Erratum in Nat Commun. 2023 Jan 12;14(1):184.

Catalytic deterioration during electrocatalytic processes is inevitable for conventional composite electrodes, which are prepared by depositing catalysts onto a rigid current collector. In contrast, metals that are liquid at near room temperature, liquid metals (LMs), are potential electrodes that are uniquely flexible and maneuverable, and whose fluidity may allow them to be more adaptive than rigid substrates. Here we demonstrate a self-healing electrocatalytic system for CO2 electroreduction using bismuth-containing Ga-based LM electrodes. Bi2O3 dispersed in the LM matrix experiences a series of electrohydrodynamic-induced structural changes when exposed to a tunable potential and finally transforms into catalytic bismuth, whose morphology can be controlled by the applied potential. The electrohydrodynamically-induced evolved electrode shows considerable electrocatalytic activity for CO2 reduction to formate. After deterioration of the electrocatalytic performance, the catalyst can be healed via simple mechanical stirring followed by in situ regeneration by applying a reducing potential. With this procedure, the electrode's original structure and catalytic activity are both recovered.

Electrochemical CO2 reduction to multicarbon products faces challenges of unsatisfactory selectivity, productivity, and long-term stability. Herein, we demonstrate CO2 electroreduction in strongly acidic electrolyte (pH ≤ 1) on electrochemically reduced porous Cu nanosheets by combining the confinement effect and cation effect to synergistically modulate the local microenvironment. A Faradaic efficiency of 83.7 ± 1.4% and partial current density of 0.56 ± 0.02 A cm-2, single-pass carbon efficiency of 54.4%, and stable electrolysis of 30 h in a flow cell are demonstrated for multicarbon products in a strongly acidic aqueous electrolyte consisting of sulfuric acid and KCl with pH ≤ 1. Mechanistically, the accumulated species (e.g., K+ and OH-) on the Helmholtz plane account for the selectivity and activity toward multicarbon products by kinetically reducing the proton coverage and thermodynamically favoring the CO2 conversion. We find that the K+ cations facilitate C-C coupling through local interaction between K+ and the key intermediate *OCCO.

Erratum in Nat Commun. 2023 Jan 12;14(1):190.

Emergent axion electrodynamics in magneto-electric media is expected to provide novel ways to detect and control material properties with electromagnetic fields. However, despite being studied intensively for over a decade, its theoretical understanding remains mostly confined to the static limit. Here, we introduce a theory of axion electrodynamics at general frequencies. We define a proper optical axion magneto-electric coupling through its relation to optical surface Hall conductivity and provide ways to calculate it in lattice systems. By employing our formulas, we show that axion electrodynamics can lead to a significant Kerr effect in thin-film antiferromagnets at wavelengths that are seemingly too long to resolve the spatial modulation of magnetism. We identify the wavelength scale above which the Kerr effect is suppressed. Our theory is particularly relevant to materials like MnBi2Te4, a topological antiferromagnet whose magneto-electric response is shown here to be dominated by the axion contribution even at optical frequencies.

Bacteria commonly live in surface-associated communities where steep gradients of antibiotics and other chemical compounds can occur. While many bacterial species move on surfaces, we know surprisingly little about how such antibiotic gradients affect cell motility. Here, we study the behaviour of the opportunistic pathogen Pseudomonas aeruginosa in stable spatial gradients of several antibiotics by tracking thousands of cells in microfluidic devices as they form biofilms. Unexpectedly, these experiments reveal that bacteria use pili-based ('twitching') motility to navigate towards antibiotics. Our analyses suggest that this behaviour is driven by a general response to the effects of antibiotics on cells. Migrating bacteria reach antibiotic concentrations hundreds of times higher than their minimum inhibitory concentration within hours and remain highly motile. However, isolating cells - using fluid-walled microfluidic devices - reveals that these bacteria are terminal and unable to reproduce. Despite moving towards their death, migrating cells are capable of entering a suicidal program to release bacteriocins that kill other bacteria. This behaviour suggests that the cells are responding to antibiotics as if they come from a competing colony growing nearby, inducing them to invade and attack. As a result, clinical antibiotics have the potential to lure bacteria to their death.

Today solid-state cooling technologies below liquid nitrogen boiling temperature (77 K), crucial to quantum information technology and probing quantum state of matter, are greatly limited due to the lack of good thermoelectric and/or thermomagnetic materials. Here, we report the discovery of colossal Nernst power factor of 3800 × 10-4 W m-1 K-2 under 5 T at 25 K and high Nernst figure-of-merit of 71 × 10-4 K-1 under 5 T at 20 K in topological semimetal NbSb2 single crystals. The observed high thermomagnetic performance is attributed to large Nernst thermopower and longitudinal electrical conductivity, and relatively low transverse thermal conductivity. The large and unsaturated Nernst thermopower is the result of the combination of highly desirable electronic structures of NbSb2 having compensated high mobility electrons and holes near Fermi level and strong phonon-drag effect. This discovery opens an avenue for exploring material option for the solid-state heat pumping below liquid nitrogen temperature.

Ca2+ influx through high-voltage-activated calcium channels (HVACCs) controls diverse cellular functions. A critical feature enabling a singular signal, Ca2+ influx, to mediate disparate functions is diversity of HVACC pore-forming α1 and auxiliary CaVβ1-CaVβ4 subunits. Selective CaVα1 blockers have enabled deciphering their unique physiological roles. By contrast, the capacity to post-translationally inhibit HVACCs based on CaVβ isoform is non-existent. Conventional gene knockout/shRNA approaches do not adequately address this deficit owing to subunit reshuffling and partially overlapping functions of CaVβ isoforms. Here, we identify a nanobody (nb.E8) that selectively binds CaVβ1 SH3 domain and inhibits CaVβ1-associated HVACCs by reducing channel surface density, decreasing open probability, and speeding inactivation. Functionalizing nb.E8 with Nedd4L HECT domain yielded Chisel-1 which eliminated current through CaVβ1-reconstituted CaV1/CaV2 and native CaV1.1 channels in skeletal muscle, strongly suppressed depolarization-evoked Ca2+ influx and excitation-transcription coupling in hippocampal neurons, but was inert against CaVβ2-associated CaV1.2 in cardiomyocytes. The results introduce an original method for probing distinctive functions of ion channel auxiliary subunit isoforms, reveal additional dimensions of CaVβ1 signaling in neurons, and describe a genetically-encoded HVACC inhibitor with unique properties.

The auditory function of the mammalian cochlea relies on two types of mechanosensory hair cells and various non-sensory supporting cells. Recent studies identified the transcription factors INSM1 and IKZF2 as regulators of outer hair cell (OHC) fate. However, the transcriptional regulation of the differentiation of inner hair cells (IHCs) and their associated inner supporting cells (ISCs) has remained enigmatic. Here, we show that the expression of the transcription factor TBX2 is restricted to IHCs and ISCs from the onset of differentiation until adulthood and examine its function using conditional deletion and misexpression approaches in the mouse. We demonstrate that TBX2 acts in prosensory progenitors as a patterning factor by specifying the inner compartment of the sensory epithelium that subsequently gives rise to IHCs and ISCs. Hair cell-specific inactivation or misexpression causes transdifferentiation of hair cells indicating a cell-autonomous function of TBX2 in inducing and maintaining IHC fate.

The question of how cell-to-cell differences in transcription rate affect RNA count distributions is fundamental for understanding biological processes underlying transcription. Answering this question requires quantitative models that are both interpretable (describing concrete biophysical phenomena) and tractable (amenable to mathematical analysis). This enables the identification of experiments which best discriminate between competing hypotheses. As a proof of principle, we introduce a simple but flexible class of models involving a continuous stochastic transcription rate driving a discrete RNA transcription and splicing process, and compare and contrast two biologically plausible hypotheses about transcription rate variation. One assumes variation is due to DNA experiencing mechanical strain, while the other assumes it is due to regulator number fluctuations. We introduce a framework for numerically and analytically studying such models, and apply Bayesian model selection to identify candidate genes that show signatures of each model in single-cell transcriptomic data from mouse glutamatergic neurons.

Eggerthella lenta is a prevalent human gut Actinobacterium implicated in drug, dietary phytochemical, and bile acid metabolism and associated with multiple human diseases. No genetic tools are currently available for the direct manipulation of E. lenta. Here, we construct shuttle vectors and develop methods to transform E. lenta and other Coriobacteriia. With these tools, we characterize endogenous E. lenta constitutive and inducible promoters using a reporter system and construct inducible expression systems, enabling tunable gene regulation. We also achieve genome editing by harnessing an endogenous type I-C CRISPR-Cas system. Using these tools to perform genetic knockout and complementation, we dissect the functions of regulatory proteins and enzymes involved in catechol metabolism, revealing a previously unappreciated family of membrane-spanning LuxR-type transcriptional regulators. Finally, we employ our genetic toolbox to study the effects of E. lenta genes on mammalian host biology. By greatly expanding our ability to study and engineer gut Coriobacteriia, these tools will reveal mechanistic details of host-microbe interactions and provide a roadmap for genetic manipulation of other understudied human gut bacteria.

The ongoing COVID-19 pandemic has demonstrated that viral diseases represent an enormous public health and economic threat to mankind and that individuals with compromised immune systems are at greater risk of complications and death from viral diseases. The development of broad-spectrum antivirals is an important part of pandemic preparedness. Here, we have engineer a series of designer cells which we term autonomous, intelligent, virus-inducible immune-like (ALICE) cells as sense-and-destroy antiviral system. After developing a destabilized STING-based sensor to detect viruses from seven different genera, we have used a synthetic signal transduction system to link viral detection to the expression of multiple antiviral effector molecules, including antiviral cytokines, a CRISPR-Cas9 module for viral degradation and the secretion of a neutralizing antibody. We perform a proof-of-concept study using multiple iterations of our ALICE system in vitro, followed by in vivo functionality testing in mice. We show that dual output ALICESaCas9+Ab system delivered by an AAV-vector inhibited viral infection in herpetic simplex keratitis (HSK) mouse model. Our work demonstrates that viral detection and antiviral countermeasures can be paired for intelligent sense-and-destroy applications as a flexible and innovative method against virus infection.

Non-coding cis-regulatory variants in animal genomes are an important driving force in the evolution of transcription regulation and phenotype diversity. However, cistrome dynamics in plants remain largely underexplored. Here, we compare the binding of GOLDEN2-LIKE (GLK) transcription factors in tomato, tobacco, Arabidopsis, maize and rice. Although the function of GLKs is conserved, most of their binding sites are species-specific. Conserved binding sites are often found near photosynthetic genes dependent on GLK for expression, but sites near non-differentially expressed genes in the glk mutant are nevertheless under purifying selection. The binding sites' regulatory potential can be predicted by machine learning model using quantitative genome features and TF co-binding information. Our study show that genome cis-variation caused wide-spread TF binding divergence, and most of the TF binding sites are genetically redundant. This poses a major challenge for interpreting the effect of individual sites and highlights the importance of quantitatively measuring TF occupancy.

A phototransistor is a promising candidate as an optical power monitor in Si photonic circuits since the internal gain of photocurrent enables high responsivity. However, state-of-the-art waveguide-coupled phototransistors suffer from a responsivity of lower than 103 A/W, which is insufficient for detecting very low power light. Here, we present a waveguide-coupled phototransistor operating at a 1.3 μm wavelength, which consists of an InGaAs ultrathin channel on a Si waveguide working as a gate electrode to increase the responsivity. The Si waveguide gate underneath the InGaAs ultrathin channel enables the effective control of transistor current without optical absorption by the gate metal. As a result, our phototransistor achieved the highest responsivity of approximately 106 A/W among the waveguide-coupled phototransistors, allowing us to detect light of 621 fW propagating in the Si waveguide. The high responsivity and the reasonable response time of approximately 100 μs make our phototransistor promising as an effective optical power monitor in Si photonic circuits.

Influenza infection continues are a persistent threat to public health. The identification and characterization of human broadly neutralizing antibodies can facilitate the development of antibody drugs and the design of universal influenza vaccines. Here, we present structural information for the human antibody PN-SIA28's heterosubtypic binding of hemagglutinin (HA) from circulating and emerging potential influenza A viruses (IAVs). Aside from group 1 and 2 conventional IAV HAs, PN-SIA28 also inhibits membrane fusion mediated by bat-origin H17 and H18 HAs. Crystallographic analyses of Fab alone or in complex with H1, H14, and H18 HA proteins reveal that PN-SIA28 binds to a highly conserved epitope in the fusion domain of different HAs, with the same CDRHs but different CDRLs for different HAs tested, distinguishing it from other structurally characterized anti-stem antibodies. The binding characteristics of PN-SIA28 provides information to support the design of increasingly potent engineered antibodies, antiviral drugs, and/or universal influenza vaccines.

Closed-loop chemical recycling provides a solution to the end-of-use problem of synthetic polymers. However, it remains a major challenge to design dynamic bonds, capable of effective bonding and reversible cleaving, for preparing chemically recyclable cross-linked polymers. Herein, we report a dynamic maleic acid tertiary amide bond based upon reversible amidation reaction between maleic anhydrides and secondary amines. This dynamic bond allows for the construction of polymer networks with tailorable and robust mechanical properties, covering strong elastomers with a tensile strength of 22.3 MPa and rigid plastics with a yield strength of 38.3 MPa. Impressively, these robust polymeric materials can be completely depolymerized in an acidic aqueous solution at ambient temperature, leading to efficient monomer recovery with >94% separation yields. Meanwhile, the recovered monomers can be used to remanufacture cross-linked polymeric materials without losing their original mechanical performance. This work unveils a general approach to design polymer networks with tunable mechanical performance and closed-loop recyclability, which will open a new avenue for sustainable polymeric materials.

Three decades of research in molecular nanomagnets have raised their magnetic memories from liquid helium to liquid nitrogen temperature thanks to a wise choice of the magnetic ion and coordination environment. Still, serendipity and chemical intuition played a main role. In order to establish a powerful framework for statistically driven chemical design, here we collected chemical and physical data for lanthanide-based nanomagnets, catalogued over 1400 published experiments, developed an interactive dashboard (SIMDAVIS) to visualise the dataset, and applied inferential statistical analysis. Our analysis shows that the Arrhenius energy barrier correlates unexpectedly well with the magnetic memory. Furthermore, as both Orbach and Raman processes can be affected by vibronic coupling, chemical design of the coordination scheme may be used to reduce the relaxation rates. Indeed, only bis-phthalocyaninato sandwiches and metallocenes, with rigid ligands, consistently present magnetic memory up to high temperature. Analysing magnetostructural correlations, we offer promising strategies for improvement, in particular for the preparation of pentagonal bipyramids, where even softer complexes are protected against molecular vibrations.

Update of bioRxiv. 2021 Dec 13;:

Author information: (1)Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. (2)Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany. (3)Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. (4)Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, 69120, Heidelberg, Germany. (5)German Cancer Consortium (DKTK), Heidelberg, Germany. (6)National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany. (7)Heidelberg Center for Personalized Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany. (8)Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, 69120, Heidelberg, Germany. (9)Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA. (10)Department of Chemistry, Centre for Molecular Science Informatics, University of Cambridge, Cambridge, CB2 1EW, UK. (11)Ludwig Center at Harvard Medical School, Boston, Massachusetts, 02115, USA. (12)School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing, 100871, China. (13)Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. (14)Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany. (15)Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany. (16)Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. l.feuerbach@dkfz-heidelberg.de.

The viscosity of magma plays a crucial role in the dynamics of the Earth: from the crystallization of a magma ocean during its initial stages to modern-day volcanic processes. However, the pressure-dependence behavior of viscosity at high pressure remains controversial. In this study, we report the results of first-principles molecular dynamics simulations of basaltic melt to show that the melt viscosity increases upon compression along each isotherm for the entire lower mantle after showing minima at ~6 GPa. However, elevated temperatures of the magma ocean translate to a narrow range of viscosity, i.e., 0.01-0.03 Pa.s. This low viscosity implies that the crystallization of the magma ocean could be complete within a few million years. These results also suggest that the crystallization of the magma ocean is likely to be fractional, thus supporting the hypothesis that present-day mantle heterogeneities could have been generated during the early crystallization of the primitive mantle.

Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.

Author information: (1)Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada. (2)Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. (3)Vector Institute, Toronto, ON, Canada. (4)Broad Institute of MIT and Harvard, Cambridge, MA, USA. (5)Harvard Medical School, Boston, MA, USA. (6)Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA. (7)Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 15 1425 Madison Ave., New York, NY, USA. (8)Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia. (9)Hartwig Medical Foundation, Science Park 408, Amsterdam, The Netherlands. (10)Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands. (11)Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands. (12)Radboud University Medical Center, Nijmegen, The Netherlands. (13)Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands. (14)Department of Medical Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. (15)Department of Pathology, Massachusetts General Hospital, Boston, MA, USA. (16)University of Toronto, Toronto, ON, Canada. (17)Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada. lincoln.stein@gmail.com. (18)Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. lincoln.stein@gmail.com. (#)Contributed equally

A three-component hydrocarboxylation of an olefin with CO2 and H2 could be regarded as a dream reaction, since it would provide a straightforward approach for the synthesis of aliphatic carboxylic acids in perfect atom economy. However, this transformation has not been realized in a direct manner under mild conditions, because boosting the carboxylation with thermodynamically stable CO2 while suppressing the rapid hydrogenation of olefin remains a challenging task. Here, we report a rhodium-catalysed reductive hydrocarboxylation of styrene derivatives with CO2 and H2 under mild conditions, in which H2 served as the terminal reductant. In this approach, the carboxylation process was largely accelerated by visible light irradiation, which was proved both experimentally and by computational studies. Hydrocarboxylation of various kinds of styrene derivatives was achieved in good yields without additional base under ambient pressure of CO2/H2 at room temperature. Mechanistic investigations revealed that use of a cationic rhodium complex was critical to achieve high hydrocarboxylation selectivity.

Author information: (1)Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. (2)European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Cambridge, UK. (3)CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Portugal. (4)BIOPIC, ICG and College of Life Sciences, Peking University, Beijing, China. (5)Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. (6)Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, 108-8639, Japan. (7)RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. (8)Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. creighto@bcm.edu. (9)Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. creighto@bcm.edu. (10)Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. creighto@bcm.edu. (11)Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. creighto@bcm.edu.

Phenotypic switching between tachyzoite and bradyzoite is the fundamental mechanism underpinning the pathogenicity and adaptability of the protozoan parasite Toxoplasma gondii. Although accumulation of cytoplasmic starch granules is a hallmark of the quiescent bradyzoite stage, the regulatory factors and mechanisms contributing to amylopectin storage in bradyzoites are incompletely known. Here, we show that T. gondii protein phosphatase 2A (PP2A) holoenzyme is composed of a catalytic subunit PP2A-C, a scaffold subunit PP2A-A and a regulatory subunit PP2A-B. Disruption of any of these subunits increased starch accumulation and blocked the tachyzoite-to-bradyzoite differentiation. PP2A contributes to the regulation of amylopectin metabolism via dephosphorylation of calcium-dependent protein kinase 2 at S679. Phosphoproteomics identified several putative PP2A holoenzyme substrates that are involved in bradyzoite differentiation. Our findings provide novel insight into the role of PP2A as a key regulator of starch metabolism and bradyzoite differentiation in T. gondii.

Observations of active turbidity currents at field scale offers a limited scope which challenges the development of theory that links flow dynamics to the morphology of submarine fans. Here we offer a framework for predicting submarine fan morphologies by simplifying critical environmental forcings such as regional slopes and properties of sediments, through densimetric Froude (ratio of inertial to gravitational forces) and Rouse numbers (ratio of settling velocity of sediments to shear velocity) of turbidity currents. We leverage a depth-average process-based numerical model to simulate an array of submarine fans and measure rugosity as a proxy for their morphological complexity. We show a systematic increase in rugosity by either increasing the densimetric Froude number or decreasing the Rouse number of turbidity currents. These trends reflect gradients in the dynamics of channel migration on the fan surface and help discriminate submarine fans that effectively sequester organic carbon rich mud in deep ocean strata.

Author information: (1)Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5S 1A8. shimin.shuai@mail.utoronto.ca. (2)Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3. shimin.shuai@mail.utoronto.ca. (3)Division of General Surgery, Toronto General Hospital, Toronto, ON, Canada, M5G 2C4. (4)Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada, M5G 1X5. (5)Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, M5S 1A8. lincoln.stein@gmail.com. (6)Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3. lincoln.stein@gmail.com.

L-Ergothioneine (ET), the 2-thioimidazole derivative of trimethylhistidine, is biosynthesized by select fungi and bacteria, notably Mycobacterium tuberculosis, and functions as a scavenger of reactive oxygen species. The extent to which ET broadly functions in bacterial cells unable to synthesize it is unknown. Here we show that spd_1642-1643 in Streptococcus pneumoniae, a Gram-positive respiratory pathogen, encodes an ET uptake ATP-binding cassette (ABC) transporter, designated EgtU. The solute binding domain (SBD) of EgtU, EgtUC, binds ET with high affinity and exquisite specificity in a cleft between the two subdomains, with cation-π interactions engaging the betaine moiety and a network of water molecules that surround the thioimidazole ring. EgtU is highly conserved among known quaternary amine compound-specific transporters and widely distributed in Firmicutes, including the human pathogens Listeria monocytogenes, as BilEB, Enterococcus faecalis and Staphylococcus aureus. ET increases the chemical diversity of the low molecular weight thiol pool in Gram-positive human pathogens and may contribute to antioxidant defenses in the infected host.

How the carbohydrate binding protein galectin-3 might act as a diabetogenic and tumorogenic factor remains to be investigated. Here we report that intracellular galectin-3 interacts with Rag GTPases and Ragulator on lysosomes. We show that galectin-3 senses lipopolysaccharide (LPS) to facilitate the interaction of Rag GTPases and Ragulator, leading to the activation of mTORC1. We find that the lipopolysaccharide/galectin-3-Rag GTPases/Ragulator-mTORC1 axis regulates a cohort of genes including GLUT1, and HK2, and PKM2 that are critically involved in glucose uptake and glycolysis. Indeed, galectin-3 deficiency severely compromises LPS-promoted glycolysis. Importantly, the expression of HK2 is significantly reduced in diabetes patients. In multiple types of cancer including hepatocellular carcinoma (HCC), galectin-3 is highly expressed, and its level of expression is positively correlated with that of HK2 and PKM2 and negatively correlated with the prognosis of HCC patients. Our study unravels that galectin-3 is a sensor of LPS, an important modulator of the mTORC1 signaling, and a critical regulator of glucose metabolism.

Mortality in children with severe malnutrition is strongly related to signs of metabolic dysfunction, such as hypoglycemia. Lower circulating tryptophan levels in children with severe malnutrition suggest a possible disturbance in the tryptophan-nicotinamide adenine dinucleotide (TRP-NAD+) pathway and subsequently in NAD+  dependent metabolism regulator sirtuin1 (SIRT1). Here we show that severe malnutrition in weanling mice, induced by 2-weeks of low protein diet feeding from weaning, leads to an impaired TRP-NAD+  pathway with decreased NAD+ levels and affects hepatic mitochondrial turnover and function. We demonstrate that stimulating the TRP-NAD+  pathway with NAD+  precursors improves hepatic mitochondrial and overall metabolic function through SIRT1 modulation. Activating SIRT1 is sufficient to induce improvement in metabolic functions. Our findings indicate that modulating the TRP-NAD+  pathway can improve liver metabolic function in a mouse model of severe malnutrition. These results could lead to the development of new interventions for children with severe malnutrition.

Author information: (1)Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON, M5G 0A3, Canada. (2)Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON, M5G 1L7, Canada. (3)Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle Room 4207, Toronto, ON, M5S 1A8, Canada. (4)Department of Human Genetics, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA, 90095, USA. (5)Department of Urology, University of California Los Angeles, 200 Medical Plaza Driveway #140, Los Angeles, CA, 90024, USA. (6)Institute of Precision Health, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA, 90024, USA. (7)Broad Stem Cell Research Centre, University of California Los Angeles, 615 Charles E Young Drive S, Los Angeles, CA, 90095, USA. (8)Jonsson Comprehensive Cancer Centre, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA, 90024, USA. (9)Computational Biology Program, Ontario Institute for Cancer Research, 661 University Ave Suite 510, Toronto, ON, M5G 0A3, Canada. Juri.Reimand@utoronto.ca. (10)Department of Medical Biophysics, University of Toronto, 101 College Street Suite 15-701, Toronto, ON, M5G 1L7, Canada. Juri.Reimand@utoronto.ca. (#)Contributed equally

A key challenge for fuel cells based on phosphoric acid doped polybenzimidazole membranes is the high Pt loading, which is required due to the low electrode performance owing to the poor mass transport and severe Pt poisoning via acid absorption on the Pt surface. Herein, these issues are well addressed by design and synthesis of effective catalyst binders based on polymers of intrinsic microporosity (PIMs) with strong hydrogen-bonding functionalities which improve phosphoric acid binding energy, and thus preferably uphold phosphoric acid in the vicinity of Pt catalyst particles to mitigate the adsorption of phosphoric acid on the Pt surface. With combination of the highly mass transport microporosity, strong hydrogen-bonds and high phosphoric acid binding energy, the tetrazole functionalized PIM binder enables an H2-O2 cell to reach a high Pt-mass specific peak power density of 3.8 W mgPt-1 at 160 °C with a low Pt loading of only 0.15 mgPt cm-2.

Author information: (1)Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. (2)Ontario Institute for Cancer Research, Toronto, Canada. (3)Department of Human Genetics, University of California, Los Angeles, USA. (4)Division of Cancer Sciences, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, UK. robert.bristow@manchester.ac.uk. (5)The Christie NHS Foundation Trust, Manchester, UK. robert.bristow@manchester.ac.uk. (6)CRUK Manchester Institute and Centre, Manchester, UK. robert.bristow@manchester.ac.uk. (7)Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. pboutros@mednet.ucla.edu. (8)Department of Human Genetics, University of California, Los Angeles, USA. pboutros@mednet.ucla.edu. (9)Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada. pboutros@mednet.ucla.edu. (10)Vector Institute for Artificial Intelligence, Toronto, Canada. pboutros@mednet.ucla.edu. (11)Department of Urology, University of California, Los Angeles, USA. pboutros@mednet.ucla.edu. (12)Jonsson Comprehensive Cancer Centre, University of California Los Angeles, Los Angeles, USA. pboutros@mednet.ucla.edu. (13)Institute for Precision Health, University of California Los Angeles, Los Angeles, USA. pboutros@mednet.ucla.edu.

When Trypanosoma brucei parasites, the causative agent of sleeping sickness, colonize the adipose tissue, they rewire gene expression. Whether this adaptation affects population behavior and disease treatment remained unknown. By using a mathematical model, we estimate that the population of adipose tissue forms (ATFs) proliferates slower than blood parasites. Analysis of the ATFs proteome, measurement of protein synthesis and proliferation rates confirm that the ATFs divide on average every 12 h, instead of 6 h in the blood. Importantly, the population of ATFs is heterogeneous with parasites doubling times ranging between 5 h and 35 h. Slow-proliferating parasites remain capable of reverting to the fast proliferation profile in blood conditions. Intravital imaging shows that ATFs are refractory to drug treatment. We propose that in adipose tissue, a subpopulation of T. brucei parasites acquire a slow growing behavior, which contributes to disease chronicity and treatment failure.

Global overturning circulation underwent significant changes in the late Miocene, driven by tectonic forcing, and impacted the global climate. Prevailing hypotheses related to the late Miocene deep water circulation (DWC) changes driven by the closure of the Central American Seaways (CAS) and its widespread impact remains untested due to the paucity of suitable records away from the CAS region. Here, we test the hypothesis of the large-scale circulation changes by providing a high-resolution record of DWC since the late Miocene (11.3 to ~2 Ma) from the north-western Indian Ocean. Our investigation reveals a progressive shift from Pacific-dominated DWC before ~9.0 Ma to the onset of a modern-like DWC system in the Indian Ocean comprising of Antarctic bottom water and northern component water during the Miocene-Pliocene transition (~6 Ma) caused by progressive shoaling of the CAS and suggests its widespread impact.

High-dimensional omics datasets provide valuable resources to determine the causal role of molecular traits in mediating the path from genotype to phenotype. Making use of molecular quantitative trait loci (QTL) and genome-wide association study (GWAS) summary statistics, we propose a multivariable Mendelian randomization (MVMR) framework to quantify the proportion of the impact of the DNA methylome (DNAm) on complex traits that is propagated through the assayed transcriptome. Evaluating 50 complex traits, we find that on average at least 28.3% (95% CI: [26.9%-29.8%]) of DNAm-to-trait effects are mediated through (typically multiple) transcripts in the cis-region. Several regulatory mechanisms are hypothesized, including methylation of the promoter probe cg10385390 (chr1:8'022'505) increasing the risk for inflammatory bowel disease by reducing PARK7 expression. The proposed integrative framework can be extended to other omics layers to identify causal molecular chains, providing a powerful tool to map and interpret GWAS signals.

In this work, the enantioselective total synthesis of (-)-quinine has been accomplished in a pot-economical manner using five reaction vessels. In the first pot, reactions involve the diphenylprolinol silyl ether-mediated Michael reaction, aza-Henry reaction, hemiaminalization, and elimination of HNO2 (five reactions), affording a chiral tetrahydropyridine with excellent enantioselectivity. In the second pot, five reactions proceed with excellent diastereoselectivity to afford a trisubstituted piperidine with the desired stereochemistry. A further five reactions are carried out in the last one-pot sequence.

Population fluctuations are widespread across the animal kingdom, especially in the order Rodentia, which includes many globally important reservoir species for zoonotic pathogens. The implications of these fluctuations for zoonotic spillover remain poorly understood. Here, we report a global empirical analysis of data describing the linkages between habitat use, population fluctuations and zoonotic reservoir status in rodents. Our quantitative synthesis is based on data collated from papers and databases. We show that the magnitude of population fluctuations combined with species' synanthropy and degree of human exploitation together distinguish most rodent reservoirs at a global scale, a result that was consistent across all pathogen types and pathogen transmission modes. Our spatial analyses identified hotspots of high transmission risk, including regions where reservoir species dominate the rodent community. Beyond rodents, these generalities inform our understanding of how natural and anthropogenic factors interact to increase the risk of zoonotic spillover in a rapidly changing world.

Early-life adversity (ELA) increases the likelihood of neuropsychiatric diagnoses, which are more prevalent in women than men. Since changes in reproductive hormone levels can also increase the probability of anxiety disorders in women, we examined the effects of ELA on adult female mice across the estrous cycle. We found that during diestrus, when progesterone levels are relatively high, ELA mice exhibit increased avoidance behavior and increased theta oscillation power in the ventral hippocampus (vHIP). We also found that diestrus ELA mice had higher levels of progesterone and lower levels of allopregnanolone, a neurosteroid metabolite of progesterone, in the vHIP compared with control-reared mice. Progesterone receptor antagonism normalized avoidance behavior in ELA mice, while treatment with a negative allosteric modulator of allopregnanolone promoted avoidance behavior in control mice. These results suggest that altered vHIP progesterone and allopregnanolone signaling during diestrus increases avoidance behavior in ELA mice.

