Single-cell genomic technologies provide an unprecedented opportunity to define molecular cell types in a data-driven fashion, but present unique data integration challenges. Many analyses require "mosaic integration", including both features shared across datasets and features exclusive to a single experiment. Previous computational integration approaches require that the input matrices share the same number of either genes or cells, and thus can use only shared features. To address this limitation, we derive a nonnegative matrix factorization algorithm for integrating single-cell datasets containing both shared and unshared features. The key advance is incorporating an additional metagene matrix that allows unshared features to inform the factorization. We demonstrate that incorporating unshared features significantly improves integration of single-cell RNA-seq, spatial transcriptomic, SNARE-seq, and cross-species datasets. We have incorporated the UINMF algorithm into the open-source LIGER R package ( https://github.com/welch-lab/liger ).

Despite the remarkable success of immunotherapy in many types of cancer, pancreatic ductal adenocarcinoma has yet to benefit. Innate immune cells are critical to anti-tumor immunosurveillance and recent studies have revealed that these populations possess a form of memory, termed trained innate immunity, which occurs through transcriptomic, epigenetic, and metabolic reprograming. Here we demonstrate that yeast-derived particulate β-glucan, an inducer of trained immunity, traffics to the pancreas, which causes a CCR2-dependent influx of monocytes/macrophages to the pancreas that display features of trained immunity. These cells can be activated upon exposure to tumor cells and tumor-derived factors, and show enhanced cytotoxicity against pancreatic tumor cells. In orthotopic models of pancreatic ductal adenocarcinoma, β-glucan treated mice show significantly reduced tumor burden and prolonged survival, which is further enhanced when combined with immunotherapy. These findings characterize the dynamic mechanisms and localization of peripheral trained immunity and identify an application of trained immunity to cancer.

Piezotronics with capacity of constructing adaptive and seamless interactions between electronics/machines and human/ambient are of value in Internet of Things, artificial intelligence and biomedical engineering. Here, we report a kind of highly sensitive strain sensor based on piezotronic tunneling junction (Ag/HfO2/n-ZnO), which utilizes the strain-induced piezoelectric potential to control the tunneling barrier height and width in parallel, and hence to synergistically modulate the electrical transport process. The piezotronic tunneling strain sensor has a high on/off ratio of 478.4 and high gauge factor of 4.8 × 105 at the strain of 0.10%, which is more than 17.8 times larger than that of a conventional Schottky-barrier based strain sensor in control group as well as some existing ZnO nanowire or nanobelt based sensors. This work provides in-depth understanding for the basic mechanism of piezotronic modulation on tunneling junction, and realizes the highly sensitive strain sensor of piezotronic tunneling junction on device scale, which has great potential in advanced micro/nano-electromechanical devices and systems.

Inexpensive and accessible sensors are accelerating data acquisition in animal ecology. These technologies hold great potential for large-scale ecological understanding, but are limited by current processing approaches which inefficiently distill data into relevant information. We argue that animal ecologists can capitalize on large datasets generated by modern sensors by combining machine learning approaches with domain knowledge. Incorporating machine learning into ecological workflows could improve inputs for ecological models and lead to integrated hybrid modeling tools. This approach will require close interdisciplinary collaboration to ensure the quality of novel approaches and train a new generation of data scientists in ecology and conservation.

Erratum in Nat Commun. 2022 Feb 25;13(1):1130.

Establishing a permanent human presence on the Moon or Mars requires a secure supply of oxygen for life support and refueling. The electrolysis of water has attracted significant attention in this regard as water-ice may exist on both the Moon and Mars. However, to date there has been no study examining how the lower gravitational fields on the Moon and Mars might affect gas-evolving electrolysis when compared to terrestrial conditions. Herein we provide experimental data on the effects of gravitational fields on water electrolysis from 0.166 g (lunar gravity) to 8 g (eight times the Earth's gravity) and show that electrolytic oxygen production is reduced by around 11% under lunar gravity with our system compared to operation at 1 g. Moreover, our results indicate that electrolytic data collected using less resource-intensive ground-based experiments at elevated gravity (>1 g) may be extrapolated to gravitational levels below 1 g.

Tousled-like kinases (TLKs) are nuclear serine-threonine kinases essential for genome maintenance and proper cell division in animals and plants. A major function of TLKs is to phosphorylate the histone chaperone proteins ASF1a and ASF1b to facilitate DNA replication-coupled nucleosome assembly, but how TLKs selectively target these critical substrates is unknown. Here, we show that TLK2 selectivity towards ASF1 substrates is achieved in two ways. First, the TLK2 catalytic domain recognizes consensus phosphorylation site motifs in the ASF1 C-terminal tail. Second, a short sequence at the TLK2 N-terminus docks onto the ASF1a globular N-terminal domain in a manner that mimics its histone H3 client. Disrupting either catalytic or non-catalytic interactions through mutagenesis hampers ASF1 phosphorylation by TLK2 and cell growth. Our results suggest that the stringent selectivity of TLKs for ASF1 is enforced by an unusual interaction mode involving mutual recognition of a short sequence motifs by both kinase and substrate.

Author information: (1)University of Cambridge, Department of Medicine, Cambridge, UK. dinesh.aggarwal@nhs.net. (2)Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. dinesh.aggarwal@nhs.net. (3)Cambridge University Hospital NHS Foundation Trust, Cambridge, UK. dinesh.aggarwal@nhs.net. (4)Wellcome Sanger Institute, Hinxton, Cambridge, UK. dinesh.aggarwal@nhs.net. (5)University of Cambridge, Department of Medicine, Cambridge, UK. (6)Cambridge University Hospital NHS Foundation Trust, Cambridge, UK. (7)Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK. (8)University of Cambridge, Department of Pathology, Division of Virology, Cambridge, UK. (9)Wellcome Sanger Institute, Hinxton, Cambridge, UK. (10)Department of Zoology, University of Oxford, Oxford, UK. (11)Institute of Evolutionary Virology, University of Edinburgh, Edinburgh, UK. (12)Public Health Directorate, Cambridgeshire County Council and Peterborough City Council, Peterborough, UK. (13)Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. (14)Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK. (15)Health, Safety & Regulated Facilities Division, University of Cambridge, Cambridge, UK. (16)University Information Services, University of Cambridge, Cambridge, UK. (17)Cambridge Covid-19 Testing Centre, Discovery Sciences, R&D, AstraZenenca, Cambridge, UK. (18)Charles River Laboratories, Chesterford Research Park, Saffron Walden, CB10 1XL, UK. (19)Institute for Manufacturing, University of Cambridge, Cambridge, UK. (20)MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK. (21)Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK. (22)Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK. (23)MRC-University of Glasgow Centre for Virus Research, Glasgow, UK. (24)University of Cambridge, Department of Medicine, Cambridge, UK. eh6@sanger.ac.uk. (25)Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. eh6@sanger.ac.uk. (26)Wellcome Sanger Institute, Hinxton, Cambridge, UK. eh6@sanger.ac.uk. (27)Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. eh6@sanger.ac.uk. (28)University of Cambridge, Department of Medicine, Cambridge, UK. njm25@cam.ac.uk. (29)Cambridge University Hospital NHS Foundation Trust, Cambridge, UK. njm25@cam.ac.uk. (30)Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK. njm25@cam.ac.uk. (31)NHS Blood and Transplant, Cambridge, UK. njm25@cam.ac.uk. (32)University of Cambridge, Department of Pathology, Division of Virology, Cambridge, UK. ig299@cam.ac.uk. (#)Contributed equally

Mitochondria host key metabolic processes vital for cellular energy provision and are central to cell fate decisions. They are subjected to unique genetic control by both nuclear DNA and their own multi-copy genome - mitochondrial DNA (mtDNA). Mutations in mtDNA often lead to clinically heterogeneous, maternally inherited diseases that display different organ-specific presentation at any stage of life. For a long time, genetic manipulation of mammalian mtDNA has posed a major challenge, impeding our ability to understand the basic mitochondrial biology and mechanisms underpinning mitochondrial disease. However, an important new tool for mtDNA mutagenesis has emerged recently, namely double-stranded DNA deaminase (DddA)-derived cytosine base editor (DdCBE). Here, we test this emerging tool for in vivo use, by delivering DdCBEs into mouse heart using adeno-associated virus (AAV) vectors and show that it can install desired mtDNA edits in adult and neonatal mice. This work provides proof-of-concept for use of DdCBEs to mutagenize mtDNA in vivo in post-mitotic tissues and provides crucial insights into potential translation to human somatic gene correction therapies to treat primary mitochondrial disease phenotypes.

Social animals actively engage in contact with conspecifics and experience stress upon isolation. However, the neural mechanisms coordinating the sensing and seeking of social contacts are unclear. Here we report that amylin-calcitonin receptor (Calcr) signaling in the medial preoptic area (MPOA) mediates affiliative social contacts among adult female mice. Isolation of females from free social interactions first induces active contact-seeking, then depressive-like behavior, concurrent with a loss of Amylin mRNA expression in the MPOA. Reunion with peers induces physical contacts, activates both amylin- and Calcr-expressing neurons, and leads to a recovery of Amylin mRNA expression. Chemogenetic activation of amylin neurons increases and molecular knockdown of either amylin or Calcr attenuates contact-seeking behavior, respectively. Our data provide evidence in support of a previously postulated origin of social affiliation in mammals.

The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.

Nickel-based complex oxides have served as a playground for decades in the quest for a copper-oxide analog of the high-temperature superconductivity. They may provide clues towards understanding the mechanism and an alternative route for high-temperature superconductors. The recent discovery of superconductivity in the infinite-layer nickelate thin films has fulfilled this pursuit. However, material synthesis remains challenging, direct demonstration of perfect diamagnetism is still missing, and understanding of the role of the interface and bulk to the superconducting properties is still lacking. Here, we show high-quality Nd0.8Sr0.2NiO2 thin films with different thicknesses and demonstrate the interface and strain effects on the electrical, magnetic and optical properties. Perfect diamagnetism is achieved, confirming the occurrence of superconductivity in the films. Unlike the thick films in which the normal-state Hall-coefficient changes signs as the temperature decreases, the Hall-coefficient of films thinner than 5.5 nm remains negative, suggesting a thickness-driven band structure modification. Moreover, X-ray absorption spectroscopy reveals the Ni-O hybridization nature in doped infinite-layer nickelates, and the hybridization is enhanced as the thickness decreases. Consistent with band structure calculations on the nickelate/SrTiO3 heterostructure, the interface and strain effect induce a dominating electron-like band in the ultrathin film, thus causing the sign-change of the Hall-coefficient.

Update of medRxiv. 2021 Jun 23;:

Mitogen-activated protein kinase (MAPK) cascades play an important role in innate immunity against various pathogens in plants and animals. However, we know very little about the importance of MAPK cascades in plant defense against viral pathogens. Here, we used a positive-strand RNA necrovirus, beet black scorch virus (BBSV), as a model to investigate the relationship between MAPK signaling and virus infection. Our findings showed that BBSV infection activates MAPK signaling, whereas viral coat protein (CP) counteracts MAPKKKα-mediated antiviral defense. CP does not directly target MAPKKKα, instead it competitively interferes with the binding of 14-3-3a to MAPKKKα in a dose-dependent manner. This results in the instability of MAPKKKα and subversion of MAPKKKα-mediated antiviral defense. Considering the conservation of 14-3-3-binding sites in the CPs of diverse plant viruses, we provide evidence that 14-3-3-MAPKKKα defense signaling module is a target of viral effectors in the ongoing arms race of defense and viral counter-defense.

Interface engineering is a proven strategy to improve the efficiency of thin film semiconductor based solar energy conversion devices. Ta3N5 thin film photoanode is a promising candidate for photoelectrochemical (PEC) water splitting. Yet, a concerted effort to engineer both the bottom and top interfaces of Ta3N5 thin film photoanode is still lacking. Here, we employ n-type In:GaN and p-type Mg:GaN to modify the bottom and top interfaces of Ta3N5 thin film photoanode, respectively. The obtained In:GaN/Ta3N5/Mg:GaN heterojunction photoanode shows enhanced bulk carrier separation capability and better injection efficiency at photoanode/electrolyte interface, which lead to a record-high applied bias photon-to-current efficiency of 3.46% for Ta3N5-based photoanode. Furthermore, the roles of the In:GaN and Mg:GaN layers are distinguished through mechanistic studies. While the In:GaN layer contributes mainly to the enhanced bulk charge separation efficiency, the Mg:GaN layer improves the surface charge inject efficiency. This work demonstrates the crucial role of proper interface engineering for thin film-based photoanode in achieving efficient PEC water splitting.

