Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca2+ concentrations and are important targets for insecticides and antiparasitic drugs. However, it is unknown how these compounds modulate ion translocation and whether there are insect-specific binding pockets. Here, we report structures of Drosophila Slo in the Ca2+-bound and Ca2+-free form and in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside. Whereas the architecture and gating mechanism of Slo channels are conserved, potential insect-specific binding pockets exist. Verruculogen inhibits K+ transport by blocking the Ca2+-induced activation signal and precludes K+ from entering the selectivity filter. Emodepside decreases the conductance by suboptimal K+ coordination and uncouples ion gating from Ca2+ and voltage sensing. Our results expand the mechanistic understanding of Slo regulation and lay the foundation for the rational design of regulators of Slo and other voltage-gated ion channels.

The CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon HDAC inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified RNF219 as an acetylation-regulated cofactor. We demonstrate that RNF219 is an active RING-type E3 ligase which stably associates with CCR4-NOT via NOT9 through a short linear motif (SLiM) embedded within the C-terminal low-complexity region of RNF219. By using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 inhibits deadenylation through the direct interaction of the α-helical SLiM with the NOT9 module. Transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, with differential requirement of its RING domain. Our results establish RNF219 as an inhibitor of CCR4-NOT-mediated deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.

Author information: (1)Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany. pascal.schlosser@uniklinik-freiburg.de. (2)Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. pascal.schlosser@uniklinik-freiburg.de. (3)Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. (4)Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA. (5)Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany. (6)Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764, Neuherberg, Bavaria, Germany. (7)TUM School of Medicine, Technical University of Munich, Munich, Germany. (8)Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. (9)Framingham Heart Study, Framingham, Massachusetts, USA. (10)Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, US. (11)Department of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA. (12)Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany. (13)Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA. (14)Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA. (15)Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. (16)Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany. (17)MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK. (18)Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK. (19)Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. (20)Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands. (21)Department of Neurobiology, Care Sciences and Society (NVS), Family Medicine and Primary Care Unit, Karolinska Institutet, Huddinge, Sweden. (22)School of Health and Social Studies, Dalarna University, Falun, Sweden. (23)Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany. (24)Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany. (25)Laboratory of Environmental Precision Health, Mailman School of Public Health, Columbia University, New York, NY, USA. (26)Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland. (27)German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany. (28)Network Aging Research, Heidelberg University, Heidelberg, Germany. (29)Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany. (30)German Cancer Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany. (31)Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany. (32)Population Health Laboratory, University of Fribourg, Fribourg, Switzerland. (33)Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands. (34)Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands. (35)Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore. (36)Department of Epidemiology and Biostatistics, Imperial College London, London, UK. (37)Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UK. (38)Imperial College Healthcare NHS Trust, London, UK. (39)Texas Biomedical Research Institute, San Antonio, USA. (40)Lothian Birth Cohorts Group, Department of Psychology, The University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK. (41)Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, the Netherlands. (42)Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. (43)Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain. (44)Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA. (45)Department of Statistics and Operations Research, University of Valencia, Valencia, Spain. (46)Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Erlangen, Germany. (47)Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany. (48)Institute of Human Genetics, Friedrich-Alexander-UniversitätErlangen-Nürnberg, 91054, Erlangen, Germany. (49)Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany. (50)DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany. (51)Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK. (52)Department of Medicine, University of Washington, Seattle, WA, 98101, USA. (53)Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA. (54)Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA. (55)Brown Foundation Institute of Molecular Medicine, McGovern Medical School, Houston, TX, 77030, USA. (56)Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. (57)Oncode Institute, Utrecht, the Netherlands. (58)Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China. (59)Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany. (60)Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (61)Department of Clinical Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands. (62)Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany. (63)German Center for Diabetes Research, Munich-Neuherberg, Germany. (64)Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. (65)Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA. (66)Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, CA, USA. (67)Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland. (68)Division of Intramural Research, Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA. (69)Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK. (70)Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014, Oulu, Finland. (71)Biocenter Oulu, University of Oulu, Oulu, Finland. (72)Unit of Primary Care, Oulu University Hospital, Oulu, Finland. (73)Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48104, USA. (74)Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia. (75)SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany. (76)Deutsches Herzzentrum München, Technische Universität München, Munich, Germany. (77)DZHK (German Centre for Cardiovascular Research), Partner site Munich Heart Alliance, Munich, Germany. (78)Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany. (79)National Heart and Lung Institute, Imperial College London, London, UK. (80)Departments of Public Health Science and Medicine, Loyola University Chicago, Maywood, IL, USA. (81)Edward Hines VA Medical Center, Hines, IL, USA. (82)Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria. (83)Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. (84)Finnish Cardiovascular Research Centre, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. (85)Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland. (86)Department of Medical Sciences, Uppsala University, Uppsala, Sweden. (87)Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA. (88)Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany. (89)Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany. (90)Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim and Augsburg, Augsburg, Germany. (91)Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria. (92)Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany. (93)Ludwig-Maximilians Universität München, Munich, Germany. (94)Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany. (95)Department of Computational Health, Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany. (96)Department of Health Services, University of Washington, Seattle, WA, 98101, USA. (97)Research centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland. (98)Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland. (99)Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland. (100)Joslin Diabetes Center, Boston, MA, USA. (101)Harvard Medical School, Boston, MA, USA. (102)Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA. (103)Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, USA. (104)Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA. (105)The George Institute for Global Health, University of New South Wales, Sydney, Australia. (106)Institute for Public Health Genetics, University of Washington, Seattle, WA, USA. (107)Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. (108)Department of Cardiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, Groningen, the Netherlands. (109)Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany. (110)Chair Neurogenetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany. (111)Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. (112)DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany. ateumer@uni-greifswald.de. (113)Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany. ateumer@uni-greifswald.de. (114)Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland. ateumer@uni-greifswald.de. (#)Contributed equally

A key challenge for the effective treatment of gastrointestinal diseases including inflammatory bowel disease is to develop an orally administered drug delivery system capable of prolonged retention in the gastrointestinal tract. Herein we report a bioadhesive liquid coacervate based on hydrogen bonding-driven nanoparticle assembly. Free from electrostatic interactions, our fluid nanoparticle-assembled coacervate demonstrates significant pH- and salt-independent structural stability and forms a physically adhesive coating on a large surface area of intestinal tract with an extended residence time of more than 2 days to mediate the sustained release of preloaded water-soluble small molecule drugs in vivo. The orally administered drug-laden nanoparticle-assembled coacervate significantly mitigates the symptoms of inflammatory bowel disease, restores the diversity of gut microbiota, reduces systemic drug exposure, and improves the therapeutic efficacy in a rat acute colitis model compared with the oral administration of the same amount of drug in solution form. We suggest that the nanoparticle-assembled coacervate provides a promising drug delivery platform for management and treatment of numerous gastrointestinal diseases where controlled drug release with extended residence time is desired.

Krill and salps are important for carbon flux in the Southern Ocean, but the extent of their contribution and the consequences of shifts in dominance from krill to salps remain unclear. We present a direct comparison of the contribution of krill and salp faecal pellets (FP) to vertical carbon flux at the Antarctic Peninsula using a combination of sediment traps, FP production, carbon content, microbial degradation, and krill and salp abundances. Salps produce 4-fold more FP carbon than krill, but the FP from both species contribute equally to the carbon flux at 300 m, accounting for 75% of total carbon. Krill FP are exported to 72% to 300 m, while 80% of salp FP are retained in the mixed layer due to fragmentation. Thus, declining krill abundances could lead to decreased carbon flux, indicating that the Antarctic Peninsula could become a less efficient carbon sink for anthropogenic CO2 in future.

Complement receptor of immunoglobulin superfamily (CRIg) is expressed on liver macrophages and directly binds complement component C3b or Gram-positive bacteria to mediate phagocytosis. CRIg plays important roles in several immune-mediated diseases, but it is not clear how its pathogen recognition and phagocytic functions maintain homeostasis and prevent disease. We previously associated cytolysin-positive Enterococcus faecalis with severity of alcohol-related liver disease. Here, we demonstrate that CRIg is reduced in liver tissues from patients with alcohol-related liver disease. CRIg-deficient mice developed more severe ethanol-induced liver disease than wild-type mice; disease severity was reduced with loss of toll-like receptor 2. CRIg-deficient mice were less efficient than wild-type mice at clearing Gram-positive bacteria such as Enterococcus faecalis that had translocated from gut to liver. Administration of the soluble extracellular domain CRIg-Ig protein protected mice from ethanol-induced steatohepatitis. Our findings indicate that ethanol impairs hepatic clearance of translocated pathobionts, via decreased hepatic CRIg, which facilitates progression of liver disease.

A characteristic clinical feature of COVID-19 is the frequent incidence of microvascular thrombosis. In fact, COVID-19 autopsy reports have shown widespread thrombotic microangiopathy characterized by extensive diffuse microthrombi within peripheral capillaries and arterioles in lungs, hearts, and other organs, resulting in multiorgan failure. However, the underlying process of COVID-19-associated microvascular thrombosis remains elusive due to the lack of tools to statistically examine platelet aggregation (i.e., the initiation of microthrombus formation) in detail. Here we report the landscape of circulating platelet aggregates in COVID-19 obtained by massive single-cell image-based profiling and temporal monitoring of the blood of COVID-19 patients (n = 110). Surprisingly, our analysis of the big image data shows the anomalous presence of excessive platelet aggregates in nearly 90% of all COVID-19 patients. Furthermore, results indicate strong links between the concentration of platelet aggregates and the severity, mortality, respiratory condition, and vascular endothelial dysfunction level of COVID-19 patients.

Legionella pneumophila is the most common cause of the severe respiratory infection known as Legionnaires' disease. However, the microorganism is typically a symbiont of free-living amoeba, and our understanding of the bacterial factors that determine human pathogenicity is limited. Here we carried out a population genomic study of 902 L. pneumophila isolates from human clinical and environmental samples to examine their genetic diversity, global distribution and the basis for human pathogenicity. We find that the capacity for human disease is representative of the breadth of species diversity although some clones are more commonly associated with clinical infections. We identified a single gene (lag-1) to be most strongly associated with clinical isolates. lag-1, which encodes an O-acetyltransferase for lipopolysaccharide modification, has been distributed horizontally across all major phylogenetic clades of L. pneumophila by frequent recent recombination events. The gene confers resistance to complement-mediated killing in human serum by inhibiting deposition of classical pathway molecules on the bacterial surface. Furthermore, acquisition of lag-1 inhibits complement-dependent phagocytosis by human neutrophils, and promoted survival in a mouse model of pulmonary legionellosis. Thus, our results reveal L. pneumophila genetic traits linked to disease and provide a molecular basis for resistance to complement-mediated killing.

Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.

Flexible actuation of droplets is crucial for biomedical and industrial applications. Hence, various approaches using optical, electrical, and magnetic forces have been exploited to actuate droplets. For broad applicability, an ideal approach should be programmable and be able to actuate droplets of arbitrary size and composition. Here we present an "additive-free" magnetic actuation method to programmably manipulate droplets of water, organic, and biological fluids of arbitrary composition, as well as solid samples, on a ferrofluid-infused porous surface. We specifically exploit the spontaneously formed ferrofluid wetting ridges to actuate droplets using spatially varying magnetic fields. We demonstrate programmed processing and analysis of biological samples in individual drops as well as the collective actuation of large ensembles of micrometer-sized droplets. Such model respiratory droplets can be accumulated for improved quantitative and sensitive bioanalysis - an otherwise prohibitively difficult task that may be useful in tracking coronavirus.

The brain extracellular matrix (ECM) consists of extremely long-lived proteins that assemble around neurons and synapses, to stabilize them. The ECM is thought to change only rarely, in relation to neuronal plasticity, through ECM proteolysis and renewed protein synthesis. We report here an alternative ECM remodeling mechanism, based on the recycling of ECM molecules. Using multiple ECM labeling and imaging assays, from super-resolution optical imaging to nanoscale secondary ion mass spectrometry, both in culture and in brain slices, we find that a key ECM protein, Tenascin-R, is frequently endocytosed, and later resurfaces, preferentially near synapses. The TNR molecules complete this cycle within ~3 days, in an activity-dependent fashion. Interfering with the recycling process perturbs severely neuronal function, strongly reducing synaptic vesicle exo- and endocytosis. We conclude that the neuronal ECM can be remodeled frequently through mechanisms that involve endocytosis and recycling of ECM proteins.

Hexagonal boron nitride (hBN) is a van der Waals semiconductor with a wide bandgap of ~ 5.96 eV. Despite the indirect bandgap characteristics of hBN, charge carriers excited by high energy electrons or photons efficiently emit luminescence at deep-ultraviolet (DUV) frequencies via strong electron-phonon interaction, suggesting potential DUV light emitting device applications. However, electroluminescence from hBN has not been demonstrated at DUV frequencies so far. In this study, we report DUV electroluminescence and photocurrent generation in graphene/hBN/graphene heterostructures at room temperature. Tunneling carrier injection from graphene electrodes into the band edges of hBN enables prominent electroluminescence at DUV frequencies. On the other hand, under DUV laser illumination and external bias voltage, graphene electrodes efficiently collect photo-excited carriers in hBN, which generates high photocurrent. Laser excitation micro-spectroscopy shows that the radiative recombination and photocarrier excitation processes in the heterostructures mainly originate from the pristine structure and the stacking faults in hBN. Our work provides a pathway toward efficient DUV light emitting and detection devices based on hBN.

Amyloid transthyretin (ATTR) amyloidosis is characterized by the abnormal accumulation of ATTR fibrils in multiple organs. However, the structure of ATTR fibrils from the eye is poorly understood. Here, we used cryo-EM to structurally characterize vitreous body ATTR fibrils. These structures were distinct from previously characterized heart fibrils, even though both have the same mutation and type A pathology. Differences were observed at several structural levels: in both the number and arrangement of protofilaments, and the conformation of the protein fibril in each layer of protofilaments. Thus, our results show that ATTR protein structure and its assembly into protofilaments in the type A fibrils can vary between patients carrying the same mutation. By analyzing and matching the interfaces between the amino acids in the ATTR fibril with those in the natively folded TTR, we are able to propose a mechanism for the structural conversion of TTR into a fibrillar form.

For the first time, lasing at NV- centers in an optically pumped diamond sample is achieved. A nanosecond train of 150-ps 532-nm laser pulses was used to pump the sample. The lasing pulses have central wavelength at 720 nm with a spectrum width of 20 nm, 1-ns duration and total energy around 10 nJ. In a pump-probe scheme, we investigate lasing conditions and gain saturation due to NV- ionization and NV0 concentration growth under high-power laser pulse pumping of diamond crystal.

Biological molecular motors transform chemical energy into mechanical work by coupling cyclic catalytic reactions to large-scale structural transitions. Mechanical deformation can be surprisingly efficient in realizing such coupling, as demonstrated by the F1FO ATP synthase. Here, we describe a synthetic molecular mechanism that transforms a rotary motion of an asymmetric camshaft into reciprocating large-scale transitions in a surrounding stator orchestrated by mechanical deformation. We design the mechanism using DNA origami, characterize its structure via cryo-electron microscopy, and examine its dynamic behavior using single-particle fluorescence microscopy and molecular dynamics simulations. While the camshaft can rotate inside the stator by diffusion, the stator's mechanics makes the camshaft pause at preferred orientations. By changing the stator's mechanical stiffness, we accelerate or suppress the Brownian rotation, demonstrating an allosteric coupling between the camshaft and the stator. Our mechanism provides a framework for manufacturing artificial nanomachines that function because of coordinated movements of their components.

Protein domains are the basic units of protein structure and function. Comparative analysis of genomes and proteomes showed that domain recombination is a main driver of multidomain protein functional diversification and some of the constraining genomic mechanisms are known. Much less is known about biophysical mechanisms that determine whether protein domains can be combined into viable protein folds. Here, we use massively parallel insertional mutagenesis to determine compatibility of over 300,000 domain recombination variants of the Inward Rectifier K+ channel Kir2.1 with channel surface expression. Our data suggest that genomic and biophysical mechanisms acted in concert to favor gain of large, structured domain at protein termini during ion channel evolution. We use machine learning to build a quantitative biophysical model of domain compatibility in Kir2.1 that allows us to derive rudimentary rules for designing domain insertion variants that fold and traffic to the cell surface. Positional Kir2.1 responses to motif insertion clusters into distinct groups that correspond to contiguous structural regions of the channel with distinct biophysical properties tuned towards providing either folding stability or gating transitions. This suggests that insertional profiling is a high-throughput method to annotate function of ion channel structural regions.

Efficient point-to-point navigation in the presence of a background flow field is important for robotic applications such as ocean surveying. In such applications, robots may only have knowledge of their immediate surroundings or be faced with time-varying currents, which limits the use of optimal control techniques. Here, we apply a recently introduced Reinforcement Learning algorithm to discover time-efficient navigation policies to steer a fixed-speed swimmer through unsteady two-dimensional flow fields. The algorithm entails inputting environmental cues into a deep neural network that determines the swimmer's actions, and deploying Remember and Forget Experience Replay. We find that the resulting swimmers successfully exploit the background flow to reach the target, but that this success depends on the sensed environmental cue. Surprisingly, a velocity sensing approach significantly outperformed a bio-mimetic vorticity sensing approach, and achieved a near 100% success rate in reaching the target locations while approaching the time-efficiency of optimal navigation trajectories.

Genome editing therapy for Duchenne muscular dystrophy (DMD) holds great promise, however, one major obstacle is delivery of the CRISPR-Cas9/sgRNA system to skeletal muscle tissues. In general, AAV vectors are used for in vivo delivery, but AAV injections cannot be repeated because of neutralization antibodies. Here we report a chemically defined lipid nanoparticle (LNP) system which is able to deliver Cas9 mRNA and sgRNA into skeletal muscle by repeated intramuscular injections. Although the expressions of Cas9 protein and sgRNA were transient, our LNP system could induce stable genomic exon skipping and restore dystrophin protein in a DMD mouse model that harbors a humanized exon sequence. Furthermore, administration of our LNP via limb perfusion method enables to target multiple muscle groups. The repeated administration and low immunogenicity of our LNP system are promising features for a delivery vehicle of CRISPR-Cas9 to treat skeletal muscle disorders.

Queuosine (Q) is a structurally complex, non-canonical RNA nucleoside. It is present in many eukaryotic and bacterial species, where it is part of the anticodon loop of certain tRNAs. In higher vertebrates, including humans, two further modified queuosine-derivatives exist - galactosyl- (galQ) and mannosyl-queuosine (manQ). The function of these low abundant hypermodified RNA nucleosides remains unknown. While the structure of galQ was elucidated and confirmed by total synthesis, the reported structure of manQ still awaits confirmation. By combining total synthesis and LC-MS-co-injection experiments, together with a metabolic feeding study of labelled hexoses, we show here that the natural compound manQ isolated from mouse liver deviates from the literature-reported structure. Our data show that manQ features an α-allyl connectivity of its sugar moiety. The yet unidentified glycosylases that attach galactose and mannose to the Q-base therefore have a maximally different constitutional connectivity preference. Knowing the correct structure of manQ will now pave the way towards further elucidation of its biological function.

The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon (IFN) responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we apply single-cell RNA sequencing and proteomics to a primary cell model of human nasal epithelium differentiated at air-liquid interface. SARS-CoV-2 demonstrates widespread tropism for nasal epithelial cell types. The host response is dominated by type I and III IFNs and interferon-stimulated gene products. This response is notably delayed in onset relative to viral gene expression and compared to other respiratory viruses. Nevertheless, once established, the paracrine IFN response begins to impact on SARS-CoV-2 replication. When provided prior to infection, recombinant IFNβ or IFNλ1 induces an efficient antiviral state that potently restricts SARS-CoV-2 viral replication, preserving epithelial barrier integrity. These data imply that the IFN-I/III response to SARS-CoV-2 initiates in the nasal airway and suggest nasal delivery of recombinant IFNs to be a potential chemoprophylactic strategy.

