The objective of the present study was to identify biological signatures of severe coronavirus disease 2019 (COVID-19) predictive of admission in the intensive care unit (ICU). Over 170 immunological markers were investigated in a 'discovery' cohort (n = 98 patients) of the Lausanne University Hospital (LUH-1). Here we report that 13 out of 49 cytokines were significantly associated with ICU admission in the three cohorts (P < 0.05 to P < 0.001), while cellular immunological markers lacked power in discriminating between ICU and non-ICU patients. The cytokine results were confirmed in two 'validation' cohorts, i.e. the French COVID-19 Study (FCS; n = 62) and a second LUH-2 cohort (n = 47). The combination of hepatocyte growth factor (HGF) and C-X-C motif chemokine ligand 13 (CXCL13) was the best predictor of ICU admission (positive and negative predictive values ranging from 81.8% to 93.1% and 85.2% to 94.4% in the 3 cohorts) and occurrence of death during patient follow-up (8.8 fold higher likelihood of death when both cytokines were increased). Of note, HGF is a pleiotropic cytokine with anti-inflammatory properties playing a fundamental role in lung tissue repair, and CXCL13, a pro-inflammatory chemokine associated with pulmonary fibrosis and regulating the maturation of B cell response. Up-regulation of HGF reflects the most powerful counter-regulatory mechanism of the host immune response to antagonize the pro-inflammatory cytokines including CXCL13 and to prevent lung fibrosis in COVID-19 patients.

Comment on Cell Metab. 2021 Jan 5;33(1):174-189.e7. Nat Commun. 2021 Mar 11;12(1):1589.

Update of bioRxiv. 2021 Apr 22;:

Comment in Bioessays. 2022 Jun;44(6):e2100297.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that is spreading rapidly, which seriously impacts global public health and economy. Thus, developing effective drugs remains urgent. We identify two potent antibodies, nCoVmab1 and nCoVmab2, targeting the SARS-CoV-2 spike protein receptor-binding domain (RBD) with high affinities from a naïve human phage-displayed Fab library. nCoVmab1 and nCoVmab2 neutralize authentic SARS-CoV-2 with picomolar and nanomolar IC50 values, respectively. No detectable defects of nCoVmab1 and nCoVmab2 are found during the preliminary druggability evaluation. nCoVmab1 could reduce viral titer and lung injury when administered prophylactically and therapeutically in human angiotensin-converting enzyme II (hACE2)-transgenic mice. Therefore, phage display platform could be efficiently used for rapid development of neutralizing monoclonal antibodies (nmabs) with clinical potential against emerging infectious diseases. In addition, we determinate epitopes in RBD of these antibodies to elucidate the neutralizing mechanism. We also convert nCoVmab1 and nCoVmab2 to their germline formats for further analysis, which reveals the contribution of somatic hypermutation (SHM) during nCoVmab1 and nCoVmab2 maturation. Our findings not only provide two highly potent nmabs against SARS-CoV-2 as prophylactic and therapeutic candidates, but also give some clues for development of anti-SARS-CoV-2 agents (e.g., drugs and vaccines) targeting the RBD.

Encapsulins are a class of microbial protein compartments defined by the viral HK97-fold of their capsid protein, self-assembly into icosahedral shells, and dedicated cargo loading mechanism for sequestering specific enzymes. Encapsulins are often misannotated and traditional sequence-based searches yield many false positive hits in the form of phage capsids. Here, we develop an integrated search strategy to carry out a large-scale computational analysis of prokaryotic genomes with the goal of discovering an exhaustive and curated set of all HK97-fold encapsulin-like systems. We find over 6,000 encapsulin-like systems in 31 bacterial and four archaeal phyla, including two novel encapsulin families. We formulate hypotheses about their potential biological functions and biomedical relevance, which range from natural product biosynthesis and stress resistance to carbon metabolism and anaerobic hydrogen production. An evolutionary analysis of encapsulins and related HK97-type virus families shows that they share a common ancestor, and we conclude that encapsulins likely evolved from HK97-type bacteriophages.

Author information: (1)St. Johns Institute of Dermatology, Kings College London, London, United Kingdom. (2)NIHR Biomedical Research Centre, Guys & St Thomas NHS Foundation Trust & King's College London, London, UK. (3)DIGNOSIS Limited, London, UK. (4)Department of Medical and Molecular Genetics, Kings College London, London, UK. (5)Sanofi, Cambridge, MA, USA. (6)Dermatology Department, Queen Elizabeth Hospital, Lewisham and Greenwich NHS Trust, London, UK. (7)Centre for Translational Bioinformatics, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, UK. (8)Dermatology Centre, Salford Royal Hospital, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK. (9)Institute of Translational and Clinical Medicine, Newcastle University Medical School and Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK. (10)St. Johns Institute of Dermatology, Kings College London, London, United Kingdom. paola.dimeglio@kcl.ac.uk. (11)NIHR Biomedical Research Centre, Guys & St Thomas NHS Foundation Trust & King's College London, London, UK. paola.dimeglio@kcl.ac.uk. (#)Contributed equally

Dopamine controls diverse behaviors and their dysregulation contributes to many disorders. Our ability to understand and manipulate the function of dopamine is limited by the heterogenous nature of dopaminergic projections, the diversity of neurons that are regulated by dopamine, the varying distribution of the five dopamine receptors (DARs), and the complex dynamics of dopamine release. In order to improve our ability to specifically modulate distinct DARs, here we develop a photo-pharmacological strategy using a Membrane anchored Photoswitchable orthogonal remotely tethered agonist for the Dopamine receptor (MP-D). Our design selectively targets D1R/D5R receptor subtypes, most potently D1R (MP-D1ago), as shown in HEK293T cells. In vivo, we targeted dorsal striatal medium spiny neurons where the photo-activation of MP-D1ago increased movement initiation, although further work is required to assess the effects of MP-D1ago on neuronal function. Our method combines ligand and cell type-specificity with temporally precise and reversible activation of D1R to control specific aspects of movement. Our results provide a template for analyzing dopamine receptors.