T cell exhaustion is a hallmark of hepatitis C virus (HCV) infection and limits protective immunity in chronic viral infections and cancer. Limited knowledge exists of the initial viral and immune dynamics that characterise exhaustion in humans. We studied longitudinal blood samples from a unique cohort of individuals with primary infection using single-cell multi-omics to identify the functions and phenotypes of HCV-specific CD8+ T cells. Early elevated IFN-γ response against the transmitted virus is associated with the rate of immune escape, larger clonal expansion, and early onset of exhaustion. Irrespective of disease outcome, we find heterogeneous subsets of progenitors of exhaustion, based on the level of PD-1 expression and loss of AP-1 transcription factors. Intra-clonal analysis shows distinct trajectories with multiple fates and evolutionary plasticity of precursor cells. These findings challenge the current paradigm on the contribution of CD8+ T cells to HCV disease outcome and provide data for future studies on T cell differentiation in human infections.

Erratum in Nat Commun. 2023 Jan 31;14(1):522.

Dodecagonal oxide quasicrystals are well established as examples of long-range aperiodic order in two dimensions. However, despite investigations by scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), low-energy electron microscopy (LEEM), photoemission spectroscopy as well as density functional theory (DFT), their structure is still controversial. Furthermore, the principles that guide the formation of quasicrystals (QCs) in oxides are elusive since the principles that are known to drive metallic QCs are expected to fail for oxides. Here we demonstrate the solution of the oxide QC structure by synchrotron-radiation based surface x-ray diffraction (SXRD) refinement of its largest-known approximant. The oxide QC formation is forced by large alkaline earth metal atoms and the reduction of their mutual electrostatic repulsion. It drives the n = 6 structure of the 2D Ti2O3 honeycomb arrangement via Stone-Wales transformations into an ordered structure with empty n = 4, singly occupied n = 7 and doubly occupied n = 10 rings, as supported by DFT.

The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. Here, we report cryo-EM structures of the type III-E gRAMPcrRNA and gRAMPcrRNA-TPR-CHAT complexes, before and after either self or non-self RNA target binding, and elucidate the mechanisms underlying RNA-targeting and non-self RNA-induced protease activation. The associated TPR-CHAT adopted a distinct conformation upon self versus non-self RNA target binding, with nucleotides at positions -1 and -2 of the CRISPR-derived RNA (crRNA) serving as a sensor. Only binding of the non-self RNA target activated the TPR-CHAT protease, leading to cleavage of Csx30 protein. Furthermore, TPR-CHAT structurally resembled eukaryotic separase, but with a distinct mechanism for protease regulation. Our findings should facilitate the development of gRAMP-based RNA manipulation tools, and advance our understanding of the virus-host discrimination process governed by a nuclease-protease Craspase during type III-E CRISPR-Cas immunity.

Metasurfaces, artificial 2D structures, have been widely used for the design of various functionalities in optics. Jones matrix, a 2×2 matrix with eight parameters, provides the most complete characterization of the metasurface structures in linear optics, and the number of free parameters (i.e., degrees of freedom, DOFs) in the Jones matrix determines the limit to what functionalities we can realize. Great efforts have been made to continuously expand the number of DOFs, and a maximal number of six has been achieved recently. However, the realization of the ultimate goal with eight DOFs (full free parameters) has been proven as a great challenge so far. Here, we show that by cascading two layer metasurfaces and utilizing the gradient descent optimization algorithm, a spatially varying Jones matrix with eight DOFs is constructed and verified numerically and experimentally in optical frequencies. Such ultimate control unlocks opportunities to design optical functionalities that are unattainable with previously known methodologies and may find wide potential applications in optical fields.

The role of non-neuronal glial cells in the regulation of adipose sympathetic nerve activity and adipocyte functions such as white adipose tissue lipid lipolysis is poorly understood. Here, we combine chemo/optogenetic manipulations of medio-basal hypothalamic astrocytes, real-time fiber photometry monitoring of white adipose tissue norepinephrine (NE) contents and nerve activities, electrophysiological recordings of local sympathetic inputs to inguinal white adipose tissue (iWAT), and adipose tissue lipid lipolytic assays to define the functional roles of hypothalamic astrocytes in the regulation of iWAT sympathetic outflow and lipolysis. Our results show that astrocyte stimulation elevates iWAT NE contents, excites sympathetic neural inputs and promotes lipolysis. Mechanistically, we find that sympathetic paravertebral ganglia (PG) partake in those astrocyte effects. We also find that astrocyte stimulation excites pro-opiomelanocortin (POMC) neurons in the arcuate nucleus of the hypothalamus (ARH), and chemogenetic inhibition of POMC neurons blunts the effects induced by astrocyte stimulation. While we cannot exclude potential roles played by other cell populations such as microglia, our findings in this study reveal a central astrocyte-peripheral adipocyte axis modulating sympathetic drive to adipose tissues and adipocyte functions, one that might serve as a target for therapeutic intervention in the treatment of obesity.

Precision oncology research is challenging outside the contexts of oncogenic addiction and/or targeted therapies. We previously showed that phosphoproteomics is a powerful approach to reveal patient subsets of interest characterized by the activity of a few kinases where the underlying genomics is complex. Here, we conduct a phosphoproteomic screening of samples from HER2-negative female breast cancer receiving neoadjuvant paclitaxel (N = 130), aiming to find candidate biomarkers of paclitaxel sensitivity. Filtering 11 candidate biomarkers through 2 independent patient sets (N = 218) allowed the identification of a subgroup of patients characterized by high levels of CDK4 and filamin-A who had a 90% chance of achieving a pCR in response to paclitaxel. Mechanistically, CDK4 regulates filamin-A transcription, which in turn forms a complex with tubulin and CLIP-170, which elicits increased binding of paclitaxel to microtubules, microtubule acetylation and stabilization, and mitotic catastrophe. Thus, phosphoproteomics allows the identification of explainable factors for predicting response to paclitaxel.

Bound states in the continuum (BICs) have received significant attention for their ability to enhance light-matter interactions across a wide range of systems, including lasers, sensors, and frequency mixers. However, many applications require degenerate or nearly degenerate high-quality factor (Q) modes, such as spontaneous parametric down conversion, non-linear four-wave mixing, and intra-cavity difference frequency mixing for terahertz generation. Previously, degenerate pairs of bound states in the continuum (BICs) have been created by fine-tuning the structure to engineer the degeneracy, yielding BICs that respond unpredictably to structure imperfections and material variations. Instead, using a group theoretic approach, we present a design paradigm based on six-fold rotational symmetry (C6) for creating degenerate pairs of symmetry-protected BICs, whose frequency splitting and Q-factors can be independently and predictably controlled, yielding a complete design phase space. Using a combination of resonator and lattice deformations in silicon metasurfaces, we experimentally demonstrate the ability to tune mode spacing from 2 nm to 110 nm while simultaneously controlling Q-factor.

Second harmonic generation is the lowest-order wave-wave nonlinear interaction occurring in, e.g., optical, radio, and magnetohydrodynamic systems. As a prototype behavior of waves, second harmonic generation is used broadly, e.g., for doubling Laser frequency. Second harmonic generation of Rossby waves has long been believed to be a mechanism of high-frequency Rossby wave generation via cascade from low-frequency waves. Here, we report the observation of a Rossby wave second harmonic generation event in the atmosphere. We diagnose signatures of two transient waves at periods of 16 and 8 days in the terrestrial middle atmosphere, using meteor-radar wind observations over the European and Asian sectors during winter 2018-2019. Their temporal evolution, frequency and wavenumber relations, and phase couplings revealed by bicoherence and biphase analyses demonstrate that the 16-day signature is an atmospheric manifestation of a Rossby wave normal mode, and its second harmonic generation gives rise to the 8-day signature. Our finding confirms the theoretically-anticipated Rossby wave nonlinearity.

To optimally adjust our behavior to changing environments we need to both adjust the speed of our decisions and movements. Yet little is known about the extent to which these processes are controlled by common or separate mechanisms. Furthermore, while previous evidence from computational models and empirical studies suggests that the basal ganglia play an important role during adjustments of decision-making, it remains unclear how this is implemented. Leveraging the opportunity to directly access the subthalamic nucleus of the basal ganglia in humans undergoing deep brain stimulation surgery, we here combine invasive electrophysiological recordings, electrical stimulation and computational modelling of perceptual decision-making. We demonstrate that, while similarities between subthalamic control of decision- and movement speed exist, the causal contribution of the subthalamic nucleus to these processes can be disentangled. Our results show that the basal ganglia independently control the speed of decisions and movement for each hemisphere during adaptive behavior.

Liquid water is a critical component of habitability. However, the production and stability of surficial liquid water can be challenging on planets outside the Habitable Zone and devoid of adequate greenhouse warming. On such cold, icy exo-Earths, basal melting of regional/global ice sheets by geothermal heat provides an alternative means of forming liquid water. Here, we model the thermophysical evolution of ice sheets to ascertain the geophysical conditions that allow liquid water to be produced and maintained at temperatures above the pressure-controlled freezing point of water ice on exo-Earths. We show that even with a modest, Moon-like geothermal heat flow, subglacial oceans of liquid water can form at the base of and within the ice sheets on exo-Earths. Furthermore, subglacial oceans may persist on exo-Earths for a prolonged period due to the billion-year half-lives of heat-producing elements responsible for geothermal heat. These subglacial oceans, often in contact with the planet's crust and shielded from the high energy radiation of their parent star by thick ice layers, may provide habitable conditions for an extended period.

The black perovskite phase of CsPbI3 is promising for optoelectronic applications; however, it is unstable under ambient conditions, transforming within minutes into an optically inactive yellow phase, a fact that has so far prevented its widespread adoption. Here we use coarse photolithography to embed a PbI2-based interfacial microstructure into otherwise-unstable CsPbI3 perovskite thin films and devices. Films fitted with a tessellating microgrid are rendered resistant to moisture-triggered decay and exhibit enhanced long-term stability of the black phase (beyond 2.5 years in a dry environment), due to increasing the phase transition energy barrier and limiting the spread of potential yellow phase formation to structurally isolated domains of the grid. This stabilizing effect is readily achieved at the device level, where unencapsulated CsPbI3 perovskite photodetectors display ambient-stable operation. These findings provide insights into the nature of phase destabilization in emerging CsPbI3 perovskite devices and demonstrate an effective stabilization procedure which is entirely orthogonal to existing approaches.

The Permo-Triassic interval encompasses three extinction events including the most dramatic biological crisis of the Phanerozoic, the latest Permian mass extinction. However, their drivers and outcomes are poorly quantified and understood for terrestrial invertebrates, which we assess here for insects. We find a pattern with three extinctions: the Roadian/Wordian (≈266.9 Ma; extinction of 64.5% insect genera), the Permian/Triassic (≈252 Ma; extinction of 82.6% insect genera), and the Ladinian/Carnian boundaries (≈237 Ma; extinction of 74.8% insect genera). We also unveil a heterogeneous effect of these extinction events across the major insect clades. Because extinction events have impacted Permo-Triassic ecosystems, we investigate the influence of abiotic and biotic factors on insect diversification dynamics and find that changes in floral assemblages are likely the strongest drivers of insects' responses throughout the Permo-Triassic. We also assess the effect of diversity dependence between three insect guilds; an effect ubiquitously found in current ecosystems. We find that herbivores held a central position in the Permo-Triassic interaction network. Our study reveals high levels of insect extinction that profoundly shaped the evolutionary history of the most diverse non-microbial lineage.

The breakdown of toll-like receptor (TLR) tolerance results in tissue damage, and hyperactivation of the TLRs and subsequent inflammatory consequences have been implicated as risk factors for more severe forms of disease and poor outcomes from various diseases including COVID-19 and metabolic (dysfunction) associated fatty liver disease (MAFLD). Here we provide evidence that membrane bound O-acyltransferase domain containing 7 (MBOAT7) is a negative regulator of TLR signalling. MBOAT7 deficiency in macrophages as observed in patients with MAFLD and in COVID-19, alters membrane phospholipid composition. We demonstrate that this is associated with a redistribution of arachidonic acid toward proinflammatory eicosanoids, induction of endoplasmic reticulum stress, mitochondrial dysfunction, and remodelling of the accessible inflammatory-related chromatin landscape culminating in macrophage inflammatory responses to TLRs. Activation of MBOAT7 reverses these effects. These outcomes are further modulated by the MBOAT7 rs8736 (T) MAFLD risk variant. Our findings suggest that MBOAT7 can potentially be explored as a therapeutic target for diseases associated with dysregulation of the TLR signalling cascade.

Solid state quantum defects are promising candidates for scalable quantum information systems which can be seamlessly integrated with the conventional semiconductor electronic devices within the 3D monolithically integrated hybrid classical-quantum devices. Diamond nitrogen-vacancy (NV) center defects are the representative examples, but the controlled positioning of an NV center within bulk diamond is an outstanding challenge. Furthermore, quantum defect properties may not be easily tuned for bulk crystalline quantum defects. In comparison, 2D semiconductors, such as transition metal dichalcogenides (TMDs), are promising solid platform to host a quantum defect with tunable properties and a possibility of position control. Here, we computationally discover a promising defect family for spin qubit realization in 2D TMDs. The defects consist of transition metal atoms substituted at chalcogen sites with desirable spin-triplet ground state, zero-field splitting in the tens of GHz, and strong zero-phonon coupling to optical transitions in the highly desirable telecom band.

Half of mammalian transcripts contain short upstream open reading frames (uORFs) that potentially regulate translation of the downstream coding sequence (CDS). The molecular mechanisms governing these events remain poorly understood. Here, we find that the non-canonical initiation factor Death-associated protein 5 (DAP5 or eIF4G2) is required for translation initiation on select transcripts. Using ribosome profiling and luciferase-based reporters coupled with mutational analysis we show that DAP5-mediated translation occurs on messenger RNAs (mRNAs) with long, structure-prone 5' leader sequences and persistent uORF translation. These mRNAs preferentially code for signalling factors such as kinases and phosphatases. We also report that cap/eIF4F- and eIF4A-dependent recruitment of DAP5 to the mRNA facilitates main CDS, but not uORF, translation suggesting a role for DAP5 in translation re-initiation. Our study reveals important mechanistic insights into how a non-canonical translation initiation factor involved in stem cell fate shapes the synthesis of specific signalling factors.

Insulin receptor (IR) signaling is central to normal metabolic control and is dysregulated in metabolic diseases such as type 2 diabetes. We report here that IR is incorporated into dynamic clusters at the plasma membrane, in the cytoplasm and in the nucleus of human hepatocytes and adipocytes. Insulin stimulation promotes further incorporation of IR into these dynamic clusters in insulin-sensitive cells but not in insulin-resistant cells, where both IR accumulation and dynamic behavior are reduced. Treatment of insulin-resistant cells with metformin, a first-line drug used to treat type 2 diabetes, can rescue IR accumulation and the dynamic behavior of these clusters. This rescue is associated with metformin's role in reducing reactive oxygen species that interfere with normal dynamics. These results indicate that changes in the physico-mechanical features of IR clusters contribute to insulin resistance and have implications for improved therapeutic approaches.

High-Entropy Alloys (HEAs) are a new family of crystalline random alloys with four or more elements in a simple unit cell, at the forefront of materials research for their exceptional mechanical properties. Their strong chemical disorder leads to mass and force-constant fluctuations which are expected to strongly reduce phonon lifetime, responsible for thermal transport, similarly to glasses. Still, the long range order would associate HEAs to crystals with a complex disordered unit cell. These two families of materials, however, exhibit very different phonon dynamics, still leading to similar thermal properties. The question arises on the positioning of HEAs in this context. Here we present an exhaustive experimental investigation of the lattice dynamics in a HEA, Fe20Co20Cr20Mn20Ni20, using inelastic neutron and X-ray scattering. We demonstrate that HEAs present unique phonon dynamics at the frontier between fully disordered and ordered materials, characterized by long-propagating acoustic phonons in the whole Brillouin zone.

The glycolytic enzyme, pyruvate kinase Pyk1 maintains telomere heterochromatin by phosphorylating histone H3T11 (H3pT11), which promotes SIR (silent information regulator) complex binding at telomeres and prevents autophagy-mediated Sir2 degradation. However, the exact mechanism of action for H3pT11 is poorly understood. Here, we report that H3pT11 directly inhibits Dot1-catalyzed H3K79 tri-methylation (H3K79me3) and uncover how this histone crosstalk regulates autophagy and telomere silencing. Mechanistically, Pyk1-catalyzed H3pT11 directly reduces the binding of Dot1 to chromatin and inhibits Dot1-catalyzed H3K79me3, which leads to transcriptional repression of autophagy genes and reduced autophagy. Despite the antagonism between H3pT11 and H3K79me3, they work together to promote the binding of SIR complex at telomeres to maintain telomere silencing. Furthermore, we identify Reb1 as a telomere-associated factor that recruits Pyk1-containing SESAME (Serine-responsive SAM-containing Metabolic Enzyme) complex to telomere regions to phosphorylate H3T11 and prevent the invasion of H3K79me3 from euchromatin into heterochromatin to maintain telomere silencing. Together, these results uncover a histone crosstalk and provide insights into dynamic regulation of silent heterochromatin and autophagy in response to cell metabolism.

Chloride homeostasis is regulated in all cellular compartments. CLC-type channels selectively transport Cl- across biological membranes. It is proposed that side-chains of pore-lining residues determine Cl- selectivity in CLC-type channels, but their spatial orientation and contributions to selectivity are not conserved. This suggests a possible role for mainchain amides in selectivity. We use nonsense suppression to insert α-hydroxy acids at pore-lining positions in two CLC-type channels, CLC-0 and bCLC-k, thus exchanging peptide-bond amides with ester-bond oxygens which are incapable of hydrogen-bonding. Backbone substitutions functionally degrade inter-anion discrimination in a site-specific manner. The presence of a pore-occupying glutamate side chain modulates these effects. Molecular dynamics simulations show backbone amides determine ion energetics within the bCLC-k pore and how insertion of an α-hydroxy acid alters selectivity. We propose that backbone-ion interactions are determinants of Cl- specificity in CLC channels in a mechanism reminiscent of that described for K+ channels.

Nutritional conditions early in human life may influence phenotypic characteristics in later generations. A male-line transgenerational pathway, triggered by the early environment, has been postulated with support from animal and a small number of human studies. Here we analyse individuals born in Uppsala Sweden 1915-29 with linked data from their children and parents, which enables us to explore the hypothesis that pre-pubertal food abundance may trigger a transgenerational effect on cancer events. We used cancer registry and cause-of-death data to analyse 3422 cancer events in grandchildren (G2) by grandparental (G0) food access. We show that variation in harvests and food access in G0 predicts cancer occurrence in G2 in a specific way: abundance among paternal grandfathers, but not any other grandparent, predicts cancer occurrence in grandsons but not in granddaughters. This male-line response is observed for several groups of cancers, suggesting a general susceptibility, possibly acquired in early embryonic development. We observed no transgenerational influence in the middle generation.

Improved response to canonical therapies requires a mechanistic understanding of dynamic tumor heterogeneity by identifying discrete cellular populations with enhanced cellular plasticity. We have previously demonstrated distinct resistance mechanisms in skin basal cell carcinomas, but a comprehensive understanding of the cellular states and markers associated with these populations remains poorly understood. Here we identify a pre-existing resistant cellular population in naive basal cell carcinoma tumors marked by the surface marker LY6D. LY6D+ tumor cells are spatially localized and possess basal cell carcinoma and squamous cell carcinoma-like features. Using computational tools, organoids, and spatial tools, we show that LY6D+ basosquamous cells represent a persister population lying on a central node along the skin lineage-associated spectrum of epithelial states with local environmental and applied therapies determining the kinetics of accumulation. Surprisingly, LY6D+ basosquamous populations exist in many epithelial tumors, such as pancreatic adenocarcinomas, which have poor outcomes. Overall, our results identify the resistant LY6D+ basosquamous population as an important clinical target and suggest strategies for future therapeutic approaches to target them.

Extrinsic and intrinsic factors impact diversity. On deep-time scales, the extrinsic impact of climate and geology are crucial, but poorly understood. Here, we use the inner ear morphology of ruminant artiodactyls to test for a deep-time correlation between a low adaptive anatomical structure and both extrinsic and intrinsic variables. We apply geometric morphometric analyses in a phylogenetic frame to X-ray computed tomographic data from 191 ruminant species. Contrasting results across ruminant clades show that neutral evolutionary processes over time may strongly influence the evolution of inner ear morphology. Extant, ecologically diversified clades increase their evolutionary rate with decreasing Cenozoic global temperatures. Evolutionary rate peaks with the colonization of new continents. Simultaneously, ecologically restricted clades show declining or unchanged rates. These results suggest that both climate and paleogeography produced heterogeneous environments, which likely facilitated Cervidae and Bovidae diversification and exemplifies the effect of extrinsic and intrinsic factors on evolution in ruminants.

Discoid lupus erythematosus (DLE) and systemic lupus erythematosus (SLE) are both types of lupus, yet the characteristics, and differences between them are not fully understood. Here we show single-cell RNA sequencing data of cutaneous lesions from DLE and SLE patients and skin tissues from healthy controls (HCs). We find significantly higher proportions of T cells, B cells and NK cells in DLE than in SLE. Expanded CCL20+ keratinocyte, CXCL1+ fibroblast, ISGhiCD4/CD8 T cell, ISGhi plasma cell, pDC, and NK subclusters are identified in DLE and SLE compared to HC. In addition, we observe higher cell communication scores between cell types such as fibroblasts and macrophage/dendritic cells in cutaneous lesions of DLE and SLE compared to HC. In summary, we clarify the heterogeneous characteristics in cutaneous lesions between DLE and SLE, and discover some specific cell subtypes and ligand-receptor pairs that indicate possible therapeutic targets of lupus erythematosus.

Although cities have risen to prominence as climate actors, emissions' data scarcity has been the primary challenge to evaluating their performance. Here we develop a scalable, replicable machine learning approach for evaluating the mitigation performance for nearly all local administrative areas in Europe from 2001-2018. By combining publicly available, spatially explicit environmental and socio-economic data with self-reported emissions data from European cities, we predict annual carbon dioxide emissions to explore trends in city-scale mitigation performance. We find that European cities participating in transnational climate initiatives have likely decreased emissions since 2001, with slightly more than half likely to have achieved their 2020 emissions reduction target. Cities who report emissions data are more likely to have achieved greater reductions than those who fail to report any data. Despite its limitations, our model provides a replicable, scalable starting point for understanding city-level climate emissions mitigation performance.

Author information: (1)Department of Human Genetics, McGill University, Montréal, QC, Canada. (2)The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada. (3)23andMe, Inc., Sunnyvale, CA, USA. (4)Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA. (5)Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK. (6)Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK. (7)NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK. (8)Lund University, Translational Neurogenetics Unit, Department of Experimental Medical Science, Lund, Sweden. (9)Sleep Disorders Unit, Pitié Salpêtrière Hospital, APHP-Sorbonne, Paris Brain Insitute and Sorbonne University, Paris, France. (10)Oxford Parkinson's Disease Centre (OPDC), University of Oxford, Oxford, UK. (11)Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK. (12)Centre d'Études Avancées en Médecine du Sommeil, Hôpital du Sacré-Cœur de Montréal, Montréal, QC, Canada. (13)Department of Psychiatry, Université de Montréal, Montréal, QC, Canada. (14)Department of Psychology, Université du Québec à Montréal, Montreal, QC, Canada. (15)Department of Neurosciences, Université de Montréal, Montréal, QC, Canada. (16)National Reference Center for Narcolepsy, Sleep Unit, Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Institute Neuroscience Montpellier Inserm, Montpellier, France. (17)Clinical Neurology Unit, Department of Neurosciences, University Hospital of Udine, Udine, Italy. (18)Department of Medicine (DAME), University of Udine, Udine, Italy. (19)Sleep Disorders Clinic, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria. (20)Department of Neurology and Centre of Clinical Neuroscience, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic. (21)Department of Neurology, Philipps-University, Marburg, Germany. (22)Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio-Emilia, Modena, Italy. (23)IRCCS, Institute of Neurological Sciences of Bologna, Bologna, Italy. (24)Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum, University of Bologna, Bologna, Italy. (25)Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy. (26)Department of Medical Sciences and Public Health, Sleep Disorder Research Center, University of Cagliari, Cagliari, Italy. (27)Paracelsus-Elena-Klinik, Kassel, Germany. (28)Department of Neurology, University Medical Centre Goettingen, Goettingen, Germany. (29)Sleep and Neurology Unit, Beau Soleil Clinic, Montpellier, France. (30)EuroMov Digital Health in Motion, University of Montpellier IMT Mines Ales, Montpellier, France. (31)University Lille North of France, Department of Clinical Neurophysiology and Sleep Center, CHU Lille, Lille, France. (32)Institute of Sleep Medicine and Neuromuscular Disorders, University of Münster, Münster, Germany. (33)Department of Neurological Sciences, Università Vita-Salute San Raffaele, Milan, Italy. (34)Laboratory for Sleep Disorders, St. Dimpna Regional Hospital, Geel, Belgium. (35)Department of Neurology, St. Dimpna Regional Hospital, Geel, Belgium. (36)Department of Neurology, Antwerp University Hospital, Edegem, Belgium. (37)Sleep disorder Unit, Carémeau Hospital, University Hospital of Nîmes, Nîmes, France. (38)Department of Neurology, Mayo Clinic, Rochester, MN, USA. (39)Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA. (40)Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA. (41)Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, UK. (42)Department of Clinical and Movement Neurosciences, University College London, Institute of Neurology, London, UK. (43)Department of Neurology, Oslo University Hospital, Oslo, Norway. (44)Data Tecnica International, Glen Echo, MD, USA. (45)Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA. (46)Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada. (47)Department of Human Genetics, McGill University, Montréal, QC, Canada. ziv.gan-or@mcgill.ca. (48)The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada. ziv.gan-or@mcgill.ca. (49)Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada. ziv.gan-or@mcgill.ca.

Dendritic cells play a key role in processing and presenting antigens to naïve T cells to prime adaptive immunity. Circadian rhythms are known to regulate many aspects of immunity; however, the role of circadian rhythms in dendritic cell function is still unclear. Here, we show greater T cell responses when mice are immunised in the middle of their rest versus their active phase. We find a circadian rhythm in antigen processing that correlates with rhythms in both mitochondrial morphology and metabolism, dependent on the molecular clock gene, Bmal1. Using Mdivi-1, a compound that promotes mitochondrial fusion, we are able to rescue the circadian deficit in antigen processing and mechanistically link mitochondrial morphology and antigen processing. Furthermore, we find that circadian changes in mitochondrial Ca2+ are central to the circadian regulation of antigen processing. Our results indicate that rhythmic changes in mitochondrial calcium, which are associated with changes in mitochondrial morphology, regulate antigen processing.

Carbon capture and utilization technology has been studied for its practical ability to reduce CO2 emissions and enable economical chemical production. The main challenge of this technology is that a large amount of thermal energy must be provided to supply high-purity CO2 and purify the product. Herein, we propose a new concept called reaction swing absorption, which produces synthesis gas (syngas) with net-zero CO2 emission through direct electrochemical CO2 reduction in a newly proposed amine solution, triethylamine. Experimental investigations show high CO2 absorption rates (>84%) of triethylamine from low CO2 concentrated flue gas. In addition, the CO Faradaic efficiency in a triethylamine supplied membrane electrode assembly electrolyzer is approximately 30% (@-200 mA cm-2), twice higher than those in conventional alkanolamine solvents. Based on the experimental results and rigorous process modeling, we reveal that reaction swing absorption produces high pressure syngas at a reasonable cost with negligible CO2 emissions. This system provides a fundamental solution for the CO2 crossover and low system stability of electrochemical CO2 reduction.

International travel contributes to the global spread of antimicrobial resistance. Travelers' diarrhea exacerbates the risk of acquiring multidrug-resistant organisms and can lead to persistent gastrointestinal disturbance post-travel. However, little is known about the impact of diarrhea on travelers' gut microbiomes, and the dynamics of these changes throughout travel. Here, we assembled a cohort of 159 international students visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. We find that gut microbiome composition changed significantly throughout travel, but taxonomic diversity remained stable. However, diarrhea disrupted this stability and resulted in an increased abundance of antimicrobial resistance genes that can remain high for weeks. We also identified taxa differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that distinguishes between these disease states. Additionally, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates and found those from travelers who experienced diarrhea encoded more antimicrobial resistance genes than those who did not. In this work, we find the gut microbiomes of international travelers' are resilient to dysbiosis; however, they are also susceptible to colonization by multidrug-resistant bacteria, a risk that is more pronounced in travelers with diarrhea.

Morphogenesis of many protozoans depends on a polarized establishment of cortical cytoskeleton containing the subpellicular microtubules (SPMTs), which are apically nucleated and anchored by the apical polar ring (APR). In malaria parasite Plasmodium, APR emerges in the host-invading stages, including the ookinete for mosquito infection. So far, the fine structure and molecular components of APR as well as the underlying mechanism of APR-mediated apical positioning of SPMTs are largely unknown. Here, we resolve an unprecedented APR structure composed of a top ring plus approximate 60 radiating spines. We report an APR-localizing and SPMT-binding protein APR2. APR2 disruption impairs ookinete morphogenesis and gliding motility, leading to Plasmodium transmission failure in mosquitoes. The APR2-deficient ookinetes display defective apical anchorage of APR and SPMT due to the impaired integrity of APR. Using protein proximity labeling, we obtain a Plasmodium ookinete APR proteome and validate ten undescribed APR proteins. Among them, APRp2 and APRp4 directly interact with APR2 and also mediate the apical anchorage of SPMTs. This study sheds light on the molecular basis of APR in the organization of Plasmodium ookinete SPMTs.

In situ vaccination is a promising strategy to convert the immunosuppressive tumor microenvironment into an immunostimulatory one with limited systemic exposure and side effect. However, sustained clinical benefits require long-term and multidimensional immune activation including innate and adaptive immunity. Here, we develop a probiotic food-grade Lactococcus lactis-based in situ vaccination (FOLactis) expressing a fusion protein of Fms-like tyrosine kinase 3 ligand and co-stimulator OX40 ligand. Intratumoural delivery of FOLactis contributes to local retention and sustained release of therapeutics to thoroughly modulate key components of the antitumour immune response, such as activation of natural killer cells, cytotoxic T lymphocytes, and conventional-type-1-dendritic cells in the tumors and tumor-draining lymph nodes. In addition, intratumoural administration of FOLactis induces a more robust tumor antigen-specific immune response and superior systemic antitumour efficacy in multiple poorly immune cell-infiltrated and anti-PD1-resistant tumors. Specific depletion of different immune cells reveals that CD8+ T and natural killer cells are crucial to the in situ vaccine-elicited tumor regression. Our results confirm that FOLactis displays an enhanced antitumour immunity and successfully converts the 'cold' tumors to 'hot' tumors.