The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments, such as Parkinsonism and dementia. Their synthesis via chemical and biological routes are therefore of industrial relevance, but suffer from several challenges. Current chemical synthesis methods involve long, multi-step reactions with harsh conditions and are not enantioselective; biological methods utilizing ergot fungi, produce an assortment of products that complicate product recovery, and are susceptible to strain degradation. Reconstituting the ergot alkaloid pathway in a strain strongly amenable for liquid fermentation, could potentially resolve these issues. In this work, we report the production of the main ergoline therapeutic precursor, D-lysergic acid, to a titre of 1.7 mg L-1 in a 1 L bioreactor. Our work demonstrates the proof-of-concept for the biological production of ergoline-derived compounds from sugar in an engineered yeast chassis.

Polyolefins with branches produced by ethylene alone via chain walking are highly desired in industry. Selective branch formation from uncontrolled chain walking is a long-standing challenge to generate exclusively branched polyolefins, however. Here we report such desirable microstructures in ethylene polymerization by using sterically constrained α-diimine nickel(II)/palladium(II) catalysts at 30 °C-90 °C that fall into industrial conditions. Branched polyethylenes with exclusive branch pattern of methyl branches (99%) and notably selective branch distribution of 1,4-Me2 unit (86%) can be generated. The ultrahigh degree of branching (>200 Me/1000 C) enables the well-defined product to mimic ethylene-propylene copolymers. More interestingly, branch distribution is predictable and computable by using a simple statistical model of p(1-p)n (p: the probability of branch formation). Mechanistic insights into the branch formation including branch pattern and branch distribution by an in-depth density functional theory (DFT) calculation are elucidated.

The possibility that Arctic sea ice loss weakens mid-latitude westerlies, promoting more severe cold winters, has sparked more than a decade of scientific debate, with apparent support from observations but inconclusive modelling evidence. Here we show that sixteen models contributing to the Polar Amplification Model Intercomparison Project simulate a weakening of mid-latitude westerlies in response to projected Arctic sea ice loss. We develop an emergent constraint based on eddy feedback, which is 1.2 to 3 times too weak in the models, suggesting that the real-world weakening lies towards the higher end of the model simulations. Still, the modelled response to Arctic sea ice loss is weak: the North Atlantic Oscillation response is similar in magnitude and offsets the projected response to increased greenhouse gases, but would only account for around 10% of variations in individual years. We further find that relationships between Arctic sea ice and atmospheric circulation have weakened recently in observations and are no longer inconsistent with those in models.

Predicting the pathogenicity of biallelic missense variants can be challenging. Here, we use a deficit of observed homozygous carriers of missense variants, versus an expected number in a set of 153,054 chip-genotyped Icelanders, to identify potentially pathogenic genotypes. We follow three missense variants with a complete deficit of homozygosity and find that their pathogenic effect in homozygous state ranges from severe childhood disease to early embryonic lethality. One of these variants is in CPSF3, a gene not previously linked to disease. From a set of clinically sequenced Icelanders, and by sequencing archival samples targeted through the Icelandic genealogy, we find four homozygous carriers. Additionally, we find two homozygous carriers of Mexican descent of another missense variant in CPSF3. All six homozygous carriers of missense variants in CPSF3 show severe intellectual disability, seizures, microcephaly, and abnormal muscle tone. Here, we show how the absence of certain homozygous genotypes from a large population set can elucidate causes of previously unexplained recessive diseases and early miscarriage.

Rho family mechano-signaling through the actin cytoskeleton positively regulates physiological TEAD/YAP transcription, while the evolutionarily conserved Hippo tumor suppressor pathway antagonizes this transcription through YAP cytoplasmic localization/degradation. The mechanisms responsible for oncogenic dysregulation of these pathways, their prevalence in tumors, as well as how such dysregulation can be therapeutically targeted are not resolved. We demonstrate that p53 DNA contact mutants in human tumors, indirectly hyperactivate RhoA/ROCK1/actomyosin signaling, which is both necessary and sufficient to drive oncogenic TEAD/YAP transcription. Moreover, we demonstrate that recurrent lesions in the Hippo pathway depend on physiological levels of ROCK1/actomyosin signaling for oncogenic TEAD/YAP transcription. Finally, we show that ROCK inhibitors selectively antagonize proliferation and motility of human tumors with either mechanism. Thus, we identify a cancer driver paradigm and a precision medicine approach for selective targeting of human malignancies driven by TEAD/YAP transcription through mechanisms that either upregulate or depend on homeostatic RhoA mechano-signaling.

The intestine is a central regulator of metabolic homeostasis. Dietary inputs are absorbed through the gut, which senses their nutritional value and relays hormonal information to other organs to coordinate systemic energy balance. However, the gut-derived hormones affecting metabolic and behavioral responses are poorly defined. Here we show that the endocrine cells of the Drosophila gut sense nutrient stress through a mechanism that involves the TOR pathway and in response secrete the peptide hormone allatostatin C, a Drosophila somatostatin homolog. Gut-derived allatostatin C induces secretion of glucagon-like adipokinetic hormone to coordinate food intake and energy mobilization. Loss of gut Allatostatin C or its receptor in the adipokinetic-hormone-producing cells impairs lipid and sugar mobilization during fasting, leading to hypoglycemia. Our findings illustrate a nutrient-responsive endocrine mechanism that maintains energy homeostasis under nutrient-stress conditions, a function that is essential to health and whose failure can lead to metabolic disorders.

DENR and MCTS1 have been identified as oncogenes in several different tumor entities. The heterodimeric DENR·MCTS1 protein complex promotes translation of mRNAs containing upstream Open Reading Frames (uORFs). We show here that DENR is phosphorylated on Serine 73 by Cyclin B/CDK1 and Cyclin A/CDK2 at the onset of mitosis, and then dephosphorylated as cells exit mitosis. Phosphorylation of Ser73 promotes mitotic stability of DENR protein and prevents its cleavage at Asp26. This leads to enhanced translation of mRNAs involved in mitosis. Indeed, we find that roughly 40% of all mRNAs with elevated translation in mitosis are DENR targets. In the absence of DENR or of Ser73 phosphorylation, cells display elevated levels of aberrant mitoses and cell death. This provides a mechanism how the cell cycle regulates translation of a subset of mitotically relevant mRNAs during mitosis.

Conductin/axin2 is a scaffold protein negatively regulating the pro-proliferative Wnt/β-catenin signaling pathway. Accumulation of scaffold proteins in condensates frequently increases their activity, but whether condensation contributes to Wnt pathway inhibition by conductin remains unclear. Here, we show that the Gαi2 subunit of trimeric G-proteins induces conductin condensation by targeting a polymerization-inhibiting aggregon in its RGS domain, thereby promoting conductin-mediated β-catenin degradation. Consistently, transient Gαi2 expression inhibited, whereas knockdown activated Wnt signaling via conductin. Colorectal cancers appear to evade Gαi2-induced Wnt pathway suppression by decreased Gαi2 expression and inactivating mutations, associated with shorter patient survival. Notably, the Gαi2-activating drug guanabenz inhibited Wnt signaling via conductin, consequently reducing colorectal cancer growth in vitro and in mouse models. In summary, we demonstrate Wnt pathway inhibition via Gαi2-triggered conductin condensation, suggesting a tumor suppressor function for Gαi2 in colorectal cancer, and pointing to the FDA-approved drug guanabenz for targeted cancer therapy.

Homologous recombination (HR) is a ubiquitous and efficient process that serves the repair of severe forms of DNA damage and the generation of genetic diversity during meiosis. HR can proceed via multiple pathways with different outcomes that may aid or impair genome stability and faithful inheritance, underscoring the importance of HR quality control. Human Bloom's syndrome (BLM, RecQ family) helicase plays central roles in HR pathway selection and quality control via unexplored molecular mechanisms. Here we show that BLM's multi-domain structural architecture supports a balance between stabilization and disruption of displacement loops (D-loops), early HR intermediates that are key targets for HR regulation. We find that this balance is markedly shifted toward efficient D-loop disruption by the presence of BLM's interaction partners Topoisomerase IIIα-RMI1-RMI2, which have been shown to be involved in multiple steps of HR-based DNA repair. Our results point to a mechanism whereby BLM can differentially process D-loops and support HR control depending on cellular regulatory mechanisms.

Liquid-liquid immiscibility has been widely observed in iron alloy systems at ambient pressure and is important for the structure and dynamics in iron cores of rocky planets. While such previously known liquid immiscibility has been demonstrated to disappear at relatively low pressures, here we report immiscible S(±Si,O)-rich liquid and H(±C)-rich liquid above ~20 GPa, corresponding to conditions of the Martian core. Mars' cosmochemically estimated core composition is likely in the miscibility gap, and the separation of two immiscible liquids could have driven core convection and stable stratification, which explains the formation and termination of the Martian planetary magnetic field. In addition, we observed liquid immiscibility in Fe-S-H(±Si,O,C) at least to 118 GPa, suggesting that it can occur in the Earth's topmost outer core and form a low-velocity layer below the core-mantle boundary.

Electrochemical oxygen reduction could proceed via either 4e--pathway toward maximum chemical-to-electric energy conversion or 2e--pathway toward onsite H2O2 production. Bulk Pt catalysts are known as the best monometallic materials catalyzing O2-to-H2O conversion, however, controversies on the reduction product selectivity are noted for atomic dispersed Pt catalysts. Here, we prepare a series of carbon supported Pt single atom catalyst with varied neighboring dopants and Pt site densities to investigate the local coordination environment effect on branching oxygen reduction pathway. Manipulation of 2e- or 4e- reduction pathways is demonstrated through modification of the Pt coordination environment from Pt-C to Pt-N-C and Pt-S-C, giving rise to a controlled H2O2 selectivity from 23.3% to 81.4% and a turnover frequency ratio of H2O2/H2O from 0.30 to 2.67 at 0.4 V versus reversible hydrogen electrode. Energetic analysis suggests both 2e- and 4e- pathways share a common intermediate of *OOH, Pt-C motif favors its dissociative reduction while Pt-S and Pt-N motifs prefer its direct protonation into H2O2. By taking the Pt-N-C catalyst as a stereotype, we further demonstrate that the maximum H2O2 selectivity can be manipulated from 70 to 20% with increasing Pt site density, providing hints for regulating the stepwise oxygen reduction in different application scenarios.

Stomatal opening requires the provision of energy in the form of ATP for proton pumping across the guard cell (GC) plasma membrane and for associated metabolic rearrangements. The source of ATP for GCs is a matter of ongoing debate that is mainly fuelled by controversies around the ability of GC chloroplasts (GCCs) to perform photosynthesis. By imaging compartment-specific fluorescent ATP and NADPH sensor proteins in Arabidopsis, we show that GC photosynthesis is limited and mitochondria are the main source of ATP. Unlike mature mesophyll cell (MC) chloroplasts, which are impermeable to cytosolic ATP, GCCs import cytosolic ATP through NUCLEOTIDE TRANSPORTER (NTT) proteins. GCs from ntt mutants exhibit impaired abilities for starch biosynthesis and stomatal opening. Our work shows that GCs obtain ATP and carbohydrates via different routes from MCs, likely to compensate for the lower chlorophyll contents and limited photosynthesis of GCCs.

Microbial biocontainment is an essential goal for engineering safe, next-generation living therapeutics. However, the genetic stability of biocontainment circuits, including kill switches, is a challenge that must be addressed. Kill switches are among the most difficult circuits to maintain due to the strong selection pressure they impart, leading to high potential for evolution of escape mutant populations. Here we engineer two CRISPR-based kill switches in the probiotic Escherichia coli Nissle 1917, a single-input chemical-responsive switch and a 2-input chemical- and temperature-responsive switch. We employ parallel strategies to address kill switch stability, including functional redundancy within the circuit, modulation of the SOS response, antibiotic-independent plasmid maintenance, and provision of intra-niche competition by a closely related strain. We demonstrate that strains harboring either kill switch can be selectively and efficiently killed inside the murine gut, while strains harboring the 2-input switch are additionally killed upon excretion. Leveraging redundant strategies, we demonstrate robust biocontainment of our kill switch strains and provide a template for future kill switch development.

Comment in Trends Endocrinol Metab. 2022 Aug;33(8):533-535.