Various stressors such as viral infection lead to the suppression of cap-dependent translation and the activation of the integrated stress response (ISR), since the stress-induced phosphorylated eukaryotic translation initiation factor 2 [eIF2(αP)] tightly binds to eIF2B to prevent it from exchanging guanine nucleotide molecules on its substrate, unphosphorylated eIF2. Sandfly fever Sicilian virus (SFSV) evades this cap-dependent translation suppression through the interaction between its nonstructural protein NSs and host eIF2B. However, its precise mechanism has remained unclear. Here, our cryo-electron microscopy (cryo-EM) analysis reveals that SFSV NSs binds to the α-subunit of eIF2B in a competitive manner with eIF2(αP). Together with SFSV NSs, eIF2B retains nucleotide exchange activity even in the presence of eIF2(αP), in line with the cryo-EM structures of the eIF2B•SFSV NSs•unphosphorylated eIF2 complex. A genome-wide ribosome profiling analysis clarified that SFSV NSs expressed in cultured human cells attenuates the ISR triggered by thapsigargin, an endoplasmic reticulum stress inducer. Furthermore, SFSV NSs introduced in rat hippocampal neurons and human induced-pluripotent stem (iPS) cell-derived motor neurons exhibits neuroprotective effects against the ISR-inducing stress. Since ISR inhibition is beneficial in various neurological disease models, SFSV NSs may be a promising therapeutic ISR inhibitor.

The understanding of turbulent flows is one of the biggest current challenges in physics, as no first-principles theory exists to explain their observed spatio-temporal intermittency. Turbulent flows may be regarded as an intricate collection of mutually-interacting vortices. This picture becomes accurate in quantum turbulence, which is built on tangles of discrete vortex filaments. Here, we study the statistics of velocity circulation in quantum and classical turbulence. We show that, in quantum flows, Kolmogorov turbulence emerges from the correlation of vortex orientations, while deviations-associated with intermittency-originate from their non-trivial spatial arrangement. We then link the spatial distribution of vortices in quantum turbulence to the coarse-grained energy dissipation in classical turbulence, enabling the application of existent models of classical turbulence intermittency to the quantum case. Our results provide a connection between the intermittency of quantum and classical turbulence and initiate a promising path to a better understanding of the latter.

Some fundamental concepts of catalysis are not fully explained but are of paramount importance for the development of improved catalysts. An example is the concept of structure insensitive reactions, where surface-normalized activity does not change with catalyst metal particle size. Here we explore this concept and its relation to surface reconstruction on a set of silica-supported Ni metal nanoparticles (mean particle sizes 1-6 nm) by spectroscopically discerning a structure sensitive (CO2 hydrogenation) from a structure insensitive (ethene hydrogenation) reaction. Using state-of-the-art techniques, inter alia in-situ STEM, and quick-X-ray absorption spectroscopy with sub-second time resolution, we have observed particle-size-dependent effects like restructuring which increases with increasing particle size, and faster restructuring for larger particle sizes during ethene hydrogenation while for CO2 no such restructuring effects were observed. Furthermore, a degree of restructuring is irreversible, and we also show that the rate of carbon diffusion on, and into nanoparticles increases with particle size. We finally show that these particle size-dependent effects induced by ethene hydrogenation, can make a structure sensitive reaction (CO2 hydrogenation), structure insensitive. We thus postulate that structure insensitive reactions are actually apparently structure insensitive, which changes our fundamental understanding of the empirical observation of structure insensitivity.

Spin-orbit coupling effect in structures with broken inversion symmetry, known as the Rashba effect, facilitates spin-orbit torques (SOTs) in heavy metal/ferromagnet/oxide structures, along with the spin Hall effect. Electric-field control of the Rashba effect is established for semiconductor interfaces, but it is challenging in structures involving metals owing to the screening effect. Here, we report that the Rashba effect in Pt/Co/AlOx structures is laterally modulated by electric voltages, generating out-of-plane SOTs. This enables field-free switching of the perpendicular magnetization and electrical control of the switching polarity. Changing the gate oxide reverses the sign of out-of-plane SOT while maintaining the same sign of voltage-controlled magnetic anisotropy, which confirms the Rashba effect at the Co/oxide interface is a key ingredient of the electric-field modulation. The electrical control of SOT switching polarity in a reversible and non-volatile manner can be utilized for programmable logic operations in spintronic logic-in-memory devices.

Monolayer transition metal dichalcogenides (1L-TMDs) have tremendous potential as atomically thin, direct bandgap semiconductors that can be used as convenient building blocks for quantum photonic devices. However, the short exciton lifetime due to the defect traps and the strong exciton-exciton interaction in TMDs has significantly limited the efficiency of exciton emission from this class of materials. Here, we show that exciton-exciton interaction in 1L-WS2 can be effectively screened using an ultra-flat Au film substrate separated by multilayers of hexagonal boron nitride. Under this geometry, induced dipolar exciton-exciton interaction becomes quadrupole-quadrupole interaction because of effective image dipoles formed within the metal. The suppressed exciton-exciton interaction leads to a significantly improved quantum yield by an order of magnitude, which is also accompanied by a reduction in the exciton-exciton annihilation (EEA) rate, as confirmed by time-resolved optical measurements. A theoretical model accounting for the screening of the dipole-dipole interaction is in a good agreement with the dependence of EEA on exciton densities. Our results suggest that fundamental EEA processes in the TMD can be engineered through proximal metallic screening, which represents a practical approach towards high-efficiency 2D light emitters.

2D electrode materials are often deployed on conductive supports for electrochemistry and there is a great need to understand fundamental electrochemical processes in this electrode configuration. Here, an integrated experimental-theoretical approach is used to resolve the key electronic interactions in outer-sphere electron transfer (OS-ET), a cornerstone elementary electrochemical reaction, at graphene as-grown on a copper electrode. Using scanning electrochemical cell microscopy, and co-located structural microscopy, the classical hexaamineruthenium (III/II) couple shows the ET kinetics trend: monolayer > bilayer > multilayer graphene. This trend is rationalized quantitatively through the development of rate theory, using the Schmickler-Newns-Anderson model Hamiltonian for ET, with the explicit incorporation of electrostatic interactions in the double layer, and parameterized using constant potential density functional theory calculations. The ET mechanism is predominantly adiabatic; the addition of subsequent graphene layers increases the contact potential, producing an increase in the effective barrier to ET at the electrode/electrolyte interface.

Photothermal microscopy has enabled highly sensitive label-free imaging of absorbers, from metallic nanoparticles to chemical bonds. Photothermal signals are conventionally detected via modulation of excitation beam and demodulation of probe beam using lock-in amplifier. While convenient, the wealth of thermal dynamics is not revealed. Here, we present a lock-in free, mid-infrared photothermal dynamic imaging (PDI) system by MHz digitization and match filtering at harmonics of modulation frequency. Thermal-dynamic information is acquired at nanosecond resolution within single pulse excitation. Our method not only increases the imaging speed by two orders of magnitude but also obtains four-fold enhancement of signal-to-noise ratio over lock-in counterpart, enabling high-throughput metabolism analysis at single-cell level. Moreover, by harnessing the thermal decay difference between water and biomolecules, water background is effectively separated in mid-infrared PDI of living cells. This ability to nondestructively probe chemically specific photothermal dynamics offers a valuable tool to characterize biological and material specimens.

D-2-Hydroxyglutarate (D-2-HG) is a metabolite involved in many physiological metabolic processes. When D-2-HG is aberrantly accumulated due to mutations in isocitrate dehydrogenase or D-2-HG dehydrogenase, it functions in a pro-oncogenic manner and is thus considered a therapeutic target and biomarker in many cancers. In this study, DhdR from Achromobacter denitrificans NBRC 15125 is identified as an allosteric transcriptional factor that negatively regulates D-2-HG dehydrogenase expression and responds to the presence of D-2-HG. Based on the allosteric effect of DhdR, a D-2-HG biosensor is developed by combining DhdR with amplified luminescent proximity homogeneous assay (AlphaScreen) technology. The biosensor is able to detect D-2-HG in serum, urine, and cell culture medium with high specificity and sensitivity. Additionally, this biosensor is used to identify the role of D-2-HG metabolism in lipopolysaccharide biosynthesis of Pseudomonas aeruginosa, demonstrating its broad usages.

Identifying the effects of genetic variation on the epigenome in disease-relevant cell types can help advance our understanding of the first molecular contributions of genetic susceptibility to disease onset. Here, we establish a genome-wide map of DNA methylation quantitative trait loci in CD4+ T-cells isolated from multiple sclerosis patients. Utilizing this map in a colocalization analysis, we identify 19 loci where the same haplotype drives both multiple sclerosis susceptibility and local DNA methylation. We also identify two distant methylation effects of multiple sclerosis susceptibility loci: a chromosome 16 locus affects PRDM8 methylation (a chromosome 4 region not previously associated with multiple sclerosis), and the aggregate effect of multiple sclerosis-associated variants in the major histocompatibility complex influences DNA methylation near PRKCA (chromosome 17). Overall, we present a new resource for a key cell type in inflammatory disease research and uncover new gene targets for the study of predisposition to multiple sclerosis.

Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway. We determine the crystal structure of NapW·NADPH complex and propose a catalytic mechanism by molecular dynamics simulation analysis. Additionally, a similar detoxification strategy is identified in the biosynthesis of saframycin A, another member of tetrahydroisoquinoline (THIQ) antibiotics. Remarkably, similar SDRs are widely spread in bacteria and able to inactive other THIQ members including the clinical anticancer drug, ET-743. These findings not only fill in the missing intracellular events of temporal-spatial shielding mode for cryptic self-resistance during THIQs biosynthesis, but also exhibit a sophisticated damage-control in secondary metabolism and general immunity toward this family of antibiotics.

Comment in Nat Rev Microbiol. 2022 Mar;20(3):125.

Histology plays an essential role in therapeutic decision-making for lung cancer patients. However, the molecular determinants of lung cancer histology are largely unknown. We conduct whole-exome sequencing and microarray profiling on 19 micro-dissected tumor regions of different histologic subtypes from 9 patients with lung cancers of mixed histology. A median of 68.9% of point mutations and 83% of copy number aberrations are shared between different histologic components within the same tumors. Furthermore, different histologic components within the tumors demonstrate similar subclonal architecture. On the other hand, transcriptomic profiling reveals shared pathways between the same histologic subtypes from different patients, which is supported by the analyses of the transcriptomic data from 141 cell lines and 343 lung cancers of different histologic subtypes. These data derived from mixed histologic subtypes in the setting of identical genetic background and exposure history support that the histologic fate of lung cancer cells is associated with transcriptomic features rather than the genomic profiles in most tumors.