Induced pluripotent stem cells (iPSCs) can in principle differentiate into any cell of the body, and have revolutionized biomedical research and regenerative medicine. Unlike their human counterparts, mouse iPSCs (miPSCs) are reported to silence transposable elements and prevent transposable element-mediated mutagenesis. Here we apply short-read or Oxford Nanopore Technologies long-read genome sequencing to 38 bulk miPSC lines reprogrammed from 10 parental cell types, and 18 single-cell miPSC clones. While single nucleotide variants and structural variants restricted to miPSCs are rare, we find 83 de novo transposable element insertions, including examples intronic to Brca1 and Dmd. LINE-1 retrotransposons are profoundly hypomethylated in miPSCs, beyond other transposable elements and the genome overall, and harbor alternative protein-coding gene promoters. We show that treatment with the LINE-1 inhibitor lamivudine does not hinder reprogramming and efficiently blocks endogenous retrotransposition, as detected by long-read genome sequencing. These experiments reveal the complete spectrum and potential significance of mutations acquired by miPSCs.

The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution.

Erratum in Nat Commun. 2023 Jan 31;14(1):524.

Tissue development and disease lead to changes in cellular organization, nuclear morphology, and gene expression, which can be jointly measured by spatial transcriptomic technologies. However, methods for jointly analyzing the different spatial data modalities in 3D are still lacking. We present a computational framework to integrate Spatial Transcriptomic data using over-parameterized graph-based Autoencoders with Chromatin Imaging data (STACI) to identify molecular and functional alterations in tissues. STACI incorporates multiple modalities in a single representation for downstream tasks, enables the prediction of spatial transcriptomic data from nuclear images in unseen tissue sections, and provides built-in batch correction of gene expression and tissue morphology through over-parameterization. We apply STACI to analyze the spatio-temporal progression of Alzheimer's disease and identify the associated nuclear morphometric and coupled gene expression features. Collectively, we demonstrate the importance of characterizing disease progression by integrating multiple data modalities and its potential for the discovery of disease biomarkers.

Interactions with commensal microbes shape host immunity on multiple levels and play a pivotal role in human health and disease. Tissue-dwelling, antigen-specific T cells are poised to respond to local insults, making their phenotype important in the relationship between host and microbes. Here we show that MHC-II restricted, commensal-reactive T cells in the colon of both humans and mice acquire transcriptional and functional characteristics associated with innate-like T cells. This cell population is abundant and conserved in the human and murine colon and endowed with polyfunctional effector properties spanning classic Th1- and Th17-cytokines, cytotoxic molecules, and regulators of epithelial homeostasis. T cells with this phenotype are increased in ulcerative colitis patients, and their presence aggravates pathology in dextran sodium sulphate-treated mice, pointing towards a pathogenic role in colitis. Our findings add to the expanding spectrum of innate-like immune cells positioned at the frontline of intestinal immune surveillance, capable of acting as sentinels of microbes and the local cytokine milieu.

Erratum in Nat Commun. 2023 Jan 25;14(1):403.

Moiré bilayer materials have recently attracted much attention following the discovery of various correlated insulating states at specific band fillings. Here we discuss the metal-insulator transitions (MITs) that have been observed in the same devices, but at fillings far from the strongly correlated regime dominated by Mott-like physics, displaying many similarities to other examples of disorder-dominated MITs. We propose a minimal theoretical model describing the interplay of interactions and disorder, which is able to capture all the universal aspects of quantum criticality, as observed in experiments performed on several devices.

Quantitative estimations of atmospheric aerosol absorption are rather uncertain due to the lack of reliable information about the global distribution. Because the information about aerosol properties is commonly provided by single-viewing photometric satellite sensors that are not sensitive to aerosol absorption. Consequently, the uncertainty in aerosol radiative forcing remains one of the largest in the Assessment Reports of the Intergovernmental Panel on Climate Change (IPCC AR5 and AR6). Here, we use multi-angular polarimeters (MAP) to provide constraints on emission of absorbing aerosol species and estimate global aerosol absorption optical depth (AAOD) and its climate effect. Our estimate of modern-era mid-visible AAOD is 0.0070 that is higher than IPCC by a factor of 1.3-1.8. The black carbon instantaneous direct radiative forcing (BC DRF) is +0.33 W/m2 [+0.17, +0.54]. The MAP constraint narrows the 95% confidence interval of BC DRF by a factor of 2 and boosts confidence in its spatial distribution.

Transplantation of mesenchymal stem cells (MSCs) holds promise to repair severe traumatic injuries. However, current transplantation practices limit the potential of this technique, either by losing the viable MSCs or reducing the performance of resident MSCs. Herein, we design a "bead-jet" printer, specialized for high-throughput intra-operative formulation and printing of MSCs-laden Matrigel beads. We show that high-density encapsulation of MSCs in Matrigel beads is able to augment MSC function, increasing MSC proliferation, migration, and extracellular vesicle production, compared with low-density bead or high-density bulk encapsulation of the equivalent number of MSCs. We find that the high-density MSCs-laden beads in sparse patterns demonstrate significantly improved therapeutic performance, by regenerating skeletal muscles approaching native-like cell density with reduced fibrosis, and regenerating skin with hair follicle growth and increased dermis thickness. MSC proliferation within 1-week post-transplantation and differentiation at 3 - 4 weeks post-transplantation are suggested to contribute therapy augmentation. We expect this "bead-jet" printing system to strengthen the potential of MSC transplantation.

CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.

The human gut microbiome has been extensively explored, while the archaeal viruses remain largely unknown. Here, we present a comprehensive analysis of the archaeal viruses from the human gut metagenomes and the existing virus collections using the CRISPR spacer and viral signature-based approach. This results in 1279 viral species, of which, 95.2% infect Methanobrevibacteria_A, 56.5% shared high identity (>95%) with the archaeal proviruses, 37.2% have a host range across archaeal species, and 55.7% are highly prevalent in the human population (>1%). A methanogenic archaeal virus-specific gene for pseudomurein endoisopeptidase (PeiW) frequently occurs in the viral sequences (n = 150). Analysis of 33 Caudoviricetes viruses with a complete genome often discovers the genes (integrase, n = 29; mazE, n = 10) regulating the viral lysogenic-lytic cycle, implying the dominance of temperate viruses in the archaeal virome. Together, our work uncovers the unexplored diversity of archaeal viruses, revealing the novel facet of the human gut microbiome.

Binary nanoparticle (NP) superlattices exhibit distinct collective plasmonic, magnetic, optical, and electronic properties. Here, we computationally demonstrate how fluid-fluid interfaces could be used to self-assemble binary systems of NPs into 2D superlattices when the NP species exhibit different miscibility with the fluids forming the interface. We develop a basin-hopping Monte Carlo (BHMC) algorithm tailored for interface-trapped structures to rapidly determine the ground-state configuration of NPs, allowing us to explore the repertoire of binary NP architectures formed at the interface. By varying the NP size ratio, interparticle interaction strength, and difference in NP miscibility with the two fluids, we demonstrate the assembly of an array of exquisite 2D periodic architectures, including AB-, AB2-, and AB3-type monolayer superlattices as well as AB-, AB2-, A3B5-, and A4B6-type bilayer superlattices. Our results suggest that the interfacial assembly approach could be a versatile platform for fabricating 2D colloidal superlattices with tunable structure and properties.

Prime editors (PEs) are powerful tools that widen the possibilities for sequence modifications during genome editing. Although methods based on the analysis of Cas9 nuclease or nickase activity have been used to predict genome-wide off-target activities of PEs, no tool that directly uses PEs for this purpose has been reported yet. In this study, we present a cell-based assay, named TAgmentation of Prime Editor sequencing (TAPE-seq), that provides genome-wide off-target candidates for PEs. TAPE-seq analyses are successfully performed using many different versions of PEs. The TAPE-seq predictions are compared with results from two other off-site prediction methods, Cas9 nuclease-based GUIDE-seq and Cas9 nickase-based Digenome-seq (nDigenome-seq). TAPE-seq shows a lower miss rate, and a higher area under the receiver operating characteristic curve compared to the other methods. TAPE-seq also identified valid off-target sites that were missed by the other methods.

Elevated body mass index (BMI) is heritable and associated with many health conditions that impact morbidity and mortality. The study of the genetic association of BMI across a broad range of common disease conditions offers the opportunity to extend current knowledge regarding the breadth and depth of adiposity-related diseases. We identify 906 (364 novel) and 41 (6 novel) genome-wide significant loci for BMI among participants of European (N~1.1 million) and African (N~100,000) ancestry, respectively. Using a BMI genetic risk score including 2446 variants, 316 diagnoses are associated in the Million Veteran Program, with 96.5% showing increased risk. A co-morbidity network analysis reveals seven disease communities containing multiple interconnected diseases associated with BMI as well as extensive connections across communities. Mendelian randomization analysis confirms numerous phenotypes across a breadth of organ systems, including conditions of the circulatory (heart failure, ischemic heart disease, atrial fibrillation), genitourinary (chronic renal failure), respiratory (respiratory failure, asthma), musculoskeletal and dermatologic systems that are deeply interconnected within and across the disease communities. This work shows that the complex genetic architecture of BMI associates with a broad range of major health conditions, supporting the need for comprehensive approaches to prevent and treat obesity.

Human sensory systems are more sensitive to common features in the environment than uncommon features. For example, small deviations from the more frequently encountered horizontal orientations can be more easily detected than small deviations from the less frequent diagonal ones. Here we find that artificial neural networks trained to recognize objects also have patterns of sensitivity that match the statistics of features in images. To interpret these findings, we show mathematically that learning with gradient descent in neural networks preferentially creates representations that are more sensitive to common features, a hallmark of efficient coding. This effect occurs in systems with otherwise unconstrained coding resources, and additionally when learning towards both supervised and unsupervised objectives. This result demonstrates that efficient codes can naturally emerge from gradient-like learning.

The evolutionary arms race between phages and bacteria, where bacteria evolve resistance to phages and phages retaliate with resistance-countering mutations, is a major driving force of molecular innovation and genetic diversification. Yet attempting to reproduce such ongoing retaliation dynamics in the lab has been challenging; laboratory coevolution experiments of phage and bacteria are typically performed in well-mixed environments and often lead to rapid stagnation with little genetic variability. Here, co-culturing motile E. coli with the lytic bacteriophage T7 on swimming plates, we observe complex spatiotemporal dynamics with multiple genetically diversifying adaptive cycles. Systematically quantifying over 10,000 resistance-infectivity phenotypes between evolved bacteria and phage isolates, we observe diversification into multiple coexisting ecotypes showing a complex interaction network with both host-range expansion and host-switch tradeoffs. Whole-genome sequencing of these evolved phage and bacterial isolates revealed a rich set of adaptive mutations in multiple genetic pathways including in genes not previously linked with phage-bacteria interactions. Synthetically reconstructing these new mutations, we discover phage-general and phage-specific resistance phenotypes as well as a strong synergy with the more classically known phage-resistance mutations. These results highlight the importance of spatial structure and migration for driving phage-bacteria coevolution, providing a concrete system for revealing new molecular mechanisms across diverse phage-bacterial systems.

Wide-field fluorescence imaging is an indispensable tool for studying large-scale biodynamics. Limited space-bandwidth product and strong light diffusion make conventional implementations incapable of high-resolution mapping of fluorescence biodistribution in three dimensions. We introduce a volumetric wide-field fluorescence microscopy based on optical astigmatism combined with fluorescence source localization, covering 5.6×5.6×0.6 mm3 imaging volume. Two alternative configurations are proposed exploiting multifocal illumination or sparse localization of point emitters, which are herein seamlessly integrated in one system. We demonstrate real-time volumetric mapping of the murine cortical microcirculation at capillary resolution without employing cranial windows, thus simultaneously delivering quantitative perfusion information across both brain hemispheres. Morphological and functional changes of cerebral vascular networks are further investigated after an acute ischemic stroke, enabling cortex-wide observation of concurrent collateral recruitment events occurring on a sub-second scale. The reported technique thus offers a wealth of unmatched possibilities for non- or minimally invasive imaging of biodynamics across scales.

The application of membrane electrode assemblies is considered a promising approach for increasing the energy efficiency of conventional alkaline water electrolysis. However, previous investigations have mostly focused on improving membrane conductivity and electrocatalyst activity. This study reports an all-in-one membrane electrode assembly obtained by de novo design. The introduction of a porous membrane readily enables the oriented intergrowth of ordered catalyst layers using solvothermal methods, leading to the formation of an all-in-one MEA for alkaline water electrolysis. This all-in-one MEA features ordered catalyst layers with large surface areas, a low-tortuosity pore structure, integrated catalyst layer/membrane interfaces, and a well-ordered OH- transfer channel. Owing to this design, a high current density of 1000 mA cm-2 is obtained at 1.57 V in 30 wt% KOH, resulting in a 94% energy efficiency. This work highlights the prospects of all-in-one membrane electrode assemblies in designing next-generation high-performance alkaline water electrolysis.

The progression of cancer from localized to metastatic disease is the primary cause of morbidity and mortality. The interplay between the tumor and its microenvironment is the key driver in this process of tumor progression. In order for tumors to progress and metastasize they must reprogram the cells that make up the microenvironment to promote tumor growth and suppress endogenous defense systems, such as the immune and inflammatory response. We have previously demonstrated that stimulation of Tsp-1 in the tumor microenvironment (TME) potently inhibits tumor growth and progression. Here, we identify a novel tumor-mediated mechanism that represses the expression of Tsp-1 in the TME via secretion of the serine protease PRSS2. We demonstrate that PRSS2 represses Tsp-1, not via its enzymatic activity, but by binding to low-density lipoprotein receptor-related protein 1 (LRP1). These findings describe a hitherto undescribed activity for PRSS2 through binding to LRP1 and represent a potential therapeutic strategy to treat cancer by blocking the PRSS2-mediated repression of Tsp-1. Based on the ability of PRSS2 to reprogram the tumor microenvironment, this discovery could lead to the development of therapeutic agents that are indication agnostic.

Organic electrochemical transistors are a promising technology for bioelectronic devices, with applications in neuromorphic computing and healthcare. The active component enabling an organic electrochemical transistor is the organic mixed ionic-electronic conductor whose optimization is critical for realizing high-performing devices. In this study, the influence of purity and molecular weight is examined for a p-type polythiophene and an n-type naphthalene diimide-based polymer in improving the performance and safety of organic electrochemical transistors. Our preparative GPC purification reduced the Pd content in the polymers and improved their organic electrochemical transistor mobility by ~60% and 80% for the p- and n-type materials, respectively. These findings demonstrate the paramount importance of removing residual Pd, which was concluded to be more critical than optimization of a polymer's molecular weight, to improve organic electrochemical transistor performance and that there is readily available improvement in performance and stability of many of the reported organic mixed ionic-electronic conductors.

The D,D-transpeptidase activity of penicillin-binding proteins (PBPs) is the well-known primary target of β-lactam antibiotics that block peptidoglycan polymerization. β-lactam-induced bacterial killing involves complex downstream responses whose causes and consequences are difficult to resolve. Here, we use the functional replacement of PBPs by a β-lactam-insensitive L,D-transpeptidase to identify genes essential to mitigate the effects of PBP inactivation by β-lactams in actively dividing bacteria. The functions of the 179 conditionally essential genes identified by this approach extend far beyond L,D-transpeptidase partners for peptidoglycan polymerization to include proteins involved in stress response and in the assembly of outer membrane polymers. The unsuspected effects of β-lactams include loss of the lipoprotein-mediated covalent bond that links the outer membrane to the peptidoglycan, destabilization of the cell envelope in spite of effective peptidoglycan cross-linking, and increased permeability of the outer membrane. The latter effect indicates that the mode of action of β-lactams involves self-promoted penetration through the outer membrane.

Microporous organic nanotubes (MONs) hold considerable promise for designing molecular-sieving membranes because of their high microporosity, customizable chemical functionalities, and favorable polymer affinity. Herein, we report the use of MONs derived from covalent organic frameworks to engineer 15-nm-thick microporous membranes via interfacial polymerization (IP). The incorporation of a highly porous and interpenetrated MON layer on the membrane before the IP reaction leads to the formation of polyamide membranes with Turing structure, enhanced microporosity, and reduced thickness. The MON-modified membranes achieve a remarkable water permeability of 41.7 L m-2 h-1 bar-1 and high retention of boron (78.0%) and phosphorus (96.8%) at alkaline conditions (pH 10), surpassing those of reported nanofiltration membranes. Molecular simulations reveal that introducing the MONs not only reduces the amine molecule diffusion toward the organic phase boundary but also increases membrane porosity and the density of water molecules around the membrane pores. This MON-regulated IP strategy provides guidelines for creating high-permeability membranes for precise nanofiltration.

Multiferroics, showing the coexistence of two or more ferroic orderings at room temperature, could harness a revolution in multifunctional devices. However, most of the multiferroic compounds known to date are not magnetically and electrically ordered at ambient conditions, so the discovery of new materials is pivotal to allow the development of the field. In this work, we show that BaFe2O4 is a previously unrecognized room temperature multiferroic. X-ray and neutron diffraction allowed to reveal the polar crystal structure of the compound as well as its antiferromagnetic behavior, confirmed by bulk magnetometry characterizations. Piezo force microscopy and electrical measurements show the polarization to be switchable by the application of an external field, while symmetry analysis and calculations based on density functional theory reveal the improper nature of the ferroelectric component. Considering the present findings, we propose BaFe2O4 as a Bi- and Pb-free model for the search of new advanced multiferroic materials.

Neuromedin U receptor 2 (NMU2), an emerging attractive target for treating obesity, has shown the capability in reducing food intake and regulating energy metabolism when activated. However, drug development of NMU2 was deferred partially due to the lack of structural information. Here, we present the cryo-electron microscopy (cryo-EM) structure of NMU2 bound to the endogenous agonist NmU-25 and Gi1 at 3.3 Å resolution. Combined with functional and computational data, the structure reveals the key factors that govern the recognition and selectivity of peptide agonist as well as non-peptide antagonist, providing the structural basis for design of novel and highly selective drugs targeting NMU2. In addition, a 25-degree rotation of Gi protein in reference to NMU2 is also observed compared in other structures of class A GPCR-Gi complexes, suggesting heterogeneity in the processes of G protein-coupled receptors (GPCRs) activation and G protein coupling.

Magnetic resonance imaging (MRI) is a non-invasive imaging technology to diagnose health conditions, showing the weakness of low sensitivity. Herein, we synthesize a contrast agent, SPIO@SiO2@MnO2, which shows decreased T1 and T2 contrast intensity in normal physiological conditions. In the acid environment of tumor or inflamed tissue, the manganese dioxide (MnO2) layer decomposes into magnetically active Mn2+ (T1-weighted), and the T1 and T2 signals are sequentially recovered. In addition, both constrast quenching-activation degrees of T1 and T2 images can be accurately regulated by the silicon dioxide (SiO2) intermediate layer between superparamagnetic iron oxide (SPIO) and MnO2. Through the "dual-contrast enhanced subtraction" imaging processing technique, the contrast sensitivity of this MRI contrast agent is enhanced to a 12.3-time difference between diseased and normal tissue. Consequently, SPIO@SiO2@MnO2 is successfully applied to trace the tiny liver metastases of approximately 0.5 mm and monitor tissue inflammation.

Lin28 RNA-binding proteins are stem-cell factors that play key roles in development. Lin28 suppresses the biogenesis of let-7 microRNAs and regulates mRNA translation. Notably, let-7 inhibits Lin28, establishing a double-negative feedback loop. The Lin28/let-7 axis resides at the interface of metabolic reprogramming and oncogenesis and is therefore a potential target for several diseases. In this study, we use compound-C1632, a drug-like Lin28 inhibitor, and show that the Lin28/let-7 axis regulates the balance between ketogenesis and lipogenesis in liver cells. Hence, Lin28 inhibition activates synthesis and secretion of ketone bodies whilst suppressing lipogenesis. This occurs at least partly via let-7-mediated inhibition of nuclear receptor co-repressor 1, which releases ketogenesis gene expression mediated by peroxisome proliferator-activated receptor-alpha. In this way, small-molecule Lin28 inhibition protects against lipid accumulation in multiple cellular and male mouse models of hepatic steatosis. Overall, this study highlights Lin28 inhibitors as candidates for the treatment of hepatic disorders of abnormal lipid deposition.

Analog spatial differentiation is used to realize edge-based enhancement, which plays an important role in data compression, microscopy, and computer vision applications. Here, a planar chip made from dielectric multilayers is proposed to operate as both first- and second-order spatial differentiator without any need to change the structural parameters. Third- and fourth-order differentiations that have never been realized before, are also experimentally demonstrated with this chip. A theoretical analysis is proposed to explain the experimental results, which furtherly reveals that more differentiations can be achieved. Taking advantages of its differentiation capability, when this chip is incorporated into conventional imaging systems as a substrate, it enhances the edges of features in optical amplitude and phase images, thus expanding the functions of standard microscopes. This planar chip offers the advantages of a thin form factor and a multifunctional wave-based analogue computing ability, which will bring opportunities in optical imaging and computing.

The most distant marsquake recorded so far by the InSight seismometer occurred at an epicentral distance of 146.3 ± 6.9o, close to the western end of Valles Marineris. On the seismogram of this event, we have identified seismic wave precursors, i.e., underside reflections off a subsurface discontinuity halfway between the marsquake and the instrument, which directly constrain the crustal structure away (about 4100-4500 km) from the InSight landing site. Here we show that the Martian crust at the bounce point between the lander and the marsquake is characterized by a discontinuity at about 20 km depth, similar to the second (deeper) intra-crustal interface seen beneath the InSight landing site. We propose that this 20-km interface, first discovered beneath the lander, is not a local geological structure but likely a regional or global feature, and is consistent with a transition from porous to non-porous Martian crustal materials.

Raine syndrome, a lethal osteosclerotic bone dysplasia in humans, is caused by loss-of-function mutations in FAM20C; however, Fam20c deficiency in mice does not recapitulate the human disorder, so the underlying pathoetiological mechanisms remain poorly understood. Here we show that FAM20C, in addition to the reported casein kinase activity, also fine-tunes the biosynthesis of chondroitin sulfate (CS) chains to impact bone homeostasis. Specifically, FAM20C with Raine-originated mutations loses the ability to interact with chondroitin 4-O-sulfotransferase-1, and is associated with reduced 4-sulfation/6-sulfation (4S/6S) ratio of CS chains and upregulated biomineralization in human osteosarcoma cells. By contrast, overexpressing chondroitin 6-O-sulfotransferase-1 reduces CS 4S/6S ratio, and induces osteoblast differentiation in vitro and higher bone mineral density in transgenic mice. Meanwhile, a potential xylose kinase activity of FAM20C does not impact CS 4S/6S ratio, and is not associated with Raine syndrome mutations. Our results thus implicate CS 4S/6S ratio imbalances caused by FAM20C mutations as a contributor of Raine syndrome etiology.

Upon the occurrence of DNA double strand breaks (DSB), the proximal histone variant H2A.X is phosphorylated as γ-H2A.X, a critical signal for consequent DSB signaling and repair pathways. Although γ-H2A.X-triggered DNA damage response (DDR) has been well-characterized in yeast and animals, the corresponding pathways in plant DDR are less well understood. Here, we show that an Arabidopsis protein γ-H2A.X-INTERACTING PROTEIN (XIP) can interact with γ-H2A.X. Its C-terminal dual-BRCT-like domain contributes to its specific interaction with γ-H2A.X. XIP-deficient seedlings display smaller meristems, inhibited growth, and higher sensitivity to DSB-inducing treatment. Loss-of-function in XIP causes transcriptome changes mimicking wild-type plants subject to replicative or genotoxic stresses. After genotoxic bleomycin treatment, more proteins with upregulated phosphorylation modifications, more DNA fragments and cell death were found in xip mutants. Moreover, XIP physically interacts with RAD51, the key recombinase in homologous recombination (HR), and somatic HR frequency is significantly reduced in xip mutants. Collectively, XIP participates in plant response to DSB and contributes to chromatin stability.

Molecular recognition is an attractive approach to designing sensitive and selective sensors for volatile organic compounds (VOCs). Although organic macrocycles and cages have been well-developed for recognising organics by their adaptive pockets in liquids, porous solids for gas detection require a deliberate design balancing adaptability and robustness. Here we report a dynamic 3D covalent organic framework (dynaCOF) constructed from an environmentally sensitive fluorophore that can undergo concerted and adaptive structural transitions upon adsorption of gas and vapours. The COF is capable of rapid and reliable detection of various VOCs, even for non-polar hydrocarbon gas under humid conditions. The adaptive guest inclusion amplifies the host-guest interactions and facilitates the differentiation of organic vapours by their polarity and sizes/shapes, and the covalently linked 3D interwoven networks ensure the robustness and coherency of the materials. The present result paves the way for multiplex fluorescence sensing of various VOCs with molecular-specific responses.

Phagocytic clearance of dying cells, termed efferocytosis, is essential for maintaining tissue homeostasis, yet our understanding of efferocytosis regulation remains incomplete. Here we perform a FACS-based, genome-wide CRISPR knockout screen in primary mouse macrophages to search for novel regulators of efferocytosis. The results show that Wdfy3 knockout in macrophages specifically impairs uptake, but not binding, of apoptotic cells due to defective actin disassembly. Additionally, WDFY3 interacts with GABARAP, thus facilitating LC3 lipidation and subsequent lysosomal acidification to permit the degradation of apoptotic cell components. Mechanistically, while the C-terminus of WDFY3 is sufficient to rescue the impaired degradation induced by Wdfy3 knockout, full-length WDFY3 is required to reconstitute the uptake of apoptotic cells. Finally, WDFY3 is also required for efficient efferocytosis in vivo in mice and in vitro in primary human macrophages. This work thus expands our knowledge of the mechanisms of macrophage efferocytosis, as well as supports genome-wide CRISPR screen as a platform for interrogating complex functional phenotypes in primary macrophages.

Dendrites of hippocampal CA1 pyramidal cells amplify clustered glutamatergic input by activation of voltage-gated sodium channels and N-methyl-D-aspartate receptors (NMDARs). NMDAR activity depends on the presence of NMDAR co-agonists such as D-serine, but how co-agonists influence dendritic integration is not well understood. Using combinations of whole-cell patch clamp, iontophoretic glutamate application, two-photon excitation fluorescence microscopy and glutamate uncaging in acute rat and mouse brain slices we found that exogenous D-serine reduced the threshold of dendritic spikes and increased their amplitude. Triggering an astrocytic mechanism controlling endogenous D-serine supply via endocannabinoid receptors (CBRs) also increased dendritic spiking. Unexpectedly, this pathway was activated by pyramidal cell activity primarily in the theta range, which required HCN channels and astrocytic CB1Rs. Therefore, astrocytes close a positive and frequency-dependent feedback loop between pyramidal cell activity and their integration of dendritic input. Its disruption in mice led to an impairment of spatial memory, which demonstrated its behavioral relevance.

Pathogenic fungi of the genus Cryptococcus can undergo two sexual cycles, involving either bisexual diploidization (after fusion of haploid cells of different mating type) or unisexual diploidization (by autodiploidization of a single cell). Here, we construct a gene-deletion library for 111 transcription factor genes in Cryptococcus deneoformans, and explore the roles of these regulatory networks in the two reproductive modes. We show that transcription factors crucial for bisexual syngamy induce the expression of known mating determinants as well as other conserved genes of unknown function. Deletion of one of these genes, which we term FMP1, leads to defects in bisexual reproduction in C. deneoformans, its sister species Cryptococcus neoformans, and the ascomycete Neurospora crassa. Furthermore, we show that a recently evolved regulatory cascade mediates pre-meiotic unisexual autodiploidization, supporting that this reproductive process is a recent evolutionary innovation. Our findings indicate that genetic circuits with different evolutionary ages govern hallmark events distinguishing unisexual and bisexual reproduction in Cryptococcus.

We investigate electroabsorption (EA) in organic semiconductor microcavities to understand whether strong light-matter coupling non-trivially alters their nonlinear optical [[Formula: see text]] response. Focusing on strongly-absorbing squaraine (SQ) molecules dispersed in a wide-gap host matrix, we find that classical transfer matrix modeling accurately captures the EA response of low concentration SQ microcavities with a vacuum Rabi splitting of [Formula: see text] meV, but fails for high concentration cavities with [Formula: see text] meV. Rather than new physics in the ultrastrong coupling regime, however, we attribute the discrepancy at high SQ concentration to a nearly dark H-aggregate state below the SQ exciton transition, which goes undetected in the optical constant dispersion on which the transfer matrix model is based, but nonetheless interacts with and enhances the EA response of the lower polariton mode. These results indicate that strong coupling can be used to manipulate EA (and presumably other optical nonlinearities) from organic microcavities by controlling the energy of polariton modes relative to other states in the system, but it does not alter the intrinsic optical nonlinearity of the organic semiconductor inside the cavity.

Genome architecture and organization play critical roles in cell life. However, it remains largely unknown how genomic loci are dynamically coordinated to regulate gene expression and determine cell fate at the single cell level. We have developed an inducible system which allows Simultaneous Imaging and Manipulation of genomic loci by Biomolecular Assemblies (SIMBA) in living cells. In SIMBA, the human heterochromatin protein 1α (HP1α) is fused to mCherry and FRB, which can be induced to form biomolecular assemblies (BAs) with FKBP-scFv, guided to specific genomic loci by a nuclease-defective Cas9 (dCas9) or a transcriptional factor (TF) carrying tandem repeats of SunTag. The induced BAs can not only enhance the imaging signals at target genomic loci using a single sgRNA, either at repetitive or non-repetitive sequences, but also recruit epigenetic modulators such as histone methyltransferase SUV39H1 to locally repress transcription. As such, SIMBA can be applied to simultaneously visualize and manipulate, in principle, any genomic locus with controllable timing in living cells.

The ability to move has introduced animals with the problem of sensory ambiguity: the position of an external stimulus could change over time because the stimulus moved, or because the animal moved its receptors. This ambiguity can be resolved with a change in neural response gain as a function of receptor orientation. Here, we developed an encoding model to capture gain modulation of visual responses in high field (7 T) fMRI data. We characterized population eye-position dependent gain fields (pEGF). The information contained in the pEGFs allowed us to reconstruct eye positions over time across the visual hierarchy. We discovered a systematic distribution of pEGF centers: pEGF centers shift from contra- to ipsilateral following pRF eccentricity. Such a topographical organization suggests that signals beyond pure retinotopy are accessible early in the visual hierarchy, providing the potential to solve sensory ambiguity and optimize sensory processing information for functionally relevant behavior.