Axons in the cerebral cortex show a broad range of myelin coverage. Oligodendrocytes establish this pattern by selecting a cohort of axons for myelination; however, the distribution of myelin on distinct neurons and extent of internode replacement after demyelination remain to be defined. Here we show that myelination patterns of seven distinct neuron subtypes in somatosensory cortex are influenced by both axon diameter and neuronal identity. Preference for myelination of parvalbumin interneurons was preserved between cortical areas with varying myelin density, suggesting that regional differences in myelin abundance arises through local control of oligodendrogenesis. By imaging loss and regeneration of myelin sheaths in vivo we show that myelin distribution on individual axons was altered but overall myelin content on distinct neuron subtypes was restored. Our findings suggest that local changes in myelination are tolerated, allowing regenerated oligodendrocytes to restore myelin content on distinct neurons through opportunistic selection of axons.

Usually, high temperature decreases the output performance of triboelectric nanogenerator because of the dissipation of triboelectric charges through the thermionic emission. Here, a temperature difference triboelectric nanogenerator is designed and fabricated to enhance the electrical output performance in high temperature environment. As the hotter friction layer's temperature of nanogenerator is 0 K to 145 K higher than the cooler part's temperature, the output voltage, current, surface charge density and output power are increased 2.7, 2.2, 3.0 and 2.9 times, respectively (from 315 V, 9.1 μA, 19.6 μC m-2, 69 μW to 858 V, 20 μA, 58.8 μC m-2, 206.7 μW). With the further increase of temperature difference from 145 K to 219 K, the surface charge density and output performance gradually decrease. At the optimal temperature difference (145 K), the largest output current density is 443 μA cm-2, which is 26.6% larger than the reported record value (350 μA cm-2).

Globally, bird migration is occurring earlier in the year, consistent with climate-related changes in breeding resources. Although often attributed to phenotypic plasticity, there is no clear demonstration of long-term population advancement in avian migration through individual plasticity. Using direct observations of bar-tailed godwits (Limosa lapponica) departing New Zealand on a 16,000-km journey to Alaska, we show that migration advanced by six days during 2008-2020, and that within-individual advancement was sufficient to explain this population-level change. However, in individuals tracked for the entire migration (50 total tracks of 36 individuals), earlier departure did not lead to earlier arrival or breeding in Alaska, due to prolonged stopovers in Asia. Moreover, changes in breeding-site phenology varied across Alaska, but were not reflected in within-population differences in advancement of migratory departure. We demonstrate that plastic responses can drive population-level changes in timing of long-distance migration, but also that behavioral and environmental constraints en route may yet limit adaptive responses to global change.

Rational design of heterostructures opens up new opportunities as an ideal catalyst system for lithium polysulfides conversion in lithium-sulfur battery. However, its traditional fabrication process is complex, which makes it difficult to reasonably control the content and distribution of each component. In this work, to rationally design the heterostructure, the atomic layer deposition is utilized to hybridize the TiO2-TiN heterostructure with the three-dimensional carbon nanotube sponge. Through optimizing the deposited thickness of TiO2 and TiN layers and adopting the annealing post-treatment, the derived coaxial sponge with uniform TiN-TiO2 heterostructure exhibits the best catalytic ability. The corresponding lithium-sulfur battery shows enhanced electrochemical performance with high specific capacity of 1289 mAh g-1 at 1 C and capacity retention of 85% after 500 cycles at 2 C. Furthermore, benefiting from the highly porous structure and interconnected conductive pathways from the sponge, its areal capacity reaches up to 21.5 mAh cm-2.

Shape displays enable people to touch simulated surfaces. A common architecture of such devices uses a mechatronic pin-matrix. Besides their complexity and high cost, these matrix displays suffer from sharp edges due to the discreet representation which reduces their ability to render a large continuous surface when sliding the hand. We propose using an engineered auxetic material actuated by a smaller number of motors. The material bends in multiple directions, feeling smooth and rigid to touch. A prototype implementation uses nine actuators on a 220 mm square section of material. It can display a range of surface curvatures under the palm of a user without aliased edges. In this work we use an auxetic skeleton to provide rigidity on a soft material and demonstrate the potential of this class of surface through user experiments.

The ancestors of cyanobacteria generated Earth's first biogenic molecular oxygen, but how they dealt with oxidative stress remains unconstrained. Here we investigate when superoxide dismutase enzymes (SODs) capable of removing superoxide free radicals evolved and estimate when Cyanobacteria originated. Our Bayesian molecular clocks, calibrated with microfossils, predict that stem Cyanobacteria arose 3300-3600 million years ago. Shortly afterwards, we find phylogenetic evidence that ancestral cyanobacteria used SODs with copper and zinc cofactors (CuZnSOD) during the Archaean. By the Paleoproterozoic, they became genetically capable of using iron, nickel, and manganese as cofactors (FeSOD, NiSOD, and MnSOD respectively). The evolution of NiSOD is particularly intriguing because it corresponds with cyanobacteria's invasion of the open ocean. Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) now demonstrate that marine geochemical records alone may not predict patterns of metal usage by phototrophs from freshwater and terrestrial habitats.