Sodium-based dual-ion batteries have received increased attention owing to their appealing cell voltage (i.e., >3 V) and cost-effective features. However, the development of high-performance anode materials is one of the key elements for exploiting this electrochemical energy storage system at practical levels. Here, we report a source-template synthetic strategy for fabricating a variety of nanowire-in-nanotube MSxTey@C (M = Mo, W, Re) structures with an in situ-grown carbon film coating, termed as nanocables. Among the various materials prepared, the MoS1.5Te0.5@C nanocables are investigated as negative electrode active material in combination with expanded graphite at the positive electrode and NaPF6-based non-aqueous electrolyte solutions for dual-ion storage in coin cell configuration. As a result, the dual-ion lab-scale cells demonstrate a prolonged cycling lifespan with 97% capacity retention over 1500 cycles and a reversible capacity of about 101 mAh g-1 at specific capacities (based on the mass of the anode) of 1.0 A g-1 and 5.0 A g-1, respectively.

The vomeronasal system plays an essential role in sensing various environmental chemical cues. Here we show that mice exposed to blood and, consequently, hemoglobin results in the activation of vomeronasal sensory neurons expressing a specific vomeronasal G protein-coupled receptor, Vmn2r88, which is mediated by the interaction site, Gly17, on hemoglobin. The hemoglobin signal reaches the medial amygdala (MeA) in both male and female mice. However, it activates the dorsal part of ventromedial hypothalamus (VMHd) only in lactating female mice. As a result, in lactating mothers, hemoglobin enhances digging and rearing behavior. Manipulation of steroidogenic factor 1 (SF1)-expressing neurons in the VMHd is sufficient to induce the hemoglobin-mediated behaviors. Our results suggest that the oxygen-carrier hemoglobin plays a role as a chemosensory signal, eliciting behavioral responses in mice in a state-dependent fashion.

Biaryl scaffolds are found in natural products and drug molecules and exhibit a wide range of biological activities. In past decade, the transition metal-catalyzed C-H arylation reaction came out as an effective tool for the construction of biaryl motifs. However, traditional transition metal-catalyzed C-H arylation reactions have limitations like harsh reaction conditions, narrow substrate scope, use of additives etc. and therefore encouraged synthetic chemists to look for alternate greener approaches. This review aims to draw a general overview on C-H bond arylation reactions for the formation of C-C bonds with the aid of different methodologies, majorly highlighting on greener and sustainable approaches.

Dissipative Kerr soliton microcombs have been recognized as a promising multi-wavelength laser source for fiber optical communications, as their comb lines possess frequency and phase stability far beyond the independent lasers. Especially, for coherent optical communications, a highly beneficial but rarely explored target is to re-generate a Kerr soliton microcomb as the receiver local oscillators that conserve the frequency and phase property of the incoming data carriers, so that to enable coherent detection with minimized optical and electrical compensations. Here, via pump laser conveying and two-point locking, we implement re-generation of a Kerr soliton microcomb that faithfully clones the frequency and phase of another microcomb sent from 50 km away. Moreover, by using the coherence-cloned soliton microcombs as carriers and local oscillators, we demonstrate terabit coherent data interconnect, wherein traditional digital processes for frequency offset estimation are totally dispensed with, and carrier phase estimation is substantially simplified via slowed-down estimation rate per channel and joint estimation among multiple channels. Our work reveals that, in addition to providing a multitude of laser tones, regulating the frequency and phase of Kerr soliton microcombs among transmitters and receivers can significantly improve optical coherent communication in terms of performance, power consumption, and simplicity.

Ultrafast infrared nano-imaging has demonstrated access to ultrafast carrier dynamics on the nanoscale in semiconductor, correlated-electron, or polaritonic materials. However, mostly limited to short-lived transient states, the contrast obtained has remained insufficient to probe important long-lived excitations, which arise from many-body interactions induced by strong perturbation among carriers, lattice phonons, or molecular vibrations. Here, we demonstrate ultrafast infrared nano-imaging based on excitation modulation and sideband detection to characterize electron and vibration dynamics with nano- to micro-second lifetimes. As an exemplary application to quantum materials, in phase-resolved ultrafast nano-imaging of the photoinduced insulator-to-metal transition in vanadium dioxide, a distinct transient nano-domain behavior is quantified. In another application to lead halide perovskites, transient vibrational nano-FTIR spatially resolves the excited-state polaron-cation coupling underlying the photovoltaic response. These examples show how heterodyne pump-probe nano-spectroscopy with low-repetition excitation extends ultrafast infrared nano-imaging to probe elementary processes in quantum and molecular materials in space and time.

Protein kinase inhibitors are amongst the most successful cancer treatments, but targetable kinases activated by genomic abnormalities are rare in T cell acute lymphoblastic leukemia. Nevertheless, kinases can be activated in the absence of genetic defects. Thus, phosphoproteomics can provide information on pathway activation and signaling networks that offer opportunities for targeted therapy. Here, we describe a mass spectrometry-based global phosphoproteomic profiling of 11 T cell acute lymphoblastic leukemia cell lines to identify targetable kinases. We report a comprehensive dataset consisting of 21,000 phosphosites on 4,896 phosphoproteins, including 217 kinases. We identify active Src-family kinases signaling as well as active cyclin-dependent kinases. We validate putative targets for therapy ex vivo and identify potential combination treatments, such as the inhibition of the INSR/IGF-1R axis to increase the sensitivity to dasatinib treatment. Ex vivo validation of selected drug combinations using patient-derived xenografts provides a proof-of-concept for phosphoproteomics-guided design of personalized treatments.

A possible engineering of materials with diverse bio- and nano-applications relies on robust self-assembly of oligonucleotides. Bottom-up approach utilizing guanine-rich DNA oligonucleotides can lead to formation of G-wires, nanostructures consisting of continuous stacks of G-quartets. However, G-wire structure and self-assembly process remain poorly understood, although they are crucial for optimizing properties needed for specific applications. Herein, we use nuclear magnetic resonance to get insights at molecular level on how chosen short, guanine-rich oligonucleotides self-assemble into G-wires, whereas complementary methods are used for their characterization. Additionally, unravelling mechanistic details enable us to guide G-wire self-assembly in a controlled manner. MD simulations provide insight why loop residues with considerably different properties, i.e., hydrogen-bond affinity, stacking interactions, electronic effects and hydrophobicity extensively increase or decrease G-wire length. Our results provide fundamental understanding of G-wire self-assembly process useful for future design of nanomaterials with specific properties.

The B-family multi-subunit DNA polymerase ζ (Polζ) is important for translesion DNA synthesis (TLS) during replication, due to its ability to extend synthesis past nucleotides opposite DNA lesions and mismatched base pairs. We present a cryo-EM structure of Saccharomyces cerevisiae Polζ with an A:C mismatch at the primer terminus. The structure shows how the Polζ active site responds to the mismatched duplex DNA distortion, including the loosening of key protein-DNA interactions and a fingers domain in an "open" conformation, while the incoming dCTP is still able to bind for the extension reaction. The structure of the mismatched DNA-Polζ ternary complex reveals insights into mechanisms that either stall or favor continued DNA synthesis in eukaryotes.

One of the most critical steps in cereal threshing is the ease with which seeds are detached from sticky glumes. Naked grains with low glume coverage have dramatically increased threshing efficiency and seed quality. Here, we demonstrate that GC1 (Glume Coverage 1), encoding an atypical G protein γ subunit, negatively regulates sorghum glume coverage. Naturally truncated variations of GC1 C-terminus accumulate at higher protein levels and affect the stability of a patatin-related phospholipase SbpPLAII-1. A strong positive selection signature around the GC1 genic region is found in the naked sorghum cultivars. Our findings reveal a crucial event during sorghum domestication through a subtle regulation of glume development by GC1 C-terminus variation, and establish a strategy for future breeding of naked grains.

An infinite number of crystal structures in a multicomponent alloy with a specific atomic ratio can be devised, although only thermodynamically-stable phases can be formed. Here, we experimentally show the first example of a layer-structured pseudo-binary alloy, theoretically called Z3-FePd3. This Z3 structure is achieved by adding a small amount of In, which is immiscible with Fe but miscible with Pd and consists of an alternate L10 (CuAu-type)-PdFePd trilayer and Pd-In ordered alloy monolayer along the c axis. First-principles calculations strongly support that the specific inter-element miscibility of In atoms stabilizes the thermodynamically-unstable Z3-FePd3 phase without significantly changing the original density of states of the Z3-FePd3 phase. Our results demonstrate that the specific inter-element miscibility can switch stable structures and manipulate the material nature with a slight composition change.

Large-scale, highly integrated and low-power-consuming hardware is becoming progressively more important for realizing optical neural networks (ONNs) capable of advanced optical computing. Traditional experimental implementations need N2 units such as Mach-Zehnder interferometers (MZIs) for an input dimension N to realize typical computing operations (convolutions and matrix multiplication), resulting in limited scalability and consuming excessive power. Here, we propose the integrated diffractive optical network for implementing parallel Fourier transforms, convolution operations and application-specific optical computing using two ultracompact diffractive cells (Fourier transform operation) and only N MZIs. The footprint and energy consumption scales linearly with the input data dimension, instead of the quadratic scaling in the traditional ONN framework. A ~10-fold reduction in both footprint and energy consumption, as well as equal high accuracy with previous MZI-based ONNs was experimentally achieved for computations performed on the MNIST and Fashion-MNIST datasets. The integrated diffractive optical network (IDNN) chip demonstrates a promising avenue towards scalable and low-power-consumption optical computational chips for optical-artificial-intelligence.

Restricted ambient temperature and slow heat replenishment in the phase transition of water molecules severely limit the performance of the evaporation-induced hydrovoltaic generators. Here we demonstrate a heat conduction effect enhanced hydrovoltaic power generator by integrating a flexible ionic thermoelectric gelatin material with a porous dual-size Al2O3 hydrovoltaic generator. In the hybrid heat conduction effect enhanced hydrovoltaic power generator, the ionic thermoelectric gelatin material can effectively improve the heat conduction between hydrovoltaic generator and near environment, thus increasing the water evaporation rate to improve the output voltage. Synergistically, hydrovoltaic generator part with continuous water evaporation can induce a constant temperature difference for the thermoelectric generator. Moreover, the system can efficiently achieve solar-to-thermal conversion to raise the temperature difference, accompanied by a stable open circuit voltage of 6.4 V for the hydrovoltaic generator module, the highest value yet.

Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus, a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions.

Transport of lipids across membranes is fundamental for diverse biological pathways in cells. Multiple ion-coupled transporters take part in lipid translocation, but their mechanisms remain largely unknown. Major facilitator superfamily (MFS) lipid transporters play central roles in cell wall synthesis, brain development and function, lipids recycling, and cell signaling. Recent structures of MFS lipid transporters revealed overlapping architectural features pointing towards a common mechanism. Here we used cysteine disulfide trapping, molecular dynamics simulations, mutagenesis analysis, and transport assays in vitro and in vivo, to investigate the mechanism of LtaA, a proton-dependent MFS lipid transporter essential for lipoteichoic acid synthesis in the pathogen Staphylococcus aureus. We reveal that LtaA displays asymmetric lateral openings with distinct functional relevance and that cycling through outward- and inward-facing conformations is essential for transport activity. We demonstrate that while the entire amphipathic central cavity of LtaA contributes to lipid binding, its hydrophilic pocket dictates substrate specificity. We propose that LtaA catalyzes lipid translocation by a 'trap-and-flip' mechanism that might be shared among MFS lipid transporters.

Randomized clinical trials (RCT) are the gold standard for informing treatment decisions. Observational studies are often plagued by selection bias, and expert-selected covariates may insufficiently adjust for confounding. We explore how unstructured clinical text can be used to reduce selection bias and improve medical practice. We develop a framework based on natural language processing to uncover interpretable potential confounders from text. We validate our method by comparing the estimated hazard ratio (HR) with and without the confounders against established RCTs. We apply our method to four cohorts built from localized prostate and lung cancer datasets from the Stanford Cancer Institute and show that our method shifts the HR estimate towards the RCT results. The uncovered terms can also be interpreted by oncologists for clinical insights. We present this proof-of-concept study to enable more credible causal inference using observational data, uncover meaningful insights from clinical text, and inform high-stakes medical decisions.

Open access to sequence data is a cornerstone of biology and biodiversity research, but has created tension under the United Nations Convention on Biological Diversity (CBD). Policy decisions could compromise research and development, unless a practical multilateral solution is implemented.