Heat extremes have grown disproportionately since the advent of industrialization and are expected to intensify further under unabated greenhouse warming, spreading unevenly across the globe. However, amplification mechanisms are highly uncertain because of the complex interplay between regional physical responses to human forcing and the statistical properties of atmospheric temperatures. Here, focusing on the latter, we explain how and to what extent the leading moments of thermal distributions sway the future trajectories of heat extremes. Crucially, we show that daily temperature variability is the key to understanding global patterns of change in the frequency and severity of the extremes and their exacerbation in many places. Variability accounts for at least half of the highly differential regional sensitivities and may well outweigh the background warming. These findings provide fundamental insights for assessing the reliability of climate models and improving their future projections.

The ability to learn Pavlovian associations from environmental cues predicting positive outcomes is critical for survival, motivating adaptive behaviours. This cued-motivated behaviour depends on the nucleus accumbens (NAc). NAc output activity mediated by spiny projecting neurons (SPNs) is regulated by dopamine, but also by cholinergic interneurons (CINs), which can release acetylcholine and glutamate via the activity of the vesicular acetylcholine transporter (VAChT) or the vesicular glutamate transporter (VGLUT3), respectively. Here we investigated behavioural and neurochemical changes in mice performing a touchscreen Pavlovian approach task by recording dopamine, acetylcholine, and calcium dynamics from D1- and D2-SPNs using fibre photometry in control, VAChT or VGLUT3 mutant mice to understand how these signals cooperate in the service of approach behaviours toward reward-predicting cues. We reveal that NAc acetylcholine-dopaminergic signalling is continuously updated to regulate striatal output underlying the acquisition of Pavlovian approach learning toward reward-predicting cues.

Devices with sensing-memory-computing capability for the detection, recognition and memorization of real time sensory information could simplify data conversion, transmission, storage, and operations between different blocks in conventional chips, which are invaluable and sought-after to offer critical benefits of accomplishing diverse functions, simple design, and efficient computing simultaneously in the internet of things (IOT) era. Here, we develop a self-powered vertical tribo-transistor (VTT) based on MXenes for multi-sensing-memory-computing function and multi-task emotion recognition, which integrates triboelectric nanogenerator (TENG) and transistor in a single device with the simple configuration of vertical organic field effect transistor (VOFET). The tribo-potential is found to be able to tune ionic migration in insulating layer and Schottky barrier height at the MXene/semiconductor interface, and thus modulate the conductive channel between MXene and drain electrode. Meanwhile, the sensing sensitivity can be significantly improved by 711 times over the single TENG device, and the VTT exhibits excellent multi-sensing-memory-computing function. Importantly, based on this function, the multi-sensing integration and multi-model emotion recognition are constructed, which improves the emotion recognition accuracy up to 94.05% with reliability. This simple structure and self-powered VTT device exhibits high sensitivity, high efficiency and high accuracy, which provides application prospects in future human-mechanical interaction, IOT and high-level intelligence.

Miniature magnetic soft machines could significantly impact minimally invasive robotics and biomedical applications. However, most soft machines are limited to solid magnetic materials, whereas further progress also relies on fluidic constructs obtained by reconfiguring liquid magnetic materials, such as ferrofluid. Here we show how harnessing the wettability of ferrofluids allows for controlled reconfigurability and the ability to create versatile soft machines. The ferrofluid droplet exhibits multimodal motions, and a single droplet can be controlled to split into multiple sub-droplets and then re-fuse back on demand. The soft droplet machine can negotiate changing terrains in unstructured environments. In addition, the ferrofluid droplets can be configured as a liquid capsule, enabling cargo delivery; a wireless omnidirectional liquid cilia matrix capable of pumping biofluids; and a wireless liquid skin, allowing multiple types of miniature soft machine construction. This work improves small magnetic soft machines' achievable complexity and boosts their future biomedical applications capabilities.

Mutation-mediated treatment resistance is one of the primary challenges for modern antibiotic and anti-cancer therapy. Yet, many resistance mutations have a substantial fitness cost and are subject to purifying selection. How emerging resistant lineages may escape purifying selection via subsequent compensatory mutations is still unclear due to the difficulty of tracking such evolutionary rescue dynamics in space and time. Here, we introduce a system of fluorescence-coupled synthetic mutations to show that the probability of evolutionary rescue, and the resulting long-term persistence of drug resistant mutant lineages, is dramatically increased in dense microbial populations. By tracking the entire evolutionary trajectory of thousands of resistant lineages in expanding yeast colonies we uncover an underlying quasi-stable equilibrium between the opposing forces of radial expansion and natural selection, a phenomenon we term inflation-selection balance. Tailored computational models and agent-based simulations corroborate the fundamental nature of the observed effects and demonstrate the potential impact on drug resistance evolution in cancer. The described phenomena should be considered when predicting multi-step evolutionary dynamics in any mechanically compact cellular population, including pathogenic microbial biofilms and solid tumors. The insights gained will be especially valuable for the quantitative understanding of response to treatment, including emerging evolution-based therapy strategies.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. Angiotensin-converting enzyme 2 (ACE2) is an entry receptor for SARS-CoV-2. The full-length membrane form of ACE2 (memACE2) undergoes ectodomain shedding to generate a shed soluble form (solACE2) that mediates SARS-CoV-2 entry via receptor-mediated endocytosis. Currently, it is not known how the physiological regulation of ACE2 shedding contributes to the etiology of COVID-19 in vivo. The present study identifies Membrane-type 1 Matrix Metalloproteinase (MT1-MMP) as a critical host protease for solACE2-mediated SARS-CoV-2 infection. SARS-CoV-2 infection leads to increased activation of MT1-MMP that is colocalized with ACE2 in human lung epithelium. Mechanistically, MT1-MMP directly cleaves memACE2 at M706-S to release solACE218-706 that binds to the SARS-CoV-2 spike proteins (S), thus facilitating cell entry of SARS-CoV-2. Human solACE218-706 enables SARS-CoV-2 infection in both non-permissive cells and naturally insusceptible C57BL/6 mice. Inhibition of MT1-MMP activities suppresses solACE2-directed entry of SARS-CoV-2 in human organoids and aged mice. Both solACE2 and circulating MT1-MMP are positively correlated in plasma of aged mice and humans. Our findings provide in vivo evidence demonstrating the contribution of ACE2 shedding to the etiology of COVID-19.

Chalcogenide aerogels (chalcogels) are amorphous structures widely known for their lack of localized structural control. This study, however, demonstrates a precise multiscale structural control through a thiostannate motif ([Sn2S6]4-)-transformation-induced self-assembly, yielding Na-Mn-Sn-S, Na-Mg-Sn-S, and Na-Sn(II)-Sn(IV)-S aerogels. The aerogels exhibited [Sn2S6]4-:Mn2+ stoichiometric-variation-induced-control of average specific surface areas (95-226 m2 g-1), thiostannate coordination networks (octahedral to tetrahedral), phase crystallinity (crystalline to amorphous), and hierarchical porous structures (micropore-intensive to mixed-pore state). In addition, these chalcogels successfully adopted the structural motifs and ion-exchange principles of two-dimensional layered metal sulfides (K2xMnxSn3-xS6, KMS-1), featuring a layer-by-layer stacking structure and effective radionuclide (Cs+, Sr2+)-control functionality. The thiostannate cluster-based gelation principle can be extended to afford Na-Mg-Sn-S and Na-Sn(II)-Sn(IV)-S chalcogels with the same structural features as the Na-Mn-Sn-S chalcogels (NMSCs). The study of NMSCs and their chalcogel family proves that the self-assembly principle of two-dimensional chalcogenide clusters can be used to design unique chalcogels with unprecedented structural hierarchy.

N6-methyladenosine (m6A), the most abundant modification of mRNA, is essential for normal development and dysregulation promotes cancer. m6A is highly enriched in the 3' untranslated region (UTR) of a large subset of mRNAs to influence mRNA stability and/or translation. However, the mechanism responsible for the observed m6A distribution remains enigmatic. Here we find the exon junction complex shapes the m6A landscape by blocking METTL3-mediated m6A modification close to exon junctions within coding sequence (CDS). Depletion of EIF4A3, a core component of the EJC, causes increased METTL3 binding and m6A modification of short internal exons, and sites close to exon-exon junctions within mRNA. Reporter gene experiments further support the role of splicing and EIF4A3 deposition in controlling m6A modification via the local steric blockade of METTL3. Our results explain how characteristic patterns of m6A mRNA modification are established and uncover a role of the EJC in shaping the m6A epitranscriptome.

The experimental investigation of matter under extreme densities and temperatures, as in astrophysical objects and nuclear fusion applications, constitutes one of the most active frontiers at the interface of material science, plasma physics, and engineering. The central obstacle is given by the rigorous interpretation of the experimental results, as even the diagnosis of basic parameters like the temperature T is rendered difficult at these extreme conditions. Here, we present a simple, approximation-free method to extract the temperature of arbitrarily complex materials in thermal equilibrium from X-ray Thomson scattering experiments, without the need for any simulations or an explicit deconvolution. Our paradigm can be readily implemented at modern facilities and corresponding experiments will have a profound impact on our understanding of warm dense matter and beyond, and open up a variety of appealing possibilities in the context of thermonuclear fusion, laboratory astrophysics, and related disciplines.

All-solid-state batteries are appealing electrochemical energy storage devices because of their high energy content and safety. However, their practical development is hindered by inadequate cycling performances due to poor reaction reversibility, electrolyte thickening and electrode passivation. Here, to circumvent these issues, we propose a fluorination strategy for the positive electrode and solid polymeric electrolyte. We develop thin laminated all-solid-state Li||FeF3 lab-scale cells capable of delivering an initial specific discharge capacity of about 600 mAh/g at 700 mA/g and a final capacity of about 200 mAh/g after 900 cycles at 60 °C. We demonstrate that the polymer electrolyte containing AlF3 particles enables a Li-ion transference number of 0.67 at 60 °C. The fluorinated polymeric solid electrolyte favours the formation of ionically conductive components in the Li metal electrode's solid electrolyte interphase, also hindering dendritic growth. Furthermore, the F-rich solid electrolyte facilitates the Li-ion storage reversibility of the FeF3-based positive electrode and decreases the interfacial resistances and polarizations at both electrodes.

Chalcogenide aerogels are receiving widespread attention due to their unique properties. Here we comment on a recent work about amorphous Na–Mn–Sn–S chalcogels featuring local structural control, and provide an outlook for the development of chalcogels and the metal-organic sulfide framework.

The development of electrocatalysts capable of efficient reduction of nitrate (NO3-) to ammonia (NH3) is drawing increasing interest for the sake of low carbon emission and environmental protection. Herein, we present a CuCo bimetallic catalyst able to imitate the bifunctional nature of copper-type nitrite reductase, which could easily remove NO2- via the collaboration of two active centers. Indeed, Co acts as an electron/proton donating center, while Cu facilitates NOx- adsorption/association. The bio-inspired CuCo nanosheet electrocatalyst delivers a 100 ± 1% Faradaic efficiency at an ampere-level current density of 1035 mA cm-2 at -0.2 V vs. Reversible Hydrogen Electrode. The NH3 production rate reaches a high activity of 4.8 mmol cm-2 h-1 (960 mmol gcat-1 h-1). A mechanistic study, using electrochemical in situ Fourier transform infrared spectroscopy and shell-isolated nanoparticle enhanced Raman spectroscopy, reveals a strong synergy between Cu and Co, with Co sites promoting the hydrogenation of NO3- to NH3 via adsorbed *H species. The well-modulated coverage of adsorbed *H and *NO3 led simultaneously to high NH3 selectivity and yield.

Studying the localized electrocatalytic activity of heterogeneous electrocatalysts is crucial for understanding electrocatalytic reactions and further improving their performance. However, correlating the electrocatalytic activity with the microscopic structure of two-dimensional (2D) electrocatalysts remains a great challenge due to the lack of in situ imaging techniques and methods of tuning structures with atomic precision. Here, we present a general method of probing the layer-dependent electrocatalytic activity of 2D materials in situ using a plasmonic imaging technique. Unlike the existing methods, this approach was used to visualize the surface charge density and electrocatalytic activity of single 2D MoS2 nanosheets, enabling the correlation of layer-dependent electrocatalytic activity with the surface charge density of single MoS2 nanosheets. This work provides insights into the electrocatalytic mechanisms of 2D transition metal dichalcogenides, and our approach can serve as a promising platform for investigating electrocatalytic reactions at the heterogeneous interface, thus guiding the rational design of high-performance electrocatalysts.

Comment on Nat Commun. 2021 Feb 2;12(1):738. Nat Commun. 2022 Dec 22;13(1):7851.

Secondary organic aerosol (SOA) contributes significantly to ambient fine particulate matter that affects climate and human health. Monoterpenes represent an important class of biogenic volatile organic compounds (VOCs) and their oxidation by nitrate radicals poses a substantial source of SOA globally. Here, we investigate the formation and properties of SOA from nitrate radical oxidation of two common monoterpenes, α-pinene and limonene. When two monoterpenes are oxidized simultaneously, we observe a ~50% enhancement in the formation of SOA from α-pinene and a ~20% reduction in limonene SOA formation. The change in SOA yields is accompanied by pronounced changes in aerosol chemical composition and volatility. These non-linear effects are not observed in a sequential oxidation experiment. Our results highlight that unlike currently assumed in atmospheric models, the interaction of products formed from individual VOCs should be accounted for to accurately describe SOA formation and its climate and health impacts.

Plasmonic MXenes are of particular interest, because of their unique electron and phonon structures and multiple surface plasmon effects, which are different from traditional plasmonic materials. However, to date, how electronic energy damp to lattice vibrations (phonons) in MXenes has not been unraveled. Here, we employed ultrafast broadband impulsive vibrational spectroscopy to identify the energy damping channels in MXenes (Ti3C2Tx and Mo2CTx). Distinctive from the well-known damping pathways, our results demonstrate a different energy damping channel, in which the Ti3C2Tx plasmonic electron energy transfers to coherent phonons by nonthermal electron mediation after Landau damping, without involving electron-electron scattering. Moreover, electrons are observed to strongly couple with A1g mode (~60 fs, 85-100%) and weakly couple with Eg mode (1-2 ps, 0-15%). Our results provide new insight into the electron-phonon interaction in MXenes, which allows the design of materials enabling efficient manipulation of electron transport and energy conversion.

Quantitative proteomics has matured into an established tool and longitudinal proteomics experiments have begun to emerge. However, no effective, simple-to-use differential expression method for longitudinal proteomics data has been released. Typically, such data is noisy, contains missing values, and has only few time points and biological replicates. To address this need, we provide a comprehensive evaluation of several existing differential expression methods for high-throughput longitudinal omics data and introduce a Robust longitudinal Differential Expression (RolDE) approach. The methods are evaluated using over 3000 semi-simulated spike-in proteomics datasets and three large experimental datasets. In the comparisons, RolDE performs overall best; it is most tolerant to missing values, displays good reproducibility and is the top method in ranking the results in a biologically meaningful way. Furthermore, RolDE is suitable for different types of data with typically unknown patterns in longitudinal expression and can be applied by non-experienced users.

Biological cell membranes can efficiently switch Na+/K+ selectivity in response to external stimuli, but achieving analogous functions in a single artificial membrane is challenging. Here, we report highly crystalline covalent organic framework (COF) membranes with well-defined nanochannels and coordinative sites (i. e., amino acid) that act as ion-selective switches to manipulate Na+ and K+ transport. The ion selectivity of the COF membrane is dynamic and can be switched between K+-selective and Na+-selective in a single membrane by applying a pH stimulus. The experimental results combined with molecular dynamics simulations reveal that the switchable Na+/K+ selectivity originates from the differentiated coordination interactions between ions and amino acids. Benefiting from the switchable Na+/K+ selectivity, we further demonstrate the membrane potential switches by varying electrolyte pH, miming the membrane polarity reversal during neural signal transduction in vivo, suggesting the great potential of these membranes for in vitro biomimetic applications.

Adverse childhood experiences (ACEs) can harm mental health across the lifespan and reduce life expectancy. We provide a commentary of evidence on the health impacts, and how creative arts and digital interventions may support prevention and recovery.

Converging lines of evidence suggest that, during the late Archean, Earth completed its transition from a stagnant-lid to a plate tectonics regime, although how and when this transition occurred is debated. The geological record indicates that some form of subduction, a key component of plate tectonics-has operated since the Mesoarchean, even though the tectonic style and timescales of burial and exhumation cycles within ancient convergent margins are poorly constrained. Here, we present a Neoarchean pressure-temperature-time (P-T-t) path from supracrustal rocks of the transpressional Yilgarn orogen (Western Australia), which documents how sea-floor-altered rocks underwent deep burial then exhumation during shortening that was unrelated to the episode of burial. Archean subduction, even if generally short-lived, was capable of producing eclogites along converging lithosphere boundaries, although exhumation processes in those environments were likely less efficient than today, such that return of high-pressure rocks to the surface was rare.

Hybrid materials capitalize on the properties of individual materials to attain a specific combination of performance assets that is not available with the individual components alone. We describe a straightforward approach to preparation of sandwich-type hybrid dynamic materials that combine metals as electrically conductive components and polymers as bending, momentum-inducing components with flexible organic crystals as mechanically compliant and optically transducive medium. The resulting hybrid materials are conductive to both electricity and light, while they also respond to changes in temperature by deformation. Depending on the metal, their conductivity ranges from 7.9 to 21.0 S µm‒1. The elements respond rapidly to temperature by curling or uncurling in about 0.2 s, which in one typical case corresponds to exceedingly fast deformation and recovery rates of 2187.5° s‒1 and 1458.3° s‒1, respectively. In cyclic operation mode, their conductivity decreases less than 1% after 10,000 thermal cycles. The mechanothermal robustness and dual functionality favors these materials as candidates for a variety of applications in organic-based optics and electronics, and expands the prospects of application of organic crystals beyond the natural limits of their dynamic performance.

Patients with multiple myeloma, an incurable malignancy of plasma cells, frequently develop osteolytic bone lesions that severely impact quality of life and clinical outcomes. Eliglustat, a U.S. Food and Drug Administration-approved glucosylceramide synthase inhibitor, reduced osteoclast-driven bone loss in preclinical in vivo models of myeloma. In combination with zoledronic acid, a bisphosphonate that treats myeloma bone disease, eliglustat provided further protection from bone loss. Autophagic degradation of TRAF3, a key step for osteoclast differentiation, was inhibited by eliglustat as evidenced by TRAF3 lysosomal and cytoplasmic accumulation. Eliglustat blocked autophagy by altering glycosphingolipid composition whilst restoration of missing glycosphingolipids rescued autophagy markers and TRAF3 degradation thus restoring osteoclastogenesis in bone marrow cells from myeloma patients. This work delineates both the mechanism by which glucosylceramide synthase inhibition prevents autophagic degradation of TRAF3 to reduce osteoclastogenesis as well as highlighting the clinical translational potential of eliglustat for the treatment of myeloma bone disease.

Appropriate processing of reward and aversive information is essential for survival. Although a critical role of serotonergic neurons in the dorsal raphe nucleus (DRN) in reward processing has been shown, the lack of rewarding effects with selective serotonin reuptake inhibitors (SSRIs) implies the presence of a discrete serotonergic system playing an opposite role to the DRN in the processing of reward and aversive stimuli. Here, we demonstrated that serotonergic neurons in the median raphe nucleus (MRN) of mice process reward and aversive information in opposite directions to DRN serotonergic neurons. We further identified MRN serotonergic neurons, including those projecting to the interpeduncular nucleus (5-HTMRN→IPN), as a key mediator of reward and aversive stimuli. Moreover, 5-HT receptors, including 5-HT2A receptors in the interpeduncular nucleus, are involved in the aversive properties of MRN serotonergic neural activity. Our findings revealed an essential function of MRN serotonergic neurons, including 5-HTMRN→IPN, in the processing of reward and aversive stimuli.

The Paleocene-Eocene Thermal Maximum (PETM) was an abrupt global warming event associated with a large injection of carbon into the ocean-atmosphere system, as evidenced by a diagnostic carbon isotope excursion (CIE). Evidence also suggests substantial hydrologic perturbations, but details have been hampered by a lack of appropriate proxies. To address this shortcoming, here we isolate and measure the isotopic composition of hydroxyl groups (OH-) in clay minerals from a highly expanded PETM section in the North Sea Basin, together with their bulk oxygen isotope composition. At this location, we show that hydroxyl O- and H-isotopes are less influenced than bulk values by clay compositional changes due to mixing and/or inherited signals and thus better track hydrologic variability. We find that clay OH- hydrogen-isotope values (δ2HOH) decrease slowly prior to the PETM and then abruptly by ∼8‰ at the CIE onset. Coincident with an increase in relative kaolinite content, this indicates increased rainfall and weathering and implies an enhanced hydrologic cycle response to global warming, particularly during the early stages of the PETM. Subsequently, δ2HOH returns to pre-PETM values well before the end of the CIE, suggesting hydrologic changes in the North Sea were short-lived relative to carbon-cycle perturbations.

The development of transition metal-catalyzed β-C-H bond activation via highly-strained 4-membered metallacycles has been a formidable task. So far, only scarce examples have been reported to undergo β-C-H bond activation via 4-membered metallacycles, and all of them rely on precious metals. In contrast, earth-abundant and inexpensive 3d transition metal-catalyzed β-C-H bond activation via 4-membered metallacycles still remains an elusive challenge. Herein, we report a phosphine oxide-ligated Ni-Al bimetallic catalyst to activate secondary benzylic C(sp3)-H bonds of formamides via 4-membered nickelacycles, providing a series of α,β-unsaturated γ-lactams in up to 97% yield.

Mutations in the lamin A/C gene (LMNA) cause dilated cardiomyopathy associated with increased activity of ERK1/2 in the heart. We recently showed that ERK1/2 phosphorylates cofilin-1 on threonine 25 (phospho(T25)-cofilin-1) that in turn disassembles the actin cytoskeleton. Here, we show that in muscle cells carrying a cardiomyopathy-causing LMNA mutation, phospho(T25)-cofilin-1 binds to myocardin-related transcription factor A (MRTF-A) in the cytoplasm, thus preventing the stimulation of serum response factor (SRF) in the nucleus. Inhibiting the MRTF-A/SRF axis leads to decreased α-tubulin acetylation by reducing the expression of ATAT1 gene encoding α-tubulin acetyltransferase 1. Hence, tubulin acetylation is decreased in cardiomyocytes derived from male patients with LMNA mutations and in heart and isolated cardiomyocytes from Lmnap.H222P/H222P male mice. In Atat1 knockout mice, deficient for acetylated α-tubulin, we observe left ventricular dilation and mislocalization of Connexin 43 (Cx43) in heart. Increasing α-tubulin acetylation levels in Lmnap.H222P/H222P mice with tubastatin A treatment restores the proper localization of Cx43 and improves cardiac function. In summary, we show for the first time an actin-microtubule cytoskeletal interplay mediated by cofilin-1 and MRTF-A/SRF, promoting the dilated cardiomyopathy caused by LMNA mutations. Our findings suggest that modulating α-tubulin acetylation levels is a feasible strategy for improving cardiac function.

Single-atom (SA) catalysts provide extensive possibilities in pursuing fantastic catalytic performances, while their preparation still suffers from metal aggregation and pore collapsing during pyrolysis. Here we report a versatile medium-induced infiltration deposition strategy for the fabrication of SAs and hetero-SAs (MaN4/MbN4@NC; Ma = Cu, Co, Ni, Mn, Mb = Co, Cu, Fe, NC = N-doped carbon). In-situ and control experiments reveal that the catalyst fabrication relies on the "step-by-step" evolution of Ma-containing metal-organic framework (MOF) template and Mb-based metal precursor, during which molten salt acts as both pore generator in the MOF transformation, and carrier for the oriented infiltration and deposition of the latter to eventually yield metal SAs embedded on hierarchically porous support. The as-prepared hetero-SAs show excellent catalytic performances in the general synthesis of 33 kinds of natural flavones. The highly efficient synthesis is further strengthened by the reliable durability of the catalyst loaded in a flow reactor. Systematic characterizations and mechanism studies suggest that the superior catalytic performances of CuN4/CoN4@NC are attributed to the facilitated O2 activating-splitting process and significantly reduced reaction energy barriers over CoN4 due to the synergetic interactions of the adjacent CuN4.

The omnipresent Na+/vacancy orderings change substantially with the composition that inevitably actuate the ionic diffusion in rechargeable batteries. Therefore, it may hold the key to the electrode design with high rate capability. Herein, the influence of Na+/vacancy ordering on Na+ mobility is demonstrated firstly through a comparative investigation in P2-Na2/3Ni1/3Mn2/3O2 and P2-Na2/3Ni0.3Mn0.7O2. The large zigzag Na+/vacancy intralayer ordering is found to accelerate Na+ migration in P2-type Na2/3Ni1/3Mn2/3O2. By theoretical simulations, it is revealed that the Na+ ordering enables the P2-type Na2/3Ni1/3Mn2/3O2 with higher diffusivities and lower activation energies of 200 meV with respect to the P3 one. The quantifying diffusional analysis further prove that the higher probability of the concerted Na+ ionic diffusion occurs in P2-type Na2/3Ni1/3Mn2/3O2 due to the appropriate ratio of high energy ordered Na ions (Naf) occupation. As a result, the interplay between the Na+/vacancy ordering and Na+ kinetic is well understood in P2-type layered cathodes.

Ultracold quantum gases are ideal sources for high-precision space-borne sensing as proposed for Earth observation, relativistic geodesy and tests of fundamental physical laws as well as for studying new phenomena in many-body physics during extended free fall. Here we report on experiments with the Cold Atom Lab aboard the International Space Station, where we have achieved exquisite control over the quantum state of single 87Rb Bose-Einstein condensates paving the way for future high-precision measurements. In particular, we have applied fast transport protocols to shuttle the atomic cloud over a millimeter distance with sub-micrometer accuracy and subsequently drastically reduced the total expansion energy to below 100 pK with matter-wave lensing techniques.

High-pressure electrical resistivity measurements reveal that the mechanical deformation of ultra-hard WB2 during compression induces superconductivity above 50 GPa with a maximum superconducting critical temperature, Tcof 17 K at 91 GPa. Upon further compression up to 187 GPa, the Tcgradually decreases. Theoretical calculations show that electron-phonon mediated superconductivity originates from the formation of metastable stacking faults and twin boundaries that exhibit a local structure resembling MgB2 (hP3, space group 191, prototype AlB2). Synchrotron x-ray diffraction measurements up to 145 GPa show that the ambient pressure hP12 structure (space group 194, prototype WB2) continues to persist to this pressure, consistent with the formation of the planar defects above 50 GPa. The abrupt appearance of superconductivity under pressure does not coincide with a structural transition but instead with the formation and percolation of mechanically-induced stacking faults and twin boundaries. The results identify an alternate route for designing superconducting materials.

Dense coding is the seminal example of how entanglement can boost qubit communication, from sending one bit to sending two bits. This is made possible by projecting separate particles onto a maximally entangled basis. We investigate more general communication tasks, in both theory and experiment, and show that simpler measurements enable strong and sometimes even optimal entanglement-assisted qubit communication protocols. Using only partial Bell state analysers for two qubits, we demonstrate quantum correlations that cannot be simulated with two bits of classical communication. Then, we show that there exists an established and operationally meaningful task for which product measurements are sufficient for the strongest possible quantum predictions based on a maximally entangled two-qubit state. Our results reveal that there are scenarios in which the power of entanglement in enhancing quantum communication can be harvested in simple and scalable optical experiments.

The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.

Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.

The assembly of biomolecules into condensates is a fundamental process underlying the organisation of the intracellular space and the regulation of many cellular functions. Mapping and characterising phase behaviour of biomolecules is essential to understand the mechanisms of condensate assembly, and to develop therapeutic strategies targeting biomolecular condensate systems. A central concept for characterising phase-separating systems is the phase diagram. Phase diagrams are typically built from numerous individual measurements sampling different parts of the parameter space. However, even when performed in microwell plate format, this process is slow, low throughput and requires significant sample consumption. To address this challenge, we present here a combinatorial droplet microfluidic platform, termed PhaseScan, for rapid and high-resolution acquisition of multidimensional biomolecular phase diagrams. Using this platform, we characterise the phase behaviour of a wide range of systems under a variety of conditions and demonstrate that this approach allows the quantitative characterisation of the effect of small molecules on biomolecular phase transitions.

Channelrhodopsins are light-gated ion channels used to control excitability of designated cells in large networks with high spatiotemporal resolution. While ChRs selective for H+, Na+, K+ and anions have been discovered or engineered, Ca2+-selective ChRs have not been reported to date. Here, we analyse ChRs and mutant derivatives with regard to their Ca2+ permeability and improve their Ca2+ affinity by targeted mutagenesis at the central selectivity filter. The engineered channels, termed CapChR1 and CapChR2 for calcium-permeable channelrhodopsins, exhibit reduced sodium and proton conductance in connection with strongly improved Ca2+ permeation at negative voltage and low extracellular Ca2+ concentrations. In cultured cells and neurons, CapChR2 reliably increases intracellular Ca2+ concentrations. Moreover, CapChR2 can robustly trigger Ca2+ signalling in hippocampal neurons. When expressed together with genetically encoded Ca2+ indicators in Drosophila melanogaster mushroom body output neurons, CapChRs mediate light-evoked Ca2+ entry in brain explants.

Enzymatic deconstruction of poly(ethylene terephthalate) (PET) is under intense investigation, given the ability of hydrolase enzymes to depolymerize PET to its constituent monomers near the polymer glass transition temperature. To date, reported PET hydrolases have been sourced from a relatively narrow sequence space. Here, we identify additional PET-active biocatalysts from natural diversity by using bioinformatics and machine learning to mine 74 putative thermotolerant PET hydrolases. We successfully express, purify, and assay 51 enzymes from seven distinct phylogenetic groups; observing PET hydrolysis activity on amorphous PET film from 37 enzymes in reactions spanning pH from 4.5-9.0 and temperatures from 30-70 °C. We conduct PET hydrolysis time-course reactions with the best-performing enzymes, where we observe differences in substrate selectivity as function of PET morphology. We employed X-ray crystallography and AlphaFold to examine the enzyme architectures of all 74 candidates, revealing protein folds and accessory domains not previously associated with PET deconstruction. Overall, this study expands the number and diversity of thermotolerant scaffolds for enzymatic PET deconstruction.