Males are generally more susceptible to impaired glucose metabolism and type 2 diabetes (T2D) than females. However, the underlying mechanisms remain to be determined. Here, we revealed that gut microbiome depletion abolished sexual dimorphism in glucose metabolism. The transfer of male donor microbiota into antibiotics-treated female mice led the recipients to be more insulin resistant. Depleting androgen via castration changed the gut microbiome of male mice to be more similar to that of females and improved glucose metabolism, while reintroducing dihydrotestosterone (DHT) reversed these alterations. More importantly, the effects of androgen on glucose metabolism were largely abolished when the gut microbiome was depleted. Next, we demonstrated that androgen modulated circulating glutamine and glutamine/glutamate (Gln/Glu) ratio partially depending on the gut microbiome, and glutamine supplementation increases insulin sensitivity in vitro. Our study identifies the effects of androgen in deteriorating glucose homeostasis partially by modulating the gut microbiome and circulating glutamine and Gln/Glu ratio, thereby contributing to the difference in glucose metabolism between the two sexes.

Cells employ highly conserved families of insertases and translocases to insert and fold proteins into membranes. How insertases insert and fold membrane proteins is not fully known. To investigate how the bacterial insertase YidC facilitates this process, we here combine single-molecule force spectroscopy and fluorescence spectroscopy approaches, and molecular dynamics simulations. We observe that within 2 ms, the cytoplasmic α-helical hairpin of YidC binds the polypeptide of the membrane protein Pf3 at high conformational variability and kinetic stability. Within 52 ms, YidC strengthens its binding to the substrate and uses the cytoplasmic α-helical hairpin domain and hydrophilic groove to transfer Pf3 to the membrane-inserted, folded state. In this inserted state, Pf3 exposes low conformational variability such as typical for transmembrane α-helical proteins. The presence of YidC homologues in all domains of life gives our mechanistic insight into insertase-mediated membrane protein binding and insertion general relevance for membrane protein biogenesis.

Receptor-interacting protein kinase 1 (RIPK1) is a key regulator of inflammation and cell death. Many sites on RIPK1, including serine 25, are phosphorylated to inhibit its kinase activity and cell death. How these inhibitory phosphorylation sites are dephosphorylated is poorly understood. Using a sensitized CRISPR whole-genome knockout screen, we discover that protein phosphatase 1 regulatory subunit 3G (PPP1R3G) is required for RIPK1-dependent apoptosis and type I necroptosis. Mechanistically, PPP1R3G recruits its catalytic subunit protein phosphatase 1 gamma (PP1γ) to complex I to remove inhibitory phosphorylations of RIPK1. A PPP1R3G mutant which does not bind PP1γ fails to rescue RIPK1 activation and cell death. Furthermore, chemical prevention of RIPK1 inhibitory phosphorylations or mutation of serine 25 of RIPK1 to alanine largely restores cell death in PPP1R3G-knockout cells. Finally, Ppp1r3g-/- mice are protected from tumor necrosis factor-induced systemic inflammatory response syndrome, confirming the important role of PPP1R3G in regulating apoptosis and necroptosis in vivo.

Shifts in landscape heterogeneity and climate can influence animal movement in ways that profoundly alter disease transmission. Water sources that are foci of animal activity have great potential to promote disease transmission, but it is unknown how this varies across a range of hosts and climatic contexts. For fecal-oral parasites, water resources can aggregate many different hosts in small areas, concentrate infectious material, and function as disease hotspots. This may be exacerbated where water is scarce and for species requiring frequent water access. Working in an East African savanna, we show via experimental and observational methods that water sources increase the density of wild and domestic herbivore feces and thus, the concentration of fecal-oral parasites in the environment, by up to two orders of magnitude. We show that this effect is amplified in drier areas and drier periods, creating dynamic and heterogeneous disease landscapes across space and time. We also show that herbivore grazing behaviors that expose them to fecal-oral parasites often increase at water sources relative to background sites, increasing potential parasite transmission at these hotspots. Critically, this effect varies by herbivore species, with strongest effects for two animals of concern for conservation and development: elephants and cattle.

The use of nitroarenes as amino sources in synthesis is challenging. Herein is reported an unusual, straightforward, and transition metal-free method for the net [3 + 2]-cycloaddition reaction of 2-azaallyl anions with nitroarenes. The products of this reaction are diverse 2,5-dihydro-1,2,4-oxadiazoles (>40 examples, up to 95% yield). This method does not require an external reductant to reduce nitroarenes, nor does it employ nitrosoarenes, which are often used in N-O cycloadditions. Instead, it is proposed that the 2-azaallyl anions, which behave as super electron donors (SEDs), deliver an electron to the nitroarene to generate a nitroarene radical anion. A downstream 2-azaallyl radical coupling with a newly formed nitrosoarene is followed by ring closure to afford the observed products. This proposed reaction pathway is supported by computational studies and experimental evidence. Overall, this method uses readily available materials, is green, and exhibits a broad scope.

mRNA expression of the DLC1 tumor suppressor gene is downregulated in many lung cancers and their derived cell lines, with DLC1 protein levels being low or absent. Although the role of increased EZH2 methyltransferase in cancer is usually attributed to its histone methylation, we unexpectedly observed that post-translational destabilization of DLC1 protein is common and attributable to its methylation by cytoplasmic EZH2, leading to CUL-4A ubiquitin-dependent proteasomal degradation of DLC1. Furthermore, siRNA knockdown of KRAS in several lines increases DLC1 protein, associated with a drastic reduction in cytoplasmic EZH2. Pharmacologic inhibition of EZH2, CUL-4A, or the proteasome can increase the steady-state level of DLC1 protein, whose tumor suppressor activity is further increased by AKT and/or SRC kinase inhibitors, which reverse the direct phosphorylation of DLC1 by these kinases. These rational drug combinations induce potent tumor growth inhibition, with markers of apoptosis and senescence, that is highly dependent on DLC1 protein.

Loss-of-function mutations in the RB1 tumour suppressor are key drivers in cancer, including osteosarcoma. RB1 loss-of-function compromises genome-maintenance and hence could yield vulnerability to therapeutics targeting such processes. Here we demonstrate selective hypersensitivity to clinically-approved inhibitors of Poly-ADP-Polymerase1,2 inhibitors (PARPi) in RB1-defective cancer cells, including an extended panel of osteosarcoma-derived lines. PARPi treatment results in extensive cell death in RB1-defective backgrounds and prolongs survival of mice carrying human RB1-defective osteosarcoma grafts. PARPi sensitivity is not associated with canonical homologous recombination defect (HRd) signatures that predict PARPi sensitivity in cancers with BRCA1,2 loss, but is accompanied by rapid activation of DNA replication checkpoint signalling, and active DNA replication is a prerequisite for sensitivity. Importantly, sensitivity in backgrounds with natural or engineered RB1 loss surpasses that seen in BRCA-mutated backgrounds where PARPi have established clinical benefit. Our work provides evidence that PARPi sensitivity extends beyond cancers identifiable by HRd and advocates PARP1,2 inhibition as a personalised strategy for RB1-mutated osteosarcoma and other cancers.

The classic two-hit model posits that both alleles of a tumor suppressor gene (TSG) must be inactivated to cause cancer. In contrast, for some oncogenes and haploinsufficient TSGs, a single genetic alteration can suffice to increase tumor fitness. Here, by quantifying the interactions between mutations and copy number alterations (CNAs) across 10,000 tumors, we show that many cancer genes actually switch between acting as one-hit or two-hit drivers. Third order genetic interactions identify the causes of some of these switches in dominance and dosage sensitivity as mutations in other genes in the same biological pathway. The correct genetic model for a gene thus depends on the other mutations in a genome, with a second hit in the same gene or an alteration in a different gene in the same pathway sometimes representing alternative evolutionary paths to cancer.

Slow slip phenomena deep in subduction zones reveal cyclic processes downdip of locked megathrusts. Here we analyze seismicity within a subducting oceanic slab, spanning ~50 major deep slow slip with tremor episodes over 17 years. Changes in rate, b-values, and stress orientations of in-slab seismicity are temporally associated with the episodes. Furthermore, although stress orientations in the slab below these slow slips may rotate slightly, in-slab orientations 20-50 km updip from there rotate farther, suggesting that previously-unrecognized transient slow slip occurs on the plate interface updip. We infer that fluid pressure propagates from slab to interface, promoting episodes of slow slip, which break mineral seals, allowing the pressure to propagate tens of km further updip along the interface where it promotes transient slow slips. The proposed methodology, based primarily on in-slab seismicity, may help monitor plate boundary conditions and slow slip phenomena, which can signal the beginning stages of megathrust earthquakes.

Characterizing time delays in molecular photoionization as a function of the ejected electron emission direction relative to the orientation of the molecule and the light polarization axis provides unprecedented insights into the attosecond dynamics induced by extreme ultraviolet or X-ray one-photon absorption, including the role of electronic correlation and continuum resonant states. Here, we report completely resolved experimental and computational angular dependence of single-photon ionization delays in NO molecules across a shape resonance, relying on synchrotron radiation and time-independent ab initio calculations. The angle-dependent time delay variations of few hundreds of attoseconds, resulting from the interference of the resonant and non-resonant contributions to the dynamics of the ejected electron, are well described using a multichannel Fano model where the time delay of the resonant component is angle-independent. Comparing these results with the same resonance computed in e-NO+ scattering highlights the connection of photoionization delays with Wigner scattering time delays.

Phosphate, a key plant nutrient, is perceived through inositol polyphosphates (InsPs) by SPX domain-containing proteins. SPX1 an inhibit the PHR2 transcription factor to maintain Pi homeostasis. How SPX1 recognizes an InsP molecule and represses transcription activation by PHR2 remains unclear. Here we show that, upon binding InsP6, SPX1 can disrupt PHR2 dimers and form a 1:1 SPX1-PHR2 complex. The complex structure reveals that SPX1 helix α1 can impose a steric hindrance when interacting with the PHR2 dimer. By stabilizing helix α1, InsP6 allosterically decouples the PHR2 dimer and stabilizes the SPX1-PHR2 interaction. In doing so, InsP6 further allows SPX1 to engage with the PHR2 MYB domain and sterically block its interaction with DNA. Taken together, our results suggest that, upon sensing the surrogate signals of phosphate, SPX1 inhibits PHR2 via a dual mechanism that attenuates dimerization and DNA binding activities of PHR2.