A new generation of earthquake catalogs developed through supervised machine-learning illuminates earthquake activity with unprecedented detail. Application of unsupervised machine learning to analyze the more complete expression of seismicity in these catalogs may be the fastest route to improving earthquake forecasting.

Biological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.

The relationship between the age-associated decline in mitochondrial function and its effect on skeletal muscle physiology and function remain unclear. In the current study, we examined to what extent physical activity contributes to the decline in mitochondrial function and muscle health during aging and compared mitochondrial function in young and older adults, with similar habitual physical activity levels. We also studied exercise-trained older adults and physically impaired older adults. Aging was associated with a decline in mitochondrial capacity, exercise capacity and efficiency, gait stability, muscle function, and insulin sensitivity, even when maintaining an adequate daily physical activity level. Our data also suggest that a further increase in physical activity level, achieved through regular exercise training, can largely negate the effects of aging. Finally, mitochondrial capacity correlated with exercise efficiency and insulin sensitivity. Together, our data support a link between mitochondrial function and age-associated deterioration of skeletal muscle.

Author information: (1)Montreal Neurological Institute, McGill University, Montréal, QC, Canada. jacob.vogel@mail.mcgill.ca. (2)Montreal Neurological Institute, McGill University, Montréal, QC, Canada. (3)Clinical Memory Research Unit, Lund University, Lund, Sweden. (4)Memory Clinic, Skåne University Hospital, Lund, Sweden. (5)Clinical Memory Research Unit, Lund University, Lund, Sweden. oskar.hansson@med.lu.se. (6)Memory Clinic, Skåne University Hospital, Lund, Sweden. oskar.hansson@med.lu.se. (#)Contributed equally

Methane (CH4) emissions from oil and natural gas (O&NG) systems are an important contributor to greenhouse gas emissions. In the United States, recent synthesis studies of field measurements of CH4 emissions at different spatial scales are ~1.5-2× greater compared to official greenhouse gas inventory (GHGI) estimates, with the production-segment as the dominant contributor to this divergence. Based on an updated synthesis of measurements from component-level field studies, we develop a new inventory-based model for CH4 emissions, for the production-segment only, that agrees within error with recent syntheses of site-level field studies and allows for isolation of equipment-level contributions. We find that unintentional emissions from liquid storage tanks and other equipment leaks are the largest contributors to divergence with the GHGI. If our proposed method were adopted in the United States and other jurisdictions, inventory estimates could better guide CH4 mitigation policy priorities.

Flat band moiré superlattices have recently emerged as unique platforms for investigating the interplay between strong electronic correlations, nontrivial band topology, and multiple isospin 'flavor' symmetries. Twisted monolayer-bilayer graphene (tMBG) is an especially rich system owing to its low crystal symmetry and the tunability of its bandwidth and topology with an external electric field. Here, we find that orbital magnetism is abundant within the correlated phase diagram of tMBG, giving rise to the anomalous Hall effect in correlated metallic states nearby most odd integer fillings of the flat conduction band, as well as correlated Chern insulator states stabilized in an external magnetic field. The behavior of the states at zero field appears to be inconsistent with simple spin and valley polarization for the specific range of twist angles we investigate, and instead may plausibly result from an intervalley coherent (IVC) state with an order parameter that breaks time reversal symmetry. The application of a magnetic field further tunes the competition between correlated states, in some cases driving first-order topological phase transitions. Our results underscore the rich interplay between closely competing correlated ground states in tMBG, with possible implications for probing exotic IVC ordering.

Forecasting the evolution of contagion dynamics is still an open problem to which mechanistic models only offer a partial answer. To remain mathematically or computationally tractable, these models must rely on simplifying assumptions, thereby limiting the quantitative accuracy of their predictions and the complexity of the dynamics they can model. Here, we propose a complementary approach based on deep learning where effective local mechanisms governing a dynamic on a network are learned from time series data. Our graph neural network architecture makes very few assumptions about the dynamics, and we demonstrate its accuracy using different contagion dynamics of increasing complexity. By allowing simulations on arbitrary network structures, our approach makes it possible to explore the properties of the learned dynamics beyond the training data. Finally, we illustrate the applicability of our approach using real data of the COVID-19 outbreak in Spain. Our results demonstrate how deep learning offers a new and complementary perspective to build effective models of contagion dynamics on networks.

Electrodermal devices that capture the physiological response of skin are crucial for monitoring vital signals, but they often require convoluted layered designs with either electronic or ionic active materials relying on complicated synthesis procedures, encapsulation, and packaging techniques. Here, we report that the ionic transport in living systems can provide a simple mode of iontronic sensing and bypass the need of artificial ionic materials. A simple skin-electrode mechanosensing structure (SEMS) is constructed, exhibiting high pressure-resolution and spatial-resolution, being capable of feeling touch and detecting weak physiological signals such as fingertip pulse under different skin humidity. Our mechanical analysis reveals the critical role of instability in high-aspect-ratio microstructures on sensing. We further demonstrate pressure mapping with millimeter-spatial-resolution using a fully textile SEMS-based glove. The simplicity and reliability of SEMS hold great promise of diverse healthcare applications, such as pulse detection and recovering the sensory capability in patients with tactile dysfunction.

