Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. We show that two consecutive mutations (R203K/G204R) in the nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found increased interaction of GSK3A kinase simultaneously with hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein. Furthermore, the host cell transcriptome analysis suggests that the mutant N protein produces dysregulated interferon response genes. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein to modulations of host-virus interactions and underline the potential of the nucleocapsid protein as a drug target during infection.

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa. Virus-induced pneumonia in humans results from animal contact, with a potential for limited onward transmission. Phenotypic changes have been suspected after a novel recombinant clade (lineage 5) caused large nosocomial outbreaks in Saudi Arabia and South Korea in 2016. However, there has been no functional assessment. Here we perform a comprehensive in vitro and ex vivo comparison of viruses from parental and recombinant virus lineages (lineage 3, n = 7; lineage 4, n = 8; lineage 5, n = 9 viruses) from Saudi Arabia, isolated immediately before and after the shift toward lineage 5. Replication of lineage 5 viruses is significantly increased. Transcriptional profiling finds reduced induction of immune genes IFNB1, CCL5, and IFNL1 in lung cells infected with lineage 5 strains. Phenotypic differences may be determined by IFN antagonism based on experiments using IFN receptor knock out and signaling inhibition. Additionally, lineage 5 is more resilient against IFN pre-treatment of Calu-3 cells (ca. 10-fold difference in replication). This phenotypic change associated with lineage 5 has remained undiscovered by viral sequence surveillance, but may be a relevant indicator of pandemic potential.

The fields of photovoltaics, photodetection and light emission have seen tremendous activity in recent years with the advent of hybrid organic-inorganic perovskites. Yet, there have been far fewer reports of perovskite-based field-effect transistors. The lateral and interfacial transport requirements of transistors make them particularly vulnerable to surface contamination and defects rife in polycrystalline films and bulk single crystals. Here, we demonstrate a spatially-confined inverse temperature crystallization strategy which synthesizes micrometre-thin single crystals of methylammonium lead halide perovskites MAPbX3 (X = Cl, Br, I) with sub-nanometer surface roughness and very low surface contamination. These benefit the integration of MAPbX3 crystals into ambipolar transistors and yield record, room-temperature field-effect mobility up to 4.7 and 1.5 cm2 V-1 s-1 in p and n channel devices respectively, with 104 to 105 on-off ratio and low turn-on voltages. This work paves the way for integrating hybrid perovskite crystals into printed, flexible and transparent electronics.

Engineering membranes for molecular separation in organic solvents is still a big challenge. When the selectivity increases, the permeability tends to drastically decrease, increasing the energy demands for the separation process. Ideally, organic solvent nanofiltration membranes should be thin to enhance the permeant transport, have a well-tailored nanoporosity and high stability in harsh solvents. Here, we introduce a trianglamine macrocycle as a molecular building block for cross-linked membranes, prepared by facile interfacial polymerization, for high-performance selective separations. The membranes were prepared via a two-in-one strategy, enabled by the amine macrocycle, by simultaneously reducing the thickness of the thin-film layers (<10 nm) and introducing permanent intrinsic porosity within the membrane (6.3 Å). This translates into a superior separation performance for nanofiltration operation, both in polar and apolar solvents. The hyper-cross-linked network significantly improved the stability in various organic solvents, while the amine host macrocycle provided specific size and charge molecular recognition for selective guest molecules separation. By employing easily customized molecular hosts in ultrathin membranes, we can significantly tailor the selectivity on-demand without compromising the overall permeability of the system.

Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved.

The energy shortage and clean water scarcity are two key challenges for global sustainable development. Near half of the total global water withdrawals is consumed by power generation plants while water desalination consumes lots of electricity. Here, we demonstrate a photovoltaics-membrane distillation (PV-MD) device that can stably produce clean water (>1.64 kg·m-2·h-1) from seawater while simultaneously having uncompromised electricity generation performance (>11%) under one Sun irradiation. Its high clean water production rate is realized by constructing multi stage membrane distillation (MSMD) device at the backside of the solar cell to recycle the latent heat of water vapor condensation in each distillation stage. This composite device can significantly reduce capital investment costs by sharing the same land and the same mounting system and thus represents a potential possibility to transform an electricity power plant from otherwise a water consumer to a fresh water producer.