Historical records of Atlantic hurricane activity, extending back to 1851, show increasing activity over time, but much or all of this trend has been attributed to lack of observations in the early portion of the record. Here we use a tropical cyclone downscaling model driven by three global climate analyses that are based mostly on sea surface temperature and surface pressure data. The results support earlier statistically-based inferences that storms were undercounted in the 19th century, but in contrast to earlier work, show increasing tropical cyclone activity through the period, interrupted by a prominent hurricane drought in the 1970s and 80 s that we attribute to anthropogenic aerosols. In agreement with earlier work, we show that most of the variability of North Atlantic tropical cyclone activity over the last century was directly related to regional rather than global climate change. Most metrics of tropical cyclones downscaled over all the tropics show weak and/or insignificant trends over the last century, illustrating the special nature of North Atlantic tropical cyclone climatology.

Βeta oscillatory activity (human: 13-35 Hz; primate: 8-24 Hz) is pervasive within the cortex and basal ganglia. Studies in Parkinson's disease patients and animal models suggest that beta-power increases with dopamine depletion. However, the exact relationship between oscillatory power, frequency and dopamine tone remains unclear. We recorded neural activity in the cortex and basal ganglia of healthy non-human primates while acutely and chronically up- and down-modulating dopamine levels. We assessed changes in beta oscillations in patients with Parkinson's following acute and chronic changes in dopamine tone. Here we show beta oscillation frequency is strongly coupled with dopamine tone in both monkeys and humans. Power, coherence between single-units and local field potentials (LFP), spike-LFP phase-locking, and phase-amplitude coupling are not systematically regulated by dopamine levels. These results demonstrate that beta frequency is a key property of pathological oscillations in cortical and basal ganglia networks.

Eph receptor tyrosine kinases play a key role in cell-cell communication. Lack of structural information on the entire multi-domain intracellular region of any Eph receptor has hindered understanding of their signaling mechanisms. Here, we use integrative structural biology to investigate the structure and dynamics of the EphA2 intracellular region. EphA2 promotes cancer malignancy through a poorly understood non-canonical form of signaling involving serine/threonine phosphorylation of the linker connecting its kinase and SAM domains. We show that accumulation of multiple linker negative charges, mimicking phosphorylation, induces cooperative changes in the EphA2 intracellular region from more closed to more extended conformations and perturbs the EphA2 juxtamembrane segment and kinase domain. In cells, linker negative charges promote EphA2 oligomerization. We also identify multiple kinases catalyzing linker phosphorylation. Our findings suggest multiple effects of linker phosphorylation on EphA2 signaling and imply that coordination of different kinases is necessary to promote EphA2 non-canonical signaling.

Yolk sac (YS) hematopoiesis is critical for the survival of the embryo and a major source of tissue-resident macrophages that persist into adulthood. Yet, the transcriptional and epigenetic regulation of YS hematopoiesis remains poorly characterized. Here we report that the epigenetic regulator Ezh2 is essential for YS hematopoiesis but dispensable for subsequent aorta-gonad-mesonephros (AGM) blood development. Loss of EZH2 activity in hemogenic endothelium (HE) leads to the generation of phenotypically intact but functionally deficient erythro-myeloid progenitors (EMPs), while the generation of primitive erythroid cells is not affected. EZH2 activity is critical for the generation of functional EMPs at the onset of the endothelial-to-hematopoietic transition but subsequently dispensable. We identify a lack of Wnt signaling downregulation as the primary reason for the production of non-functional EMPs. Together, our findings demonstrate a critical and stage-specific role of Ezh2 in modulating Wnt signaling during the generation of EMPs from YS HE.

Steviol glycosides are the intensely sweet components of extracts from Stevia rebaudiana. These molecules comprise an invariant steviol aglycone decorated with variable glycans and could widely serve as a low-calorie sweetener. However, the most desirable steviol glycosides Reb D and Reb M, devoid of unpleasant aftertaste, are naturally produced only in trace amounts due to low levels of specific β (1-2) glucosylation in Stevia. Here, we report the biochemical and structural characterization of OsUGT91C1, a glycosyltransferase from Oryza sativa, which is efficient at catalyzing β (1-2) glucosylation. The enzyme's ability to bind steviol glycoside substrate in three modes underlies its flexibility to catalyze β (1-2) glucosylation in two distinct orientations as well as β (1-6) glucosylation. Guided by the structural insights, we engineer this enzyme to enhance the desirable β (1-2) glucosylation, eliminate β (1-6) glucosylation, and obtain a promising catalyst for the industrial production of naturally rare but palatable steviol glycosides.

Memory formation and reinstatement are thought to lock to the hippocampal theta rhythm, predicting that encoding and retrieval processes appear rhythmic themselves. Here, we show that rhythmicity can be observed in behavioral responses from memory tasks, where participants indicate, using button presses, the timing of encoding and recall of cue-object associative memories. We find no evidence for rhythmicity in button presses for visual tasks using the same stimuli, or for questions about already retrieved objects. The oscillations for correctly remembered trials center in the slow theta frequency range (1-5 Hz). Using intracranial EEG recordings, we show that the memory task induces temporally extended phase consistency in hippocampal local field potentials at slow theta frequencies, but significantly more for remembered than forgotten trials, providing a potential mechanistic underpinning for the theta oscillations found in behavioral responses.

Silencing of a subset of germline genes is dependent upon DNA methylation (DNAme) post-implantation. However, these genes are generally hypomethylated in the blastocyst, implicating alternative repressive pathways before implantation. Indeed, in embryonic stem cells (ESCs), an overlapping set of genes, including germline "genome-defence" (GGD) genes, are upregulated following deletion of the H3K9 methyltransferase SETDB1 or subunits of the non-canonical PRC1 complex PRC1.6. Here, we show that in pre-implantation embryos and naïve ESCs (nESCs), hypomethylated promoters of germline genes bound by the PRC1.6 DNA-binding subunits MGA/MAX/E2F6 are enriched for RING1B-dependent H2AK119ub1 and H3K9me3. Accordingly, repression of these genes in nESCs shows a greater dependence on PRC1.6 than DNAme. In contrast, GGD genes are hypermethylated in epiblast-like cells (EpiLCs) and their silencing is dependent upon SETDB1, PRC1.6/RING1B and DNAme, with H3K9me3 and DNAme establishment dependent upon MGA binding. Thus, GGD genes are initially repressed by PRC1.6, with DNAme subsequently engaged in post-implantation embryos.

Is the world quantum? An active research line in quantum foundations is devoted to exploring what constraints can rule out the postquantum theories that are consistent with experimentally observed results. We explore this question in the context of epistemics, and ask whether agreement between observers can serve as a physical principle that must hold for any theory of the world. Aumann's seminal Agreement Theorem states that two observers (of classical systems) cannot agree to disagree. We propose an extension of this theorem to no-signaling settings. In particular, we establish an Agreement Theorem for observers of quantum systems, while we construct examples of (postquantum) no-signaling boxes where observers can agree to disagree. The PR box is an extremal instance of this phenomenon. These results make it plausible that agreement between observers might be a physical principle, while they also establish links between the fields of epistemics and quantum information that seem worthy of further exploration.

The sugar fucose is expressed on mammalian cell membranes as part of glycoconjugates and mediates essential physiological processes. The aberrant expression of fucosylated glycans has been linked to pathologies such as cancer, inflammation, infection, and genetic disorders. Tools to modulate fucose expression on living cells are needed to elucidate the biological role of fucose sugars and the development of potential therapeutics. Herein, we report a class of fucosylation inhibitors directly targeting de novo GDP-fucose biosynthesis via competitive GMDS inhibition. We demonstrate that cell permeable fluorinated rhamnose 1-phosphate derivatives (Fucotrim I & II) are metabolic prodrugs that are metabolized to their respective GDP-mannose derivatives and efficiently inhibit cellular fucosylation.

Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy with a complex microenvironment. Dichotomous tumour-promoting and -restrictive roles have been ascribed to the tumour microenvironment, however the effects of individual stromal subsets remain incompletely characterised. Here, we describe how heterocellular Oncostatin M (OSM) - Oncostatin M Receptor (OSMR) signalling reprograms fibroblasts, regulates tumour growth and metastasis. Macrophage-secreted OSM stimulates inflammatory gene expression in cancer-associated fibroblasts (CAFs), which in turn induce a pro-tumourigenic environment and engage tumour cell survival and migratory signalling pathways. Tumour cells implanted in Osm-deficient (Osm-/-) mice display an epithelial-dominated morphology, reduced tumour growth and do not metastasise. Moreover, the tumour microenvironment of Osm-/- animals exhibit increased abundance of α smooth muscle actin positive myofibroblasts and a shift in myeloid and T cell phenotypes, consistent with a more immunogenic environment. Taken together, these data demonstrate how OSM-OSMR signalling coordinates heterocellular interactions to drive a pro-tumourigenic environment in PDA.

Confidence, the subjective estimate of decision quality, is a cognitive process necessary for learning from mistakes and guiding future actions. The origins of confidence judgments resulting from economic decisions remain unclear. We devise a task and computational framework that allowed us to formally tease apart the impact of various sources of confidence in value-based decisions, such as uncertainty emerging from encoding and decoding operations, as well as the interplay between gaze-shift dynamics and attentional effort. In line with canonical decision theories, trial-to-trial fluctuations in the precision of value encoding impact economic choice consistency. However, this uncertainty has no influence on confidence reports. Instead, confidence is associated with endogenous attentional effort towards choice alternatives and down-stream noise in the comparison process. These findings provide an explanation for confidence (miss)attributions in value-guided behaviour, suggesting mechanistic influences of endogenous attentional states for guiding decisions and metacognitive awareness of choice certainty.

Female intrasexual competition can be intense in cooperatively breeding species, with some dominant breeders (matriarchs) limiting reproduction in subordinates via aggression, eviction or infanticide. In males, such tendencies bidirectionally link to testosterone, but in females, there has been little systematic investigation of androgen-mediated behaviour within and across generations. In 22 clans of wild meerkats (Suricata suricatta), we show that matriarchs 1) express peak androgen concentrations during late gestation, 2) when displaying peak feeding competition, dominance behaviour, and evictions, and 3) relative to subordinates, produce offspring that are more aggressive in early development. Late-gestation antiandrogen treatment of matriarchs 4) specifically reduces dominance behaviour, is associated with infrequent evictions, decreases social centrality within the clan, 5) increases aggression in cohabiting subordinate dams, and 6) reduces offspring aggression. These effects implicate androgen-mediated aggression in the operation of female sexual selection, and intergenerational transmission of masculinised phenotypes in the evolution of meerkat cooperative breeding.