Polarized epithelial cells can organize into complex structures with a characteristic central lumen. Lumen formation requires that cells coordinately orient their polarity axis so that the basolateral domain is on the outside and apical domain inside epithelial structures. Here we show that the transmembrane aminopeptidase, CD13, is a key determinant of epithelial polarity orientation. CD13 localizes to the apical membrane and associates with an apical complex with Par6. CD13-deficient cells display inverted polarity in which apical proteins are retained on the outer cell periphery and fail to accumulate at an intercellular apical initiation site. Here we show that CD13 is required to couple apical protein cargo to Rab11-endosomes and for capture of endosomes at the apical initiation site. This role in polarity utilizes the short intracellular domain but is independent of CD13 peptidase activity.

Climate change is a critical factor affecting biodiversity. However, the quantitative relationship between temperature change and extinction is unclear. Here, we analyze magnitudes and rates of temperature change and extinction rates of marine fossils through the past 450 million years (Myr). The results show that both the rate and magnitude of temperature change are significantly positively correlated with the extinction rate of marine animals. Major mass extinctions in the Phanerozoic can be linked to thresholds in climate change (warming or cooling) that equate to magnitudes >5.2 °C and rates >10 °C/Myr. The significant relationship between temperature change and extinction still exists when we exclude the five largest mass extinctions of the Phanerozoic. Our findings predict that a temperature increase of 5.2 °C above the pre-industrial level at present rates of increase would likely result in mass extinction comparable to that of the major Phanerozoic events, even without other, non-climatic anthropogenic impacts.

Erratum in Nat Commun. 2021 Sep 3;12(1):5334.

Mycobacterium tuberculosis can adapt to changing environments by non-heritable mechanisms. Frame-shifting insertions and deletions (indels) may also participate in adaptation through gene disruption, which could be reversed by secondary introduction of a frame-restoring indel. We present ScarTrek, a program that scans genomic data for indels, including those that together disrupt and restore a gene's reading frame, producing "frame-shift scars" suggestive of reversible gene inactivation. We use ScarTrek to analyze 5977 clinical M. tuberculosis isolates. We show that indel frequency inversely correlates with genomic linguistic complexity and varies with gene-position and gene-essentiality. Using ScarTrek, we detect 74 unique frame-shift scars in 48 genes, with a 3.74% population-level incidence of unique scar events. We find multiple scars in the ESX-1 gene cluster. Six scars show evidence of convergent evolution while the rest shared a common ancestor. Our results suggest that sequential indels are a mechanism for reversible gene silencing and adaptation in M. tuberculosis.

Bone metastasis is an incurable complication of breast cancer. In advanced stages, patients with estrogen-positive tumors experience a significantly higher incidence of bone metastasis (>87%) compared to estrogen-negative patients (<56%). To understand the mechanism of this bone-tropism of ER+ tumor, and to identify liquid biopsy biomarkers for patients with high risk of bone metastasis, the secreted extracellular vesicles and cytokines from bone-tropic breast cancer cells are examined in this study. Both exosomal miR-19a and Integrin-Binding Sialoprotein (IBSP) are found to be significantly upregulated and secreted from bone-tropic ER+ breast cancer cells, increasing their levels in the circulation of patients. IBSP is found to attract osteoclast cells and create an osteoclast-enriched environment in the bone, assisting the delivery of exosomal miR-19a to osteoclast to induce osteoclastogenesis. Our findings reveal a mechanism by which ER+ breast cancer cells create a microenvironment favorable for colonization in the bone. These two secreted factors can also serve as effective biomarkers for ER+ breast cancer to predict their risks of bone metastasis. Furthermore, our screening of a natural compound library identifies chlorogenic acid as a potent inhibitor for IBSP-receptor binding to suppress bone metastasis of ER+ tumor, suggesting its preventive use for bone recurrence in ER+ patients.

The energy demand for heating and cooling buildings is changing with global warming. Using proxies of climate-driven energy demand based on the heating and cooling Degree-Days methodology applied to thirty global climate model simulations, we show that, over all continental areas, the climate-driven energy demand trends for heating and cooling were weak, changing by less than 10% from 1950 to 1990, but become stronger from 1990 to 2030, changing by more than 10%. With the multi-model mean, the increasing trends in cooling energy demand are more pronounced than the decreasing trends in heating. The changes in cooling, however, are highly variable depending on individual simulations, ranging from a few to several hundred percent in most of the densely populated mid-latitude areas. This work presents an example of the challenges that accompany future energy demand quantification as a result of the uncertainty in the projected climate.

From physics to engineering, biology and social science, natural and artificial systems are characterized by interconnected topologies whose features - e.g., heterogeneous connectivity, mesoscale organization, hierarchy - affect their robustness to external perturbations, such as targeted attacks to their units. Identifying the minimal set of units to attack to disintegrate a complex network, i.e. network dismantling, is a computationally challenging (NP-hard) problem which is usually attacked with heuristics. Here, we show that a machine trained to dismantle relatively small systems is able to identify higher-order topological patterns, allowing to disintegrate large-scale social, infrastructural and technological networks more efficiently than human-based heuristics. Remarkably, the machine assesses the probability that next attacks will disintegrate the system, providing a quantitative method to quantify systemic risk and detect early-warning signals of system's collapse. This demonstrates that machine-assisted analysis can be effectively used for policy and decision-making to better quantify the fragility of complex systems and their response to shocks.