The precise precursor supply is a precondition for controllable growth of two-dimensional (2D) transition metal dichalcogenides (TMDs). Although great efforts have been devoted to modulating the transition metal supply, few effective methods of chalcogen feeding control were developed. Here we report a strategy of using active chalcogen monomer supply to grow high-quality TMDs in a robust and controllable manner, e.g., MoS2 monolayers perform representative photoluminescent circular helicity of ~92% and electronic mobility of ~42 cm2V-1s-1. Meanwhile, a uniform quaternary TMD alloy with three different anions, i.e., MoS2(1-x-y)Se2xTe2y, was accomplished. Our mechanism study revealed that the active chalcogen monomers can bind and diffuse freely on a TMD surface, which enables the effective nucleation, reaction, vacancy healing and alloy formation during the growth. Our work offers a degree of freedom for the controllable synthesis of 2D compounds and their alloys, benefiting the development of high-end devices with desired 2D materials.

Plastic deformation in crystals is mediated by the motion of line defects known as dislocations. For decades, dislocation activity has been treated as a homogeneous, smooth continuous process. However, it is now recognized that plasticity can be determined by long-range correlated and intermittent collective dislocation processes, known as avalanches. Here we demonstrate in body-centered cubic Nb how the long-range and scale-free dynamics at room temperature are progressively quenched out with decreasing temperature, eventually revealing intermittency with a characteristic length scale that approaches the Burgers vector itself. Plasticity is shown to be bimodal across the studied temperature regime, with conventional thermally-activated smooth plastic flow ('mild') coexisting with sporadic bursts ('wild') controlled by athermal screw dislocation activity, thereby violating the classical notion of temperature-dependent screw dislocation motion at low temperatures. An abrupt increase of the athermal avalanche component is identified at the critical temperature of the material. Our results indicate that plasticity at any scale can be understood in terms of the coexistence of these mild and wild modes of deformation, which could help design better alloys by suppressing one of the two modes in desired temperature windows.

Ionic covalent organic framework membranes (iCOFMs) hold great promise in ion conduction-relevant applications because the high content and monodispersed ionic groups could afford superior ion conduction. The key to push the upper limit of ion conductivity is to maximize the ion exchange capacity (IEC). Here, we explore iCOFMs with a superhigh ion exchange capacity of 4.6 mmol g-1, using a dual-activation interfacial polymerization strategy. Fukui function is employed as a descriptor of monomer reactivity. We use Brønsted acid to activate aldehyde monomers in organic phase and Brønsted base to activate ionic amine monomers in water phase. After the dual-activation, the reaction between aldehyde monomer and amine monomer at the water-organic interface is significantly accelerated, leading to iCOFMs with high crystallinity. The resultant iCOFMs display a prominent proton conductivity up to 0.66 S cm-1, holding great promise in ion transport and ionic separation applications.

Postoperative abdominal infectious complication (AIC) is associated with metastasis in locally advanced gastric cancer (GC) patients after radical gastrectomy. However, the underlying mechanism remains unclear. Herein, we report that neutrophil extracellular traps (NETs), the DNA meshes released by neutrophils in response to infection, could promote GC cells proliferation, invasion, migration and epithelial-mesenchymal transition dependent on TGF-β signaling. Then we model nude mice with cecal puncture without ligation to simulate postoperative AIC and find that NETs in peripheral blood and ascites fluid facilitate GC cells extravasation and implantation into liver and peritoneum for proliferation and metastasis. Notably, TGF-β signaling inhibitor LY 2157299 could effectively impede liver and peritoneal metastasis but not concurrently aggravate sepsis in those AIC-bearing nude mice. These findings implicate that targeting downstream effectors of NETs such as TGF-β signaling might provide potential therapeutic prospect to reduce the risk of GC metastasis.

Author information: (1)University of Cambridge, Department of Medicine, Cambridge, UK. dinesh.aggarwal@nhs.net. (2)Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. dinesh.aggarwal@nhs.net. (3)Cambridge University Hospital NHS Foundation Trust, Cambridge, UK. dinesh.aggarwal@nhs.net. (4)Wellcome Sanger Institute, Hinxton, Cambridge, UK. dinesh.aggarwal@nhs.net. (5)Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK. (6)Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. (7)Imperial College London, Department of Infectious Disease Epidemiology, London, UK. (8)University of Cambridge, Cambridge University Libraries, Cambridge, UK. (9)Public Health England National Infections Service, Field Service, Leeds, UK. (10)Public Health England, National Infections Service, Field Service, Nottingham, UK. (11)University of Cambridge, Department of Medicine, Cambridge, UK. (12)Cambridge University Hospital NHS Foundation Trust, Cambridge, UK. (13)Wellcome Sanger Institute, Hinxton, Cambridge, UK. (14)University of Cambridge, Department of Medicine, Cambridge, UK. eh6@sanger.ac.uk. (15)Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK. eh6@sanger.ac.uk. (16)Wellcome Sanger Institute, Hinxton, Cambridge, UK. eh6@sanger.ac.uk. (17)University of Cambridge, Department of Public Health and Primary Care, Cambridge, UK. eh6@sanger.ac.uk. (#)Contributed equally

The antiviral immune response to SARS-CoV-2 infection can limit viral spread and prevent development of pneumonic COVID-19. However, the protective immunological response associated with successful viral containment in the upper airways remains unclear. Here, we combine a multi-omics approach with longitudinal sampling to reveal temporally resolved protective immune signatures in non-pneumonic and ambulatory SARS-CoV-2 infected patients and associate specific immune trajectories with upper airway viral containment. We see a distinct systemic rather than local immune state associated with viral containment, characterized by interferon stimulated gene (ISG) upregulation across circulating immune cell subsets in non-pneumonic SARS-CoV2 infection. We report reduced cytotoxic potential of Natural Killer (NK) and T cells, and an immune-modulatory monocyte phenotype associated with protective immunity in COVID-19. Together, we show protective immune trajectories in SARS-CoV2 infection, which have important implications for patient prognosis and the development of immunomodulatory therapies.

Time-restricted feeding (TRF) improves metabolic health. Both early TRF (eTRF, food intake restricted to the early part of the day) and mid-day TRF (mTRF, food intake restricted to the middle of the day) have been shown to have metabolic benefits. However, the two regimens have yet to be thoroughly compared. We conducted a five-week randomized trial to compare the effects of the two TRF regimens in healthy individuals without obesity (ChiCTR2000029797). The trial has completed. Ninety participants were randomized to eTRF (n=30), mTRF (n=30), or control groups (n=30) using a computer-based random-number generator. Eighty-two participants completed the entire five-week trial and were analyzed (28 in eTRF, 26 in mTRF, 28 in control groups). The primary outcome was the change in insulin resistance. Researchers who assessed the outcomes were blinded to group assignment, but participants and care givers were not. Here we show that eTRF was more effective than mTRF at improving insulin sensitivity. Furthermore, eTRF, but not mTRF, improved fasting glucose, reduced total body mass and adiposity, ameliorated inflammation, and increased gut microbial diversity. No serious adverse events were reported during the trial. In conclusion, eTRF showed greater benefits for insulin resistance and related metabolic parameters compared with mTRF. Clinical Trial Registration URL: http://www.chictr.org.cn/showproj.aspx?proj=49406 .

During decidualization in rodents, uterine stroma undergoes extensive reprograming into distinct cells, forming the discrete regions defined as the primary decidual zone (PDZ), the secondary decidual zone (SDZ) and the layer of undifferentiated stromal cells respectively. Here we show that uterine deletion of Men1, a member of the histone H3K4 methyltransferase complex, disrupts the terminal differentiation of stroma, resulting in chaotic decidualization and pregnancy failure. Genome-wide epigenetic profile reveals that Men1 binding in chromatin recapitulates H3K4me3 distribution. Further transcriptomic investigation demonstrates that Men1 directly regulates the expression of PTX3, an extra-cellular trap for FGF2 in decidual cells. Decreased Ptx3 upon Men1 ablation leads to aberrant activation of ERK1/2 in the SDZ due to the unrestrained FGF2 signal emanated from undifferentiated stromal cells, which blunt BMP2 induction and decidualization. In brief, our study provides genetic and molecular mechanisms for epigenetic rewiring mediated decidual regionalization by Men1 and sheds new light on pregnancy maintenance.

The bacterial microbiota works as a community that consists of many individual organisms, i.e., cells. To fully understand the function of bacterial microbiota, individual cells must be identified; however, it is difficult with current techniques. Here, we develop a method, Barcoding Bacteria for Identification and Quantification (BarBIQ), which classifies single bacterial cells into taxa-named herein cell-based operational taxonomy units (cOTUs)-based on cellularly barcoded 16S rRNA sequences with single-base accuracy, and quantifies the cell number for each cOTU in the microbiota in a high-throughput manner. We apply BarBIQ to murine cecal microbiotas and quantify in total 3.4 × 105 bacterial cells containing 810 cOTUs. Interestingly, we find location-dependent global differences in the cecal microbiota depending on the dietary vitamin A deficiency, and more differentially abundant cOTUs at the proximal location than the distal location. Importantly, these location differences are not clearly shown by conventional 16S rRNA gene-amplicon sequencing methods, which quantify the 16S rRNA genes, not the cells. Thus, BarBIQ enables microbiota characterization with the identification and quantification of individual constituent bacteria, which is a cornerstone for microbiota studies.

Author information: (1)Department of Genetics, Stanford University, Stanford, CA, USA. (2)Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. (3)School of Medicine, Stanford University, Stanford, CA, USA. (4)Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa. (5)SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa. (6)School of Human Development and Health, University of Southampton, Southampton, UK. (7)MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. (8)INDEPTH Network, East Legon, Accra, Ghana. (9)Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. Scott.Hazelhurst@wits.ac.za. (10)School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa. Scott.Hazelhurst@wits.ac.za. (11)Department of Genetics, Stanford University, Stanford, CA, USA. asbhatt@stanford.edu. (12)School of Medicine, Stanford University, Stanford, CA, USA. asbhatt@stanford.edu. (13)Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA. asbhatt@stanford.edu. (#)Contributed equally

Short-term memory deficits have been associated with prefrontal cortex (PFC) dysfunction in Alzheimer's disease (AD) and AD mouse models. Extratelencephalic projection (ET) neurons in the PFC play a key role in short-term working memory, but the mechanism between ET neuronal dysfunction in the PFC and short-term memory impairment in AD is not well understood. Here, using fiber photometry and optogenetics, we found reduced neural activity in the ET neurons in the medial prefrontal cortex (mPFC) of the 5×FAD mouse model led to object recognition memory (ORM) deficits. Activation of ET neurons in the mPFC of 5×FAD mice rescued ORM impairment, and inhibition of ET neurons in the mPFC of wild type mice impaired ORM expression. ET neurons in the mPFC that project to supramammillary nucleus were necessary for ORM expression. Viral tracing and in vivo recording revealed that mPFC ET neurons received fewer cholinergic inputs from the basal forebrain in 5×FAD mice. Furthermore, activation of cholinergic fibers in the mPFC rescued ORM deficits in 5×FAD mice, while acetylcholine deficiency reduced the response of ET neurons in the mPFC to familiar objects. Taken together, our results revealed a neural mechanism behind ORM impairment in 5×FAD mice.

UV-DDB, consisting of subunits DDB1 and DDB2, recognizes UV-induced photoproducts during global genome nucleotide excision repair (GG-NER). We recently demonstrated a noncanonical role of UV-DDB in stimulating base excision repair (BER) which raised several questions about the timing of UV-DDB arrival at 8-oxoguanine (8-oxoG), and the dependency of UV-DDB on the recruitment of downstream BER and NER proteins. Using two different approaches to introduce 8-oxoG in cells, we show that DDB2 is recruited to 8-oxoG immediately after damage and colocalizes with 8-oxoG glycosylase (OGG1) at sites of repair. 8-oxoG removal and OGG1 recruitment is significantly reduced in the absence of DDB2. NER proteins, XPA and XPC, also accumulate at 8-oxoG. While XPC recruitment is dependent on DDB2, XPA recruitment is DDB2-independent and transcription-coupled. Finally, DDB2 accumulation at 8-oxoG induces local chromatin unfolding. We propose that DDB2-mediated chromatin decompaction facilitates the recruitment of downstream BER proteins to 8-oxoG lesions.