Pore size uniformity is one of the most critical parameters in determining membrane separation performance. Recently, a novel type of conjugated microporous polymers (CMPs) has shown uniform pore size and high porosity. However, their brittle nature has prevented them from preparing robust membranes. Inspired by the skin-core architecture of spider silk that offers both high strength and high ductility, herein we report an electropolymerization process to prepare a CMP membrane from a rigid carbazole monomer, 2,2',7,7'-tetra(carbazol-9-yl)-9,9'-spirobifluorene, inside a robust carbon nanotube scaffold. The obtained membranes showed superior mechanical strength and ductility, high surface area, and uniform pore size of approximately 1 nm. The superfast solvent transport and excellent molecular sieving well surpass the performance of most reported polymer membranes. Our method makes it possible to use rigid CMPs membranes in pressure-driven membrane processes, providing potential applications for this important category of polymer materials.

Spatial transcriptomics technologies are used to profile transcriptomes while preserving spatial information, which enables high-resolution characterization of transcriptional patterns and reconstruction of tissue architecture. Due to the existence of low-resolution spots in recent spatial transcriptomics technologies, uncovering cellular heterogeneity is crucial for disentangling the spatial patterns of cell types, and many related methods have been proposed. Here, we benchmark 18 existing methods resolving a cellular deconvolution task with 50 real-world and simulated datasets by evaluating the accuracy, robustness, and usability of the methods. We compare these methods comprehensively using different metrics, resolutions, spatial transcriptomics technologies, spot numbers, and gene numbers. In terms of performance, CARD, Cell2location, and Tangram are the best methods for conducting the cellular deconvolution task. To refine our comparative results, we provide decision-tree-style guidelines and recommendations for method selection and their additional features, which will help users easily choose the best method for fulfilling their concerns.

Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. PIFE has been explained by an increase in local viscosity due to the presence of the protein residues. This explanation, however, denies the opposite effect of fluorescence quenching. This work offers a perspective for understanding PIFE mechanism and reports the observation of a phenomenon that we name protein-induced fluorescence quenching (PIFQ), which exhibits an opposite effect to PIFE. A detailed characterization of these two fluorescence modulations reveals that the initial fluorescence state of the labeled mediator (DNA) determines whether this mediator-conjugated dye undergoes PIFE or PIFQ upon protein binding. This key role of the mediator DNA provides a protocol for the experimental design to obtain either PIFQ or PIFE, on-demand. This makes the arbitrary nature of the current experimental design obsolete, allowing for proper integration of both PIFE and PIFQ with existing bulk and single-molecule fluorescence techniques.

Selection and dispersal are ecological processes that have contrasting roles in the assembly of communities. Variable selection diversifies and strong dispersal homogenizes them. However, we do not know whether dispersal homogenizes communities directly via immigration or indirectly via weakening selection across habitats due to physical transfer of material, e.g., water mixing in aquatic ecosystems. Here we examine how dispersal homogenizes a simplified synthetic bacterial metacommunity, using a sequencing-independent approach based on flow cytometry and mathematical modeling. We show that dispersal homogenizes the metacommunity via immigration, not via weakening selection, and even when immigration is four times slower than growth. This finding challenges the current view that dispersal homogenizes communities only at high rates and explains why communities are homogeneous at small spatial scales. It also offers a benchmark for sequence-based studies in natural microbial communities where immigration rates can be inferred solely by using neutral models.

Proper disposal of industrial brine has been a critical environmental challenge. Zero liquid discharge (ZLD) brine treatment holds great promise to the brine disposal, but its application is limited by the intensive energy consumption of its crystallization process. Here we propose a new strategy that employs an advanced solar crystallizer coupled with a salt crystallization inhibitor to eliminate highly concentrated waste brine. The rationally designed solar crystallizer exhibited a high water evaporation rate of 2.42 kg m-2 h-1 under one sun illumination when treating real concentrated seawater reverse osmosis (SWRO) brine (21.6 wt%). The solar crystallizer array showed an even higher water evaporation rate of 48.0 kg m-2 per day in the outdoor field test, suggesting a great potential for practical application. The solar crystallizer design and the salt crystallization inhibition strategy proposed and confirmed in this work provide a low-cost and sustainable solution for industrial brine disposal with ZLD.