Studying naturalistic animal behavior remains a difficult objective. Recent machine learning advances have enabled limb localization; however, extracting behaviors requires ascertaining the spatiotemporal patterns of these positions. To provide a link from poses to actions and their kinematics, we developed B-SOiD - an open-source, unsupervised algorithm that identifies behavior without user bias. By training a machine classifier on pose pattern statistics clustered using new methods, our approach achieves greatly improved processing speed and the ability to generalize across subjects or labs. Using a frameshift alignment paradigm, B-SOiD overcomes previous temporal resolution barriers. Using only a single, off-the-shelf camera, B-SOiD provides categories of sub-action for trained behaviors and kinematic measures of individual limb trajectories in any animal model. These behavioral and kinematic measures are difficult but critical to obtain, particularly in the study of rodent and other models of pain, OCD, and movement disorders.

Plasmablastic lymphoma (PBL) represents a rare and aggressive lymphoma subtype frequently associated with immunosuppression. Clinically, patients with PBL are characterized by poor outcome. The current understanding of the molecular pathogenesis is limited. A hallmark of PBL represents its plasmacytic differentiation with loss of B-cell markers and, in 60% of cases, its association with Epstein-Barr virus (EBV). Roughly 50% of PBLs harbor a MYC translocation. Here, we provide a comprehensive integrated genomic analysis using whole exome sequencing (WES) and genome-wide copy number determination in a large cohort of 96 primary PBL samples. We identify alterations activating the RAS-RAF, JAK-STAT, and NOTCH pathways as well as frequent high-level amplifications in MCL1 and IRF4. The functional impact of these alterations is assessed using an unbiased shRNA screen in a PBL model. These analyses identify the IRF4 and JAK-STAT pathways as promising molecular targets to improve outcome of PBL patients.

Superconducting computing promises enhanced computational power in both classical and quantum approaches. Yet, scalable and fast superconducting memories are not implemented. Here, we propose a fully superconducting memory cell based on the hysteretic phase-slip transition existing in long aluminum nanowire Josephson junctions. Embraced by a superconducting ring, the memory cell codifies the logic state in the direction of the circulating persistent current, as commonly defined in flux-based superconducting memories. But, unlike the latter, the hysteresis here is a consequence of the phase-slip occurring in the long weak link and associated to the topological transition of its superconducting gap. This disentangles our memory scheme from the large-inductance constraint, thus enabling its miniaturization. Moreover, the strong activation energy for phase-slip nucleation provides a robust topological protection against stochastic phase-slips and magnetic-flux noise. These properties make the Josephson phase-slip memory a promising solution for advanced superconducting classical logic architectures or flux qubits.

Nanographenes have kindled considerable interest in the fields of materials science and supramolecular chemistry as a result of their unique self-assembling and optoelectronic properties. Encapsulating the contorted nanographenes inside artificial receptors, however, remains challenging. Herein, we report the design and synthesis of a trigonal prismatic hexacationic cage, which has a large cavity and adopts a relatively flexible conformation. It serves as a receptor, not only for planar coronene, but also for contorted nanographene derivatives with diameters of approximately 15 Å and thicknesses of 7 Å. A comprehensive investigation of the host-guest interactions in the solid, solution and gaseous states by experimentation and theoretical calculations reveals collectively an induced-fit binding mechanism with high binding affinities between the cage and the nanographenes. Notably, the photostability of the nanographenes is improved significantly by the ultrafast deactivation of their excited states within the cage. Encapsulating the contorted nanographenes inside the cage provides a noncovalent strategy for regulating their photoreactivity.

Parkinson's disease (PD) is characterised by the emergence of beta frequency oscillatory synchronisation across the cortico-basal-ganglia circuit. The relationship between the anatomy of this circuit and oscillatory synchronisation within it remains unclear. We address this by combining recordings from human subthalamic nucleus (STN) and internal globus pallidus (GPi) with magnetoencephalography, tractography and computational modelling. Coherence between supplementary motor area and STN within the high (21-30 Hz) but not low (13-21 Hz) beta frequency range correlated with 'hyperdirect pathway' fibre densities between these structures. Furthermore, supplementary motor area activity drove STN activity selectively at high beta frequencies suggesting that high beta frequencies propagate from the cortex to the basal ganglia via the hyperdirect pathway. Computational modelling revealed that exaggerated high beta hyperdirect pathway activity can provoke the generation of widespread pathological synchrony at lower beta frequencies. These findings suggest a spectral signature and a pathophysiological role for the hyperdirect pathway in PD.

Calcitonin receptor (Calcr)-expressing neurons of the nucleus tractus solitarius (NTS; CalcrNTS cells) contribute to the long-term control of food intake and body weight. Here, we show that Prlh-expressing NTS (PrlhNTS) neurons represent a subset of CalcrNTS cells and that Prlh expression in these cells restrains body weight gain in the face of high fat diet challenge in mice. To understand the relationship of PrlhNTS cells to hypothalamic feeding circuits, we determined the ability of PrlhNTS-mediated signals to overcome enforced activation of AgRP neurons. We found that PrlhNTS neuron activation and Prlh overexpression in PrlhNTS cells abrogates AgRP neuron-driven hyperphagia and ameliorates the obesity of mice deficient in melanocortin signaling or leptin. Thus, enhancing Prlh-mediated neurotransmission from the NTS dampens hypothalamically-driven hyperphagia and obesity, demonstrating that NTS-mediated signals can override the effects of orexigenic hypothalamic signals on long-term energy balance.