A pressing challenge facing the aviation industry is to aggressively reduce greenhouse gas emissions in the face of increasing demand for aviation fuels. Climate goals such as carbon-neutral growth from 2020 onwards require continuous improvements in technology, operations, infrastructure, and most importantly, reductions in aviation fuel life cycle emissions. The Carbon Offsetting Scheme for International Aviation of the International Civil Aviation Organization provides a global market-based measure to group all possible emissions reduction measures into a joint program. Using a bottom-up, engineering-based modeling approach, this study provides the first estimates of life cycle greenhouse gas emissions from petroleum jet fuel on regional and global scales. Here we show that not all petroleum jet fuels are the same as the country-level life cycle emissions of petroleum jet fuels range from 81.1 to 94.8 gCO2e MJ-1, with a global volume-weighted average of 88.7 gCO2e MJ-1. These findings provide a high-resolution baseline against which sustainable aviation fuel and other emissions reduction opportunities can be prioritized to achieve greater emissions reductions faster.

Silk is a unique, remarkably strong biomaterial made of simple protein building blocks. To date, no synthetic method has come close to reproducing the properties of natural silk, due to the complexity and insufficient understanding of the mechanism of the silk fiber formation. Here, we use a combination of bulk analytical techniques and nanoscale analytical methods, including nano-infrared spectroscopy coupled with atomic force microscopy, to probe the structural characteristics directly, transitions, and evolution of the associated mechanical properties of silk protein species corresponding to the supramolecular phase states inside the silkworm's silk gland. We found that the key step in silk-fiber production is the formation of nanoscale compartments that guide the structural transition of proteins from their native fold into crystalline β-sheets. Remarkably, this process is reversible. Such reversibility enables the remodeling of the final mechanical characteristics of silk materials. These results open a new route for tailoring silk processing for a wide range of new material formats by controlling the structural transitions and self-assembly of the silk protein's supramolecular phases.

Protein modification by ubiquitin-like proteins (UBLs) amplifies limited genome information and regulates diverse cellular processes, including translation, autophagy and antiviral pathways. Ubiquitin-fold modifier 1 (UFM1) is a UBL covalently conjugated with intracellular proteins through ufmylation, a reaction analogous to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control at the ER and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here we identify a UFM1 substrate, NADH-cytochrome b5 reductase 3 (CYB5R3), that localizes on the ER membrane. Ufmylation of CYB5R3 depends on the E3 components UFL1 and UFBP1 on the ER, and converts CYB5R3 into its inactive form. Ufmylated CYB5R3 is recognized by UFBP1 through the UFM1-interacting motif, which plays an important role in the further uyfmylation of CYB5R3. Ufmylated CYB5R3 is degraded in lysosomes, which depends on the autophagy-related protein Atg7- and the autophagy-adaptor protein CDK5RAP3. Mutations of CYB5R3 and genes involved in the UFM1 system cause hereditary developmental disorders, and ufmylation-defective Cyb5r3 knock-in mice exhibit microcephaly. Our results indicate that CYB5R3 ufmylation induces ER-phagy, which is indispensable for brain development.

Coxsackievirus A16 (CVA16) causes hand, foot and mouth disease in infants and young children. However, no vaccine or anti-viral agent is currently available for CVA16. Here, the functions and working mechanisms of two CVA16-specific neutralizing monoclonal antibodies (MAbs), 9B5 and 8C4, are comprehensively investigated. Both 9B5 and 8C4 display potent neutralization in vitro and prophylactic and therapeutic efficacy in a mouse model of CVA16 infection. Mechanistically, 9B5 exerts neutralization primarily through inhibiting CVA16 attachment to cell surface via blockade of CVA16 binding to its attachment receptor, heparan sulfate, whereas 8C4 functions mainly at the post-attachment stage of CVA16 entry by interfering with the interaction between CVA16 and its uncoating receptor SCARB2. Cryo-EM studies show that 9B5 and 8C4 target distinct epitopes located at the 5-fold and 3-fold protrusions of CVA16 capsids, respectively, and exhibit differential binding preference to three forms of naturally occurring CVA16 particles. Moreover, 9B5 and 8C4 are compatible in formulating an antibody cocktail which displays the ability to prevent virus escape seen with individual MAbs. Together, our work elucidates the functional and structural basis of CVA16 antibody-mediated neutralization and protection, providing important information for design and development of effective CVA16 vaccines and antibody therapies.

Phase contrast microscopy has played a central role in the development of modern biology, geology, and nanotechnology. It can visualize the structure of translucent objects that remains hidden in regular optical microscopes. The optical layout of a phase contrast microscope is based on a 4 f image processing setup and has essentially remained unchanged since its invention by Zernike in the early 1930s. Here, we propose a conceptually new approach to phase contrast imaging that harnesses the non-local optical response of a guided-mode-resonator metasurface. We highlight its benefits and demonstrate the imaging of various phase objects, including biological cells, polymeric nanostructures, and transparent metasurfaces. Our results showcase that the addition of this non-local metasurface to a conventional microscope enables quantitative phase contrast imaging with a 0.02π phase accuracy. At a high level, this work adds to the growing body of research aimed at the use of metasurfaces for analog optical computing.

The developments of pure organic room-temperature phosphorescence (RTP) materials with circularly polarized luminescence (CPL) have significantly facilitated the future integration and systemization of luminescent material in fundamental science and technological applications. Here, a type of photoinduced circularly polarized RTP materials are constructed by homogeneously dispersing phosphorescent chiral helical substituted polyacetylenes into a processable poly(methyl methacrylate) (PMMA) matrix. These substituted polyacetylenes play vital roles in the propagation of CPL and present prominently optical characteristics with high absorption and luminescent dissymmetric factors up to 0.029 (gabs) and 0.019 (glum). The oxygen consumption properties of the films under UV light irradiation endow materials with dynamic chiro-optical functionality, which can leverage of light to precisely control and manipulate the circularly polarized RTP properties with the remarkable advantages of being contactless, wireless and fatigue-resistant. Significantly, the distinct materials with dynamic properties can be used as anti-counterfeiting materials involving photoprogrammability.

Marine heatwaves can have disastrous impacts on ecosystems and marine industries. Given their potential consequences, it is important to understand how broad-scale climate variability influences the probability of localised extreme events. Here, we employ an advanced data-mining methodology, archetype analysis, to identify large scale patterns and teleconnections that lead to marine extremes in certain regions. This methodology is applied to the Australasian region, where it identifies instances of anomalous sea-surface temperatures, frequently associated with marine heatwaves, as well as the broadscale oceanic and atmospheric conditions associated with those extreme events. Additionally, we use archetype analysis to assess the ability of a low-resolution climate model to accurately represent the teleconnection patterns associated with extreme climate variability, and discuss the implications for the predictability of these impactful events.

Structured Illumination Microscopy, SIM, is one of the most powerful optical imaging methods available to visualize biological environments at subcellular resolution. Its limitations stem from a difficulty of imaging in multiple color channels at once, which reduces imaging speed. Furthermore, there is substantial experimental complexity in setting up SIM systems, preventing a widespread adoption. Here, we present Machine-learning Assisted, Interferometric Structured Illumination Microscopy, MAI-SIM, as an easy-to-implement method for live cell super-resolution imaging at high speed and in multiple colors. The instrument is based on an interferometer design in which illumination patterns are generated, rotated, and stepped in phase through movement of a single galvanometric mirror element. The design is robust, flexible, and works for all wavelengths. We complement the unique properties of the microscope with an open source machine-learning toolbox that permits real-time reconstructions to be performed, providing instant visualization of super-resolved images from live biological samples.

Bandgap gradient is a proven approach for improving the open-circuit voltages (VOCs) in Cu(In,Ga)Se2 and Cu(Zn,Sn)Se2 thin-film solar cells, but has not been realized in Cd(Se,Te) thin-film solar cells, a leading thin-film solar cell technology in the photovoltaic market. Here, we demonstrate the realization of a bandgap gradient in Cd(Se,Te) thin-film solar cells by introducing a Cd(O,S,Se,Te) region with the same crystal structure of the absorber near the front junction. The formation of such a region is enabled by incorporating oxygenated CdS and CdSe layers. We show that the introduction of the bandgap gradient reduces the hole density in the front junction region and introduces a small spike in the band alignment between this and the absorber regions, effectively suppressing the nonradiative recombination therein and leading to improved VOCs in Cd(Se,Te) solar cells using commercial SnO2 buffers. A champion device achieves an efficiency of 20.03% with a VOC of 0.863 V.

Electrostatic adsorption is an important complement to the mechanical filtration for high-efficiency air filtering. However, the electrostatic charge decays with time, especially in humid conditions. In this work, a self-charging air filter is presented to capture airborne particles in an efficient and long-lasting manner without the need of external power sources. Leveraging the triboelectric effect between the electrospun poly(vinylidene fluoride) nanofiber film and nylon fabric, the self-charging air filter-based mask excited by breathing can continuously replenish electrostatic charges. As a result, its effective lifespan is up to 60 hours (including 30 hours of wearing), with a minimum filtration efficiency of 95.8% for 0.3-μm particles. The filtration efficiency and lifespan are significantly higher than those of a commercial surgical mask. Furthermore, we uncover the quantitative relation between filtration efficiency and surface electrostatic potential. This work provides an effective strategy to significantly prolong the electrostatic adsorption efficacy for high-performance air-filtering masks.

Protein micropatterning enables robust control of cell positioning on electron-microscopy substrates for cryogenic electron tomography (cryo-ET). However, the combination of regulated cell boundaries and the underlying electron-microscopy substrate (EM-grids) provides a poorly understood microenvironment for cell biology. Because substrate stiffness and morphology affect cellular behavior, we devised protocols to characterize the nanometer-scale details of the protein micropatterns on EM-grids by combining cryo-ET, atomic force microscopy, and scanning electron microscopy. Measuring force displacement characteristics of holey carbon EM-grids, we found that their effective spring constant is similar to physiological values expected from skin tissues. Despite their apparent smoothness at light-microscopy resolution, spatial boundaries of the protein micropatterns are irregular at nanometer scale. Our protein micropatterning workflow provides the means to steer both positioning and morphology of cell doublets to determine nanometer details of punctate adherens junctions. Our workflow serves as the foundation for studying the fundamental structural changes governing cell-cell signaling.

Standard genome-wide association studies (GWASs) rely on analyzing a single trait at a time. However, many human phenotypes are complex and composed by multiple correlated traits. Here we introduce C-GWAS, a method for combining GWAS summary statistics of multiple potentially correlated traits. Extensive computer simulations demonstrated increased statistical power of C-GWAS compared to the minimal p-values of multiple single-trait GWASs (MinGWAS) and the current state-of-the-art method for combining single-trait GWASs (MTAG). Applying C-GWAS to a meta-analysis dataset of 78 single trait facial GWASs from 10,115 Europeans identified 56 study-wide suggestively significant loci with multi-trait effects on facial morphology of which 17 are novel loci. Using data from additional 13,622 European and Asian samples, 46 (82%) loci, including 9 (53%) novel loci, were replicated at nominal significance with consistent allele effects. Functional analyses further strengthen the reliability of our C-GWAS findings. Our study introduces the C-GWAS method and makes it available as computationally efficient open-source R package for widespread future use. Our work also provides insights into the genetic architecture of human facial appearance.

The development of new antibacterial drugs with different mechanisms of action is urgently needed to address antimicrobial resistance. MraY is an essential membrane enzyme required for bacterial cell wall synthesis. Sphaerimicins are naturally occurring macrocyclic nucleoside inhibitors of MraY and are considered a promising target in antibacterial discovery. However, developing sphaerimicins as antibacterials has been challenging due to their complex macrocyclic structures. In this study, we construct their characteristic macrocyclic skeleton via two key reactions. Having then determined the structure of a sphaerimicin analogue bound to MraY, we use a structure-guided approach to design simplified sphaerimicin analogues. These analogues retain potency against MraY and exhibit potent antibacterial activity against Gram-positive bacteria, including clinically isolated drug resistant strains of S. aureus and E. faecium. Our study combines synthetic chemistry, structural biology, and microbiology to provide a platform for the development of MraY inhibitors as antibacterials against drug-resistant bacteria.

Erratum in Nat Commun. 2023 Jan 11;14(1):158.

Current therapies for autoimmune diseases, such as multiple sclerosis (MS), induce broad suppression of the immune system, potentially promoting opportunistic infections. Here, we report an immunosuppressive biomaterial-based therapeutic vaccine carrying self-antigen and tolerance-inducing inorganic nanoparticles to treat experimental autoimmune encephalomyelitis (EAE), a mouse model mimicking human MS. Immunization with self-antigen-loaded mesoporous nanoparticles generates Foxp3+ regulatory T-cells in spleen and systemic immune tolerance in EAE mice, reducing central nervous system-infiltrating antigen-presenting cells (APCs) and autoreactive CD4+ T-cells. Introducing reactive oxygen species (ROS)-scavenging cerium oxide nanoparticles (CeNP) to self-antigen-loaded nanovaccine additionally suppresses activation of APCs and enhances antigen-specific immune tolerance, inducing recovery in mice from complete paralysis at the late, chronic stage of EAE, which shows similarity to chronic human MS. This study clearly shows that the ROS-scavenging capability of catalytic inorganic nanoparticles could be utilized to enhance tolerogenic features in APCs, leading to antigen-specific immune tolerance, which could be exploited in treating MS.

Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-PP1 complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion enhances global KSHV gene expression and overall viral replication. Mechanistically, PNUTS requires PP1 interaction, binds viral RNAs downstream of polyadenylation sites, and restricts transcription readthrough of viral genes. Surprisingly, PNUTS also represses productive elongation at the 5´ ends of the KSHV reporter and the KSHV T1.4 RNA. From these data, we conclude that PNUTS' activity constitutes an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions.

Robust translation elongation of any given amino acid sequence is required to shape proteomes. Nevertheless, nascent peptides occasionally destabilize ribosomes, since consecutive negatively charged residues in bacterial nascent chains can stochastically induce discontinuation of translation, in a phenomenon termed intrinsic ribosome destabilization (IRD). Here, using budding yeast and a human factor-based reconstituted translation system, we show that IRD also occurs in eukaryotic translation. Nascent chains enriched in aspartic acid (D) or glutamic acid (E) in their N-terminal regions alter canonical ribosome dynamics, stochastically aborting translation. Although eukaryotic ribosomes are more robust to ensure uninterrupted translation, we find many endogenous D/E-rich peptidyl-tRNAs in the N-terminal regions in cells lacking a peptidyl-tRNA hydrolase, indicating that the translation of the N-terminal D/E-rich sequences poses an inherent risk of failure. Indeed, a bioinformatics analysis reveals that the N-terminal regions of ORFs lack D/E enrichment, implying that the translation defect partly restricts the overall amino acid usage in proteomes.

Alcohols are ubiquitous in chemistry and are native functionalities in many natural products and bioactive molecules. As such, a strategy that utilizes hydroxy-containing compounds to develop bond disconnection and bond formation process would achieve molecular diversity. Herein we utilize bench-stable N-alkoxyphthalimides prepared from alcohols to couple with glycine derivatives via radical process under visible light irradiation, providing a variety of unnatural amino acid (UAA) and peptide derivatives. The approach allows to rapidly deconstruct molecular complexity via β-fragmentation such as saclareolide, β-pinene and camphor and provides products with unique scaffolds, which show inhibition toward the pathogenic fungi growth.

Bordetella pertussis (Bp), the causative agent of pertussis, continues to circulate despite widespread vaccination programs. An important question is whether and how (sub)clinical infections shape immune memory to Bp, particularly in populations primed with acellular pertussis vaccines (aP). Here, we examine the prevalence of mucosal antibodies against non-vaccine antigens in aP-primed children and adolescents of the BERT study (NCT03697798), using antibody binding to a Bp mutant strain lacking aP antigens (Bp_mut). Our study identifies increased levels of mucosal IgG and IgA binding to Bp_mut in older aP-primed individuals, suggesting different Bp exposure between aP-primed birth cohorts, in line with pertussis disease incidence data. To examine whether Bp exposure influences vaccination responses, we measured mucosal antibody responses to aP booster vaccination as a secondary study outcome. Although booster vaccination induces significant increases in mucosal antibodies to Bp in both cohorts, the older age group that had higher baseline antibodies to Bp_ mut shows increased persistence of antibodies after vaccination.

N6-methyladenosine (m6A) modification of mRNAs affects many biological processes. However, the function of m6A in plant photosynthesis remains unknown. Here, we demonstrate that m6A modification is crucial for photosynthesis during photodamage caused by high light stress in plants. The m6A modification levels of numerous photosynthesis-related transcripts are changed after high light stress. We determine that the Arabidopsis m6A writer VIRILIZER (VIR) positively regulates photosynthesis, as its genetic inactivation drastically lowers photosynthetic activity and photosystem protein abundance under high light conditions. The m6A levels of numerous photosynthesis-related transcripts decrease in vir mutants, extensively reducing their transcript and translation levels, as revealed by multi-omics analyses. We demonstrate that VIR associates with the transcripts of genes encoding proteins with functions related to photoprotection (such as HHL1, MPH1, and STN8) and their regulatory proteins (such as regulators of transcript stability and translation), promoting their m6A modification and maintaining their stability and translation efficiency. This study thus reveals an important mechanism for m6A-dependent maintenance of photosynthetic efficiency in plants under high light stress conditions.

Diurnal rainfall offshore propagation (OP) shapes the timing and intensity of coastal rainfall and thus impacts both nature and society. Previous OP studies have rarely compared various coasts, and a consensus regarding physical mechanisms has not been reached on a global scale. Here, we provide the global climatology of observed OP, which propagates across ~78% of all coasts and accounts for ~59% of the coastal precipitation. Generally, OP is facilitated by low latitudes, high moisture conditions and offshore background winds. OP at low latitudes in a high-moisture environment is mainly caused by inertia-gravity waves due to the land-sea thermal contrast, whereas OP at higher latitudes is significantly influenced by background winds under trapped land-sea breeze circulation conditions. Slower near-shore OP might be modulated by density currents. Our results provide a guide for global OP hotspots and suggest relative contributions of mechanisms from a statistical perspective.

Mechanisms by which specific histone modifications regulate distinct gene networks remain little understood. We investigated how H3K79me2, a modification catalyzed by DOT1L and previously considered a general transcriptional activation mark, regulates gene expression during cardiogenesis. Embryonic cardiomyocyte ablation of Dot1l revealed that H3K79me2 does not act as a general transcriptional activator, but rather regulates highly specific transcriptional networks at two critical cardiogenic junctures: embryonic cardiogenesis, where it was particularly important for left ventricle-specific genes, and postnatal cardiomyocyte cell cycle withdrawal, with Dot1L mutants having more mononuclear cardiomyocytes and prolonged cardiomyocyte cell cycle activity. Mechanistic analyses revealed that H3K79me2 in two distinct domains, gene bodies and regulatory elements, synergized to promote expression of genes activated by DOT1L. Surprisingly, H3K79me2 in specific regulatory elements also contributed to silencing genes usually not expressed in cardiomyocytes. These results reveal mechanisms by which DOT1L successively regulates left ventricle specification and cardiomyocyte cell cycle withdrawal.

Developing dynamic organic ultralong room-temperature phosphorescent (URTP) materials is of practical importance in various applications but remains a challenge due to the difficulty in manipulating aggregate structures. Herein, we report a dish-like molecular architecture via a bottom-up way, featuring guest-responsive dynamic URTP. Through controlling local fragment motions in the molecular architecture, fascinating dynamic URTP performances can be achieved in response to reversible accommodation of various guests, including solvents, alkyl bromides and even carbon dioxide. Large-scale regulations of phosphorescence lifetime (100-fold) and intensity (10-fold) can be realized, presenting a maximum phosphorescence efficiency and lifetime of 78.8% and 483.1 ms, respectively. Moreover, such a dish-like molecular architecture is employed for temperature-dependent multiple information encryption and visual identification of linear alkyl bromides. This work can not only deepen our understanding to construct multifunctional organic aggregates, but also facilitate the design of high-performance dynamic URTP materials and enrich their practical applications.

Intracellular Ca2+ dysregulation is a key marker in septic cardiac dysfunction; however, regulation of the classic Ca2+ regulatory modules cannot successfully abolish this symptom. Here we show that the knockout of transient receptor potential canonical (TRPC) channel isoforms TRPC1 and TRPC6 can ameliorate LPS-challenged heart failure and prolong survival in mice. The LPS-triggered Ca2+ release from the endoplasmic reticulum both in cardiomyocytes and macrophages is significantly inhibited by Trpc1 or Trpc6 knockout. Meanwhile, TRPC's molecular partner - calmodulin - is uncoupled during Trpc1 or Trpc6 deficiency and binds to TLR4's Pococurante site and atypical isoleucine-glutamine-like motif to block the inflammation cascade. Blocking the C-terminal CaM/IP3R binding domain in TRPC with chemical inhibitor could obstruct the Ca2+ leak and TLR4-mediated inflammation burst, demonstrating a cardioprotective effect in endotoxemia and polymicrobial sepsis. Our findings provide insight into the pathogenesis of endotoxemic cardiac dysfunction and suggest a novel approach for its treatment.

Physicians write clinical notes with abbreviations and shorthand that are difficult to decipher. Abbreviations can be clinical jargon (writing "HIT" for "heparin induced thrombocytopenia"), ambiguous terms that require expertise to disambiguate (using "MS" for "multiple sclerosis" or "mental status"), or domain-specific vernacular ("cb" for "complicated by"). Here we train machine learning models on public web data to decode such text by replacing abbreviations with their meanings. We report a single translation model that simultaneously detects and expands thousands of abbreviations in real clinical notes with accuracies ranging from 92.1%-97.1% on multiple external test datasets. The model equals or exceeds the performance of board-certified physicians (97.6% vs 88.7% total accuracy). Our results demonstrate a general method to contextually decipher abbreviations and shorthand that is built without any privacy-compromising data.

Formamidinium lead iodide (FAPbI3) perovskites are promising emitters for near-infrared light-emitting diodes. However, their performance is still limited by defect-assisted nonradiative recombination and band offset-induced carrier aggregation at the interface. Herein, we introduce a couple of cadmium salts with acetate or halide anion into the FAPbI3 perovskite precursors to synergistically passivate the material defects and optimize the device band structure. Particularly, the perovskite analogs, containing zero-dimensional formamidinium cadmium iodide, one-dimensional δ-FAPbI3, two-dimensional FA2FAn-1PbnI3n+1, and three-dimensional α-FAPbI3, can be obtained in one pot and play a pivotal and positive role in energy transfer in the formamidinium iodide-rich lead-based perovskite films. As a result, the near-infrared FAPbI3-based devices deliver a maximum external quantum efficiency of 24.1% together with substantially improved operational stability. Combining our findings on defect passivation and energy transfer, we also achieve near-infrared light communication with device twins of light emitting and unprecedented self-driven detection.

LAT assembly into a two-dimensional protein condensate is a prominent feature of antigen discrimination by T cells. Here, we use single-molecule imaging techniques to resolve the spatial position and temporal duration of each pMHC:TCR molecular binding event while simultaneously monitoring LAT condensation at the membrane. An individual binding event is sufficient to trigger a LAT condensate, which is self-limiting, and neither its size nor lifetime is correlated with the duration of the originating pMHC:TCR binding event. Only the probability of the LAT condensate forming is related to the pMHC:TCR binding dwell time. LAT condenses abruptly, but after an extended delay from the originating binding event. A LAT mutation that facilitates phosphorylation at the PLC-γ1 recruitment site shortens the delay time to LAT condensation and alters T cell antigen specificity. These results identify a function for the LAT protein condensation phase transition in setting antigen discrimination thresholds in T cells.

Transformation pathways for the land sector in line with the Paris Agreement depend on the assumption of globally implemented greenhouse gas (GHG) emission pricing, and in some cases also on inclusive socio-economic development and sustainable land-use practices. In such pathways, the majority of GHG emission reductions in the land system is expected to come from low- and middle-income countries, which currently account for a large share of emissions from agriculture, forestry and other land use (AFOLU). However, in low- and middle-income countries the economic, financial and institutional barriers for such transformative changes are high. Here, we show that if sustainable development in the land sector remained highly unequal and limited to high-income countries only, global AFOLU emissions would remain substantial throughout the 21st century. Our model-based projections highlight that overcoming global inequality is critical for land-based mitigation in line with the Paris Agreement. While also a scenario purely based on either global GHG emission pricing or on inclusive socio-economic development would achieve the stringent emissions reductions required, only the latter ensures major co-benefits for other Sustainable Development Goals, especially in low- and middle-income regions.

Light initiates chloroplast biogenesis in Arabidopsis by eliminating PHYTOCHROME-INTERACTING transcription FACTORs (PIFs), which in turn de-represses nuclear photosynthesis genes, and synchronously, generates a nucleus-to-plastid (anterograde) signal that activates the plastid-encoded bacterial-type RNA polymerase (PEP) to transcribe plastid photosynthesis genes. However, the identity of the anterograde signal remains frustratingly elusive. The main challenge has been the difficulty to distinguish regulators from the plethora of necessary components for plastid transcription and other essential chloroplast functions, such as photosynthesis. Here, we show that the genome-wide induction of nuclear photosynthesis genes is insufficient to activate the PEP. PEP inhibition is imposed redundantly by multiple PIFs and requires PIF3's activator activity. Among the nuclear-encoded components of the PEP holoenzyme, we identify four light-inducible, PIF-repressed sigma factors as anterograde signals. Together, our results elucidate that light-dependent inhibition of PIFs activates plastid photosynthesis genes via sigma factors as anterograde signals in parallel with the induction of nuclear photosynthesis genes.

Recent studies have shown that G protein coupled receptors (GPCRs) show selective and promiscuous coupling to different Gα protein subfamilies and yet the mechanisms of the range of coupling preferences remain unclear. Here, we use Molecular Dynamics (MD) simulations on ten GPCR:G protein complexes and show that the location (spatial) and duration (temporal) of intermolecular contacts at the GPCR:Gα protein interface play a critical role in how GPCRs selectively interact with G proteins. We identify that some GPCR:G protein interface contacts are common across Gα subfamilies and others specific to Gα subfamilies. Using large scale data analysis techniques on the MD simulation snapshots we derive a spatio-temporal code for contacts that confer G protein selective coupling and validated these contacts using G protein activation BRET assays. Our results demonstrate that promiscuous GPCRs show persistent sampling of the common contacts more than G protein specific contacts. These findings suggest that GPCRs maintain contact with G proteins through a common central interface, while the selectivity comes from G protein specific contacts at the periphery of the interface.

Metabolic engineering has become an attractive method for the efficient production of natural products. However, one important pre-requisite is to establish the biosynthetic pathways. Many commercially interesting molecules cannot be biosynthesized as their native biochemical pathways are not fully elucidated. Cis-α-irone, a top-end perfumery molecule, is an example. Retrobiosynthetic pathway design by employing promiscuous enzymes provides an alternative solution to this challenge. In this work, we design a synthetic pathway to produce cis-α-irone with a promiscuous methyltransferase (pMT). Using structure-guided enzyme engineering strategies, we improve pMT activity and specificity towards cis-α-irone by >10,000-fold and >1000-fold, respectively. By incorporating the optimized methyltransferase into our engineered microbial cells, ~86 mg l-1 cis-α-irone is produced from glucose in a 5 l bioreactor. Our work illustrates that integrated retrobiosynthetic pathway design and enzyme engineering can offer opportunities to expand the scope of natural molecules that can be biosynthesized.

Regular patterns can form spontaneously in chemical reaction-diffusion systems under non-equilibrium conditions as proposed by Alan Turing. Here, we found that regular patterns can be generated in uphill-diffusion solution systems without a chemical reaction process through both in-situ and ex-situ observations. Organic semiconductor solution is confined between two parallel plates with controlled micron/submicron-meter distance to minimize convection of the liquid and avoid spinodal precipitation at equilibrium. The solvent evaporation concentrates the solution gradually into an oversaturated non-equilibrium condition, under which a phase-transition occurs and ordered concentration-waves are generated. By proper tuning of the experimental parameter, multiple regular patterns with micro/nano-meter scaled features (line, square-grid, zig-zag, and fence-like patterns etc.) were observed. We explain the observed phenomenon as Turing-pattern generation resulted from uphill-diffusion and solution oversaturation. The generated patterns in the solutions can be condensed onto substrates to form structured micro/nanomaterials. We have fabricated organic semiconductor devices with such patterned materials to demonstrate the potential applications. Our observation may serve as a milestone in the progress towards a fundamental understanding of pattern formation in nature, like in biosystem, and pave a new avenue in developing self-assembling techniques of micro/nano structured materials.

Thermochromic window develops as a competitive solution for carbon emissions due to comprehensive advantages of its passivity and effective utilization of energy. How to further enhance the solar modulation ([Formula: see text]) of thermochromic windows while ensuring high luminous transmittance ([Formula: see text]) becomes the latest challenge to touch the limit of energy efficiency. Here, we show a smart window combining mechanochromism with thermochromism by self-rolling of vanadium dioxide (VO2) nanomembranes to enhance multi-level solar modulation. The mechanochromism is introduced by the temperature-controlled regulation of curvature of rolled-up smart window, which benefits from effective strain adjustment in VO2 nanomembranes upon the phase transition. Under geometry design and optimization, the rolled-up smart window with high [Formula: see text] and [Formula: see text] is achieved for the modulation of indoor temperature self-adapted to seasons and climate. Furthermore, such rolled-up smart window enables high infrared reflectance after triggered phase transition and acts as a smart lens protective cover for strong radiation. This work supports the feasibility of self-rolling technology in smart windows and lens protection, which promises broad interest and practical applications of self-adapting devices and systems for smart building, intelligent sensors and actuators with the perspective of energy efficiency.

Many organisms produce stunning optical displays based on structural color instead of pigmentation. This structural or photonic color is achieved through the interaction of light with intricate micro-/nano-structures, which are "grown" from strong, sustainable biological materials such as chitin, keratin, and cellulose. In contrast, current synthetic structural colored materials are usually brittle, inert, and produced via energy-intensive processes, posing significant challenges to their practical uses. Inspired by the brilliantly colored peacock feathers which selectively grow keratin-based photonic structures with different photonic bandgaps, we develop a self-growing photonic composite system in which the photonic bandgaps and hence the coloration can be easily tuned. This is achieved via the selective growth of the polymer matrix with polymerizable compounds as feeding materials in a silica nanosphere-polymer composite system, thus effectively modulating the photonic bandgaps without compromising nanostructural order. Such strategy not only allows the material system to continuously vary its colors and patterns in an on-demand manner, but also endows it with many appealing properties, including flexibility, toughness, self-healing ability, and reshaping capability. As this innovative self-growing method is simple, inexpensive, versatile, and scalable, we foresee its significant potential in meeting many emerging requirements for various applications of structural color materials.