Carotenoid cleavage dioxygenases (CCDs) form hormones and signaling molecules. Here we show that a member of an overlooked plant CCD subfamily from rice, that we name Zaxinone Synthase (ZAS), can produce zaxinone, a novel apocarotenoid metabolite in vitro. Loss-of-function mutants (zas) contain less zaxinone, exhibit retarded growth and showed elevated levels of strigolactones (SLs), a hormone that determines plant architecture, mediates mycorrhization and facilitates infestation by root parasitic weeds, such as Striga spp. Application of zaxinone can rescue zas phenotypes, decrease SL content and release and promote root growth in wild-type seedlings. In conclusion, we show that zaxinone is a key regulator of rice development and biotic interactions and has potential for increasing crop growth and combating Striga, a severe threat to global food security.

Transgenes are prone to progressive silencing due to their structure, copy number, and genomic location. In C. elegans, repressive mechanisms are particularly strong in the germline with almost fully penetrant transgene silencing in simple extrachromosomal arrays and frequent silencing of single-copy transgene insertions. A class of non-coding DNA, Periodic An/Tn Clusters (PATCs) can prevent transgene-silencing in repressive chromatin or from small interfering RNAs (piRNAs). Here, we describe design rules (codon-optimization, intron and PATC inclusion, elevated temperature (25 °C), and vector backbone removal) for efficient germline expression from arrays in wildtype animals. We generate web-based tools to analyze PATCs and reagents for the convenient assembly of PATC-rich transgenes. An extensive collection of silencing resistant fluorescent proteins (e.g., gfp, mCherry, and tagBFP) can be used for dissecting germline regulatory elements and a set of enhanced enzymes (Mos1 transposase, Cas9, Cre, and Flp recombinases) enable efficient genetic engineering in C. elegans.

Heat stress is being exacerbated by global warming, jeopardizing human and social sustainability. As a result, reliable and energy-efficient cooling methods are highly sought-after. Here, we report a polyacrylate film fabricated by self-moisture-absorbing hygroscopic hydrogel for efficient hybrid passive cooling. Using one of the lowest-cost industrial materials (e.g., sodium polyacrylate), we demonstrate radiative cooling by reducing solar heating with high solar reflectance (0.93) while maximizing thermal emission with high mid-infrared emittance (0.99). Importantly, the manufacturing process utilizes only atmospheric moisture and requires no additional chemicals or energy consumption, making it a completely green process. Under sunlight illumination of 800 W m-2, the surface temperature of the film was reduced by 5 °C under a partly cloudy sky observed at Buffalo, NY. Combined with its hygroscopic feature, this film can simultaneously introduce evaporative cooling that is independent of access to the clear sky. The hybrid passive cooling approach is projected to decrease global carbon emissions by 118.4 billion kg/year compared to current air-conditioning facilities powered by electricity. Given its low-cost raw materials and excellent molding feature, the film can be manufactured through simple and cost-effective roll-to-roll processes, making it suitable for future building construction and personal thermal management needs.

High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.

Architected materials that actively respond to external stimuli hold tantalizing prospects for applications in energy storage, wearable electronics, and bioengineering. Molybdenum disulfide, an excellent two-dimensional building block, is a promising candidate for lithium-ion battery anode. However, the stacked and brittle two-dimensional layered structure limits its rate capability and electrochemical stability. Here we report the dewetting-induced manufacturing of two-dimensional molybdenum disulfide nanosheets into a three-dimensional foam with a structural hierarchy across seven orders of magnitude. Our molybdenum disulfide foam provides an interpenetrating network for efficient charge transport, rapid ion diffusion, and mechanically resilient and chemically stable support for electrochemical reactions. These features induce a pseudocapacitive energy storage mechanism involving molybdenum redox reactions, confirmed by in-situ X-ray absorption near edge structure. The extraordinary electrochemical performance of molybdenum disulfide foam outperforms most reported molybdenum disulfide-based Lithium-ion battery anodes and state-of-the-art materials. This work opens promising inroads for various applications where special properties arise from hierarchical architecture.