Manmade high-performance polymers are typically non-biodegradable and derived from petroleum feedstock through energy intensive processes involving toxic solvents and byproducts. While engineered microbes have been used for renewable production of many small molecules, direct microbial synthesis of high-performance polymeric materials remains a major challenge. Here we engineer microbial production of megadalton muscle titin polymers yielding high-performance fibers that not only recapture highly desirable properties of natural titin (i.e., high damping capacity and mechanical recovery) but also exhibit high strength, toughness, and damping energy - outperforming many synthetic and natural polymers. Structural analyses and molecular modeling suggest these properties derive from unique inter-chain crystallization of folded immunoglobulin-like domains that resists inter-chain slippage while permitting intra-chain unfolding. These fibers have potential applications in areas from biomedicine to textiles, and the developed approach, coupled with the structure-function insights, promises to accelerate further innovation in microbial production of high-performance materials.

The COVID-19 lockdown reduced human mobility and led to immediate insights into how humans impact nature. Yet the strongest ecological impacts are likely to come. As we emerge from the pandemic, governments should avoid prioritizing short-term economic gains that compromise ecosystems and the services they provide humanity. Instead, the pandemic can be a pivot point for societal transformation to value longer term ecosystem and economic sustainability.

Animals maintain metabolic homeostasis by modulating the activity of specialized organs that adjust internal metabolism to external conditions. However, the hormonal signals coordinating these functions are incompletely characterized. Here we show that six neurosecretory cells in the Drosophila central nervous system respond to circulating nutrient levels by releasing Capa hormones, homologs of mammalian neuromedin U, which activate the Capa receptor (CapaR) in peripheral tissues to control energy homeostasis. Loss of Capa/CapaR signaling causes intestinal hypomotility and impaired nutrient absorption, which gradually deplete internal nutrient stores and reduce organismal lifespan. Conversely, increased Capa/CapaR activity increases fluid and waste excretion. Furthermore, Capa/CapaR inhibits the release of glucagon-like adipokinetic hormone from the corpora cardiaca, which restricts energy mobilization from adipose tissue to avoid harmful hyperglycemia. Our results suggest that the Capa/CapaR circuit occupies a central node in a homeostatic program that facilitates the digestion and absorption of nutrients and regulates systemic energy balance.

Update of bioRxiv. 2021 Mar 10;:

Non-contact triboelectric nanogenerator (TENG) enabled for both high conversion efficiency and durability is appropriate to harvest random micro energy owing to the advantage of low driving force. However, the low output (<10 μC m-2) of non-contact TENG caused by the drastic charge decay limits its application. Here, we propose a floating self-excited sliding TENG (FSS-TENG) by a self-excited amplification between rotator and stator to achieve self-increased charge density, and the air breakdown model of non-contact TENG is given for a maximum charge density. The charge density up to 71.53 μC m-2 is achieved, 5.46 times as that of the traditional floating TENG. Besides, the high output enables it to continuously power small electronics at 3 m s-1 weak wind. This work provides an effective strategy to address the low output of floating sliding TENG, and can be easily adapted to capture the varied micro mechanical energies anywhere.

Placenta accreta spectrum (PAS) is a high-risk obstetrical condition associated with significant morbidity and mortality. Current clinical screening modalities for PAS are not always conclusive. Here, we report a nanostructure-embedded microchip that efficiently enriches both single and clustered circulating trophoblasts (cTBs) from maternal blood for detecting PAS. We discover a uniquely high prevalence of cTB-clusters in PAS and subsequently optimize the device to preserve the intactness of these clusters. Our feasibility study on the enumeration of cTBs and cTB-clusters from 168 pregnant women demonstrates excellent diagnostic performance for distinguishing PAS from non-PAS. A logistic regression model is constructed using a training cohort and then cross-validated and tested using an independent cohort. The combined cTB assay achieves an Area Under ROC Curve of 0.942 (throughout gestation) and 0.924 (early gestation) for distinguishing PAS from non-PAS. Our assay holds the potential to improve current diagnostic modalities for the early detection of PAS.

Direct current (DC) converters play an essential role in electronic circuits. Conventional high-efficiency DC voltage converters, especially step-up type, rely on switching operation, where energy is periodically stored within and released from inductors and/or capacitors connected in a variety of circuit topologies. Since these energy storage components, especially inductors, are fundamentally difficult to scale down, miniaturization of switching converters proves challenging. Furthermore, the resulting switching currents produce significant electromagnetic noise. To overcome the limitations of switching converters, photonic transformers, where voltage conversion is achieved through light emission and detection processes, have been demonstrated. However, the demonstrated efficiency is significantly below that of the switching converter. Here we perform a detailed balance analysis and show that with a monolithically integrated design that enables efficient photon transport, the photonic transformer can operate with a near-unity conversion efficiency and high voltage conversion ratio. We validate the theory with a transformer constructed with off-the-shelf discrete components. Our experiment showcases near noiseless operation and a voltage conversion ratio that is significantly higher than obtained in previous photonic transformers. Our findings point to the possibility of a high-performance optical solution to miniaturizing DC power converters and improving the electromagnetic compatibility and quality of electrical power.