Wood is a remarkable material with great cultural, economic, and biogeochemical importance. However, our understanding of its formation is poor. Key properties that have not been explained include the anatomy of growth rings (with consistent transitions from low-density earlywood to high density latewood), strong temperature-dependence of latewood density (used for historical temperature reconstructions), the regulation of cell size, and overall growth-temperature relationships in conifer and ring-porous tree species. We have developed a theoretical framework based on observations on Pinus sylvestris L. in northern Sweden. The observed anatomical properties emerge from our framework as a consequence of interactions in time and space between the production of new cells, the dynamics of developmental zone widths, and the distribution of carbohydrates across the developing wood. Here we find that the diffusion of carbohydrates is critical to determining final ring anatomy, potentially overturning current understanding of how wood formation responds to environmental variability and transforming our interpretation of tree rings as proxies of past climates.

Serious concerns exist about potentially reinforcing negative effects of climate change and land conversion on biodiversity. Here, we investigate the tandem and interacting roles of climate warming and land-use change as predictors of shifts in the regional distributions of 1701 plant species in Sweden over 60 years. We show that species associated with warmer climates have increased, while grassland specialists have declined. Our results also support the hypothesis that climate warming and vegetation densification through grazing abandonment have synergistic effects on species distribution change. Local extinctions were related to high levels of warming but were reduced by grassland retention. In contrast, colonisations occurred more often in areas experiencing high levels of both climate and land-use change. Strong temperature increases were experienced by species across their ranges, indicating time lags in expected warming-related local extinctions. Our results highlight that the conservation of threatened species relies on both reduced greenhouse gas emissions and the retention and restoration of valuable habitat.

Dietary composition affects food preference in animals. High sugar intake suppresses sweet sensation from insects to humans, but the molecular basis of this suppression is largely unknown. Here, we reveal that sugar intake in Drosophila induces the gut to express and secrete Hedgehog (Hh) into the circulation. We show that the midgut secreted Hh localize to taste sensilla and suppresses sweet sensation, perception, and preference. We further find that the midgut Hh inhibits Hh signalling in the sweet taste neurons. Our electrophysiology studies demonstrate that the midgut Hh signal also suppresses bitter taste and some odour responses, affecting overall food perception and preference. We further show that the level of sugar intake during a critical window early in life, sets the adult gut Hh expression and sugar perception. Our results together reveal a bottom-up feedback mechanism involving a "gut-taste neuron axis" that regulates food sensation and preference.

Groundwater provides nearly half of irrigation water supply, and it enables resilience during drought, but in many regions of the world, it remains poorly, if at all managed. In heavily agricultural regions like California's Central Valley, where groundwater management is being slowly implemented over a 27-year period that began in 2015, groundwater provides two-thirds or more of irrigation water during drought, which has led to falling water tables, drying wells, subsiding land, and its long-term disappearance. Here we use nearly two decades of observations from NASA's GRACE satellite missions and show that the rate of groundwater depletion in the Central Valley has been accelerating since 2003 (1.86 km3/yr, 1961-2021; 2.41 km3/yr, 2003-2021; 8.58 km3/yr, 2019-2021), a period of megadrought in southwestern North America. Results suggest the need for expedited implementation of groundwater management in the Central Valley to ensure its availability during the increasingly intense droughts of the future.

Strong light-matter interaction in cavity environments is emerging as a promising approach to control chemical reactions in a non-intrusive and efficient manner. The underlying mechanism that distinguishes between steering, accelerating, or decelerating a chemical reaction has, however, remained unclear, hampering progress in this frontier area of research. We leverage quantum-electrodynamical density-functional theory to unveil the microscopic mechanism behind the experimentally observed reduced reaction rate under cavity induced resonant vibrational strong light-matter coupling. We observe multiple resonances and obtain the thus far theoretically elusive but experimentally critical resonant feature for a single strongly coupled molecule undergoing the reaction. While we describe only a single mode and do not explicitly account for collective coupling or intermolecular interactions, the qualitative agreement with experimental measurements suggests that our conclusions can be largely abstracted towards the experimental realization. Specifically, we find that the cavity mode acts as mediator between different vibrational modes. In effect, vibrational energy localized in single bonds that are critical for the reaction is redistributed differently which ultimately inhibits the reaction.

Graphene's original promise to succeed silicon faltered due to pervasive edge disorder in lithographically patterned deposited graphene and the lack of a new electronics paradigm. Here we demonstrate that the annealed edges in conventionally patterned graphene epitaxially grown on a silicon carbide substrate (epigraphene) are stabilized by the substrate and support a protected edge state. The edge state has a mean free path that is greater than 50 microns, 5000 times greater than the bulk states and involves a theoretically unexpected Majorana-like zero-energy non-degenerate quasiparticle that does not produce a Hall voltage. In seamless integrated structures, the edge state forms a zero-energy one-dimensional ballistic network with essentially dissipationless nodes at ribbon-ribbon junctions. Seamless device structures offer a variety of switching possibilities including quantum coherent devices at low temperatures. This makes epigraphene a technologically viable graphene nanoelectronics platform that has the potential to succeed silicon nanoelectronics.

Methods capable of manipulating bacterial colonization are of great significance for modulating host-microbiota relationships. Here, we describe a strategy of in-situ chemical reaction-mediated covalent localization of bacteria. Through a simple one-step imidoester reaction, primary amino groups on bacterial surface can be converted to free thiols under cytocompatible conditions. Surface thiolation is applicable to modify diverse strains and the number of introduced thiols per bacterium can be easily tuned by varying feed ratios. These chemically reactive bacteria are able to spontaneously bond with mucous layer by catalyst-free thiol-disulfide exchange between mucin-associated disulfides and newly converted thiols on bacterial surface and show thiolation level-dependent attachment. Bacteria optimized with 9.3 × 107 thiols per cell achieve 170-fold higher attachment in mucin-enriched jejunum, a challenging location for gut microbiota to colonize. As a proof-of-concept application for microbiota transplantation, covalent bonding-assisted localization of an oral probiotic in the jejunum generates an improved remission of jejunal mucositis. Our findings demonstrate that transforming bacteria with a reactive surface provides an approach to chemically control bacterial localization, which is highly desirable for developing next-generation bacterial living bioagents.

The crustal accretion along mid-ocean ridges is known to be spreading-rate dependent. Along fast-spreading ridges, two-dimensional sheet-like mantle upwelling creates relatively uniform crust. In contrast, the crust formed along slow-spreading ridges shows large along-axis thickness variations with thicker crust at segment centres, which is hypothesised to be due a three-dimensional plume-like mantle upwelling or due to focused melt migration to segment centres. Using wide-angle seismic data acquired from the equatorial Atlantic Ocean, here we show that the crustal thickness is nearly uniform (~5.5 km) across five crustal segments for crust formed at the slow-spreading Mid-Atlantic Ridge with age varying from 8 to 70 Ma. The crustal velocities indicate that this crust is predominantly of magmatic origin. We suggest that this uniform magmatic crustal accretion is due to a two-dimensional sheet-like mantle upwelling facilitated by the long-offset transform faults in the equatorial Atlantic region and the presence of a high concentration of volatiles in the primitive melt in the mantle.

Erratum in Nat Commun. 2023 Jan 19;14(1):325.

Microwave photonics has adopted a number of important concepts and technologies over the recent pasts, including photonic integration, versatile programmability, and techniques for enhancing key radio frequency performance metrics such as the noise figure and the dynamic range. However, to date, these aspects have not been achieved simultaneously in a single circuit. Here, we report a multi-functional photonic integrated circuit that enables programmable filtering functions with record-high performance. We demonstrate reconfigurable filter functions with record-low noise figure and a RF notch filter with ultra-high dynamic range. We achieve this unique feature using versatile complex spectrum tailoring enabled by an all integrated modulation transformer and a double injection ring resonator as a multi-function optical filtering component. Our work breaks the conventional and fragmented approach of integration, functionality and performance that currently prevents the adoption of integrated MWP systems in real applications.

Dysregulation of mTOR complex 1 (mTORC1) activity drives neuromuscular junction (NMJ) structural instability during aging; however, downstream targets mediating this effect have not been elucidated. Here, we investigate the roles of two mTORC1 phosphorylation targets for mRNA translation, ribosome protein S6 kinase 1 (S6K1) and eukaryotic translation initiation factor 4E-binding protein 1 (4EBP1), in regulating NMJ structural instability induced by aging and sustained mTORC1 activation. While myofiber-specific deletion of S6k1 has no effect on NMJ structural integrity, 4EBP1 activation in murine muscle induces drastic morphological remodeling of the NMJ with enhancement of synaptic transmission. Mechanistically, structural modification of the NMJ is attributed to increased satellite cell activation and enhanced post-synaptic acetylcholine receptor (AChR) turnover upon 4EBP1 activation. Considering that loss of post-synaptic myonuclei and reduced NMJ turnover are features of aging, targeting 4EBP1 activation could induce NMJ renewal by expanding the pool of post-synaptic myonuclei as an alternative intervention to mitigate sarcopenia.

The demands for cost-effective solar fuels have triggered extensive research in artificial photosynthesis, yet the efforts in designing high-performance particulate photocatalysts are largely impeded by inefficient charge separation. Because charge separation in a particulate photocatalyst is driven by asymmetric interfacial energetics between its reduction and oxidation sites, enhancing this process demands nanoscale tuning of interfacial energetics on the prerequisite of not impairing the kinetics and selectivity for surface reactions. In this study, we realize this target with a general strategy involving the application of a core/shell type cocatalyst that is demonstrated on various photocatalytic systems. The promising H2O2 generation efficiency validate our perspective on tuning interfacial energetics for enhanced charge separation and photosynthesis performance. Particularly, this strategy is highlighted on a BiVO4 system for overall H2O2 photosynthesis with a solar-to-H2O2 conversion of 0.73%.

Erratum in Nat Commun. 2023 Feb 6;14(1):650.

Photomedicine has gained great attention due to its nontoxicity, good selectivity and small trauma. However, owing to the limited penetration of light and difficult monitoring of the photo-media therapies, it is challenging to apply photomedical treatment in deep tissue as they may damage normal tissues. Herein, a thermal regulated interventional photomedicine based on a temperature-adaptive hydrogel fiber-based optical waveguide (THFOW) is proposed, capable of eliminating deeply seated tumor cells while lowering risks of overtemperature (causes the death of healthy cells around the tumor). The THFOW is fabricated by an integrated homogeneous-dynamic-crosslinking-spinning method, and shows a remarkable soft tissue-affinity (low cytotoxicity, swelling stability, and soft tissue-like Young's modulus). Moreover, the THFOW shows an excellent light propagation property with different wavenumbers (especially -0.32 dB cm-1 with 915 nm laser light), and temperature-gated light propagation effect. The THFOW and relevant therapeutic strategy offer a promising application for intelligent photomedicine in deep issue.

Although the importance of virus-specific cytotoxic T lymphocytes (CTL) in virus clearance is evident in COVID-19, the characteristics of virus-specific CTLs related to disease severity have not been fully explored. Here we show that the phenotype of virus-specific CTLs against immunoprevalent epitopes in COVID-19 convalescents might differ according to the course of the disease. We establish a cellular screening method that uses artificial antigen presenting cells, expressing HLA-A*24:02, the costimulatory molecule 4-1BBL, SARS-CoV-2 structural proteins S, M, and N and non-structural proteins ORF3a and nsp6/ORF1a. The screen implicates SARS-CoV-2 M protein as a frequent target of IFNγ secreting CD8+ T cells, and identifies M198-206 as an immunoprevalent epitope in our cohort of HLA-A*24:02 positive convalescent COVID-19 patients recovering from mild, moderate and severe disease. Further exploration of M198-206-specific CD8+ T cells with single cell RNA sequencing reveals public TCRs in virus-specific CD8+ T cells, and shows an exhausted phenotype with less differentiated status in cells from the severe group compared to cells from the moderate group. In summary, this study describes a method to identify T cell epitopes, indicate that dysfunction of virus-specific CTLs might be an important determinant of clinical outcomes.

Red giants are stars in the late stages of stellar evolution. Because they have exhausted the supply of hydrogen in their core, they burn the hydrogen in the surrounding shell . Once the helium in the core starts fusing, the star enters the clump phase, which is identified as a striking feature in the color-magnitude diagram. Since clump stars share similar observational properties, they are heavily used in astrophysical studies, as probes of distance, extinction through the galaxy, galaxy density, and stellar chemical evolution. In this work, we perform the detailed observational characterization of the deepest layers of clump stars using asteroseismic data from Kepler. We find evidence for large core structural discontinuities in about 6.7% of the stars in our sample, implying that the region of mixing beyond the convective core boundary has a radiative thermal stratification. These stars are otherwise similar to the remaining stars in our sample, which may indicate that the building of the discontinuities is an intermittent phenomenon.

Valley pseudospin is an electronic degree of freedom that promises highly efficient information processing applications. However, valley-polarized excitons usually have short pico-second lifetimes, which limits the room-temperature applicability of valleytronic devices. Here, we demonstrate room-temperature valley transistors that operate by generating free carrier valley polarization with a long lifetime. This is achieved by electrostatic manipulation of the non-trivial band topology of the Weyl semiconductor tellurium (Te). We observe valley-polarized diffusion lengths of more than 7 μm and fabricate valley transistors with an ON/OFF ratio of 105 at room temperature. Moreover, we demonstrate an ion insertion/extraction device structure that enables 32 non-volatile memory states with high linearity and symmetry in the Te valley transistor. With ultralow power consumption (~fW valley contribution), we enable the inferring process of artificial neural networks, exhibiting potential for applications in low-power neuromorphic computing.

Large-scale arrays of quantum-dot spin qubits in Si/SiGe quantum wells require large or tunable energy splittings of the valley states associated with degenerate conduction band minima. Existing proposals to deterministically enhance the valley splitting rely on sharp interfaces or modifications in the quantum well barriers that can be difficult to grow. Here, we propose and demonstrate a new heterostructure, the "Wiggle Well", whose key feature is Ge concentration oscillations inside the quantum well. Experimentally, we show that placing Ge in the quantum well does not significantly impact our ability to form and manipulate single-electron quantum dots. We further observe large and widely tunable valley splittings, from 54 to 239 μeV. Tight-binding calculations, and the tunability of the valley splitting, indicate that these results can mainly be attributed to random concentration fluctuations that are amplified by the presence of Ge alloy in the heterostructure, as opposed to a deterministic enhancement due to the concentration oscillations. Quantitative predictions for several other heterostructures point to the Wiggle Well as a robust method for reliably enhancing the valley splitting in future qubit devices.

Direct visualization of point mutations in situ can be informative for studying genetic diseases and nuclear biology. We describe a direct hybridization genome imaging method with single-nucleotide sensitivity, single guide genome oligopaint via local denaturation fluorescence in situ hybridization (sgGOLDFISH), which leverages the high cleavage specificity of eSpCas9(1.1) variant combined with a rationally designed guide RNA to load a superhelicase and reveal probe binding sites through local denaturation. The guide RNA carries an intentionally introduced mismatch so that while wild-type target DNA sequence can be efficiently cleaved, a mutant sequence with an additional mismatch (e.g., caused by a point mutation) cannot be cleaved. Because sgGOLDFISH relies on genomic DNA being cleaved by Cas9 to reveal probe binding sites, the probes will only label the wild-type sequence but not the mutant sequence. Therefore, sgGOLDFISH has the sensitivity to differentiate the wild-type and mutant sequences differing by only a single base pair. Using sgGOLDFISH, we identify base-editor-modified and unmodified progeroid fibroblasts from a heterogeneous population, validate the identification through progerin immunofluorescence, and demonstrate accurate sub-nuclear localization of point mutations.

Programmable, RNA-guided nucleases are diverse enzymes that have been repurposed for biotechnological applications. However, to further expand the therapeutic application of these tools there is a need for targetable systems that are small enough to be delivered efficiently. Here, we mined an extensive genome-resolved metagenomics database and identified families of uncharacterized RNA-guided, compact nucleases (between 450 and 1,050 aa). We report that Cas9d, a new CRISPR type II subtype, contains Zinc-finger motifs and high arginine content, features that we also found in nucleases related to HEARO effectors. These enzymes exhibit diverse biochemical characteristics and are broadly targetable. We show that natural Cas9d enzymes are capable of genome editing in mammalian cells with >90% efficiency, and further engineered nickase variants into the smallest base editors active in E. coli and human cells. Their small size, broad targeting potential, and translatability suggest that Cas9d and HEARO systems will enable a variety of genome editing applications.

The design of adsorbents for rapid, selective extraction of ultra-trace amounts of gold from complex liquids is desirable from both an environmental and economical point of view. However, the development of such materials remains challenging. Herein, we report the fabrication of two vinylene-linked two-dimensional silver(I)-organic frameworks prepared via Knoevenagel condensation. This material enables selective sensing of gold with a low limit of detection of 60 ppb, as well as selective uptake of ultra-trace gold from complex aqueous mixtures including distilled water with 15 competing metal ions, leaching solution of electronic waste (e-waste), wastewater, and seawater. The present adsorbent delivers a gold adsorption capacity of 954 mg g-1, excellent selectivity and reusability, and can rapidly and selectively extract ultra-trace gold from seawater down to ~20 ppb (94% removal in 10 minutes). In addition, the purity of recovered gold from e-waste reaches 23.8 Karat (99.17% pure).

Carbon dioxide capture is essential to achieve net-zero emissions. A hurdle to the design of improved capture materials is the lack of adequate tools to characterise how CO2 adsorbs. Solid-state nuclear magnetic resonance (NMR) spectroscopy is a promising probe of CO2 capture, but it remains challenging to distinguish different adsorption products. Here we perform a comprehensive computational investigation of 22 amine-functionalised metal-organic frameworks and discover that 17O NMR is a powerful probe of CO2 capture chemistry that provides excellent differentiation of ammonium carbamate and carbamic acid species. The computational findings are supported by 17O NMR experiments on a series of CO2-loaded frameworks that clearly identify ammonium carbamate chain formation and provide evidence for a mixed carbamic acid - ammonium carbamate adsorption mode. We further find that carbamic acid formation is more prevalent in this materials class than previously believed. Finally, we show that our methods are readily applicable to other adsorbents, and find support for ammonium carbamate formation in amine-grafted silicas. Our work paves the way for investigations of carbon capture chemistry that can enable materials design.

The vertebrate main-body axis is laid down during embryonic stages in an anterior-to-posterior (head-to-tail) direction, driven and supplied by posteriorly located progenitors. Whilst posterior expansion and segmentation appears broadly uniform along the axis, there is developmental and evolutionary support for at least two discrete modules controlling processes within different axial regions: a trunk and a tail module. Here, we identify Nuclear receptor subfamily 6 group A member 1 (Nr6a1) as a master regulator of trunk development in the mouse. Specifically, Nr6a1 was found to control vertebral number and segmentation of the trunk region, autonomously from other axial regions. Moreover, Nr6a1 was essential for the timely progression of Hox signatures, and neural versus mesodermal cell fate choice, within axial progenitors. Collectively, Nr6a1 has an axially-restricted role in all major cellular and tissue-level events required for vertebral column formation, supporting the view that changes in Nr6a1 levels may underlie evolutionary changes in axial formulae.

Van der Waals (vdW) magnet heterostructures have emerged as new platforms to explore exotic magnetic orders and quantum phenomena. Here, we study heterostructures of layered antiferromagnets, CrI3 and CrCl3, with perpendicular and in-plane magnetic anisotropy, respectively. Using magneto-optical Kerr effect microscopy, we demonstrate out-of-plane magnetic order in the CrCl3 layer proximal to CrI3, with ferromagnetic interfacial coupling between the two. Such an interlayer exchange field leads to higher critical temperature than that of either CrI3 or CrCl3 alone. We further demonstrate significant electric-field control of the coercivity, attributed to the naturally broken structural inversion symmetry of the heterostructure allowing unprecedented direct coupling between electric field and interfacial magnetism. These findings illustrate the opportunity to explore exotic magnetic phases and engineer spintronic devices in vdW heterostructures.

Recovering molecular information remains a grand challenge in the widely used holographic and computational imaging technologies. To address this challenge, we developed a computational mid-infrared photothermal microscope, termed Bond-selective Intensity Diffraction Tomography (BS-IDT). Based on a low-cost brightfield microscope with an add-on pulsed light source, BS-IDT recovers both infrared spectra and bond-selective 3D refractive index maps from intensity-only measurements. High-fidelity infrared fingerprint spectra extraction is validated. Volumetric chemical imaging of biological cells is demonstrated at a speed of ~20 s per volume, with a lateral and axial resolution of ~350 nm and ~1.1 µm, respectively. BS-IDT's application potential is investigated by chemically quantifying lipids stored in cancer cells and volumetric chemical imaging on Caenorhabditis elegans with a large field of view (~100 µm x 100 µm).

Preantral follicles are often used as models for cryopreservation and in vitro culture due to their easy availability. As a promising approach for mammalian fertility preservation, vitrification of preantral follicles requires high concentrations of highly toxic penetrating cryoprotective agents (up to 6 M). Here, we accomplish low-concentration-penetrating cryoprotective agent (1.5 M) vitrification of mouse preantral follicles encapsulated in hydrogel by nanowarming. We find that compared with conventional water bath warming, the viability of preantral follicles is increased by 33%. Moreover, the cavity formation rate of preantral follicles after in vitro culture is comparable to the control group without vitrification. Furthermore, the percentage of MII oocytes developed from the vitrified follicles, and the birth rate of offspring following in vitro fertilization and embryo transfer are also similar to the control group. Our results provide a step towards nontoxic vitrification by utilizing the synergistic cryoprotection effect of microencapsulation and nanowarming.

Herein, we employ a galvanic replacement approach to create atomically dispersed Au on degradable zero-valent Cu nanocubes for tumor treatments on female mice. Controlling the addition of precursor HAuCl4 allows for the fabrication of different atomic ratios of AuxCuy. X-ray absorption near edge spectra indicates that Au and Cu are the predominant oxidation states of zero valence. This suggests that the charges of Au and Cu remain unchanged after galvanic replacement. Specifically, Au0.02Cu0.98 composition reveals the enhanced •OH generation following O2 → H2O2 → •OH. The degradable Au0.02Cu0.98 released Cu+ and Cu2+ resulting in oxygen reduction and Fenton-like reactions. Simulation studies indicate that Au single atoms boot zero-valent copper to reveal the catalytic capability of Au0.02Cu0.98 for O2 → H2O2 → •OH as well. Instead of using endogenous H2O2, H2O2 can be sourced from the O2 in the air through the use of nanocubes. Notably, the Au0.02Cu0.98 structure is degradable and renal-clearable.

We develop a novel approach to analysing decarbonisation strategies by linking global resource inventories with demographic systems. Our 'mine-town systems' approach establishes an empirical basis for examining the spatial extent of the transition and demographic effects of changing energy systems. The research highlights an urgent need for targeted macro-level planning as global markets see a decline in thermal coal and a ramp up of other mining commodities. Our findings suggest that ramping up energy transition metals (ETM) could be more disruptive to demographic systems than ramping down coal. The data shows asymmetry in the distribution of risks: mine-town systems within the United States are most sensitive to coal phase-out, while systems in Australia and Canada are most sensitive to ETM phase-in. A complete phase-out of coal could disrupt demographic systems with a minimum of 33.5 million people, and another 115.7 million people if all available ETM projects enter production.

Electronic patches, based on various mechanisms, allow continuous and noninvasive monitoring of biomolecules on the skin surface. However, to date, such devices are unable to sense biomolecules in deep tissues, which have a stronger and faster correlation with the human physiological status than those on the skin surface. Here, we demonstrate a photoacoustic patch for three-dimensional (3D) mapping of hemoglobin in deep tissues. This photoacoustic patch integrates an array of ultrasonic transducers and vertical-cavity surface-emitting laser (VCSEL) diodes on a common soft substrate. The high-power VCSEL diodes can generate laser pulses that penetrate >2 cm into biological tissues and activate hemoglobin molecules to generate acoustic waves, which can be collected by the transducers for 3D imaging of the hemoglobin with a high spatial resolution. Additionally, the photoacoustic signal amplitude and temperature have a linear relationship, which allows 3D mapping of core temperatures with high accuracy and fast response. With access to biomolecules in deep tissues, this technology adds unprecedented capabilities to wearable electronics and thus holds significant implications for various applications in both basic research and clinical practice.

Histone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease.

Artificial neural networks are known to suffer from catastrophic forgetting: when learning multiple tasks sequentially, they perform well on the most recent task at the expense of previously learned tasks. In the brain, sleep is known to play an important role in incremental learning by replaying recent and old conflicting memory traces. Here we tested the hypothesis that implementing a sleep-like phase in artificial neural networks can protect old memories during new training and alleviate catastrophic forgetting. Sleep was implemented as off-line training with local unsupervised Hebbian plasticity rules and noisy input. In an incremental learning framework, sleep was able to recover old tasks that were otherwise forgotten. Previously learned memories were replayed spontaneously during sleep, forming unique representations for each class of inputs. Representational sparseness and neuronal activity corresponding to the old tasks increased while new task related activity decreased. The study suggests that spontaneous replay simulating sleep-like dynamics can alleviate catastrophic forgetting in artificial neural networks.

The reduction of carbon dioxide using electrochemical cells is an appealing technology to store renewable electricity in a chemical form. The preferential adsorption of oxygen over carbon atoms of intermediates could improve the methanol selectivity due to the retention of C-O bond. However, the adsorbent-surface interaction is mainly related to the d states of transition metals in catalysts, thus it is difficult to promote the formation of oxygen-bound intermediates without affecting the carbon affinity. This paper describes the construction of a molybdenum-based metal carbide catalyst that promotes the formation and adsorption of oxygen-bound intermediates, where the sp states in catalyst are enabled to participate in the bonding of intermediates. A high Faradaic efficiency of 80.4% for methanol is achieved at -1.1 V vs. the standard hydrogen electrode.

Unreliable predictions can occur when an artificial intelligence (AI) system is presented with data it has not been exposed to during training. We demonstrate the use of conformal prediction to detect unreliable predictions, using histopathological diagnosis and grading of prostate biopsies as example. We digitized 7788 prostate biopsies from 1192 men in the STHLM3 diagnostic study, used for training, and 3059 biopsies from 676 men used for testing. With conformal prediction, 1 in 794 (0.1%) predictions is incorrect for cancer diagnosis (compared to 14 errors [2%] without conformal prediction) while 175 (22%) of the predictions are flagged as unreliable when the AI-system is presented with new data from the same lab and scanner that it was trained on. Conformal prediction could with small samples (N = 49 for external scanner, N = 10 for external lab and scanner, and N = 12 for external lab, scanner and pathology assessment) detect systematic differences in external data leading to worse predictive performance. The AI-system with conformal prediction commits 3 (2%) errors for cancer detection in cases of atypical prostate tissue compared to 44 (25%) without conformal prediction, while the system flags 143 (80%) unreliable predictions. We conclude that conformal prediction can increase patient safety of AI-systems.

The development of cancer therapies is limited by the availability of suitable drug targets. Potential candidate drug targets can be identified based on the concept of synthetic lethality (SL), which refers to pairs of genes for which an aberration in either gene alone is non-lethal, but co-occurrence of the aberrations is lethal to the cell. Here, we present SLIdR (Synthetic Lethal Identification in R), a statistical framework for identifying SL pairs from large-scale perturbation screens. SLIdR successfully predicts SL pairs even with small sample sizes while minimizing the number of false positive targets. We apply SLIdR to Project DRIVE data and find both established and potential pan-cancer and cancer type-specific SL pairs consistent with findings from literature and drug response screening data. We experimentally validate two predicted SL interactions (ARID1A-TEAD1 and AXIN1-URI1) in hepatocellular carcinoma, thus corroborating the ability of SLIdR to identify potential drug targets.

Accurate, in-depth mapping of proteins on whole-tissue levels provides comprehensive insights into the spatially-organized regulatory processes/networks in tissues, but is challenging. Here we describe a micro-scaffold assisted spatial proteomics (MASP) strategy, based on spatially-resolved micro-compartmentalization of tissue using a 3D-printed micro-scaffold, capable of mapping thousands of proteins across a whole-tissue slice with excellent quantitative accuracy/precision. The pipeline includes robust tissue micro-compartmentalization with precisely-preserved spatial information, reproducible procurement and preparation of the micro-specimens, followed by sensitive LC-MS analysis and map generation by a MAsP app. The mapping accuracy was validated by comparing the MASP-generated maps of spiked-in peptides and brain-region-specific markers with known patterns, and by correlating the maps of the two protein components of the same heterodimer. The MASP was applied in mapping >5000 cerebral proteins in the mouse brain, encompassing numerous important brain markers, regulators, and transporters, where many of these proteins had not previously been mapped on the whole-tissue level.

Numerous studies have demonstrated that biodiversity drives ecosystem functioning, yet how biodiversity loss alters ecosystems functioning and stability in the long-term lacks experimental evidence. We report temporal effects of species richness on community productivity, stability, species asynchrony, and complementarity, and how the relationships among them change over 17 years in a grassland biodiversity experiment. Productivity declined more rapidly in less diverse communities resulting in temporally strengthening positive effects of richness on productivity, complementarity, and stability. In later years asynchrony played a more important role in increasing community stability as the negative effect of richness on population stability diminished. Only during later years did species complementarity relate to species asynchrony. These results show that species complementarity and asynchrony can take more than a decade to develop strong stabilizing effects on ecosystem functioning in diverse plant communities. Thus, the mechanisms stabilizing ecosystem functioning change with community age.

Synthesis planning programs trained on chemical reaction data can design efficient routes to new molecules of interest, but are limited in their ability to leverage rare chemical transformations. This challenge is acute for enzymatic reactions, which are valuable due to their selectivity and sustainability but are few in number. We report a retrosynthetic search algorithm using two neural network models for retrosynthesis-one covering 7984 enzymatic transformations and one 163,723 synthetic transformations-that balances the exploration of enzymatic and synthetic reactions to identify hybrid synthesis plans. This approach extends the space of retrosynthetic moves by thousands of uniquely enzymatic one-step transformations, discovers routes to molecules for which synthetic or enzymatic searches find none, and designs shorter routes for others. Application to (-)-Δ9 tetrahydrocannabinol (THC) (dronabinol) and R,R-formoterol (arformoterol) illustrates how our strategy facilitates the replacement of metal catalysis, high step counts, or costly enantiomeric resolution with more elegant hybrid proposals.

