sets of 100-300 genes where reduced CRISPR measurements can produce genome-scale loss-of-function predictions across >18,000 genes. Thus, it is possible to reduce in vitro CRISPR libraries by orders of magnitude-with some information loss-when we remove redundant genes and not redundant sgRNAs.

Norovirus Protease Structure and Antivirals Development.

Human norovirus (HuNoV) infection is a global health and economic burden. Currently, there are no licensed HuNoV vaccines or antiviral drugs available. The protease encoded by the HuNoV genome plays a critical role in virus replication by cleaving the polyprotein and is an excellent target for developing small-molecule inhibitors. The current strategy for developing HuNoV protease inhibitors is by targeting the enzyme's active site and designing inhibitors that bind to the substrate-binding pockets located near the active site. However, subtle differential conformational flexibility in response to the different substrates in the polyprotein and structural differences in the active site and substrate-binding pockets across different genogroups, hamper the development of effective broad-spectrum inhibitors. A comparative analysis of the available HuNoV protease structures may provide valuable insight for identifying novel strategies for the design and development of such inhibitors. The goal of this review is to provide such analysis together with an overview of the current status of the design and development of HuNoV protease inhibitors.

Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40 T.

Marine extremophiles produce cold-adapted and/or salt-tolerant enzymes to survive in harsh conditions. These enzymes are naturally evolved with unique structural features that confer a high level of flexibility, solubility and substrate-binding ability compared to mesophilic and thermostable homologs. Here, we identified and characterized an amylase, SdG5A, from the marine bacterium Saccharophagus degradans 2-40 T . We expressed the protein in Bacillus subtilis and found that the purified SdG5A enabled highly specific production of maltopentaose, an important health-promoting food and nutrition component. Notably, SdG5A exhibited outstanding cold adaptation and salt tolerance, retaining approximately 30 and 70% of its maximum activity at 4°C and in 3 M NaCl, respectively. It converted 68 and 83% of starch into maltooligosaccharides at 4 and 25°C, respectively, within 24 h, with 79% of the yield being the maltopentaose. By analyzing the structure of SdG5A, we found that the C-terminal carbohydrate-binding module (CBM) coupled with an extended linker, displayed a relatively high negative charge density and superior conformational flexibility compared to the whole protein and the catalytic domain. Consistent with our bioinformatics analysis, truncation of the linker-CBM region resulted in a significant loss in activities at low temperature and high salt concentration. This highlights the linker-CBM acting as the critical component for the protein to carry out its activity in biologically unfavorable condition. Together, our study indicated that these unique properties of SdG5A have great potential for both basic research and industrial applications in food, biology, and medical and pharmaceutical fields.

Electronic characteristics of BRCA1 mutations in DNA.

The efficient and low-cost way for gene mutation detection and identification are conducive for the detection of disease. Here, we report the electronic characteristics of the gene of breast cancer 1 in four common mutation types: duplication, single nucleotide variant, deletion, and indel. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. The magnitude of conductance of these DNA molecules and mutational changes are found to be detectable experimentally. In this study, we also find the significant mutation type dependent on the change of conductance. Hence these mutations are expected to be identifiable. We find deletion type mutation shows the largest change in relative conductance (~97%), whereas the indel mutation shows the smallest change in relative conductance (~27%). Therefore, this work presents a possibility of electronic detection and identification of mutations in DNA, which could be an efficient method as compared to the conventional methods.

Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins.

Prenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible ß-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.