The rational design of molecules with desired properties is a long-standing challenge in chemistry. Generative neural networks have emerged as a powerful approach to sample novel molecules from a learned distribution. Here, we propose a conditional generative neural network for 3d molecular structures with specified chemical and structural properties. This approach is agnostic to chemical bonding and enables targeted sampling of novel molecules from conditional distributions, even in domains where reference calculations are sparse. We demonstrate the utility of our method for inverse design by generating molecules with specified motifs or composition, discovering particularly stable molecules, and jointly targeting multiple electronic properties beyond the training regime.

Acoustic graphene plasmons (AGPs) have ultrastrong field confinement and low loss, which have been applied for quantum effect exploration and ångström-thick material sensing. However, the exploration of in-plane scattering of AGPs is still lacking, although it is essential for the manipulation of ultraconfined optical fields down to atomic level. Here, by using scattering-type scanning near-field optical microscopy (s-SNOM), we show that the mid-infrared AGPs can be strongly scattered by atomic level height steps, even though the step height of the scatterer is four orders of magnitude smaller than the incident free wavelength. This effect can be attributed to larger back scattering of AGPs than that of the traditional graphene plasmons. Besides, the scattering of AGPs by individual scatterers can be controlled via electrical back gating. Our work suggests a feasible way to control confined optical fields with atomic level height nanostructures, which can be used for ultra-compacted strong light-matter interactions.

The MORDOR trial in Niger, Malawi, and Tanzania found that biannual mass distribution of azithromycin to children younger than 5 years led to a 13.5% reduction in all-cause mortality (NCT02048007). To help elucidate the mechanism for mortality reduction, we report IgG responses to 11 malaria, bacterial, and protozoan pathogens using a multiplex bead assay in pre-specified substudy of 30 communities in the rural Niger placebo-controlled trial over a three-year period (n = 5642 blood specimens, n = 3814 children ages 1-59 months). Mass azithromycin reduces Campylobacter spp. force of infection by 29% (hazard ratio = 0.71, 95% CI: 0.56, 0.89; P = 0.004) but serological measures show no significant differences between groups for other pathogens against a backdrop of high transmission. Results align with a recent microbiome study in the communities. Given significant sequelae of Campylobacter infection among preschool aged children, our results support an important mechanism through which biannual mass distribution of azithromycin likely reduces mortality in Niger.

Translating ribosomes unwind mRNA secondary structures by three basepairs each elongation cycle. Despite the ribosome helicase, certain mRNA stem-loops stimulate programmed ribosomal frameshift by inhibiting translation elongation. Here, using mutagenesis, biochemical and single-molecule experiments, we examine whether high stability of three basepairs, which are unwound by the translating ribosome, is critical for inducing ribosome pauses. We find that encountering frameshift-inducing mRNA stem-loops from the E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) hinders A-site tRNA binding and slows down ribosome translocation by 15-20 folds. By contrast, unwinding of first three basepairs adjacent to the mRNA entry channel slows down the translating ribosome by only 2-3 folds. Rather than high thermodynamic stability, specific length and structure enable regulatory mRNA stem-loops to stall translation by forming inhibitory interactions with the ribosome. Our data provide the basis for rationalizing transcriptome-wide studies of translation and searching for novel regulatory mRNA stem-loops.

Despite global warming and Arctic sea-ice loss, on average the Antarctic sea-ice extent has not declined since 1979 when satellite data became available. In contrast, climate model simulations tend to exhibit strong negative sea-ice trends for the same period. This Antarctic sea-ice paradox leads to low confidence in 21st-century sea-ice projections. Here we present multi-resolution climate change projections that account for Southern Ocean mesoscale eddies. The high-resolution configuration simulates stable September Antarctic sea-ice extent that is not projected to decline until the mid-21st century. We argue that one reason for this finding is a more realistic ocean circulation that increases the equatorward heat transport response to global warming. As a result, the ocean becomes more efficient at moderating the anthropogenic warming around Antarctica and hence at delaying sea-ice decline. Our study suggests that explicitly simulating Southern Ocean eddies is necessary for providing Antarctic sea-ice projections with higher confidence.

Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) are promising molecules for therapeutic or prophylactic interventions. Beyond neutralization, bNAbs exert Fc-dependent functions including antibody-dependent cellular cytotoxicity and activation of the complement. Here, we show that a subset of bNAbs targeting the CD4 binding site and the V1/V2 or V3 loops inhibit viral release from infected cells. We combined immunofluorescence, scanning electron microscopy, transmission electron microscopy and immunogold staining to reveal that some bNAbs form large aggregates of virions at the surface of infected cells. This activity correlates with the capacity of bNAbs to bind to Env at the cell surface and to neutralize cell-free viral particles. We further show that antibody bivalency is required for viral retention, and that aggregated virions are neutralized. We have thus identified an additional antiviral activity of bNAbs, which block HIV-1 release by tethering viral particles at the surface of infected cells.

The choroid plexus secretes cerebrospinal fluid and is critical for the development and function of the brain. In the telencephalon, the choroid plexus epithelium arises from the Wnt- expressing cortical hem. Canonical Wnt signaling pathway molecules such as nuclear β-CATENIN are expressed in the mouse and human embryonic choroid plexus epithelium indicating that this pathway is active. Point mutations in human β-CATENIN are known to result in the constitutive activation of canonical Wnt signaling. In a mouse model that recapitulates this perturbation, we report a loss of choroid plexus epithelial identity and an apparent transformation of this tissue to a neuronal identity. Aspects of this phenomenon are recapitulated in human embryonic stem cell derived organoids. The choroid plexus is also disrupted when β-Catenin is conditionally inactivated. Together, our results indicate that canonical Wnt signaling is required in a precise and regulated manner for normal choroid plexus development in the mammalian brain.

RNA polymerase III (Pol III) transcribes noncoding RNA, including transfer RNA (tRNA), and is commonly targeted during cancer and viral infection. We find that Herpes Simplex Virus-1 (HSV-1) stimulates tRNA expression 10-fold. Perturbation of host tRNA synthesis requires nuclear viral entry, but not synthesis of specific viral transcripts. tRNA with a specific codon bias were not targeted-rather increased transcription was observed from euchromatic, actively transcribed loci. tRNA upregulation is linked to unique crosstalk between the Pol II and III transcriptional machinery. While viral infection results in depletion of Pol II on host mRNA promoters, we find that Pol II binding to tRNA loci increases. Finally, we report Pol III and associated factors bind the viral genome, which suggests a previously unrecognized role in HSV-1 gene expression. These findings provide insight into mechanisms by which HSV-1 alters the host nuclear environment, shifting key processes in favor of the pathogen.

Author information: (1)deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. gyda.bjornsdottir@decode.is. (2)deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. (3)Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland. (4)School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland. (5)Landspitali University Hospital, Reykjavik, Iceland. (6)Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark. (7)Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. (8)Danish Headache Center, Dept. Neurology, Rigshospitalet-Glostrup, Glostrup, Denmark. (9)Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. (10)Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark. (11)Lundbeck Foundation for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. (12)Department of Orthopaedic Surgery, CAG ROAD-Research OsteoArthritis Denmark, Copenhagen University Hospital, Hvidovre, Denmark. (13)Research Unit for Musculoskeletal Function and Physiotherapy, Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark. (14)The Research Unit PROgrez, Department of Physiotherapy and Occupational Therapy, Næstved-Slagelse-Ringsted Hospitals, Næstved, Denmark. (15)Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark. (16)Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark. (17)Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark. (18)Department of Neurosurgery, Landspitali University Hospital, Reykjavik, Iceland. (19)Health Care Institution of West Iceland, Stykkisholmur, Iceland. (20)Statens Serum Institut, Copenhagen, Copenhagen, Denmark. (21)deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. thorgeir.thorgeirsson@decode.is. (22)deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. kstefans@decode.is. (23)Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland. kstefans@decode.is.

Inhibition of the master growth regulator mTORC1 (mechanistic target of rapamycin complex 1) slows ageing across phyla, in part by reducing protein synthesis. Various stresses globally suppress protein synthesis through the integrated stress response (ISR), resulting in preferential translation of the transcription factor ATF-4. Here we show in C. elegans that inhibition of translation or mTORC1 increases ATF-4 expression, and that ATF-4 mediates longevity under these conditions independently of ISR signalling. ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production. This H2S boost increases protein persulfidation, a protective modification of redox-reactive cysteines. The ATF-4/CTH-2/H2S pathway also mediates longevity and increased stress resistance from mTORC1 suppression. Increasing H2S levels, or enhancing mechanisms that H2S influences through persulfidation, may represent promising strategies for mobilising therapeutic benefits of the ISR, translation suppression, or mTORC1 inhibition.

Analysis of manganese mineral occurrences and valence states demonstrate oxidation of Earth's crust through time. Changes in crustal redox state are critical to Earth's evolution, but few methods exist for evaluating spatially averaged crustal redox state through time. Manganese (Mn) is a redox-sensitive metal whose variable oxidation states and abundance in crustal minerals make it a useful tracer of crustal oxidation. We find that the average oxidation state of crustal Mn occurrences has risen in the last 1 billion years in response to atmospheric oxygenation following a 66 ± 1 million-year time lag. We interpret this lag as the average time necessary to equilibrate the shallow crust to atmospheric oxygen fugacity. This study employs large mineralogical databases to evaluate geochemical conditions through Earth's history, and we propose that this and other mineral data sets form an important class of proxies that constrain the evolving redox state of various Earth reservoirs.

The homo-dimeric bacterial membrane protein EmrE effluxes polyaromatic cationic substrates in a proton-coupled manner to cause multidrug resistance. We recently determined the structure of substrate-bound EmrE in phospholipid bilayers by measuring hundreds of protein-ligand HN-F distances for a fluorinated substrate, 4-fluoro-tetraphenylphosphonium (F4-TPP+), using solid-state NMR. This structure was solved at low pH where one of the two proton-binding Glu14 residues is protonated. Here, to understand how substrate transport depends on pH, we determine the structure of the EmrE-TPP complex at high pH, where both Glu14 residues are deprotonated. The high-pH complex exhibits an elongated and hydrated binding pocket in which the substrate is similarly exposed to the two sides of the membrane. In contrast, the low-pH complex asymmetrically exposes the substrate to one side of the membrane. These pH-dependent EmrE conformations provide detailed insights into the alternating-access model, and suggest that the high-pH conformation may facilitate proton binding in the presence of the substrate, thus accelerating the conformational change of EmrE to export the substrate.

Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.

Prevalence of Mycobacterium abscessus infections is increasing in patients with respiratory comorbidities. After initial colonisation, M. abscessus smooth colony (S) variants can undergo an irreversible genetic switch into highly inflammatory, rough colony (R) variants, often associated with a decline in pulmonary function. Here, we use an adult zebrafish model of chronic infection with R and S variants to study M. abscessus pathogenesis in the context of fully functioning host immunity. We show that infection with an R variant causes an inflammatory immune response that drives necrotic granuloma formation through host TNF signalling, mediated by the tnfa, tnfr1 and tnfr2 gene products. T cell-dependent immunity is stronger against the R variant early in infection, and regulatory T cells associate with R variant granulomas and limit bacterial growth. In comparison, an S variant proliferates to high burdens but appears to be controlled by TNF-dependent innate immunity early during infection, resulting in delayed granuloma formation. Thus, our work demonstrates the applicability of adult zebrafish to model persistent M. abscessus infection, and illustrates differences in the immunopathogenesis induced by R and S variants during granulomatous infection.

Erratum in Nat Commun. 2022 Mar 17;13(1):1575.

Despite recent advances in cancer immunotherapy, certain tumor types, such as Glioblastomas, are highly resistant due to their tumor microenvironment disabling the anti-tumor immune response. Here we show, by applying an in-silico multidimensional model integrating spatially resolved and single-cell gene expression data of 45,615 immune cells from 12 tumor samples, that a subset of Interleukin-10-releasing HMOX1+ myeloid cells, spatially localizing to mesenchymal-like tumor regions, drive T-cell exhaustion and thus contribute to the immunosuppressive tumor microenvironment. These findings are validated using a human ex-vivo neocortical glioblastoma model inoculated with patient derived peripheral T-cells to simulate the immune compartment. This model recapitulates the dysfunctional transformation of tumor infiltrating T-cells. Inhibition of the JAK/STAT pathway rescues T-cell functionality both in our model and in-vivo, providing further evidence of IL-10 release being an important driving force of tumor immune escape. Our results thus show that integrative modelling of single cell and spatial transcriptomics data is a valuable tool to interrogate the tumor immune microenvironment and might contribute to the development of successful immunotherapies.