The vast tropical Pacific is home to the majority of tropical cyclones (TCs) which threaten the rim countries every year. The TC genesis is nourished by warm sea surface temperatures (SSTs). During El Niño, the western Pacific warm pool extends eastward. However, the number of TCs does not increase significantly with the expanding warm pool and it remains comparable between El Niño and La Niña. Here, we show that the subsurface heat content change counteracts the favorable SSTs in the tropical central-north Pacific. Due to the anomalous positive wind stress curl, the 26 °C isotherm shoals during El Niño over this region and the heat content diminishes in the tropical central-north Pacific, even though warm SST anomalies prevail. This negative correlation between SST and 26 °C isotherm depth anomalies is opposite to the positive correlation in the tropical eastern and western Pacific. This is critical because quantifying the dynamics of the subsurface ocean provides insight into TC genesis. The trend in TC genesis continues to be debated. Future projections must account for the net effect of the surface-subsurface dynamics on TCs, especially given the expected El Niño-like pattern over the tropical Pacific under global warming.

Photosynthesis converts light energy to chemical energy to fuel life on earth. Light energy is harvested by antenna pigments and transferred to reaction centers (RCs) to drive the electron transfer (ET) reactions. Here, we present cryo-electron microscopy (cryo-EM) structures of two forms of the RC from the microaerophilic Chloracidobacterium thermophilum (CabRC): one containing 10 subunits, including two different cytochromes; and the other possessing two additional subunits, PscB and PscZ. The larger form contained 2 Zn-bacteriochlorophylls, 16 bacteriochlorophylls, 10 chlorophylls, 2 lycopenes, 2 hemes, 3 Fe4S4 clusters, 12 lipids, 2 Ca2+ ions and 6 water molecules, revealing a type I RC with an ET chain involving two hemes and a hybrid antenna containing bacteriochlorophylls and chlorophylls. Our results provide a structural basis for understanding the excitation energy and ET within the CabRC and offer evolutionary insights into the origin and adaptation of photosynthetic RCs.

Update of bioRxiv. 2022 Jun 30;:

Due to the interest in the origin of life and the need to synthesize new functional materials, the study of the origin of chirality has been given significant attention. The mechanism of chirality transfer at molecular and supramolecular levels remains underexplored. Herein, we study the mechanism of chirality transfer of N, N'-bis (octadecyl)-L-/D-(anthracene-9-carboxamide)-glutamic diamide (L-/D-GAn) supramolecular chiral self-assembled at the air/water interface by chiral sum-frequency generation vibrational spectroscopy (chiral SFG) and molecular dynamics (MD) simulations. We observe long-range chirality transfer in the systems. The chirality of Cα-H is transferred first to amide groups and then transferred to the anthracene unit, through intermolecular hydrogen bonds and π-π stacking to produce an antiparallel β-sheet-like structure, and finally it is transferred to the end of hydrophobic alkyl chains at the interface. These results are relevant for understanding the chirality origin in supramolecular systems and the rational design of supramolecular chiral materials.

Author information: (1)Centro de Física de Materiales (CSIC-UPV/EHU), San Sebastián, E-20018, Spain. (2)Donostia International Physics Center (DIPC), San Sebastián, E-20018, Spain. (3)Ikerbasque, Basque Foundation for Science, Bilbao, E-48009, Spain. (4)Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO-CINQA), University of the Basque Country (UPV/EHU), San Sebastián, E-20018, Spain. (5)Department of Applied Chemistry, University of the Basque Country (UPV/EHU), San Sebastián, E-20018, Spain. (6)Centro de Física de Materiales (CSIC-UPV/EHU), San Sebastián, E-20018, Spain. celia.rogero@csic.es. (7)Donostia International Physics Center (DIPC), San Sebastián, E-20018, Spain. celia.rogero@csic.es.

The medial ganglionic eminence (MGE) produces both locally-projecting interneurons, which migrate long distances to structures such as the cortex as well as projection neurons that occupy subcortical nuclei. Little is known about what regulates the migratory behavior and axonal projections of these two broad classes of neurons. We find that St18 regulates the migration and morphology of MGE neurons in vitro. Further, genetic loss-of-function of St18 in mice reveals a reduction in projection neurons of the globus pallidus pars externa. St18 functions by influencing cell fate in MGE lineages as we observe a large expansion of nascent cortical interneurons at the expense of putative GPe neurons in St18 null embryos. Downstream of St18, we identified Cbx7, a component of Polycomb repressor complex 1, and find that it is essential for projection neuron-like migration but not morphology. Thus, we identify St18 as a key regulator of projection neuron vs. interneuron identity.

The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in endowing seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5' gene end distribution and facilitates chromatin opening at regulatory regions in seeds. During germination, H3.3 is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3' gene end, correlating with gene body DNA methylation and the restriction of chromatin accessibility and cryptic transcription at this region. Our results suggest a fundamental role of H3.3 in initiating chromatin accessibility at regulatory regions in seed and licensing the embryonic to post-embryonic transition.

A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation.

Atmospheric ammonia (NH3) and ammonium (NH4+) can substantially influence air quality, ecosystems, and climate. NH3 volatilization from fertilizers and wastes (v-NH3) has long been assumed to be the primary NH3 source, but the contribution of combustion-related NH3 (c-NH3, mainly fossil fuels and biomass burning) remains unconstrained. Here, we collated nitrogen isotopes of atmospheric NH3 and NH4+ and established a robust method to differentiate v-NH3 and c-NH3. We found that the relative contribution of the c-NH3 in the total NH3 emissions reached up to 40 ± 21% (6.6 ± 3.4 Tg N yr-1), 49 ± 16% (2.8 ± 0.9 Tg N yr-1), and 44 ± 19% (2.8 ± 1.3 Tg N yr-1) in East Asia, North America, and Europe, respectively, though its fractions and amounts in these regions generally decreased over the past decades. Given its importance, c-NH3 emission should be considered in making emission inventories, dispersion modeling, mitigation strategies, budgeting deposition fluxes, and evaluating the ecological effects of atmospheric NH3 loading.

Flapping wings produce lift and thrust in bio-inspired aerial robots, leading to quiet, safe and efficient flight. However, to extend their application scope, these robots must perch and land, a feat widely demonstrated by birds. Despite recent progress, flapping-wing vehicles, or ornithopters, are to this day unable to stop their flight. In this paper, we present a process to autonomously land an ornithopter on a branch. This method describes the joint operation of a pitch-yaw-altitude flapping flight controller, an optical close-range correction system and a bistable claw appendage design that can grasp a branch within 25 milliseconds and re-open. We validate this method with a 700 g robot and demonstrate the first autonomous perching flight of a flapping-wing robot on a branch, a result replicated with a second robot. This work paves the way towards the application of flapping-wing robots for long-range missions, bird observation, manipulation, and outdoor flight.

Abundant heterogeneous immune cells infiltrate lesions in chronic inflammatory diseases and characterization of these cells is needed to distinguish disease-promoting from bystander immune cells. Here, we investigate the landscape of non-communicable inflammatory skin diseases (ncISD) by spatial transcriptomics resulting in a large repository of 62,000 spatially defined human cutaneous transcriptomes from 31 patients. Despite the expected immune cell infiltration, we observe rather low numbers of pathogenic disease promoting cytokine transcripts (IFNG, IL13 and IL17A), i.e. >125 times less compared to the mean expression of all other genes over lesional skin sections. Nevertheless, cytokine expression is limited to lesional skin and presented in a disease-specific pattern. Leveraging a density-based spatial clustering method, we identify specific responder gene signatures in direct proximity of cytokines, and confirm that detected cytokine transcripts initiate amplification cascades of up to thousands of specific responder transcripts forming localized epidermal clusters. Thus, within the abundant and heterogeneous infiltrates of ncISD, only a low number of cytokine transcripts and their translated proteins promote disease by initiating an inflammatory amplification cascade in their local microenvironment.

Frequent heatwaves under global warming can increase the risk of preterm birth (PTB), which in turn will affect physical health and human potential over the life course. However, what remains unknown is the extent to which anthropogenic climate change has contributed to such burdens. We combine health impact and economic assessment methods to comprehensively evaluate the entire heatwave-related PTB burden in dimensions of health, human capital and economic costs. Here, we show that during 2010-2020, an average of 13,262 (95%CI 6,962-18,802) PTBs occurred annually due to heatwave exposure in China. In simulated scenarios, 25.8% (95%CI 17.1%-34.5%) of heatwave-related PTBs per year on average can be attributed to anthropogenic climate change, which further result in substantial human capital losses, estimated at over $1 billion costs. Our findings will provide additional impetus for introducing more stringent climate mitigation policies and also call for more sufficient adaptations to reduce heatwave detriments to newborn.

An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.

Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa, an untreatable form of blindness. Gene therapy is a promising treatment for PRPF31-retinitis pigmentosa, however, there are currently no suitable animal models in which to develop AAV-mediated gene augmentation. Here we establish Prpf31 mutant mouse models using AAV-mediated CRISPR/Cas9 knockout, and characterize the resulting retinal degeneration phenotype. Mouse models with early-onset morphological and functional impairments like those in patients were established, providing new platforms in which to investigate pathogenetic mechanisms and develop therapeutic methods. AAV-mediated PRPF31 gene augmentation restored the retinal structure and function in a rapidly degenerating mouse model, demonstrating the first in vivo proof-of-concept for AAV-mediated gene therapy to treat PRPF31-retinitis pigmentosa. AAV-CRISPR/Cas9-PRPF31 knockout constructs also mediated efficient PRPF31 knockout in human and non-human primate retinal explants, laying a foundation for establishing non-human primate models using the method developed here.

Classically the human life-course is characterized by youth, middle age and old age. A wide range of biological, health and cognitive functions vary across this life-course. Here, using reported sleep duration from 730,187 participants across 63 countries, we find three distinct phases in the adult human life-course: early adulthood (19-33yrs), mid-adulthood (34-53yrs), and late adulthood (54+yrs). They appear stable across culture, gender, education and other demographics. During the third phase, where self-reported sleep duration increases with age, cognitive performance, as measured by spatial navigation, was found to have an inverted u-shape relationship with reported sleep duration: optimal performance peaks at 7 hours reported sleep. World-wide self-reported sleep duration patterns are geographically clustered, and are associated with economy, culture, and latitude.

Nacre is generally regarded as tough body armor, but it was often smashed by predators with a certain striking speed. Nacre-like architectures have been demonstrated to dissipate abundant energy by tablets sliding at static or specific low-speed loads, but whether they're still impact-resistant templates in a wide range of impact velocities remains unclear. Here, we find an anomalous phenomenon that nacre-like structures show superior energy-dissipation ability only in a narrow range of low impact velocities, while they exhibit lower impact resistance than laminated structures when impact velocity exceeds a critical value. This is because the tablets sliding in nacre-like structure occurs earlier and wider at low impact velocities, while it becomes localized at excessive impact velocities. Such anomalous phenomenon remains under different structural sizes and boundary conditions. It further inspires us to propose a hybrid architecture design strategy that achieves optimal impact resistance in a wide range of impact velocities.

Hydrogen (H2) is expected to play a crucial role in reducing greenhouse gas emissions. However, hydrogen losses to the atmosphere impact atmospheric chemistry, including positive feedback on methane (CH4), the second most important greenhouse gas. Here we investigate through a minimalist model the response of atmospheric methane to fossil fuel displacement by hydrogen. We find that CH4 concentration may increase or decrease depending on the amount of hydrogen lost to the atmosphere and the methane emissions associated with hydrogen production. Green H2 can mitigate atmospheric methane if hydrogen losses throughout the value chain are below 9 ± 3%. Blue H2 can reduce methane emissions only if methane losses are below 1%. We address and discuss the main uncertainties in our results and the implications for the decarbonization of the energy sector.

Being the first intrinsic antiferromagnetic (AFM) topological insulator (TI), MnBi2Te4 is argued to be a topological axion state in its even-layer form due to the antiparallel magnetization between the top and bottom layers. Here we combine both transport and scanning microwave impedance microscopy (sMIM) to investigate such axion state in atomically thin MnBi2Te4 with even-layer thickness at zero magnetic field. While transport measurements show a zero Hall plateau signaturing the axion state, sMIM uncovers an unexpected edge state raising questions regarding the nature of the "axion state". Based on our model calculation, we propose that the edge state of even-layer MnBi2Te4 at zero field is derived from gapped helical edge states of the quantum spin Hall effect with time-reversal-symmetry breaking, when a crossover from a three-dimensional TI MnBi2Te4 to a two-dimensional TI occurs. Our finding thus signifies the richness of topological phases in MnB2Te4 that has yet to be fully explored.

A high-fat diet increases the risk of insulin resistance, type-2 diabetes, and non-alcoholic steato-hepatitis. Here we identified two heat-shock proteins, Heat-Shock-Protein70 and Glucose-Regulated Protein78, which are increased in the jejunum of rats on a high-fat diet. We demonstrated a causal link between these proteins and hepatic and whole-body insulin-resistance, as well as the metabolic response to bariatric/metabolic surgery. Long-term continuous infusion of Heat-Shock-Protein70 and Glucose-Regulated Protein78 caused insulin-resistance, hyperglycemia, and non-alcoholic steato-hepatitis in rats on a chow diet, while in rats on a high-fat diet continuous infusion of monoclonal antibodies reversed these phenotypes, mimicking metabolic surgery. Infusion of these proteins or their antibodies was also associated with shifts in fecal microbiota composition. Serum levels of Heat-Shock-Protein70 and Glucose-Regulated Protein78were elevated in patients with non-alcoholic steato-hepatitis, but decreased following metabolic surgery. Understanding the intestinal regulation of metabolism may provide options to reverse metabolic diseases.

Biomolecular condensates form via coupled associative and segregative phase transitions of multivalent associative macromolecules. Phase separation coupled to percolation is one example of such transitions. Here, we characterize molecular and mesoscale structural descriptions of condensates formed by intrinsically disordered prion-like low complexity domains (PLCDs). These systems conform to sticker-and-spacers architectures. Stickers are cohesive motifs that drive associative interactions through reversible crosslinking and spacers affect the cooperativity of crosslinking and overall macromolecular solubility. Our computations reproduce experimentally measured sequence-specific phase behaviors of PLCDs. Within simulated condensates, networks of reversible inter-sticker crosslinks organize PLCDs into small-world topologies. The overall dimensions of PLCDs vary with spatial location, being most expanded at and preferring to be oriented perpendicular to the interface. Our results demonstrate that even simple condensates with one type of macromolecule feature inhomogeneous spatial organizations of molecules and interfacial features that likely prime them for biochemical activity.

The epicardium, a mesothelial cell tissue that encompasses vertebrate hearts, supports heart regeneration after injury through paracrine effects and as a source of multipotent progenitors. However, the progenitor state in the adult epicardium has yet to be defined. Through single-cell RNA-sequencing of isolated epicardial cells from uninjured and regenerating adult zebrafish hearts, we define the epithelial and mesenchymal subsets of the epicardium. We further identify a transiently activated epicardial progenitor cell (aEPC) subpopulation marked by ptx3a and col12a1b expression. Upon cardiac injury, aEPCs emerge from the epithelial epicardium, migrate to enclose the wound, undergo epithelial-mesenchymal transition (EMT), and differentiate into mural cells and pdgfra+hapln1a+ mesenchymal epicardial cells. These EMT and differentiation processes are regulated by the Tgfβ pathway. Conditional ablation of aEPCs blocks heart regeneration through reduced nrg1 expression and mesenchymal cell number. Our findings identify a transient progenitor population of the adult epicardium that is indispensable for heart regeneration and highlight it as a potential target for enhancing cardiac repair.

Open-conduit basaltic volcanoes can be characterised by sudden large explosive events (paroxysms) that interrupt normal effusive and mild explosive activity. In June-August 2019, one major explosion and two paroxysms occurred at Stromboli volcano (Italy) within only 64 days. Here, via a multifaceted approach using clinopyroxene, we show arrival of mafic recharges up to a few days before the onset of these events and their effects on the eruption pattern at Stromboli, as a prime example of a persistently active, open-conduit basaltic volcano. Our data indicate a rejuvenated Stromboli plumbing system where the extant crystal mush is efficiently permeated by recharge magmas with minimum remobilisation promoting a direct linkage between the deeper and the shallow reservoirs that sustains the currently observed larger variability of eruptive behaviour. Our approach provides vital insights into magma dynamics and their effects on monitoring signals demonstrating the power of petrological studies in interpreting patterns of surficial activity.

Single-cell multimodal sequencing technologies are developed to simultaneously profile different modalities of data in the same cell. It provides a unique opportunity to jointly analyze multimodal data at the single-cell level for the identification of distinct cell types. A correct clustering result is essential for the downstream complex biological functional studies. However, combining different data sources for clustering analysis of single-cell multimodal data remains a statistical and computational challenge. Here, we develop a novel multimodal deep learning method, scMDC, for single-cell multi-omics data clustering analysis. scMDC is an end-to-end deep model that explicitly characterizes different data sources and jointly learns latent features of deep embedding for clustering analysis. Extensive simulation and real-data experiments reveal that scMDC outperforms existing single-cell single-modal and multimodal clustering methods on different single-cell multimodal datasets. The linear scalability of running time makes scMDC a promising method for analyzing large multimodal datasets.

When the atomic layers in a non-centrosymmetric van der Waals structure slide against each other, the interfacial charge transfer results in a reversal of the structure's spontaneous polarization. This phenomenon is known as sliding ferroelectricity and it is markedly different from conventional ferroelectric switching mechanisms relying on ion displacement. Here, we present layer dependence as a new dimension to control sliding ferroelectricity. By fabricating 3 R MoS2 of various thicknesses into dual-gate field-effect transistors, we obtain anomalous intermediate polarization states in multilayer (more than bilayer) 3 R MoS2. Using results from ab initio density functional theory calculations, we propose a generalized model to describe the ferroelectric switching process in multilayer 3 R MoS2 and to explain the formation of these intermediate polarization states. This work reveals the critical roles layer number and interlayer dipole coupling play in sliding ferroelectricity and presents a new strategy for the design of novel sliding ferroelectric devices.

Volatiles are vital ingredients for a habitable planet. Angrite meteorites sample the most volatile-depleted planetesimal in the Solar System, particularly for the alkali elements. They are prime targets for investigating the formation of volatile-poor rocky planets, yet their exceptionally low volatile content presents a major analytical challenge. Here, we leverage improved sensitivity and precision of K isotopic analysis to constrain the mechanism of extreme K depletion (>99.8%) in angrites. In contrast with the isotopically heavy Moon and Vesta, we find that angrites are strikingly depleted in the heavier K isotopes, which is best explained by partial recondensation of vaporized K following extensive evaporation on the angrite parent body (APB) during magma-ocean stage. Therefore, the APB may provide a rare example of isotope fractionation controlled by condensation, rather than evaporation, at a planetary scale. Furthermore, nebula-wide K isotopic variations primarily reflect volatility-driven fractionations instead of presolar nucleosynthetic heterogeneity proposed previously.

Programmed death receptor-1 (PD-1) blockade have achieved some efficacy but only in a fraction of patients with hepatocellular carcinoma (HCC). Programmed cell death 1 ligand 1 (PD-L1) binds to its receptor PD1 on T cells to dampen antigen-tumor immune responses. However, the mechanisms underlying PD-L1 regulation are not fully elucidated. Herein, we identify that tumoral Prdm1 overexpression inhibits cell growth in immune-deficient mouse models. Further, tumoral Prdm1 overexpression upregulates PD-L1 levels, dampening anti-tumor immunity in vivo, and neutralizes the anti-tumor efficacy of Prdm1 overexpression in immune-competent mouse models. Mechanistically, PRDM1 enhances USP22 transcription, thus reducing SPI1 protein degradation through deubiquitination, which enhances PD-L1 transcription. Functionally, PD-1 mAb treatment reinforces the efficacy of Prdm1-overexpressing HCC immune-competent mouse models. Collectively, we demonstrate that the PRDM1-USP22-SPI1 axis regulates PD-L1 levels, resulting in infiltrated CD8+ T cell exhaustion. Furthermore, PRDM1 overexpression combined with PD-(L)1 mAb treatment provides a therapeutic strategy for HCC treatment.

Quasi-periodic pulsations (QPPs) are frequently detected in solar and stellar flares, but the underlying physical mechanisms are still to be ascertained. Here, we show microwave QPPs during a solar flare originating from quasi-periodic magnetic reconnection at the flare current sheet. They appear as two vertically detached but closely related sources with the brighter ones located at flare loops and the weaker ones along the stretched current sheet. Although the brightness temperatures of the two microwave sources differ greatly, they vary in phase with periods of about 10-20 s and 30-60 s. The gyrosynchrotron-dominated microwave spectra also present a quasi-periodic soft-hard-soft evolution. These results suggest that relevant high-energy electrons are accelerated by quasi-periodic reconnection, likely arising from the modulation of magnetic islands within the current sheet as validated by a 2.5-dimensional magnetohydrodynamic simulation.

Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the availability of three-dimensional structures of phytochromes and other two-component proteins, the conformational changes, which lead to activation of the protein, are not understood. We reveal cryo electron microscopy structures of the complete phytochrome from Deinoccocus radiodurans in its resting and photoactivated states at 3.6 Å and 3.5 Å resolution, respectively. Upon photoactivation, the photosensory core module hardly changes its tertiary domain arrangement, but the connector helices between the photosensory and the histidine kinase modules open up like a zipper, causing asymmetry and disorder in the effector domains. The structures provide a framework for atom-scale understanding of signaling in phytochromes, visualize allosteric communication over several nanometers, and suggest that disorder in the dimeric arrangement of the effector domains is important for phosphatase activity in a two-component system. The results have implications for the development of optogenetic applications.

The brain is a major sanctuary site for metastatic cancer cells that evade systemic therapies. Through pre-clinical pharmacological, biological, and molecular studies, we characterize the functional link between drug resistance and central nervous system (CNS) relapse in Epidermal Growth Factor Receptor- (EGFR-) mutant non-small cell lung cancer, which can progress in the brain when treated with the CNS-penetrant EGFR inhibitor osimertinib. Despite widespread osimertinib distribution in vivo, the brain microvascular tumor microenvironment (TME) is associated with the persistence of malignant cell sub-populations, which are poised to proliferate in the brain as osimertinib-resistant lesions over time. Cellular and molecular features of this poised state are regulated through a Ras homolog family member A (RhoA) and Serum Responsive Factor (SRF) gene expression program. RhoA potentiates the outgrowth of disseminated tumor cells on osimertinib treatment, preferentially in response to extracellular laminin and in the brain. Thus, we identify pre-existing and adaptive features of metastatic and drug-resistant cancer cells, which are enhanced by RhoA/SRF signaling and the brain TME during the evolution of osimertinib-resistant disease.

Multifunctional hydrogel with asymmetric and reversible adhesion characteristics is essential to handle the obstructions towards bioapplications of trauma removal and postoperative tissue synechia. Herein, we developed a responsively reversible and asymmetrically adhesive Janus hydrogel that enables on-demand stimuli-triggered detachment for efficient myocardial infarction (MI) repair, and synchronously prevents tissue synechia and inflammatory intrusion after surgery. In contrast with most irreversibly and hard-to-removable adhesives, this Janus hydrogel exhibited a reversible adhesion capability and can be noninvasively detached on-demand just by slight biologics. It is interesting that the adhesion behaves exhibited a molecularly encoded adhesion-adaptive stiffening feature similar to the self-protective stress-strain effect of biological tissues. In vitro and in vivo experiments demonstrated that Janus hydrogel can promote the maturation and functions of cardiomyocytes, and facilitate MI repair by reducing oxidative damage and inflammatory response, reconstructing electrical conduction and blood supply in infarcted area. Furthermore, no secondary injury and tissue synechia were triggered after transplantation of Janus hydrogel. This smart Janus hydrogel reported herein offers a potential strategy for clinically transformable cardiac patch and anti-postoperative tissue synechia barrier.

CRISPR technology holds significant promise for biological studies and gene therapies because of its high flexibility and efficiency when applied in mammalian cells. But endonuclease (e.g., Cas9) potentially generates undesired edits; thus, there is an urgent need to comprehensively identify off-target sites so that the genotoxicities can be accurately assessed. To date, it is still challenging to streamline the entire process to specifically label and efficiently enrich the cleavage sites from unknown genomic locations. Here we develop PEAC-seq, in which we adopt the Prime Editor to insert a sequence-optimized tag to the editing sites and enrich the tagged regions with site-specific primers for high throughput sequencing. Moreover, we demonstrate that PEAC-seq could identify DNA translocations, which are more genotoxic but usually overlooked by other off-target detection methods. As PEAC-seq does not rely on exogenous oligodeoxynucleotides to label the editing site, we also conduct in vivo off-target identification as proof of concept. In summary, PEAC-seq provides a comprehensive and streamlined strategy to identify CRISPR off-targeting sites in vitro and in vivo, as well as DNA translocation events. This technique further diversified the toolkit to evaluate the genotoxicity of CRISPR applications in research and clinics.

Surface plasmons, which allow tight confinement of light, suffer from high intrinsic electronic losses. It has been shown that stimulated emission from excited electrons can transfer energy to plasmons and compensate for the high intrinsic losses. To-date, these realizations have relied on introducing an external gain media coupled to the surface plasmon. Here, we propose that plasmons in two-dimensional materials with closely located electron and hole Fermi pockets can be amplified, when an electrical current bias is applied along the displaced electron-hole pockets, without the need for an external gain media. As a prototypical example, we consider WTe2 from the family of 1T[Formula: see text]-MX2 materials, whose electronic structure can be described within a type-II tilted massive Dirac model. We find that the nonlocal plasmonic response experiences prominent gain for experimentally accessible currents on the order of mAμm-1. Furthermore, the group velocity of the plasmon found from the isofrequency curves imply that the amplified plasmons are highly collimated along a direction perpendicular to the Dirac node tilt when the electrical current is applied along it.

Climate and land-use changes are main drivers of insect declines, but their combined effects have not yet been quantified over large spatiotemporal scales. We analysed changes in the distribution (mean occupancy of squares) of 390 insect species (butterflies, grasshoppers, dragonflies), using 1.45 million records from across bioclimatic gradients of Switzerland between 1980 and 2020. We found no overall decline, but strong increases and decreases in the distributions of different species. For species that showed strongest increases (25% quantile), the average proportion of occupied squares increased in 40 years by 0.128 (95% credible interval: 0.123-0.132), which equals an average increase in mean occupancy of 71.3% (95% CI: 67.4-75.1%) relative to their 40-year mean occupancy. For species that showed strongest declines (25% quantile), the average proportion decreased by 0.0660 (95% CI: 0.0613-0.0709), equalling an average decrease in mean occupancy of 58.3% (95% CI: 52.2-64.4%). Decreases were strongest for narrow-ranged, specialised, and cold-adapted species. Short-term distribution changes were associated to both climate changes and regional land-use changes. Moreover, interactive effects between climate and regional land-use changes confirm that the various drivers of global change can have even greater impacts on biodiversity in combination than alone. In contrast, 40-year distribution changes were not clearly related to regional land-use changes, potentially reflecting mixed changes in local land use after 1980. Climate warming however was strongly linked to 40-year changes, indicating its key role in driving insect trends of temperate regions in recent decades.

The fine equilibrium of bone homeostasis is maintained by bone-forming osteoblasts and bone-resorbing osteoclasts. Here, we show that TAM receptors MERTK and TYRO3 exert reciprocal effects in osteoblast biology: Osteoblast-targeted deletion of MERTK promotes increased bone mass in healthy mice and mice with cancer-induced bone loss, whereas knockout of TYRO3 in osteoblasts shows the opposite phenotype. Functionally, the interaction of MERTK with its ligand PROS1 negatively regulates osteoblast differentiation via inducing the VAV2-RHOA-ROCK axis leading to increased cell contractility and motility while TYRO3 antagonizes this effect. Consequently, pharmacologic MERTK blockade by the small molecule inhibitor R992 increases osteoblast numbers and bone formation in mice. Furthermore, R992 counteracts cancer-induced bone loss, reduces bone metastasis and prolongs survival in preclinical models of multiple myeloma, breast- and lung cancer. In summary, MERTK and TYRO3 represent potent regulators of bone homeostasis with cell-type specific functions and MERTK blockade represents an osteoanabolic therapy with implications in cancer and beyond.

A highly promising route to scale millions of qubits is to use quantum photonic integrated circuits (PICs), where deterministic photon sources, reconfigurable optical elements, and single-photon detectors are monolithically integrated on the same silicon chip. The isolation of single-photon emitters, such as the G centers and W centers, in the optical telecommunication O-band, has recently been realized in silicon. In all previous cases, however, single-photon emitters were created uncontrollably in random locations, preventing their scalability. Here, we report the controllable fabrication of single G and W centers in silicon wafers using focused ion beams (FIB) with high probability. We also implement a scalable, broad-beam implantation protocol compatible with the complementary-metal-oxide-semiconductor (CMOS) technology to fabricate single telecom emitters at desired positions on the nanoscale. Our findings unlock a clear and easily exploitable pathway for industrial-scale photonic quantum processors with technology nodes below 100 nm.

As one of the most predominant interannual variabilities, the Indian Ocean Dipole (IOD) exerts great socio-economic impacts globally, especially on Asia, Africa, and Australia. While enormous efforts have been made since its discovery to improve both climate models and statistical methods for better prediction, current skills in IOD predictions are mostly limited up to three months ahead. Here, we challenge this long-standing problem using a multi-task deep learning model that we name MTL-NET. Hindcasts of the IOD events during the past four decades indicate that the MTL-NET can predict the IOD well up to 7-month ahead, outperforming most of world-class dynamical models used for comparison in this study. Moreover, the MTL-NET can help assess the importance of different predictors and correctly capture the nonlinear relationships between the IOD and predictors. Given its merits, the MTL-NET is demonstrated to be an efficient model for improved IOD prediction.

Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids and clonal expansion, yet the distribution and dynamics of ESC-R genes in different ecological compartments are poorly understood. Here we use whole genome sequence data of Enterobacterales isolates of human and animal origin from Europe and North America and identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant in North America in humans and farm animals, only later emerging in Europe. In contrast, specific extended-spectrum β-lactamases (ESBLs) were initially common in animals from Europe and later emerged in North America. This study identifies differences in the relative importance of plasmids and clonal expansion across different compartments for the spread of different ESC-R genes. Understanding the mechanisms of transmission will be critical in the design of interventions to reduce the spread of antimicrobial resistance.

Mechanical strain is a powerful tuning knob for excitons, Coulomb-bound electron-hole complexes dominating optical properties of two-dimensional semiconductors. While the strain response of bright free excitons is broadly understood, the behaviour of dark free excitons (long-lived excitations that generally do not couple to light due to spin and momentum conservation) or localized excitons related to defects remains mostly unexplored. Here, we study the strain behaviour of these fragile many-body states on pristine suspended WSe2 kept at cryogenic temperatures. We find that under the application of strain, dark and localized excitons in monolayer WSe2-a prototypical 2D semiconductor-are brought into energetic resonance, forming a new hybrid state that inherits the properties of the constituent species. The characteristics of the hybridized state, including an order-of-magnitude enhanced light/matter coupling, avoided-crossing energy shifts, and strain tunability of many-body interactions, are all supported by first-principles calculations. The hybridized excitons reported here may play a critical role in the operation of single quantum emitters based on WSe2. Furthermore, the techniques we developed may be used to fingerprint unidentified excitonic states.