Long non-coding RNAs (lncRNAs) constitute a poorly studied class of transcripts with emerging roles in key cellular processes. Despite efforts to characterize lncRNAs across a wide range of species, these molecules remain largely unexplored in most eukaryotic microbes, including yeast pathogens of the Candida clade. Here, we analyze thousands of publicly available sequencing datasets to infer and characterize the lncRNA repertoires of five major Candida pathogens: Candida albicans, Candida tropicalis, Candida parapsilosis, Candida auris and Candida glabrata. Our results indicate that genomes of these species encode hundreds of lncRNAs that show levels of evolutionary constraint intermediate between those of intergenic genomic regions and protein-coding genes. Despite their low sequence conservation across the studied species, some lncRNAs are syntenic and are enriched in shared sequence motifs. We find co-expression of lncRNAs with certain protein-coding transcripts, hinting at potential functional associations. Finally, we identify lncRNAs that are differentially expressed during infection of human epithelial cells for four of the studied species. Our comprehensive bioinformatic analyses of Candida lncRNAs pave the way for future functional characterization of these transcripts.

Erratum in Nat Commun. 2022 Mar 28;13(1):1749.

The much-needed renewable alternatives to fossil fuel can be achieved efficiently and sustainably by converting solar energy to fuels via hydrogen generation from water or CO2 reduction. Herein, a soft processable metal-organic hybrid material is developed and studied for photocatalytic activity towards H2 production and CO2 reduction to CO and CH4 under visible light as well as direct sunlight irradiation. A tetrapodal low molecular weight gelator (LMWG) is synthesized by integrating tetrathiafulvalene (TTF) and terpyridine (TPY) derivatives through amide linkages and results in TPY-TTF LMWG. The TPY-TTF LMWG acts as a linker, and self-assembly of this gelator molecules with ZnII ions results in a coordination polymer gel (CPG); Zn-TPY-TTF. The Zn-TPY-TTF CPG shows high photocatalytic activity towards H2 production (530 μmol g-1h-1) and CO2 reduction to CO (438 μmol g-1h-1, selectivity > 99%) regulated by charge-transfer interactions. Furthermore, in situ stabilization of Pt nanoparticles on CPG (Pt@Zn-TPY-TTF) enhances H2 evolution (14727 μmol g-1h-1). Importantly, Pt@Zn-TPY-TTF CPG produces CH4 (292 μmol g-1h-1, selectivity > 97%) as CO2 reduction product instead of CO. The real-time CO2 reduction reaction is monitored by in situ DRIFT study, and the plausible mechanism is derived computationally.

Since 2020, the COVID-19 pandemic has urged event holders to shift conferences online. Virtual and hybrid conferences are greener alternatives to in-person conferences, yet their environmental sustainability has not been fully assessed. Considering food, accommodation, preparation, execution, information and communication technology, and transportation, here we report comparative life cycle assessment results of in-person, virtual, and hybrid conferences and consider carbon footprint trade-offs between in-person participation and hybrid conferences. We find that transitioning from in-person to virtual conferencing can substantially reduce the carbon footprint by 94% and energy use by 90%. For the sake of maintaining more than 50% of in-person participation, carefully selected hubs for hybrid conferences have the potential to slash carbon footprint and energy use by two-thirds. Furthermore, switching the dietary type of future conferences to plant-based diets and improving energy efficiencies of the information and communication technology sector can further reduce the carbon footprint of virtual conferences.

The flow of the Greenland Ice Sheet is controlled by subglacial processes and conditions that depend on the geological provenance and temperature of the crust beneath it, neither of which are adequately known. Here we present a seismic velocity model of the uppermost 5 km of the Greenlandic crust. We show that slow velocities in the upper crust tend to be associated with major outlet glaciers along the ice-sheet margin, and elevated geothermal heat flux along the Iceland hotspot track inland. Outlet glaciers particularly susceptible to basal slip over deformable subglacial sediments include Jakobshavn, Helheim and Kangerdlussuaq, while geothermal warming and softening of basal ice may affect the onset of faster ice flow at Petermann Glacier and the Northeast Greenland Ice Stream. Interactions with the solid earth therefore control the past, present and future dynamics of the Greenland Ice Sheet and must be adequately explored and implemented in ice sheet models.

Pyroclastic surges are lethal hazards from volcanoes that exhibit enormous destructiveness through dynamic pressures of 100-102 kPa inside flows capable of obliterating reinforced buildings. However, to date, there are no measurements inside these currents to quantify the dynamics of this important hazard process. Here we show, through large-scale experiments and the first field measurement of pressure inside pyroclastic surges, that dynamic pressure energy is mostly carried by large-scale coherent turbulent structures and gravity waves. These perpetuate as low-frequency high-pressure pulses downcurrent, form maxima in the flow energy spectra and drive a turbulent energy cascade. The pressure maxima exceed mean values, which are traditionally estimated for hazard assessments, manifold. The frequency of the most energetic coherent turbulent structures is bounded by a critical Strouhal number of ~0.3, allowing quantitative predictions. This explains the destructiveness of real-world flows through the development of c. 1-20 successive high-pressure pulses per minute. This discovery, which is also applicable to powder snow avalanches, necessitates a re-evaluation of hazard models that aim to forecast and mitigate volcanic hazard impacts globally.

Copper serves as a co-factor for a host of metalloenzymes that contribute to malignant progression. The orally bioavailable copper chelating agent tetrathiomolybdate (TM) has been associated with a significant survival benefit in high-risk triple negative breast cancer (TNBC) patients. Despite these promising data, the mechanisms by which copper depletion impacts metastasis are poorly understood and this remains a major barrier to advancing TM to a randomized phase II trial. Here, using two independent TNBC models, we report a discrete subpopulation of highly metastatic SOX2/OCT4+ cells within primary tumors that exhibit elevated intracellular copper levels and a marked sensitivity to TM. Global proteomic and metabolomic profiling identifies TM-mediated inactivation of Complex IV as the primary metabolic defect in the SOX2/OCT4+ cell population. We also identify AMPK/mTORC1 energy sensor as an important downstream pathway and show that AMPK inhibition rescues TM-mediated loss of invasion. Furthermore, loss of the mitochondria-specific copper chaperone, COX17, restricts copper deficiency to mitochondria and phenocopies TM-mediated alterations. These findings identify a copper-metabolism-metastasis axis with potential to enrich patient populations in next-generation therapeutic trials.

The ocean moderates the world's climate through absorption of heat and carbon, but how much carbon the ocean will continue to absorb remains unknown. The North Atlantic Ocean west (Baffin Bay/Labrador Sea) and east (Fram Strait/Greenland Sea) of Greenland features the most intense absorption of anthropogenic carbon globally; the biological carbon pump (BCP) contributes substantially. As Arctic sea-ice melts, the BCP changes, impacting global climate and other critical ocean attributes (e.g. biodiversity). Full understanding requires year-round observations across a range of ice conditions. Here we present such observations: autonomously collected Eulerian continuous 24-month time-series in Fram Strait. We show that, compared to ice-unaffected conditions, sea-ice derived meltwater stratification slows the BCP by 4 months, a shift from an export to a retention system, with measurable impacts on benthic communities. This has implications for ecosystem dynamics in the future warmer Arctic where the seasonal ice zone is expected to expand.

Nonsteroidal anti-inflammatory drugs (NSAIDs), including salicylic acid (SA), target mammalian cyclooxygenases. In plants, SA is a defense hormone that regulates NON-EXPRESSOR OF PATHOGENESIS RELATED GENES 1 (NPR1), the master transcriptional regulator of immunity-related genes. We identify that the oxicam-type NSAIDs tenoxicam (TNX), meloxicam, and piroxicam, but not other types of NSAIDs, exhibit an inhibitory effect on immunity to bacteria and SA-dependent plant immune response. TNX treatment decreases NPR1 levels, independently from the proposed SA receptors NPR3 and NPR4. Instead, TNX induces oxidation of cytosolic redox status, which is also affected by SA and regulates NPR1 homeostasis. A cysteine labeling assay reveals that cysteine residues in NPR1 can be oxidized in vitro, leading to disulfide-bridged oligomerization of NPR1, but not in vivo regardless of SA or TNX treatment. Therefore, this study indicates that oxicam inhibits NPR1-mediated SA signaling without affecting the redox status of NPR1.

Because of its compatibility with semiconductor-based technologies, hafnia (HfO2) is today's most promising ferroelectric material for applications in electronics. Yet, knowledge on the ferroic and electromechanical response properties of this all-important compound is still lacking. Interestingly, HfO2 has recently been predicted to display a negative longitudinal piezoelectric effect, which sets it apart from classic ferroelectrics (e.g., perovskite oxides like PbTiO3) and is reminiscent of the behavior of some organic compounds. The present work corroborates this behavior, by first-principles calculations and an experimental investigation of HfO2 thin films using piezoresponse force microscopy. Further, the simulations show how the chemical coordination of the active oxygen atoms is responsible for the negative longitudinal piezoelectric effect. Building on these insights, it is predicted that, by controlling the environment of such active oxygens (e.g., by means of an epitaxial strain), it is possible to change the sign of the piezoelectric response of the material.

Several members of the FGF family have been identified as potential regulators of glucose homeostasis. We previously reported that a low threshold of FGF-induced FGF receptor 1c (FGFR1c) dimerization and activity is sufficient to evoke a glucose lowering activity. We therefore reasoned that ligand identity may not matter, and that besides paracrine FGF1 and endocrine FGF21, other cognate paracrine FGFs of FGFR1c might possess such activity. Indeed, via a side-by-side testing of multiple cognate FGFs of FGFR1c in diabetic mice we identified the paracrine FGF4 as a potent anti-hyperglycemic FGF. Importantly, we found that like FGF1, the paracrine FGF4 is also more efficacious than endocrine FGF21 in lowering blood glucose. We show that paracrine FGF4 and FGF1 exert their superior glycemic control by targeting skeletal muscle, which expresses copious FGFR1c but lacks β-klotho (KLB), an obligatory FGF21 co-receptor. Mechanistically, both FGF4 and FGF1 upregulate GLUT4 cell surface abundance in skeletal muscle in an AMPKα-dependent but insulin-independent manner. Chronic treatment with rFGF4 improves insulin resistance and suppresses adipose macrophage infiltration and inflammation. Notably, unlike FGF1 (a pan-FGFR ligand), FGF4, which has more restricted FGFR1c binding specificity, has no apparent effect on food intake. The potent anti-hyperglycemic and anti-inflammatory properties of FGF4 testify to its promising potential for use in the treatment of T2D and related metabolic disorders.