Inflammation triggers secondary brain damage after stroke. The meninges and other CNS border compartments serve as invasion sites for leukocyte influx into the brain thus promoting tissue damage after stroke. However, the post-ischemic immune response of border compartments compared to brain parenchyma remains poorly characterized. Here, we deeply characterize tissue-resident leukocytes in meninges and brain parenchyma and discover that leukocytes respond differently to stroke depending on their site of residence. We thereby discover a unique phenotype of myeloid cells exclusive to the brain after stroke. These stroke-associated myeloid cells partially resemble neurodegenerative disease-associated microglia. They are mainly of resident microglial origin, partially conserved in humans and exhibit a lipid-phagocytosing phenotype. Blocking markers specific for these cells partially ameliorates stroke outcome thus providing a potential therapeutic target. The injury-response of myeloid cells in the CNS is thus compartmentalized, adjusted to the type of injury and may represent a therapeutic target.

Heterotetrameric glutamate receptors are essential for the development, function, and plasticity of spine synapses but how they are organized to achieve this is not known. Here we show that the nanoscale organization of glutamate receptors containing specific subunits define distinct subsynaptic features. Glutamate receptors containing GluA2 or GluN1 subunits establish nanomodular elements precisely positioned relative to Synaptotagmin-1 positive presynaptic release sites that scale with spine size. Glutamate receptors containing GluA1 or GluN2B specify features that exhibit flexibility: GluA1-subunit containing AMPARs are found in larger spines, while GluN2B-subunit containing NMDARs are enriched in the smallest spines with neither following a strict modular organization. Given that the precise positioning of distinct classes of glutamate receptors is linked to diverse events including cell death and synaptic plasticity, this unexpectedly robust synaptic nanoarchitecture provides a resilient system, where nanopositioned glutamate receptor heterotetramers define specific subsynaptic regions of individual spine synapses.

Palladium catalyst turnover by reoxidation of a low-valent Pd species dominates the proceeding of an efficient oxidative transformation, but the state-of-the-art catalysis approaches still have great challenges from the perspectives of high efficiency, atom-economy and environmental-friendliness. Herein, we report a new strategy for addressing Pd reoxidation problem by the fabrication of spatially proximate IrIII photocatalyst and PdII catalyst into metal-organic framework (MOF), affording MOFs based Pd/photoredox catalysts UiO-67-Ir-PdX2 (X = OAc, TFA), which are systematically evaluated using three representative Pd-catalyzed oxidation reactions. Owing to the stabilization of single-site Pd and Ir catalysts by MOFs framework as well as the proximity of them favoring fast electron transfer, UiO-67-Ir-PdX2, under visible light, exhibits up to 25 times of Pd catalyst turnover number than the existing catalysis systems. Mechanism investigations theoretically corroborate the capability of MOFs based Pd/photoredox catalysis to regulate the competitive processes of Pd0 aggregation and reoxidation in Pd-catalyzed oxidation reactions.

The increased complexity of infrastructure systems has resulted in critical interdependencies between multiple networks-communication systems require electricity, while the normal functioning of the power grid relies on communication systems. These interdependencies have inspired an extensive literature on coupled multilayer networks, assuming a hard interdependence, where a component failure in one network causes failures in the other network, resulting in a cascade of failures across multiple systems. While empirical evidence of such hard failures is limited, the repair and recovery of a network requires resources typically supplied by other networks, resulting in documented interdependencies induced by the recovery process. In this work, we explore recovery coupling, capturing the dependence of the recovery of one system on the instantaneous functional state of another system. If the support networks are not functional, recovery will be slowed. Here we collected data on the recovery time of millions of power grid failures, finding evidence of universal nonlinear behavior in recovery following large perturbations. We develop a theoretical framework to address recovery coupling, predicting quantitative signatures different from the multilayer cascading failures. We then rely on controlled natural experiments to separate the role of recovery coupling from other effects like resource limitations, offering direct evidence of how recovery coupling affects a system's functionality.

The evergrowing plastic production and the caused concerns of plastic waste accumulation have stimulated the need for waste plastic chemical recycling/valorization. Current methods suffer from harsh reaction conditions and long reaction time. Herein we demonstrate a non-thermal plasma-assisted method for rapid hydrogenolysis of polystyrene (PS) at ambient temperature and atmospheric pressure, generating high yield (>40 wt%) of C1-C3 hydrocarbons and ethylene being the dominant gas product (Selectivity of ethylene, SC2H4 > 70%) within ~10 min. The fast reaction kinetics is attributed to highly active hydrogen plasma, which can effectively break bonds in polymer and initiate hydrogenolysis under mild condition. Efficient hydrogenolysis of post-consumer PS materials using this method is also demonstrated, suggesting a promising approach for fast retrieval of small molecular hydrocarbon modules from plastic materials as well as a good capability to process waste plastics in complicated conditions.

The formation of pre-metastatic niche is a key step in the metastatic burden. The pluripotent factor Lin28B is frequently expressed in breast tumors and is particularly upregulated in the triple negative breast cancer subtype. Here, we demonstrate that Lin28B promotes lung metastasis of breast cancer by building an immune-suppressive pre-metastatic niche. Lin28B enables neutrophil recruitment and N2 conversion. The N2 neutrophils are then essential for immune suppression in pre-metastatic lung by PD-L2 up-regulation and a dysregulated cytokine milieu. We also identify that breast cancer-released exosomes with low let-7s are a prerequisite for Lin28B-induced immune suppression. Moreover, Lin28B-induced breast cancer stem cells are the main sources of low-let-7s exosomes. Clinical data further verify that high Lin28B and low let-7s in tumors are both indicators for poor prognosis and lung metastasis in breast cancer patients. Together, these data reveal a mechanism by which Lin28B directs the formation of an immune-suppressive pre-metastatic niche.

Monolayers of two-dimensional van der Waals materials exhibit novel electronic phases distinct from their bulk due to the symmetry breaking and reduced screening in the absence of the interlayer coupling. In this work, we combine angle-resolved photoemission spectroscopy and scanning tunneling microscopy/spectroscopy to demonstrate the emergence of a unique insulating 2 × 1 dimer ground state in monolayer 1T-IrTe2 that has a large band gap in contrast to the metallic bilayer-to-bulk forms of this material. First-principles calculations reveal that phonon and charge instabilities as well as local bond formation collectively enhance and stabilize a charge-ordered ground state. Our findings provide important insights into the subtle balance of interactions having similar energy scales that occurs in the absence of strong interlayer coupling, which offers new opportunities to engineer the properties of 2D monolayers.

Development of hyperproducing strains is important for biomanufacturing of biochemicals and biofuels but requires extensive efforts to engineer cellular metabolism and discover functional components. Herein, we optimize and use the CRISPR-assisted editing and CRISPRi screening methods to convert a wild-type Corynebacterium glutamicum to a hyperproducer of L-proline, an amino acid with medicine, feed, and food applications. To facilitate L-proline production, feedback-deregulated variants of key biosynthetic enzyme γ-glutamyl kinase are screened using CRISPR-assisted single-stranded DNA recombineering. To increase the carbon flux towards L-proline biosynthesis, flux-control genes predicted by in silico analysis are fine-tuned using tailored promoter libraries. Finally, an arrayed CRISPRi library targeting all 397 transporters is constructed to discover an L-proline exporter Cgl2622. The final plasmid-, antibiotic-, and inducer-free strain produces L-proline at the level of 142.4 g/L, 2.90 g/L/h, and 0.31 g/g. The CRISPR-assisted strain development strategy can be used for engineering industrial-strength strains for efficient biomanufacturing.

V2p and V2i antibodies (Abs) that are specific for epitopes in the V1V2 region of the HIV gp120 envelope (Env) do not effectively neutralize HIV but mediate Fc-dependent anti-viral activities that have been correlated with protection from, or control of HIV, SIV and SHIV infections. Here, we describe a novel molecular toolbox that allows the discrimination of antigenically and functionally distinct polyclonal V2 Ab responses. We identify different patterns of V2 Ab induction by SHIV infection and three separate vaccine regimens that aid in fine-tuning an optimized immunization protocol for inducing V2p and V2i Abs. We observe no, or weak and sporadic V2p and V2i Abs in non-vaccinated SHIV-infected NHPs, but strong V2p and/or V2i Ab responses after immunization with a V2-targeting vaccine protocol. The V2-focused vaccination is superior to both natural infection and to immunization with whole Env constructs for inducing functional V2p- and V2i-specific responses. Strikingly, levels of V2-directed Abs correlate inversely with Abs specific for peptides of V3 and C5. These data demonstrate that a V1V2-targeting vaccine has advantages over the imprecise targeting of SIV/SHIV infections and of whole Env-based immunization regimens for inducing a more focused functional V2p- and V2i-specific Ab response.

Dysregulation of the balance between pro-inflammatory and anti-inflammatory macrophages has a key function in the pathogenesis of Duchenne muscular dystrophy (DMD), a fatal genetic disease. We postulate that an evolutionarily ancient protective mechanism against infection, known as trained immunity, drives pathological inflammation in DMD. Here we show that bone marrow-derived macrophages from a murine model of DMD (mdx) exhibit cardinal features of trained immunity, consisting of transcriptional hyperresponsiveness associated with metabolic and epigenetic remodeling. The hyperresponsive phenotype is transmissible by bone marrow transplantation to previously healthy mice and persists for up to 11 weeks post-transplant. Mechanistically, training is induced by muscle extract in vitro. The functional and epigenetic changes in bone marrow-derived macrophages from dystrophic mice are TLR4-dependent. Adoptive transfer experiments further support the TLR4-dependence of trained macrophages homing to damaged muscles from the bone marrow. Collectively, this suggests that a TLR4-regulated, memory-like capacity of innate immunity induced at the level of the bone marrow promotes dysregulated inflammation in DMD.

The SARS-CoV-2 Delta variant is currently the dominant circulating strain in the world. Uncovering the structural basis of the enhanced transmission and altered immune sensitivity of Delta is particularly important. Here we present cryo-EM structures revealing two conformational states of Delta spike and S/ACE2 complex in four states. Our cryo-EM analysis suggests that RBD destabilizations lead to population shift towards the more RBD-up and S1 destabilized fusion-prone state, beneficial for engagement with ACE2 and shedding of S1. Noteworthy, we find the Delta T478K substitution plays a vital role in stabilizing and reshaping the RBM loop473-490, enhancing interaction with ACE2. Collectively, increased propensity for more RBD-up states and the affinity-enhancing T478K substitution together contribute to increased ACE2 binding, providing structural basis of rapid spread of Delta. Moreover, we identify a previously generated MAb 8D3 as a cross-variant broadly neutralizing antibody and reveal that 8D3 binding induces a large K478 side-chain orientation change, suggesting 8D3 may use an "induced-fit" mechanism to tolerate Delta T478K mutation. We also find that all five RBD-targeting MAbs tested remain effective on Delta, suggesting that Delta well preserves the neutralizing antigenic landscape in RBD. Our findings shed new lights on the pathogenicity and antibody neutralization of Delta.

Rare species, which represent a large fraction of the taxa in ecological assemblages, account for much of the biological diversity on Earth. These species make substantial contributions to ecosystem functioning, and are targets of conservation policy. Here we adopt an integrated approach, combining information on the rarity of species trait combinations, and their spatial restrictedness, to quantify the biogeography of rare fish (a taxon with almost 13,000 species) in the world's oceans. We find concentrations of rarity, in excess of what is predicted by a null expectation, near the coasts and at higher latitudes. We also observe mismatches between these rarity hotspots and marine protected areas. This pattern is repeated for both major groupings of fish, the Actinopterygii (bony fish) and Elasmobranchii (sharks, skates and rays). These results uncover global patterns of rarity that were not apparent from earlier work, and highlight the importance of using metrics that incorporate information on functional traits in the conservation and management of global marine fishes.