The lunar surface is ancient and well-preserved, recording Solar System history and planetary evolution processes. Ancient basin-scale impacts excavated lunar mantle rocks, which are expected to remain present on the surface. Sampling these rocks would provide insight into fundamental planetary processes, including differentiation and magmatic evolution. There is contention among lunar scientists as to what lithologies make up the upper lunar mantle, and where they may have been exposed on the surface. We review dynamical models of lunar differentiation in the context of recent experiments and spacecraft data, assessing candidate lithologies, their distribution, and implications for lunar evolution.

Integration of solid-state microchips into soft-matter, and stretchable printed electronics has been the biggest challenge against their scalable fabrication. We introduce, Pol-Gel, a simple technique for self-soldering, self-encapsulation, and self-healing, that allows low cost, scalable, and rapid fabrication of hybrid microchip-integrated ultra-stretchable circuits. After digitally printing the circuit, and placing the microchips, we trigger a Polymer-Gel transition in physically cross-linked block copolymers substrate, and silver liquid metal composite ink, by exposing the circuits to the solvent vapor. Once in the gel state, microchips penetrate to the ink and the substrate (Self-Soldering), and the ink penetrates to the substrate (Self-encapsulation). Maximum strain tolerance of ~1200% for printed stretchable traces, and >500% for chip-integrated soft circuits is achieved, which is 5x higher than the previous works. We demonstrate condensed soft-matter patches and e-textiles with integrated sensors, processors, and wireless communication, and repairing of a fully cut circuits through Pol-Gel.

Dynamically adapting the allocation of COVID-19 vaccines to the evolving epidemiological situation could be key to reduce COVID-19 burden. Here we developed a data-driven mechanistic model of SARS-CoV-2 transmission to explore optimal vaccine prioritization strategies in China. We found that a time-varying vaccination program (i.e., allocating vaccines to different target groups as the epidemic evolves) can be highly beneficial as it is capable of simultaneously achieving different objectives (e.g., minimizing the number of deaths and of infections). Our findings suggest that boosting the vaccination capacity up to 2.5 million first doses per day (0.17% rollout speed) or higher could greatly reduce COVID-19 burden, should a new wave start to unfold in China with reproduction number ≤1.5. The highest priority categories are consistent under a broad range of assumptions. Finally, a high vaccination capacity in the early phase of the vaccination campaign is key to achieve large gains of strategic prioritizations.

The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of which is the type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with the parS DNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood. Here, we report the cryo-EM structure of the Vibrio cholerae ParA2 filament bound to DNA, as well as the crystal structures of this protein in various nucleotide states. These structures show that ParA forms a left-handed filament on DNA, stabilized by nucleotide binding, and that ParA undergoes profound structural rearrangements upon DNA binding and filament assembly. Collectively, our data suggest the structural basis for ParA's cooperative binding to DNA and the formation of high ParA density regions on the nucleoid.

Obesity results from a caloric imbalance between energy intake, absorption and expenditure. In both rodents and humans, diet-induced thermogenesis contributes to energy expenditure and involves the activation of brown adipose tissue (BAT). We hypothesize that environmental toxicants commonly used as food additives or pesticides might reduce BAT thermogenesis through suppression of uncoupling protein 1 (UCP1) and this may contribute to the development of obesity. Using a step-wise screening approach, we discover that the organophosphate insecticide chlorpyrifos suppresses UCP1 and mitochondrial respiration in BAT at concentrations as low as 1 pM. In mice housed at thermoneutrality and fed a high-fat diet, chlorpyrifos impairs BAT mitochondrial function and diet-induced thermogenesis, promoting greater obesity, non-alcoholic fatty liver disease (NAFLD) and insulin resistance. This is associated with reductions in cAMP; activation of p38MAPK and AMPK; protein kinases critical for maintaining UCP1 and mitophagy, respectively in BAT. These data indicate that the commonly used pesticide chlorpyrifos, suppresses diet-induced thermogenesis and the activation of BAT, suggesting its use may contribute to the obesity epidemic.

Author information: (1)Chair of Statistics and Econometrics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. johannes.bracher@kit.edu. (2)Computational Statistics Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. johannes.bracher@kit.edu. (3)Chair of Statistics and Econometrics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. (4)Computational Statistics Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. (5)Robert Koch Institute (RKI), Berlin, Germany. (6)London School of Hygiene and Tropical Medicine, London, UK. (7)Frankfurt Institute for Advanced Studies, Frankfurt, Germany. (8)Sloan School of Management, Massachusetts Institute of Technology, Cambridge, MA, USA. (9)MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK. (10)Wroclaw University of Science and Technology, Wroclaw, Poland. (11)Economic and Social Statistics Department, University of Trier, Trier, Germany. (12)Information Systems and Modeling, Los Alamos National Laboratory, Los Alamos, NM, USA. (13)Jülich Supercomputing Centre, Forschungszentrum Jülich, Jülich, Germany. (14)Institute of Informatics, University of Warsaw, Warsaw, Poland. (15)Department of Computer Science, University of California, Los Angeles, CA, USA. (16)Institute of Mathematics, Technische Universität Ilmenau, Ilmenau, Germany. (17)Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany. (18)Swiss Data Science Center, ETH Zurich and EPFL, Lausanne, Switzerland. (19)Operations Research Center, Massachusetts Institute of Technology, Cambridge, MA, USA. (20)Statistical Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, USA. (21)Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland. (22)Ming Hsieh Department of Computer and Electrical Engineering, University of Southern California, Los Angeles, CA, USA. (23)Institute for Stochastics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. (24)Chair of Statistics and Econometrics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. melanie.schienle@kit.edu.