Growth of the Andes has been attributed to Cenozoic subduction. Although climatic and tectonic processes have been proposed to be first-order mechanisms, their interaction and respective contributions remain largely unclear. Here, we apply three-dimensional, fully-dynamic subduction models to investigate the effect of trench-axial sediment transport and subduction on Andean growth, a mechanism that involves both climatic and tectonic processes. We find that the thickness of trench-fill sediments, a proxy of plate coupling (with less sediments causing stronger coupling), exerts an important influence on the pattern of crustal shortening along the Andes. The southward migrating Juan Fernandez Ridge acts as a barrier to the northward flowing trench sediments, thus expanding the zone of plate coupling southward through time. Consequently, the predicted history of Andean shortening is consistent with observations. Southward expanding crustal shortening matches the kinematic history of inferred compression. These results demonstrate the importance of climate-tectonic interaction on mountain building.

Mendelian Randomisation (MR) is an increasingly popular approach that estimates the causal effect of risk factors on complex human traits. While it has seen several extensions that relax its basic assumptions, most suffer from two major limitations; their under-exploitation of genome-wide markers, and sensitivity to the presence of a heritable confounder of the exposure-outcome relationship. To overcome these limitations, we propose a Latent Heritable Confounder MR (LHC-MR) method applicable to association summary statistics, which estimates bi-directional causal effects, direct heritabilities, and confounder effects while accounting for sample overlap. We demonstrate that LHC-MR outperforms several existing MR methods in a wide range of simulation settings and apply it to summary statistics of 13 complex traits. Besides several concordant results with other MR methods, LHC-MR unravels new mechanisms (how disease diagnosis might lead to improved lifestyle) and reveals new causal effects (e.g. HDL cholesterol being protective against high systolic blood pressure), hidden from standard MR methods due to a heritable confounder of opposite effect direction.

DNA owes its remarkable photostability to its building blocks-the nucleosides-that efficiently dissipate the energy acquired upon ultraviolet light absorption. The mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy experiments with broad spectral coverage and state-of-the-art mixed quantum-classical dynamics with spectral signal simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. We track the wave packet motion from the Franck-Condon region to the conical intersections (CIs) with the ground state and observe spectral signatures of excited-state vibrational modes. 5mUrd exhibits an order of magnitude longer lifetime with respect to Urd due to the solvent reorganization needed to facilitate bulky methyl group motions leading to the CI. This activates potentially lesion-inducing dynamics such as ring opening. Involvement of the 1nπ* state is found to be negligible.

Machine-learned force fields combine the accuracy of ab initio methods with the efficiency of conventional force fields. However, current machine-learned force fields typically ignore electronic degrees of freedom, such as the total charge or spin state, and assume chemical locality, which is problematic when molecules have inconsistent electronic states, or when nonlocal effects play a significant role. This work introduces SpookyNet, a deep neural network for constructing machine-learned force fields with explicit treatment of electronic degrees of freedom and nonlocality, modeled via self-attention in a transformer architecture. Chemically meaningful inductive biases and analytical corrections built into the network architecture allow it to properly model physical limits. SpookyNet improves upon the current state-of-the-art (or achieves similar performance) on popular quantum chemistry data sets. Notably, it is able to generalize across chemical and conformational space and can leverage the learned chemical insights, e.g. by predicting unknown spin states, thus helping to close a further important remaining gap for today's machine learning models in quantum chemistry.

Interleukin-7 receptor α (encoded by IL7R) is essential for lymphoid development. Whether acute lymphoblastic leukemia (ALL)-related IL7R gain-of-function mutations can trigger leukemogenesis remains unclear. Here, we demonstrate that lymphoid-restricted mutant IL7R, expressed at physiological levels in conditional knock-in mice, establishes a pre-leukemic stage in which B-cell precursors display self-renewal ability, initiating leukemia resembling PAX5 P80R or Ph-like human B-ALL. Full transformation associates with transcriptional upregulation of oncogenes such as Myc or Bcl2, downregulation of tumor suppressors such as Ikzf1 or Arid2, and major IL-7R signaling upregulation (involving JAK/STAT5 and PI3K/mTOR), required for leukemia cell viability. Accordingly, maximal signaling drives full penetrance and early leukemia onset in homozygous IL7R mutant animals. Notably, we identify 2 transcriptional subgroups in mouse and human Ph-like ALL, and show that dactolisib and sphingosine-kinase inhibitors are potential treatment avenues for IL-7R-related cases. Our model, a resource to explore the pathophysiology and therapeutic vulnerabilities of B-ALL, demonstrates that IL7R can initiate this malignancy.

Interrogation of cellular metabolism with high-throughput screening approaches can unravel contextual biology and identify cancer-specific metabolic vulnerabilities. To systematically study the consequences of distinct metabolic perturbations, we assemble a comprehensive metabolic drug library (CeMM Library of Metabolic Drugs; CLIMET) covering 243 compounds. We, next, characterize it phenotypically in a diverse panel of myeloid leukemia cell lines and primary patient cells. Analysis of the drug response profiles reveals that 77 drugs affect cell viability, with the top effective compounds targeting nucleic acid synthesis, oxidative stress, and the PI3K/mTOR pathway. Clustering of individual drug response profiles stratifies the cell lines into five functional groups, which link to specific molecular and metabolic features. Mechanistic characterization of selective responses to the PI3K inhibitor pictilisib, the fatty acid synthase inhibitor GSK2194069, and the SLC16A1 inhibitor AZD3965, bring forth biomarkers of drug response. Phenotypic screening using CLIMET represents a valuable tool to probe cellular metabolism and identify metabolic dependencies at large.

Ecosystems face both local hazards, such as over-exploitation, and global hazards, such as climate change. Since the impact of local hazards attenuates with distance from humans, local extinction risk should decrease with remoteness, making faraway areas safe havens for biodiversity. However, isolation and reduced anthropogenic disturbance may increase ecological specialization in remote communities, and hence their vulnerability to secondary effects of diversity loss propagating through networks of interacting species. We show this to be true for reef fish communities across the globe. An increase in fish-coral dependency with the distance of coral reefs from human settlements, paired with the far-reaching impacts of global hazards, increases the risk of fish species loss, counteracting the benefits of remoteness. Hotspots of fish risk from fish-coral dependency are distinct from those caused by direct human impacts, increasing the number of risk hotspots by ~30% globally. These findings might apply to other ecosystems on Earth and depict a world where no place, no matter how remote, is safe for biodiversity, calling for a reconsideration of global conservation priorities.

The resistive switching effect in memristors typically stems from the formation and rupture of localized conductive filament paths, and HfO2 has been accepted as one of the most promising resistive switching materials. However, the dynamic changes in the resistive switching process, including the composition and structure of conductive filaments, and especially the evolution of conductive filament surroundings, remain controversial in HfO2-based memristors. Here, the conductive filament system in the amorphous HfO2-based memristors with various top electrodes is revealed to be with a quasi-core-shell structure consisting of metallic hexagonal-Hf6O and its crystalline surroundings (monoclinic or tetragonal HfOx). The phase of the HfOx shell varies with the oxygen reservation capability of the top electrode. According to extensive high-resolution transmission electron microscopy observations and ab initio calculations, the phase transition of the conductive filament shell between monoclinic and tetragonal HfO2 is proposed to depend on the comprehensive effects of Joule heat from the conductive filament current and the concentration of oxygen vacancies. The quasi-core-shell conductive filament system with an intrinsic barrier, which prohibits conductive filament oxidation, ensures the extreme scalability of resistive switching memristors. This study renovates the understanding of the conductive filament evolution in HfO2-based memristors and provides potential inspirations to improve oxide memristors for nonvolatile storage-class memory applications.

Recent years have witnessed incredible growth in RNA therapeutics, which has benefited significantly from decades of research on lipid nanoparticles, specifically its key component—the ionizable lipid. This comment discusses the major ionizable lipid types, and provides perspectives for future development.

Global warming is expected to not only impact mean temperatures but also temperature variability, substantially altering climate extremes. Here we show that human-caused changes in internal year-to-year temperature variability are expected to emerge from the unforced range by the end of the 21st century across climate model initial-condition large ensembles forced with a strong global warming scenario. Different simulated changes in globally averaged regional temperature variability between models can be explained by a trade-off between strong increases in variability on tropical land and substantial decreases in high latitudes, both shown by most models. This latitudinal pattern of temperature variability change is consistent with loss of sea ice in high latitudes and changes in vegetation cover in the tropics. Instrumental records are broadly in line with this emerging pattern, but have data gaps in key regions. Paleoclimate proxy reconstructions support the simulated magnitude and distribution of temperature variability. Our findings strengthen the need for urgent mitigation to avoid unprecedented changes in temperature variability.

When a solid object impacts on the surface of a liquid, extremely high pressure develops at the site of contact. Von Karman's study of this classical physics problem showed that the pressure on the bottom surface of the impacting body approaches infinity for flat impacts. Yet, in contrast to the high pressures found from experience and in previous studies, we show that a flat-bottomed cylinder impacting a pool of liquid can decrease the local pressure sufficiently to cavitate the liquid. Cavitation occurs because the liquid is slightly compressible and impact creates large pressure waves that reflect from the free surface to form negative pressure regions. We find that an impact velocity as low as ~3 m/s suffices to cavitate the liquid and propose a new cavitation number to predict cavitation onset in low-speed solid-liquid impact-scenarios. These findings imply that localized cavitation could occur in impacts such as boat slamming, cliff jumping, and ocean landing of spacecraft.