IL-18 is emerging as an IL-22-induced and epithelium-derived cytokine which contributes to host defence against intestinal infection and inflammation. In contrast to its known role in Goblet cells, regulation of barrier function at the molecular level by IL-18 is much less explored. Here we show that IL-18 is a bona fide IL-22-regulated gate keeper for intestinal epithelial barrier. IL-22 promotes crypt immunity both via induction of phospho-Stat3 binding to the Il-18 gene promoter and via Il-18 independent mechanisms. In organoid culture, while IL-22 primarily increases organoid size and inhibits expression of stem cell genes, IL-18 preferentially promotes organoid budding and induces signature genes of Lgr5+ stem cells via Akt-Tcf4 signalling. During adherent-invasive E. coli (AIEC) infection, systemic administration of IL-18 corrects compromised T-cell IFNγ production and restores Lysozyme+ Paneth cells in Il-22-/- mice, but IL-22 administration fails to restore these parameters in Il-18-/- mice, thereby placing IL-22-Stat3 signalling upstream of the IL-18-mediated barrier defence function. IL-18 in return regulates Stat3-mediated anti-microbial response in Paneth cells, Akt-Tcf4-triggered expansion of Lgr5+ stem cells to facilitate tissue repair, and AIEC clearance by promoting IFNγ+ T cells.

Cell-based immunotherapies can provide safe and effective treatments for various disorders including autoimmunity, cancer, and excessive proinflammatory events in sepsis or viral infections. However, to achieve this goal there is a need for deeper understanding of mechanisms of the intercellular interactions. Regulatory T cells (Tregs) are a lymphocyte subset that maintain peripheral tolerance, whilst mesenchymal stem cells (MSCs) are multipotent nonhematopoietic progenitor cells. Despite coming from different origins, Tregs and MSCs share immunoregulatory properties that have been tested in clinical trials. Here we demonstrate how direct and indirect contact with allogenic MSCs improves Tregs' potential for accumulation of immunosuppressive adenosine and suppression of conventional T cell proliferation, making them more potent therapeutic tools. Our results also demonstrate that direct communication between Tregs and MSCs is based on transfer of active mitochondria and fragments of plasma membrane from MSCs to Tregs, an event that is HLA-dependent and associates with HLA-C and HLA-DRB1 eplet mismatch load between Treg and MSC donors.

The catalytic asymmetric borylation of conjugated carbonyls followed by stereoselective intramolecular cascade cyclizations with in situ generated chiral enolates are extremely rare. Herein, we report the enantioselective Cu(I)-catalyzed β-borylation/Michael addition on prochiral enone-tethered 2,5-cyclohexadienones. This asymmetric desymmetrization strategy has a broad range of substrate scope to generate densely functionalized bicyclic enones bearing four contiguous stereocenters with excellent yield, enantioselectivity, and diastereoselectivity. One-pot borylation/cyclization/oxidation via the sequential addition of sodium perborate reagent affords the corresponding alcohols without affecting yield and enantioselectivity. The synthetic potential of this reaction is explored through gram-scale reactions and further chemoselective transformations on products. DFT calculations explain the requirement of the base in an equimolar ratio in the reaction, as it leads to the formation of a lithium-enolate complex to undergo C-C bond formation via a chair-like transition state, with a barrier that is 22.5 kcal/mol more favourable than that of the copper-enolate complex.

Patients with hematological malignancies have impaired immune response after two doses of BNT162b2 (Pfizer/BioNTech) vaccine against SARS-CoV-2. Here, in this observational study (registration number HDH F20210324145532), we measure SARS-CoV-2 anti-Spike antibodies, neutralizing antibodies and T-cell responses after immune stimulation with a third dose (D3) of the same vaccine in patients with chronic lymphocytic leukemia (n = 13), B cell non-Hodgkin lymphoma (n = 14), and multiple myeloma (n = 16)). No unexpected novel side effects are reported. Among 25 patients with positive anti-S titers before D3, 23 (92%) patients increase their anti-S and neutralizing antibody titer after D3. All 18 (42%) initially seronegative patients remain negative. D3 increases the median IFN-γ secretion in the whole cohort and induces IFN-γ secretion in a fraction of seronegative patients. Our data thus support the use of a third vaccine dose amongst patients with lymphoid malignancies, even though some of them will still have vaccine failure.

Epstein-Barr virus (EBV) is reportedly the first identified human tumor virus, and is closely related to the occurrence and development of nasopharyngeal carcinoma (NPC), gastric carcinoma (GC), and several lymphomas. PD-L1 expression is elevated in EBV-positive NPC and GC tissues; however, the specific mechanisms underlying the EBV-dependent promotion of PD-L1 expression to induce immune escape warrant clarification. EBV encodes 44 mature miRNAs. In this study, we find that EBV-miR-BART11 and EBV-miR-BART17-3p upregulate the expression of PD-L1 in EBV-associated NPC and GC. Furthermore, EBV-miR-BART11 targets FOXP1, EBV-miR-BART17-3p targets PBRM1, and FOXP1 and PBRM1 bind to the enhancer region of PD-L1 to inhibit its expression. Therefore, EBV-miR-BART11 and EBV-miR-BART17-3p inhibit FOXP1 and PBRM1, respectively, and enhance the transcription of PD-L1 (CD274, http://www.ncbi.nlm.nih.gov/gene/29126 ), resulting in the promotion of tumor immune escape, which provides insights into potential targets for EBV-related tumor immunotherapy.

Recent advances in thermally localized solar evaporation hold significant promise for vapor generation, seawater desalination, wastewater treatment, and medical sterilization. However, salt accumulation is one of the key bottlenecks for reliable adoption. Here, we demonstrate highly efficient (>80% solar-to-vapor conversion efficiency) and salt rejecting (20 weight % salinity) solar evaporation by engineering the fluidic flow in a wick-free confined water layer. With mechanistic modeling and experimental characterization of salt transport, we show that natural convection can be triggered in the confined water. More notably, there exists a regime enabling simultaneous thermal localization and salt rejection, i.e., natural convection significantly accelerates salt rejection while inducing negligible additional heat loss. Furthermore, we show the broad applicability by integrating this confined water layer with a recently developed contactless solar evaporator and report an improved efficiency. This work elucidates the fundamentals of salt transport and offers a low-cost strategy for high-performance solar evaporation.

Time crystals are periodic states exhibiting spontaneous symmetry breaking in either time-independent or periodically-driven quantum many-body systems. Spontaneous modification of discrete time-translation symmetry in periodically-forced physical systems can create a discrete time crystal (DTC) constituting a state of matter possessing properties like temporal rigid long-range order and coherence, which are inherently desirable for quantum computing and information processing. Despite their appeal, experimental demonstrations of DTCs are scarce and significant aspects of their behavior remain unexplored. Here, we report the experimental observation and theoretical investigation of DTCs in a Kerr-nonlinear optical microcavity. Empowered by the self-injection locking of two independent lasers with arbitrarily large frequency separation simultaneously to two same-family cavity modes and a dissipative Kerr soliton, this versatile platform enables realizing long-awaited phenomena such as defect-carrying DTCs and phase transitions. Combined with monolithic microfabrication, this room-temperature system paves the way for chip-scale time crystals supporting real-world applications outside sophisticated laboratories.

The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.

Optogenetic methods provide efficient cell-specific modulations, and the ability of simultaneous neural activation and inhibition in the same brain region of freely moving animals is highly desirable. Here we report bidirectional neuronal activity manipulation accomplished by a wireless, dual-color optogenetic probe in synergy with the co-expression of two spectrally distinct opsins (ChrimsonR and stGtACR2) in a rodent model. The flexible probe comprises vertically assembled, thin-film microscale light-emitting diodes with a lateral dimension of 125 × 180 µm2, showing colocalized red and blue emissions and enabling chronic in vivo operations with desirable biocompatibilities. Red or blue irradiations deterministically evoke or silence neurons co-expressing the two opsins. The probe interferes with dopaminergic neurons in the ventral tegmental area of mice, increasing or decreasing dopamine levels. Such bidirectional regulations further generate rewarding and aversive behaviors and interrogate social interactions among multiple mice. These technologies create numerous opportunities and implications for brain research.

Frequent prothrombin time (PT) and international normalized ratio (INR) testing is critical for millions of people on lifelong anticoagulation with warfarin. Currently, testing is performed in hospital laboratories or with expensive point-of-care devices limiting the ability to test frequently and affordably. We report a proof-of-concept PT/INR testing system that uses the vibration motor and camera on smartphones to track micro-mechanical movements of a copper particle. The smartphone system computed the PT/INR with inter-class correlation coefficients of 0.963 and 0.966, compared to a clinical-grade coagulation analyzer for 140 plasma samples and demonstrated similar results for 80 whole blood samples using a single drop of blood (10 μl). When tested with 79 blood samples with coagulopathic conditions, the smartphone system demonstrated a correlation of 0.974 for both PT/INR. Given the ubiquity of smartphones in the global setting, this proof-of-concept technology may provide affordable and effective PT and INR testing in low-resource environments.

Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.

Microbial composition and functions in the rhizosphere-an important microbial hotspot-are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions. The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin-antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11-182%), while genes involved in nitrification were strongly depleted.

Varicella caused by the primary infection of varicella-zoster virus (VZV) exerts a considerable disease burden globally. Current varicella vaccines consisting of the live-attenuated vOka strain of VZV are generally safe and effective. However, vOka retains full neurovirulence and can establish latency and reactivate to cause herpes zoster in vaccine recipients, raising safety concerns. Here, we rationally design a live-attenuated varicella vaccine candidate, v7D. This virus replicates like wild-type virus in MRC-5 fibroblasts and human PBMCs, the carrier for VZV dissemination, but is severely impaired for infection of human skin and neuronal cells. Meanwhile, v7D shows immunogenicity comparable to vOka both in vitro and in multiple small animal species. Finally, v7D is proven well-tolerated and immunogenic in nonhuman primates. Our preclinical data suggest that v7D is a promising candidate as a safer live varicella vaccine with reduced risk of vaccine-related complications, and could inform the design of other herpes virus vaccines.

Small RNA pathways play key and diverse regulatory roles in C. elegans, but our understanding of their conservation and contributions in other nematodes is limited. We analyzed small RNA pathways in the divergent parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that associate with secondary 5'-triphosphate 22-24G-RNAs. These small RNAs target repetitive sequences or mature mRNAs and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Even in the absence of a piRNA pathway, Ascaris CSR-1 may still function to "license" as well as fine-tune or repress gene expression. Ascaris ALG-4 and its associated 26G-RNAs target and likely repress specific mRNAs during testis meiosis. Ascaris WAGO small RNAs demonstrate target plasticity changing their targets between repeats and mRNAs during development. We provide a unique and comprehensive view of mRNA and small RNA expression throughout spermatogenesis. Overall, our study illustrates the conservation, divergence, dynamics, and flexibility of small RNA pathways in nematodes.

In optical communications, sphere shaping is used to limit the energy of lightwaves to within a certain value over a period. This minimizes the energy required to contain information, allowing the rate of information transmission to approach the theoretical limit if the transmission medium is linear. However, when shaped lightwaves are transmitted through optical fiber, Kerr nonlinearity manifests itself as nonlinear interference in a peculiar way, potentially lowering communications capacity. In this article, we show that the impact of sphere shaping on Kerr nonlinearity varies with chromatic dispersion, shaping block length and symbol rate, and that this impact can be predicted using a novel statistical measure of light energy. As a practical consequence, by optimally controlling the parameters of sphere-shaped lightwaves, it is experimentally demonstrated that the information rate can be increased by up to 25% in low-dispersion channels on a 2824 km dispersion-managed wavelength-division multiplexed optical fiber link.

Alopecia areata is a complex genetic disease that results in hair loss due to the autoimmune-mediated attack of the hair follicle. We previously defined a role for both rare and common variants in our earlier GWAS and linkage studies. Here, we identify rare variants contributing to Alopecia Areata using a whole exome sequencing and gene-level burden analyses approach on 849 Alopecia Areata patients compared to 15,640 controls. KRT82 is identified as an Alopecia Areata risk gene with rare damaging variants in 51 heterozygous Alopecia Areata individuals (6.01%), achieving genome-wide significance (p = 2.18E-07). KRT82 encodes a hair-specific type II keratin that is exclusively expressed in the hair shaft cuticle during anagen phase, and its expression is decreased in Alopecia Areata patient skin and hair follicles. Finally, we find that cases with an identified damaging KRT82 variant and reduced KRT82 expression have elevated perifollicular CD8 infiltrates. In this work, we utilize whole exome sequencing to successfully identify a significant Alopecia Areata disease-relevant gene, KRT82, and reveal a proposed mechanism for rare variant predisposition leading to disrupted hair shaft integrity.