Sex differences in the lifetime risk and expression of disease are well-known. Preclinical research targeted at improving treatment, increasing health span, and reducing the financial burden of health care, has mostly been conducted on male animals and cells. The extent to which sex differences in phenotypic traits are explained by sex differences in body weight remains unclear. We quantify sex differences in the allometric relationship between trait value and body weight for 363 phenotypic traits in male and female mice, recorded in >2 million measurements from the International Mouse Phenotyping Consortium. We find sex differences in allometric parameters (slope, intercept, residual SD) are common (73% traits). Body weight differences do not explain all sex differences in trait values but scaling by weight may be useful for some traits. Our results show sex differences in phenotypic traits are trait-specific, promoting case-specific approaches to drug dosage scaled by body weight in mice.

Brown adipose tissue plays a central role in the regulation of the energy balance by expending energy to produce heat. NAD+-dependent deacylase sirtuins have widely been recognized as positive regulators of brown adipose tissue thermogenesis. However, here we reveal that SIRT7, one of seven mammalian sirtuins, suppresses energy expenditure and thermogenesis by regulating brown adipose tissue functions. Whole-body and brown adipose tissue-specific Sirt7 knockout mice have higher body temperature and energy expenditure. SIRT7 deficiency increases the protein level of UCP1, a key regulator of brown adipose tissue thermogenesis. Mechanistically, we found that SIRT7 deacetylates insulin-like growth factor 2 mRNA-binding protein 2, an RNA-binding protein that inhibits the translation of Ucp1 mRNA, thereby enhancing its inhibitory action on Ucp1. Furthermore, SIRT7 attenuates the expression of batokine genes, such as fibroblast growth factor 21. In conclusion, we propose that SIRT7 serves as an energy-saving factor by suppressing brown adipose tissue functions.

Although ocular manifestations are reported in patients with COVID-19, consensus on ocular tropism of SARS-CoV-2 is lacking. Here, we infect K18-hACE2 transgenic mice with SARS-CoV-2 using various routes. We observe ocular manifestation and retinal inflammation with production of pro-inflammatory cytokines in the eyes of intranasally (IN)-infected mice. Intratracheal (IT) infection results in dissemination of the virus from the lungs to the brain and eyes via trigeminal and optic nerves. Ocular and neuronal invasions are confirmed using intracerebral (IC) infection. Notably, the eye-dropped (ED) virus does not cause lung infection and becomes undetectable with time. Ocular and neurotropic distribution of the virus in vivo is evident in fluorescence imaging with an infectious clone of SARS-CoV-2-mCherry. The ocular tropic and neuroinvasive characteristics of SARS-CoV-2 are confirmed in wild-type Syrian hamsters. Our data can improve the understanding regarding viral transmission and clinical characteristics of SARS-CoV-2 and help in improving COVID-19 control procedures.

Ultrahigh-resolution patterning with high-throughput and high-fidelity is highly in demand for expanding the potential of organic light-emitting diodes (OLEDs) from mobile and TV displays into near-to-eye microdisplays. However, current patterning techniques so far suffer from low resolution, consecutive pattern for RGB pixelation, low pattern fidelity, and throughput issue. Here, we present a silicone engineered anisotropic lithography of the organic light-emitting semiconductor (OLES) that in-situ forms a non-volatile etch-blocking layer during reactive ion etching. This unique feature not only slows the etch rate but also enhances the anisotropy of etch direction, leading to gain delicate control in forming ultrahigh-density multicolor OLES patterns (up to 4500 pixels per inch) through photolithography. This patterning strategy inspired by silicon etching chemistry is expected to provide new insights into ultrahigh-density OLED microdisplays.

Presynaptic homeostatic plasticity (PHP) adaptively enhances neurotransmitter release following diminished postsynaptic glutamate receptor (GluR) functionality to maintain synaptic strength. While much is known about PHP expression mechanisms, postsynaptic induction remains enigmatic. For over 20 years, diminished postsynaptic Ca2+ influx was hypothesized to reduce CaMKII activity and enable retrograde PHP signaling at the Drosophila neuromuscular junction. Here, we have interrogated inductive signaling and find that active CaMKII colocalizes with and requires the GluRIIA receptor subunit. Next, we generated Ca2+-impermeable GluRs to reveal that both CaMKII activity and PHP induction are Ca2+-insensitive. Rather, a GluRIIA C-tail domain is necessary and sufficient to recruit active CaMKII. Finally, chimeric receptors demonstrate that the GluRIIA tail constitutively occludes retrograde homeostatic signaling by stabilizing active CaMKII. Thus, the physical loss of the GluRIIA tail is sensed, rather than reduced Ca2+, to enable retrograde PHP signaling, highlighting a unique, Ca2+-independent control mechanism for CaMKII in gating homeostatic plasticity.

Evaporative loss of interception (Ei) is the first process occurring during rainfall, yet its role in large-scale surface water balance has been largely underexplored. Here we show that Ei can be inferred from flux tower evapotranspiration measurements using physics-informed hybrid machine learning models built under wet versus dry conditions. Forced by satellite and reanalysis data, this framework provides an observationally constrained estimate of Ei, which is on average 84.1 ± 1.8 mm per year and accounts for 8.6 ± 0.2% of total rainfall globally during 2000-2020. Rainfall frequency regulates long-term average Ei changes, and rainfall intensity, rather than vegetation attributes, determines the fraction of Ei in gross precipitation (Ei/P). Rain events have become less frequent and more intense since 2000, driving a global decline in Ei (and Ei/P) by 4.9% (6.7%). This suggests that ongoing rainfall changes favor a partitioning towards more soil moisture and runoff, benefiting ecosystem functions but simultaneously increasing flood risks.

Garnet-type Li7La3Zr2O12 (LLZO) solid electrolytes (SE) demonstrates appealing ionic conductivity properties for all-solid-state lithium metal battery applications. However, LLZO (electro)chemical stability in contact with the lithium metal electrode is not satisfactory for developing practical batteries. To circumvent this issue, we report the preparation of various doped cubic-phase LLZO SEs without vacancy formation (i.e., Li = 7.0 such as Li7La3Zr0.5Hf0.5Sc0.5Nb0.5O12 and Li7La3Zr0.4Hf0.4Sn0.4Sc0.4Ta0.4O12). The entropy-driven synthetic approach allows access to hidden chemical space in cubic-phase garnet and enables lower solid-state synthesis temperature as the cubic-phase nucleation decreases from 750 to 400 °C. We demonstrate that the SEs with Li = 7.0 show better reduction stability against lithium metal compared to SE with low lithium contents and identical atomic species (i.e., Li = 6.6 such as Li6.6La3Zr0.4Hf0.4Sn0.4Sc0.2Ta0.6O12). Moreover, when a Li7La3Zr0.4Hf0.4Sn0.4Sc0.4Ta0.4O12 pellet is tested at 60 °C in coin cell configuration with a Li metal negative electrode, a LiNi1/3Co1/3Mn1/3O2-based positive electrode and an ionic liquid-based electrolyte at the cathode|SE interface, discharge capacity retention of about 92% is delivered after 700 cycles at 0.8 mA/cm2 and 60 °C.

To assess mortality risks and burdens associated with short-term exposure to wildfire-related fine particulate matter with diameter ≤ 2.5 μm (PM2.5), we collect daily mortality data from 2000 to 2016 for 510 immediate regions in Brazil, the most wildfire-prone area. We integrate data from multiple sources with a chemical transport model at the global scale to isolate daily concentrations of wildfire-related PM2.5 at a 0.25 × 0.25 resolution. With a two-stage time-series approach, we estimate (i) an increase of 3.1% (95% confidence interval [CI]: 2.4, 3.9%) in all-cause mortality, 2.6% (95%CI: 1.5, 3.8%) in cardiovascular mortality, and 7.7% (95%CI: 5.9, 9.5) in respiratory mortality over 0-14 days with each 10 μg/m3 increase in daily wildfire-related PM2.5; (ii) 0.65% of all-cause, 0.56% of cardiovascular, and 1.60% of respiratory mortality attributable to acute exposure to wildfire-related PM2.5, corresponding to 121,351 all-cause deaths, 29,510 cardiovascular deaths, and 31,287 respiratory deaths during the study period. In this study, we find stronger associations in females and adults aged ≥ 60 years, and geographic difference in the mortality risks and burdens.

During the last decade lead halide perovskites have shown great potential for photovoltaic applications. However, the stability of perovskite solar cells still restricts commercialization, and lack of properly implemented unified stability testing and disseminating standards makes it difficult to compare historical stability data for evaluating promising routes towards better device stability. Here, we propose a single indicator to describe device stability that normalizes the stability results with respect to different environmental stress conditions which enables a direct comparison of different stability results. Based on this indicator and an open dataset of heterogeneous stability data of over 7000 devices, we have conducted a statistical analysis to assess the effect of different stability improvement strategies. This provides important insights for achieving more stable perovskite solar cells and we also provide suggestions for future directions in the perovskite solar cell field based on big data utilization.

The conversion of inexpensive aqueous ammonia (NH3·H2O) into value-added primary amines by N-H insertion persists as a longstanding challenge in chemistry because of the tendency of Lewis basic ammonia (NH3) to bind and inhibit metal catalysts. Herein, we report a chemoselective carbene N-H insertion of NH3·H2O using a TpBr3Ag-catalyzed two-phase system. Coordination by a homoscorpionate TpBr3 ligand renders silver compatible with NH3 and H2O and enables the generation of electrophilic silver carbene. Water promotes subsequent [1,2]-proton shift to generate N-H insertion products with high chemoselectivity. The result of the reaction is the coupling of an inorganic nitrogen source with either diazo compounds or N-triftosylhydrazones to produce useful primary amines. Further investigations elucidate the reaction mechanism and the origin of chemoselectivity.

Eps15-homology domain containing proteins (EHDs) are eukaryotic, dynamin-related ATPases involved in cellular membrane trafficking. They oligomerize on membranes into filaments that induce membrane tubulation. While EHD crystal structures in open and closed conformations were previously reported, little structural information is available for the membrane-bound oligomeric form. Consequently, mechanistic insights into the membrane remodeling mechanism have remained sparse. Here, by using cryo-electron tomography and subtomogram averaging, we determined structures of nucleotide-bound EHD4 filaments on membrane tubes of various diameters at an average resolution of 7.6 Å. Assembly of EHD4 is mediated via interfaces in the G-domain and the helical domain. The oligomerized EHD4 structure resembles the closed conformation, where the tips of the helical domains protrude into the membrane. The variation in filament geometry and tube radius suggests a spontaneous filament curvature of approximately 1/70 nm-1. Combining the available structural and functional data, we suggest a model for EHD-mediated membrane remodeling.

After myocardial infarction the innate immune response is pivotal in clearing of tissue debris as well as scar formation, but exaggerated cytokine and chemokine secretion with subsequent leukocyte infiltration also leads to further tissue damage. Here, we address the value of targeting a previously unknown a disintegrin and metalloprotease 10 (ADAM10)/CX3CL1 axis in the regulation of neutrophil recruitment early after MI. We show that myocardial ADAM10 is distinctly upregulated in myocardial biopsies from patients with ischemia-driven cardiomyopathy. Intriguingly, upon MI in mice, pharmacological ADAM10 inhibition as well as genetic cardiomycyte-specific ADAM10 deletion improves survival with markedly enhanced heart function and reduced scar size. Mechanistically, abolished ADAM10-mediated CX3CL1 ectodomain shedding leads to diminished IL-1β-dependent inflammation, reduced neutrophil bone marrow egress as well as myocardial tissue infiltration. Thus, our data shows a conceptual insight into how acute MI induces chemotactic signaling via ectodomain shedding in cardiomyocytes.

Natural superlattice structures MnBi2Te4(Bi2Te3)n (n = 1, 2, ...), in which magnetic MnBi2Te4 layers are separated by nonmagnetic Bi2Te3 layers, hold band topology, magnetism and reduced interlayer coupling, providing a promising platform for the realization of exotic topological quantum states. However, their magnetism in the two-dimensional limit, which is crucial for further exploration of quantum phenomena, remains elusive. Here, complex ferromagnetic-antiferromagnetic coexisting ground states that persist down to the 2-septuple layers limit are observed and comprehensively investigated in MnBi4Te7 (n = 1) and MnBi6Te10 (n = 2). The ubiquitous Mn-Bi site mixing modifies or even changes the sign of the subtle interlayer magnetic interactions, yielding a spatially inhomogeneous interlayer coupling. Further, a tunable exchange bias effect, arising from the coupling between the ferromagnetic and antiferromagnetic components in the ground state, is observed in MnBi2Te4(Bi2Te3)n (n = 1, 2), which provides design principles and material platforms for future spintronic devices. Our work highlights a new approach toward the fine-tuning of magnetism and paves the way for further study of quantum phenomena in MnBi2Te4(Bi2Te3)n (n = 1, 2) as well as their magnetic applications.

Although mitochondrial activity is critical for angiogenesis, its mechanism is not entirely clear. Here we show that mice with endothelial deficiency of any one of the three nuclear genes encoding for mitochondrial proteins, transcriptional factor (TFAM), respiratory complex IV component (COX10), or redox protein thioredoxin 2 (TRX2), exhibit retarded retinal vessel growth and arteriovenous malformations (AVM). Single-cell RNA-seq analyses indicate that retinal ECs from the three mutant mice have increased TGFβ signaling and altered gene expressions associated with vascular maturation and extracellular matrix, correlating with vascular malformation and increased basement membrane thickening in microvesels of mutant retinas. Mechanistic studies suggest that mitochondrial dysfunction from Tfam, Cox10, or Trx2 depletion induces a mitochondrial localization and MAPKs-mediated phosphorylation of SMAD2, leading to enhanced ALK5-SMAD2 signaling. Importantly, pharmacological blockade of ALK5 signaling or genetic deficiency of SMAD2 prevented retinal vessel growth retardation and AVM in all three mutant mice. Our studies uncover a novel mechanism whereby mitochondrial dysfunction via the ALK5-SMAD2 signaling induces retinal vascular malformations, and have therapeutic values for the alleviation of angiogenesis-associated human retinal diseases.

BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.

Key to the success of legumes is the ability to form and maintain optimal symbiotic nodules that enable them to balance the trade-off between symbiosis and plant growth. Cytokinin is essential for homeostatic regulation of nodulation, but the mechanism remains incompletely understood. Here, we show that a B-type response regulator GmRR11d mediates systemic inhibition of nodulation. GmRR11d is induced by rhizobia and low level cytokinin, and GmRR11d can suppress the transcriptional activity of GmNSP1 on GmNIN1a to inhibit soybean nodulation. GmRR11d positively regulates cytokinin response and its binding on the GmNIN1a promoter is enhanced by cytokinin. Intriguingly, rhizobial induction of GmRR11d and its function are dependent upon GmNARK that is a CLV1-like receptor kinase and inhibits nodule number in shoots. Thus, GmRR11d governs a transcriptional program associated with nodulation attenuation and cytokinin response activation essential for systemic regulation of nodulation.

Monosynaptic viral tracers are essential tools for dissecting neuronal connectomes and for targeted delivery of molecular sensors and effectors. Viral toxicity and complex multi-injection protocols are major limiting application barriers. To overcome these barriers, we developed an anterograde monosynaptic H129Amp tracer system based on HSV-1 strain H129. The H129Amp tracer system consists of two components: an H129-dTK-T2-pacFlox helper which assists H129Amp tracer's propagation and transneuronal monosynaptic transmission. The shared viral features of tracer/helper allow for simultaneous single-injection and subsequent high expression efficiency from multiple-copy of expression cassettes in H129Amp tracer. These improvements of H129Amp tracer system shorten experiment duration from 28-day to 5-day for fast-bright monosynaptic tracing. The lack of toxic viral genes in the H129Amp tracer minimizes toxicity in postsynaptic neurons, thus offering the potential for functional anterograde mapping and long-term tracer delivery of genetic payloads. The H129Amp tracer system is a powerful tracing tool for revealing neuronal connectomes.

Knowledge of the transcriptional programs underpinning the functions of human kidney cell populations at homeostasis is limited. We present a single-cell perspective of healthy human kidney from 19 living donors, with equal contribution from males and females, profiling the transcriptome of 27677 cells to map human kidney at high resolution. Sex-based differences in gene expression within proximal tubular cells were observed, specifically, increased anti-oxidant metallothionein genes in females and aerobic metabolism-related genes in males. Functional differences in metabolism were confirmed in proximal tubular cells, with male cells exhibiting higher oxidative phosphorylation and higher levels of energy precursor metabolites. We identified kidney-specific lymphocyte populations with unique transcriptional profiles indicative of kidney-adapted functions. Significant heterogeneity in myeloid cells was observed, with a MRC1+LYVE1+FOLR2+C1QC+ population representing a predominant population in healthy kidney. This study provides a detailed cellular map of healthy human kidney, and explores the complexity of parenchymal and kidney-resident immune cells.

Distinct families of eukaryotic deubiquitinases (DUBs) are regulators of ubiquitin signaling. Here, we report on the presence of an additional DUB class broadly distributed in eukaryotes and several bacteria. The only described members of this family are the large tegument proteins of herpesviruses, which are attached to the outside of the viral capsid. By using a bioinformatics screen, we have identified distant homologs of this VTD (Viral tegument-like DUB) family in vertebrate transposons, fungi, insects, nematodes, cnidaria, protists and bacteria. While some VTD activities resemble viral tegument DUBs in that they favor K48-linked ubiquitin chains, other members are highly specific for K6- or K63-linked ubiquitin chains. The crystal structures of K48- and K6-specific members reveal considerable differences in ubiquitin recognition. The VTD family likely evolved from non-DUB proteases and spread through transposons, many of which became 'domesticated', giving rise to the Drosophila male sterile (3)76Ca gene and several nematode genes with male-specific expression.

Unconventional nonequilibrium phases with restricted correlation spreading and slow entanglement growth have been proposed to emerge in systems with confined excitations, calling their thermalization dynamics into question. Here, we show that in confined systems the thermalization dynamics after a quantum quench instead exhibits multiple stages with well separated time scales. As an example, we consider the confined Ising spin chain, in which domain walls in the ordered phase form bound states reminiscent of mesons. The system first relaxes towards a prethermal state, described by a Gibbs ensemble with conserved meson number. The prethermal state arises from rare events in which mesons are created in close vicinity, leading to an avalanche of scattering events. Only at much later times a true thermal equilibrium is achieved in which the meson number conservation is violated by a mechanism akin to the Schwinger effect. The discussed prethermalization dynamics is directly relevant to generic one-dimensional, many-body systems with confined excitations.

The p53 transcription factor is a master regulator of cellular stress responses inhibited by repressors such as MDM2 and the phosphatase PPM1D. Activation of p53 with pharmacological inhibitors of its repressors is being tested in clinical trials for cancer therapy, but efficacy has been limited by poor induction of tumor cell death. We demonstrate that dual inhibition of MDM2 and PPM1D induces apoptosis in multiple cancer cell types via amplification of the p53 transcriptional program through the eIF2α-ATF4 pathway. PPM1D inhibition induces phosphorylation of eIF2α, ATF4 accumulation, and ATF4-dependent enhancement of p53-dependent transactivation upon MDM2 inhibition. Dual inhibition of p53 repressors depletes heme and induces HRI-dependent eIF2α phosphorylation. Pharmacological induction of eIF2α phosphorylation synergizes with MDM2 inhibition to induce cell death and halt tumor growth in mice. These results demonstrate that PPM1D inhibits both the p53 network and the integrated stress response controlled by eIF2α-ATF4, with clear therapeutic implications.

Fluorescence laser-scanning microscopy (LSM) is experiencing a revolution thanks to new single-photon (SP) array detectors, which give access to an entirely new set of single-photon information. Together with the blooming of new SP LSM techniques and the development of tailored SP array detectors, there is a growing need for (i) DAQ systems capable of handling the high-throughput and high-resolution photon information generated by these detectors, and (ii) incorporating these DAQ protocols in existing fluorescence LSMs. We developed an open-source, low-cost, multi-channel time-tagging module (TTM) based on a field-programmable gate array that can tag in parallel multiple single-photon events, with 30 ps precision, and multiple synchronisation events, with 4 ns precision. We use the TTM to demonstrate live-cell super-resolved fluorescence lifetime image scanning microscopy and fluorescence lifetime fluctuation spectroscopy. We expect that our BrightEyes-TTM will support the microscopy community in spreading SP-LSM in many life science laboratories.

Alpine plants have evolved a tight seasonal cycle of growth and senescence to cope with a short growing season. The potential growing season length (GSL) is increasing because of climate warming, possibly prolonging plant growth above- and belowground. We tested whether growth dynamics in typical alpine grassland are altered when the natural GSL (2-3 months) is experimentally advanced and thus, prolonged by 2-4 months. Additional summer months did not extend the growing period, as canopy browning started 34-41 days after the start of the season, even when GSL was more than doubled. Less than 10% of roots were produced during the added months, suggesting that root growth was as conservative as leaf growth. Few species showed a weak second greening under prolonged GSL, but not the dominant sedge. A longer growing season under future climate may therefore not extend growth in this widespread alpine community, but will foster species that follow a less strict phenology.

The quantum limit (QL) of an electron liquid, realised at strong magnetic fields, has long been proposed to host a wealth of strongly correlated states of matter. Electronic states in the QL are, for example, quasi-one dimensional (1D), which implies perfectly nested Fermi surfaces prone to instabilities. Whereas the QL typically requires unreachably strong magnetic fields, the topological semimetal ZrTe5 has been shown to reach the QL at fields of only a few Tesla. Here, we characterize the QL of ZrTe5 at fields up to 64 T by a combination of electrical-transport and ultrasound measurements. We find that the Zeeman effect in ZrTe5 enables an efficient tuning of the 1D Landau band structure with magnetic field. This results in a Lifshitz transition to a 1D Weyl regime in which perfect charge neutrality can be achieved. Since no instability-driven phase transitions destabilise the 1D electron liquid for the investigated field strengths and temperatures, our analysis establishes ZrTe5 as a thoroughly understood platform for potentially inducing more exotic interaction-driven phases at lower temperatures.

Information related to the diverse and dynamic metabolite composition of the small intestine is crucial for the diagnosis and treatment of various diseases. However, our current understanding of the physiochemical dynamics of metabolic processes within the small intestine is limited due to the lack of in situ access to the intestinal environment. Here, we report a demonstration of a battery-free ingestible biosensing system for monitoring metabolites in the small intestine. As a proof of concept, we monitor the intestinal glucose dynamics on a porcine model. Battery-free operation is achieved through a self-powered glucose biofuel cell/biosensor integrated into a circuit that performs energy harvesting, biosensing, and wireless telemetry via a power-to-frequency conversion scheme using magnetic human body communication. Such long-term biochemical analysis could potentially provide critical information regarding the complex and dynamic small intestine metabolic profiles.

Many elusive quantum phenomena emerge from a quantum system interacting with its classical environment. Quantum simulators enable us to program this interaction by using measurement operations. Measurements generally remove part of the entanglement built between the qubits in a simulator. While in simple cases entanglement may disappear at a constant rate as we measure qubits one by one, the evolution of entanglement under measurements for a given class of quantum states is generally unknown. We show that consecutive measurements of qubits in a simulator can lead to criticality, separating two phases of entanglement. Using up to 48 qubits, we prepare an entangled superposition of ground states to a classical spin model. Progressively measuring the qubits drives the simulator through an observable vitrification point and into a spin glass phase of entanglement. Our findings suggest coupling to a classical environment may drive critical phenomena in more general quantum states.

Liquid crystal (LC) phases are in between solids and liquids with properties of both. Nematic LCs composed of rod-like molecules or particles exhibit long-range orientational order, yielding characteristic birefringence, but they lack positional order, allowing them to flow like a liquid. This combination of properties as well as their sensitivity to external fields make nematic LCs fundamental for optical applications e.g. liquid crystal displays (LCDs). When rod-like particles become bent, spontaneous bend deformations arise in the LC, leading to geometric frustration which can be resolved by complementary twist or splay deformations forming intriguing twist-bend (NTB) and splay-bend (NSB) nematic phases. Here, we show experimentally that the elusive NSB phases can be stabilized in systems of polydisperse micron-sized bent silica rods. Our results open avenues for the realization of NTB and NSB phases of colloidal and molecular LCs.

Comprehensive integration of structural and functional connectivity data is required to model brain functions accurately. While resources for studying the structural connectivity of non-human primate brains already exist, their integration with functional connectivity data has remained unavailable. Here we present a comprehensive resource that integrates the most extensive awake marmoset resting-state fMRI data available to date (39 marmoset monkeys, 710 runs, 12117 mins) with previously published cellular-level neuronal tracing data (52 marmoset monkeys, 143 injections) and multi-resolution diffusion MRI datasets. The combination of these data allowed us to (1) map the fine-detailed functional brain networks and cortical parcellations, (2) develop a deep-learning-based parcellation generator that preserves the topographical organization of functional connectivity and reflects individual variabilities, and (3) investigate the structural basis underlying functional connectivity by computational modeling. This resource will enable modeling structure-function relationships and facilitate future comparative and translational studies of primate brains.

Author information: (1)Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark. pmun@food.dtu.dk. (2)Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark. (3)Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK. (4)Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden. (5)Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands.

Single-cell data integration can provide a comprehensive molecular view of cells. However, how to integrate heterogeneous single-cell multi-omics as well as spatially resolved transcriptomic data remains a major challenge. Here we introduce uniPort, a unified single-cell data integration framework that combines a coupled variational autoencoder (coupled-VAE) and minibatch unbalanced optimal transport (Minibatch-UOT). It leverages both highly variable common and dataset-specific genes for integration to handle the heterogeneity across datasets, and it is scalable to large-scale datasets. uniPort jointly embeds heterogeneous single-cell multi-omics datasets into a shared latent space. It can further construct a reference atlas for gene imputation across datasets. Meanwhile, uniPort provides a flexible label transfer framework to deconvolute heterogeneous spatial transcriptomic data using an optimal transport plan, instead of embedding latent space. We demonstrate the capability of uniPort by applying it to integrate a variety of datasets, including single-cell transcriptomics, chromatin accessibility, and spatially resolved transcriptomic data.

Childhood allergic diseases, including asthma, rhinitis and eczema, are prevalent conditions that share strong genetic and environmental components. Diagnosis relies on clinical history and measurements of allergen-specific IgE. We hypothesize that a multi-omics model could accurately diagnose childhood allergic disease. We show that nasal DNA methylation has the strongest predictive power to diagnose childhood allergy, surpassing blood DNA methylation, genetic risk scores, and environmental factors. DNA methylation at only three nasal CpG sites classifies allergic disease in Dutch children aged 16 years well, with an area under the curve (AUC) of 0.86. This is replicated in Puerto Rican children aged 9-20 years (AUC 0.82). DNA methylation at these CpGs additionally detects allergic multimorbidity and symptomatic IgE sensitization. Using nasal single-cell RNA-sequencing data, these three CpGs associate with influx of T cells and macrophages that contribute to allergic inflammation. Our study suggests the potential of methylation-based allergy diagnosis.

Association genetic studies and genome-scale CRISPR screens have recently identified ARF3 and TMEM251/LYSET/GCAF as Golgi-resident factors essential to brain and skeletal development. Here we discuss how even though the consequences of mutations in these genes affect endosomal and lysosomal compartments, the problem originates in the Golgi complex and may involve either the identity of the carrier vesicles or that of cargo molecules.

Despite dominating industrial processes, heterogeneous catalysts remain challenging to characterize and control. This is largely attributable to the diversity of potentially active sites at the catalyst-reactant interface and the complex behaviour that can arise from interactions between active sites. Surface-supported, single-site molecular catalysts aim to bring together benefits of both heterogeneous and homogeneous catalysts, offering easy separability while exploiting molecular design of reactivity, though the presence of a surface is likely to influence reaction mechanisms. Here, we use metal-organic coordination to build reactive Fe-terpyridine sites on the Ag(111) surface and study their activity towards CO and C2H4 gaseous reactants using low-temperature ultrahigh-vacuum scanning tunnelling microscopy, scanning tunnelling spectroscopy, and atomic force microscopy supported by density-functional theory models. Using a site-by-site approach at low temperature to visualize the reaction pathway, we find that reactants bond to the Fe-tpy active sites via surface-bound intermediates, and investigate the role of the substrate in understanding and designing single-site catalysts on metallic supports.

The synthesis of ammonia from atmospheric dinitrogen, nitrogen fixation, is one of the essential reactions for human beings. Because the current industrial nitrogen fixation depends on dihydrogen produced from fossil fuels as raw material, the development of a nitrogen fixation reaction that relies on the energy provided by renewable energy, such as visible light, is an important research goal from the viewpoint of sustainable chemistry. Herein, we establish an iridium- and molybdenum-catalysed process for synthesizing ammonia from dinitrogen under ambient reaction conditions and visible light irradiation. In this reaction system, iridium complexes and molybdenum triiodide complexes bearing N-heterocyclic carbene-based pincer ligands act as cooperative catalysts to activate 9,10-dihydroacridine and dinitrogen, respectively. The reaction of dinitrogen with 9,10-dihydroacridine is not thermodynamically favoured, and it only takes place under visible light irradiation. Therefore, the described reaction system is one that affords visible light energy-driven ammonia formation from dinitrogen catalytically.

T cell development requires the coordinated rearrangement of T cell receptor (TCR) gene segments and the expression of either αβ or γδ TCR. However, whether and how de novo synthesis of nutrients contributes to thymocyte commitment to either lineage remains unclear. Here, we find that T cell-specific deficiency in glutamine:fructose-6-phosphate aminotransferase 1 (GFAT1), the rate-limiting enzyme of the de novo hexosamine biosynthesis pathway (dn-HBP), attenuates hexosamine levels, blunts N-glycosylation of TCRβ chains, reduces surface expression of key developmental receptors, thus impairing αβ-T cell ontogeny. GFAT1 deficiency triggers defects in N-glycans, increases the unfolded protein response, and elevates  γδ-T cell numbers despite reducing γδ-TCR diversity. Enhancing TCR expression or PI3K/Akt signaling does not reverse developmental defects. Instead, dietary supplementation with the salvage metabolite, glucosamine, and an α-ketoglutarate analogue partially restores αβ-T cell development in GFAT1T-/- mice, while fully rescuing it in ex vivo fetal thymic organ cultures. Thus, dn-HBP fulfils, while salvage nutrients partially satisfy, the elevated demand for hexosamines during early T cell development.