Controlling the properties of heavy element complexes, such as those containing berkelium, is challenging because relativistic effects, spin-orbit and ligand-field splitting, and complex metal-ligand bonding, all dictate the final electronic states of the molecules. While the first two of these are currently beyond experimental control, covalent M‒L interactions could theoretically be boosted through the employment of chelators with large polarizabilities that substantially shift the electron density in the molecules. This theory is tested by ligating BkIII with 4'-(4-nitrophenyl)-2,2':6',2"-terpyridine (terpy*), a ligand with a large dipole. The resultant complex, Bk(terpy*)(NO3)3(H2O)·THF, is benchmarked with its closest electrochemical analog, Ce(terpy*)(NO3)3(H2O)·THF. Here, we show that enhanced Bk‒N interactions with terpy* are observed as predicted. Unexpectedly, induced polarization by terpy* also creates a plane in the molecules wherein the M‒L bonds trans to terpy* are shorter than anticipated. Moreover, these molecules are highly anisotropic and rhombic EPR spectra for the CeIII complex are reported.

Bacteriorhodopsin is a seven-helix light-driven proton-pump that was structurally and functionally extensively studied. Despite a wealth of data, the single molecule kinetics of the reaction cycle remain unknown. Here, we use high-speed atomic force microscopy methods to characterize the single molecule kinetics of wild-type bR exposed to continuous light and short pulses. Monitoring bR conformational changes with millisecond temporal resolution, we determine that the cytoplasmic gate opens 2.9 ms after photon absorption, and stays open for proton capture for 13.2 ms. Surprisingly, a previously active protomer cannot be reactivated for another 37.6 ms, even under excess continuous light, giving a single molecule reaction cycle of ~20 s-1. The reaction cycle slows at low light where the closed state is prolonged, and at basic or acidic pH where the open state is extended.

Global warming is considered a major threat to Earth's lakes water budgets and quality. However, flow regulation, over-exploitation, lack of hydrological data, and disparate evaluation methods hamper comparative global estimates of lake vulnerability to evaporation. We have analyzed the stable isotope composition of 1257 global lakes and we find that most lakes depend on precipitation and groundwater recharge subsequently altered by catchment and lake evaporation processes. Isotope mass-balance modeling shows that ca. 20% of water inflow in global lakes is lost through evaporation and ca. 10% of lakes in arid and temperate zones experience extreme evaporative losses >40 % of the total inflow. Precipitation amount, limnicity, wind speed, relative humidity, and solar radiation are predominant controls on lake isotope composition and evaporation, regardless of the climatic zone. The promotion of systematic global isotopic monitoring of Earth's lakes provides a direct and comparative approach to detect the impacts of climatic and catchment-scale changes on water-balance and evaporation trends.

Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, PHT4;4 encoding a chloroplastic ascorbate transporter and bZIP58, encoding a nuclear transcription factor, which prevent the downregulation of photosynthesis genes leading to the stay-green phenotype under iron-phosphorus deficiency. Joint limitation of these nutrients induces ascorbate accumulation by activating expression of an ascorbate biosynthesis gene, VTC4, which requires bZIP58. Furthermore, we demonstrate that chloroplastic ascorbate transport prevents the downregulation of photosynthesis genes under iron-phosphorus combined deficiency through modulation of ROS homeostasis. Our study uncovers a ROS-mediated chloroplastic retrograde signaling pathway to adapt photosynthesis to nutrient availability.

While aldehydes represent a classic class of electrophilic synthons, the corresponding acyl radicals are inherently nucleophilic, which exhibits umpolung reactivity. Generation of acyl radicals typically requires noble metal catalysts or excess oxidants to be added. Herein, we report a convenient and green approach to access acyl radicals, capitalizing on neutral eosin Y-enabled hydrogen atom transfer (HAT) photocatalysis with aldehydes. The generated acyl radicals underwent SOMOphilic substitutions with various functionalized sulfones (X-SO2R') to deliver value-added acyl products. The merger of eosin Y photocatalysis and sulfone-based SOMOphiles provides a versatile platform for a wide array of aldehydic C-H functionalizations, including fluoromethylthiolation, arylthiolation, alkynylation, alkenylation and azidation. The present protocol features green characteristics, such as being free of metals, harmful oxidants and additives; step-economic; redox-neutral; and amenable to scale-up assisted by continuous-flow technology.

Inverse-electron-demand-hetero-Diels-Alder reactions of alkenes with α,β-unsaturated keto compounds allow rapid access to the tetrahydropyran ring found in numerous natural products and bioactive molecules. Despite its synthetic interest, catalytic asymmetric versions of this process remain underdeveloped, especially regarding the use of non-activated alkenes reacting with α,β-unsaturated ketone or aldehyde, for which no report can be found in the literature. Herein, we describe the catalytic inverse-electron-demand-hetero-Diels-Alder reactions between neutral alkenes and an α,β-unsaturated ketones or aldehydes to produce a variety of trans-fused [5,6,8] tricyclic structures containing a central, chiral tetrahydropyran ring. This complex transformation, which is achieved using a chiral phosphoric acid, allows for the formation of four stereogenic centers in a single step with high regio-, diastereo- and enantioselectivity (up to 99% ee). Such level of stereocontrol could be achieved by a key remote double hydrogen atom bonding interaction between the linear substrate and the catalyst.

Sustained ryanodine receptor (RyR) Ca2+ leak is associated with pathological conditions such as heart failure or skeletal muscle weakness. We report that a single session of sprint interval training (SIT), but not of moderate intensity continuous training (MICT), triggers RyR1 protein oxidation and nitrosylation leading to calstabin1 dissociation in healthy human muscle and in in vitro SIT models (simulated SIT or S-SIT). This is accompanied by decreased sarcoplasmic reticulum Ca2+ content, increased levels of mitochondrial oxidative phosphorylation proteins, supercomplex formation and enhanced NADH-linked mitochondrial respiratory capacity. Mechanistically, (S-)SIT increases mitochondrial Ca2+ uptake in mouse myotubes and muscle fibres, and decreases pyruvate dehydrogenase phosphorylation in human muscle and mouse myotubes. Countering Ca2+ leak or preventing mitochondrial Ca2+ uptake blunts S-SIT-induced adaptations, a result supported by proteomic analyses. Here we show that triggering acute transient Ca2+ leak through RyR1 in healthy muscle may contribute to the multiple health promoting benefits of exercise.

Interfacial moiré superlattices in van der Waals vertical assemblies effectively reconstruct the crystal symmetry, leading to opportunities for investigating exotic quantum states. Notably, a two-dimensional nanosheet has top and bottom open surfaces, allowing the specific case of doubly aligned super-moiré lattice to serve as a toy model for studying the tunable lattice symmetry and the complexity of related electronic structures. Here, we show that by doubly aligning a graphene monolayer to both top and bottom encapsulating hexagonal boron nitride (h-BN), multiple conductivity minima are observed away from the main Dirac point, which are sensitively tunable with respect to the small twist angles. Moreover, our experimental evidences together with theoretical calculations suggest correlated insulating states at integer fillings of -5, -6, -7 electrons per moiré unit cell, possibly due to inter-valley coherence. Our results provide a way to construct intriguing correlations in 2D electronic systems in the weak interaction regime.

RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. In recent years, a growing number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework that identifies modifications from these data. Our strategy compares an RNA sample of interest against a non-modified control sample, not requiring a training set and allowing the use of replicates. We show that Nanocompore can detect different RNA modifications with position accuracy in vitro, and we apply it to profile m6A in vivo in yeast and human RNAs, as well as in targeted non-coding RNAs. We confirm our results with orthogonal methods and provide novel insights on the co-occurrence of multiple modified residues on individual RNA molecules.

CRISPR-based genetic engineering tools aimed to bias sex ratios, or drive effector genes into animal populations, often integrate the transgenes into autosomal chromosomes. However, in species with heterogametic sex chromsomes (e.g. XY, ZW), sex linkage of endonucleases could be beneficial to drive the expression in a sex-specific manner to produce genetic sexing systems, sex ratio distorters, or even sex-specific gene drives, for example. To explore this possibility, here we develop a transgenic line of Drosophila melanogaster expressing Cas9 from the Y chromosome. We functionally characterize the utility of this strain for both sex selection and gene drive finding it to be quite effective. To explore its utility for population control, we built mathematical models illustrating its dynamics as compared to other state-of-the-art systems designed for both population modification and suppression. Taken together, our results contribute to the development of current CRISPR genetic control tools and demonstrate the utility of using sex-linked Cas9 strains for genetic control of animals.

Prior research indicates that lower resting-state functional coupling between two brain networks, lateral frontoparietal network (LFPN) and default mode network (DMN), relates to cognitive test performance, for children and adults. However, most of the research that led to this conclusion has been conducted with non-representative samples of individuals from higher-income backgrounds, and so further studies including participants from a broader range of socioeconomic backgrounds are required. Here, in a pre-registered study, we analyzed resting-state fMRI from 6839 children ages 9-10 years from the ABCD dataset. For children from households defined as being above poverty (family of 4 with income > $25,000, or family of 5+ with income > $35,000), we replicated prior findings; that is, we found that better performance on cognitive tests correlated with weaker LFPN-DMN coupling. For children from households defined as being in poverty, the direction of association was reversed, on average: better performance was instead directionally related to stronger LFPN-DMN connectivity, though there was considerable variability. Among children in households below poverty, the direction of this association was predicted in part by features of their environments, such as school type and parent-reported neighborhood safety. These results highlight the importance of including representative samples in studies of child cognitive development.

Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.

The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, -2 and -3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.

Cancer cells acquire genetic heterogeneity to escape from immune surveillance during tumor evolution, but a systematic approach to distinguish driver from passenger mutations is lacking. Here we investigate the impact of different immune pressure on tumor clonal dynamics and immune evasion mechanism, by combining massive parallel sequencing of immune edited tumors and CRISPR library screens in syngeneic mouse tumor model and co-culture system. We find that the core microRNA (miRNA) biogenesis and targeting machinery maintains the sensitivity of cancer cells to PD-1-independent T cell-mediated cytotoxicity. Genetic inactivation of the machinery or re-introduction of ANKRD52 frequent patient mutations dampens the JAK-STAT-interferon-γ signaling and antigen presentation in cancer cells, largely by abolishing miR-155-targeted silencing of suppressor of cytokine signaling 1 (SOCS1). Expression of each miRNA machinery component strongly correlates with intratumoral T cell infiltration in nearly all human cancer types. Our data indicate that the evolutionarily conserved miRNA pathway can be exploited by cancer cells to escape from T cell-mediated elimination and immunotherapy.