Submarine eruptions that lead to the formation of new volcanic islands are rare and far from being fully understood; only a few such eruptions have been witnessed since Surtsey Island emerged to the south of Iceland in the 1960s. Here we report on two new volcanic islands that were formed in the Zubair archipelago of the southern Red Sea in 2011-2013. Using high-resolution optical satellite images, we find that the new islands grew rapidly during their initial eruptive phases and that coastal erosion significantly modified their shapes within months. Satellite radar data indicate that two north-south-oriented dykes, much longer than the small islands might suggest, fed the eruptions. These events occurred contemporaneously with several local earthquake swarms of the type that typically accompany magma intrusions. Earthquake activity has been affecting the southern Red Sea for decades, suggesting the presence of a magmatically active zone that has previously escaped notice.

Trapping air at the solid-liquid interface is a promising strategy for reducing frictional drag and desalting water, although it has thus far remained unachievable without perfluorinated coatings. Here, we report on biomimetic microtextures composed of doubly reentrant cavities (DRCs) and reentrant cavities (RCs) that can enable even intrinsically wetting materials to entrap air for long periods upon immersion in liquids. Using SiO2/Si wafers as the model system, we demonstrate that while the air entrapped in simple cylindrical cavities immersed in hexadecane is lost after 0.2 s, the air entrapped in the DRCs remained intact even after 27 days (~106 s). To understand the factors and mechanisms underlying this ten-million-fold enhancement, we compared the behaviors of DRCs, RCs and simple cavities of circular and non-circular shapes on immersion in liquids of low and high vapor pressures through high-speed imaging, confocal microscopy, and pressure cells. Those results might advance the development of coating-free liquid repellent surfaces.

Conjugated polymer films, which can conduct both ionic and electronic charges, are central to building soft electronic sensors and actuators. Despite the possible interplay between light absorption and the mixed conductivity of these materials in aqueous biological media, no single polymer film has been utilized to create a solar-switchable organic bioelectronic circuit that relies on a fully reversible and redox reaction-free potentiometric photodetection and current modulation. Here we demonstrate that the absorption of light by an electron and cation-transporting polymer film reversibly modulates its electrochemical potential and conductivity in an aqueous electrolyte, which is harnessed to design an n-type photo-electrochemical transistor (n-OPECT). By controlling the intensity of light incident on the n-type polymeric gate electrode, we generate transistor output characteristics that mimic the modulation of the polymeric channel current achieved through gate voltage control. The micron-scale n-OPECT exhibits a high signal-to-noise ratio and an excellent sensitivity to low light intensities. We demonstrate three direct applications of the n-OPECT, i.e., a photoplethysmogram recorder, a light-controlled inverter circuit, and a light-gated artificial synapse, underscoring the suitability of this platform for a myriad of biomedical applications that involve light intensity changes.

Cascade processes are gaining momentum in heterogeneous catalysis. The combination of several catalytic solids within one reactor has shown great promise for the one-step valorization of C1-feedstocks. The combination of metal-based catalysts and zeolites in the gas phase hydrogenation of CO2 leads to a large degree of product selectivity control, defined mainly by zeolites. However, a great deal of mechanistic understanding remains unclear: metal-based catalysts usually lead to complex product compositions that may result in unexpected zeolite reactivity. Here we present an in-depth multivariate analysis of the chemistry involved in eight different zeolite topologies when combined with a highly active Fe-based catalyst in the hydrogenation of CO2 to olefins, aromatics, and paraffins. Solid-state NMR spectroscopy and computational analysis demonstrate that the hybrid nature of the active zeolite catalyst and its preferred CO2-derived reaction intermediates (CO/ester/ketone/hydrocarbons, i.e., inorganic-organic supramolecular reactive centers), along with 10 MR-zeolite topology, act as descriptors governing the ultimate product selectivity.