Molecular forces induced by optical excitations are connected to a wide range of phenomena, from chemical bond dissociation to intricate biological processes that underpin vision. Commonly, the description of optical excitations requires the solution of computationally demanding electronic Bethe-Salpeter equation (BSE). However, when studying non-covalent interactions in large-scale systems, more efficient methods are desirable. Here we introduce an effective approach based on coupled quantum Drude oscillators (cQDO) as represented by the many-body dispersion model. We find that the cQDO Hamiltonian yields semi-quantitative agreement with BSE calculations and that both attractive and repulsive optical van der Waals (vdW) forces can be induced by light. These optical-vdW interactions dominate over vdW dispersion in the long-distance regime, showing a complexity that grows with system size. Evidence of highly non-local forces in the human formaldehyde dehydrogenase 1MC5 protein suggests the ability to selectively activate collective molecular vibrations by photoabsorption, in agreement with recent experiments.

The miniaturization of ferroelectric devices in non-volatile memories requires the device to maintain stable switching behavior as the thickness scales down to nanometer scale, which requires the coercive field to be sufficiently large. Recently discovered metal-free perovskites exhibit advantages such as structural tunability and solution-processability, but they are disadvantaged by a lower coercive field compared to inorganic perovskites. Herein, we demonstrate that the coercive field (110 kV/cm) in metal-free ferroelectric perovskite MDABCO-NH4-(PF6)3 (MDABCO = N-methyl-N'-diazabicyclo[2.2.2]octonium) is one order larger than MDABCO-NH4-I3 (12 kV/cm) owing to the stronger intermolecular hydrogen bonding in the former. Using isotope experiments, the ferroelectric-to-paraelectric phase transition temperature and coercive field are verified to be strongly influenced by hydrogen bonds. Our work highlights that the coercive field of organic ferroelectrics can be tailored by tuning the strength of hydrogen bonding.

Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.

T follicular helper (Tfh) cells provide signals to initiate and maintain the germinal center (GC) reaction and are crucial for the generation of robust, long-lived antibody responses, but how the GC microenvironment affects Tfh cells is not well understood. Here we develop an in vivo T cell-intrinsic CRISPR-knockout screen to evaluate Tfh and Th1 cells in an acute viral infection model to identify regulators of Tfh cells in their physiological setting. Using a screen of druggable-targets, alongside genetic, transcriptomic and cellular analyses, we identify a function of HIF-1α in suppressing mTORC1-mediated and Myc-related pathways, and provide evidence that VHL-mediated degradation of HIF-1α is required for Tfh development; an expanded in vivo CRISPR screen reveals multiple components of these pathways that regulate Tfh versus Th1 cells, including signaling molecules, cell-cycle regulators, nutrient transporters, metabolic enzymes and autophagy mediators. Collectively, our data serve as a resource for studying Tfh versus Th1 decisions, and implicate the VHL-HIF-1α axis in fine-tuning Tfh generation.

Electrochemical reduction of CO2 (CO2ER) has received significant attention due to its potential to sustainably produce valuable fuels and chemicals. However, the reaction mechanism is still not well understood. One vital debate is whether the rate-limiting step (RLS) is dominated by the availability of protons, the conversion of water molecules, or the adsorption of CO2. This paper describes insights into the RLS by investigating pH dependency and kinetic isotope effect with respect to the rate expression of CO2ER. Focusing on electrocatalysts geared towards two-electron transfer reactions, we find the generation rates of CO and formate to be invariant with either pH or deuteration of the electrolyte over Au, Ag, Sn, and In. We elucidate the RLS of two-electron transfer CO2ER to be the adsorption of CO2 onto the surface of electrocatalysts. We expect this finding to provide guidance for improving CO2ER activity through the enhancement of the CO2 adsorption processes by strategies such as surface modification of catalysts as well as careful control of pressure and interfacial electric field within reactors.

In the biosynthesis sterols an enzyme-catalyzed demethylation is achieved via a stepwise oxidative transformation of alcohols to olefins. The overall demethylation proceeds through two sequential monooxygenation reactions and a subsequent dehydroformylative saturation. To mimic the desaturation processes observed in nature, we have successfully integrated photoredox proton-coupled electron transfer (PCET) and cobaloxime chemistry for the acceptorless dehydrogenation of alcohols. The state-of-the-art remote and precise desaturation of ketones proceeds efficiently through the activation of cyclic alcohols using bond-dissociation free energy (BDFE) as thermodynamic driving force. The resulting transient alkoxyl radical allows C-C bond scission to generate the carbon-centered radical remote to the carbonyl moiety. This key intermediate is subsequently combined with cobaloxime photochemistry to furnish the alkene. Moreover, the mild protocol can be extended to desaturation of linear alcohols as well as aromatic hydrocarbons. Application to bioactive molecules and natural product derivatives is also presented.

Type 2 diabetes is associated with insulin resistance, impaired pancreatic β-cell insulin secretion, and nonalcoholic fatty liver disease. Tissue-specific SWELL1 ablation impairs insulin signaling in adipose, skeletal muscle, and endothelium, and impairs β-cell insulin secretion and glycemic control. Here, we show that ICl,SWELL and SWELL1 protein are reduced in adipose and β-cells in murine and human diabetes. Combining cryo-electron microscopy, molecular docking, medicinal chemistry, and functional studies, we define a structure activity relationship to rationally-design active derivatives of a SWELL1 channel inhibitor (DCPIB/SN-401), that bind the SWELL1 hexameric complex, restore SWELL1 protein, plasma membrane trafficking, signaling, glycemic control and islet insulin secretion via SWELL1-dependent mechanisms. In vivo, SN-401 restores glycemic control, reduces hepatic steatosis/injury, improves insulin-sensitivity and insulin secretion in murine diabetes. These findings demonstrate that SWELL1 channel modulators improve SWELL1-dependent systemic metabolism in Type 2 diabetes, representing a first-in-class therapeutic approach for diabetes and nonalcoholic fatty liver disease.

The evolution of microbial parasites involves the counterplay between natural selection forcing parasites to improve and genetic drifts forcing parasites to lose genes and accumulate deleterious mutations. Here, to understand how this counterplay occurs at the scale of individual macromolecules, we describe cryo-EM structure of ribosomes from Encephalitozoon cuniculi, a eukaryote with one of the smallest genomes in nature. The extreme rRNA reduction in E. cuniculi ribosomes is accompanied with unparalleled structural changes, such as the evolution of previously unknown molten rRNA linkers and bulgeless rRNA. Furthermore, E. cuniculi ribosomes withstand the loss of rRNA and protein segments by evolving an ability to use small molecules as structural mimics of degenerated rRNA and protein segments. Overall, we show that the molecular structures long viewed as reduced, degenerated, and suffering from debilitating mutations possess an array of compensatory mechanisms that allow them to remain active despite the extreme molecular reduction.

The mitigation potential of vegetation-driven biophysical effects is strongly influenced by the background climate and will therefore be influenced by global warming. Based on an ensemble of remote sensing datasets, here we first estimate the temperature sensitivities to changes in leaf area over the period 2003-2014 as a function of key environmental drivers. These sensitivities are then used to predict temperature changes induced by future leaf area dynamics under four scenarios. Results show that by 2100, under high-emission scenario, greening will likely mitigate land warming by 0.71 ± 0.40 °C, and 83% of such effect (0.59 ± 0.41 °C) is driven by the increase in plant carbon sequestration, while the remaining cooling (0.12 ± 0.05 °C) is due to biophysical land-atmosphere interactions. In addition, our results show a large potential of vegetation to reduce future land warming in the very-stringent scenario (35 ± 20% of the overall warming signal), whereas this effect is limited to 11 ± 6% under the high-emission scenario.

Knowledge of the sound velocity of core materials is essential to explain the observed anomalously low shear wave velocity (VS) and high Poisson's ratio (σ) in the solid inner core. To date, neither VS nor σ of Fe and Fe-Si alloy have been measured under core conditions. Here, we present VS and σ derived from direct measurements of the compressional wave velocity, bulk sound velocity, and density of Fe and Fe-8.6 wt%Si up to ~230 GPa and ~5400 K. The new data show that neither the effect of temperature nor incorporation of Si would be sufficient to explain the observed low VS and high σ of the inner core. A possible solution would add carbon (C) into the solid inner core that could further decrease VS and increase σ. However, the physical property-based Fe-Si-C core models seemingly conflict with the partitioning behavior of Si and C between liquid and solid Fe.

We study the real-life effect of an unprecedented rapid mass vaccination campaign. Following a large outbreak of the Beta variant in the district of Schwaz/Austria, 100,000 doses of BNT162b2 (Pfizer/BioNTech) were procured to mass vaccinate the entire adult population of the district between the 11th and 16th of March 2021. This made the district the first widely inoculated region in Europe. We examine the effect of this campaign on the number of infections, cases of variants of concern, hospital and ICU admissions. We compare Schwaz with (i) a control group of highly similar districts, and (ii) with populations residing in municipalities along the border of Schwaz which were just excluded from the campaign. We find large and significant decreases for all outcomes after the campaign. Our results suggest that rapid mass vaccination is an effective tool to curb the spread of SARS-CoV-2.

Erratum in Nat Commun. 2022 Feb 16;13(1):986.

In vivo electron transfer processes are closely related to the activation of signaling pathways, and, thus, affect various life processes. Indeed, the signaling pathway activation of key molecules may be associated with certain diseases. For example, epidermal growth factor receptor (EGFR) activation is related to the occurrence and development of tumors. Hence, monitoring the activation of EGFR-related signaling pathways can help reveal the progression of tumor development. However, it is challenging for current detection methods to monitor the activation of specific signaling pathways in complex biochemical reactions. Here we designed a highly sensitive and specific nanoprobe that enables in vivo imaging of electronic transfer over a broad range of spatial and temporal scales. By using the ferrocene-DNA polymer "wire", the electrons transferred in a biochemical reaction can flow to persistent luminescent nanoparticles and change their electron distribution, thereby altering the optical signal of the particles. This electron transfer-triggered imaging probe enables mapping the activation of EGFR-related signaling pathways in a temporally and spatially precise manner. By offering precise visualization of signaling activity, this approach may offer a general platform not only for understanding molecular mechanisms in various biological processes but also for promoting disease therapies and drug evaluation.

Spin-orbit interaction has established itself as a key player in the emergent phenomena in modern condensed matter, including topological insulator, spin liquid and spin-dependent transports. However, its function is rather limited to adding topological nature to band kinetics, leaving behind the growing interest in the direct interplay with electron correlation. Here, we prove by our spinor line graph theory that a very strong spin-orbit interaction realized in 5d pyrochlore electronic systems generates multiply degenerate perfect flat bands. Unlike any of the previous flat bands, the electrons in this band localize in real space by destructively interfering with each other in a spin selective manner governed by the SU(2) gauge field. These electrons avoid the Coulomb interaction by self-organizing their localized wave functions, which may lead to a flat-band state with a stiff spin chirality. It also causes perfectly trimerized charge ordering, which may explain the recently discovered exotic low-temperature insulating phase of CsW2O6.

Lima1 is an extensively studied prognostic marker of malignancy and is also considered to be a tumour suppressor, but its role in a developmental context of non-transformed cells is poorly understood. Here, we characterise the expression pattern and examined the function of Lima1 in mouse embryos and pluripotent stem cell lines. We identify that Lima1 expression is controlled by the naïve pluripotency circuit and is required for the suppression of membrane blebbing, as well as for proper mitochondrial energetics in embryonic stem cells. Moreover, forcing Lima1 expression enables primed mouse and human pluripotent stem cells to be incorporated into murine pre-implantation embryos. Thus, Lima1 is a key effector molecule that mediates the pluripotency control of membrane dynamics and cellular metabolism.

Animals retain some but not all experiences in long-term memory (LTM). Sleep supports LTM retention across animal species. It is well established that learning experiences enhance post-learning sleep. However, the underlying mechanisms of how learning mediates sleep for memory retention are not clear. Drosophila males display increased amounts of sleep after courtship learning. Courtship learning depends on Mushroom Body (MB) neurons, and post-learning sleep is mediated by the sleep-promoting ventral Fan-Shaped Body neurons (vFBs). We show that post-learning sleep is regulated by two opposing output neurons (MBONs) from the MB, which encode a measure of learning. Excitatory MBONs-γ2α'1 becomes increasingly active upon increasing time of learning, whereas inhibitory MBONs-β'2mp is activated only by a short learning experience. These MB outputs are integrated by SFS neurons, which excite vFBs to promote sleep after prolonged but not short training. This circuit may ensure that only longer or more intense learning experiences induce sleep and are thereby consolidated into LTM.