Converting incoming photons to electrical current is the key operation principle of optical photodetectors and it enables a host of emerging quantum information technologies. The leading approach for continuous and efficient detection in the optical domain builds on semiconductor photodiodes. However, there is a paucity of efficient and continuous photon detectors in the microwave regime, because photon energies are four to five orders of magnitude lower therein and conventional photodiodes do not have that sensitivity. Here we tackle this gap and demonstrate how microwave photons can be efficiently and continuously converted to electrical current in a high-quality, semiconducting nanowire double quantum dot resonantly coupled to a cavity. In particular, in our photodiode device, an absorbed photon gives rise to a single electron tunneling through the double dot, with a conversion efficiency reaching 6%.

The gastrointestinal tract may be a site of origin for α-synuclein pathology in idiopathic Parkinson's disease (PD). Disruption of the autophagy-lysosome pathway (ALP) may contribute to α-synuclein aggregation. Here we examined epigenetic alterations in the ALP in the appendix by deep sequencing DNA methylation at 521 ALP genes. We identified aberrant methylation at 928 cytosines affecting 326 ALP genes in the appendix of individuals with PD and widespread hypermethylation that is also seen in the brain of individuals with PD. In mice, we find that DNA methylation changes at ALP genes induced by chronic gut inflammation are greatly exacerbated by α-synuclein pathology. DNA methylation changes at ALP genes induced by synucleinopathy are associated with the ALP abnormalities observed in the appendix of individuals with PD specifically involving lysosomal genes. Our work identifies epigenetic dysregulation of the ALP which may suggest a potential mechanism for accumulation of α-synuclein pathology in idiopathic PD.

Mycobacterium abscessus (MAB) is an emerging pathogen that leads to chronic lung infections. To date, the global population structure of non-cystic fibrosis (CF) MAB and evolutionary patterns of drug resistance emergence have not been investigated. Here we construct a global dataset of 1,279 MAB whole genomes from CF or non-CF patients. We utilize whole genome analysis to assess relatedness, phylogeography, and drug resistance evolution. MAB isolates from CF and non-CF hosts are interspersed throughout the phylogeny, such that the majority of dominant circulating clones include isolates from both populations, indicating that global spread of MAB clones is not sequestered to CF contexts. We identify a large clade of M. abscessus harboring the erm(41) T28C mutation, predicted to confer macrolide susceptibility in this otherwise macrolide-resistant species. Identification of multiple evolutionary events within this clade, consistent with regain of wild type, intrinsic macrolide resistance, underscores the critical importance of macrolides in MAB.

Concatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures. Here, to provide a model system for such biological systems, we demonstrate autonomous lifecycles of DNA nanotubes (DNTs) by two concatenated CRNs using different thermodynamic principles: (1) ATP-powered ligation/restriction of DNA components and (2) input strand-mediated DNA strand displacement (DSD) using energy gains provided in DNA toeholds. This allows to achieve hierarchical non-equilibrium systems by concurrent ATP-powered ligation-induced DSD for activating DNT self-assembly and restriction-induced backward DSD reactions for triggering DNT degradation. We introduce indirect and direct activation of DNT self-assemblies, and orthogonal molecular recognition allows ATP-fueled self-sorting of transient multicomponent DNTs. Coupling ATP dissipation to DNA nanostructures via programmable DSD is a generic concept which should be widely applicable to organize other DNA nanostructures, and enable the design of automatons and life-like systems of higher structural complexity.

Efficient and selective CO2 electroreduction into chemical fuels promises to alleviate environmental pollution and energy crisis, but it relies on catalysts with controllable product selectivity and reaction path. Here, by means of first-principles calculations, we identify six ferroelectric catalysts comprising transition-metal atoms anchored on In2Se3 monolayer, whose catalytic performance can be controlled by ferroelectric switching based on adjusted d-band center and occupation of supported metal atoms. The polarization dependent activation allows effective control of the limiting potential of CO2 reduction on TM@In2Se3 (TM = Ni, Pd, Rh, Nb, and Re) as well as the reaction paths and final products on Nb@In2Se3 and Re@In2Se3. Interestingly, the ferroelectric switching can even reactivate the stuck catalytic CO2 reduction on Zr@In2Se3. The fairly low limiting potential and the unique ferroelectric controllable CO2 catalytic performance on atomically dispersed transition-metals on In2Se3 clearly distinguish them from traditional single atom catalysts, and open an avenue toward improving catalytic activity and selectivity for efficient and controllable electrochemical CO2 reduction reaction.

The microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating the microbiome into quantitative genetics can help untangle complexities of host-microbiome evolution. We describe two general ways in which the microbiome may affect host evolutionary potential: by shifting the mean host phenotype and by changing the variance in host phenotype in the population. We synthesize the literature across diverse taxa and discuss how these scenarios could shape the host response to selection. We conclude by outlining key avenues of research to improve our understanding of the complex interplay between hosts and microbiomes.

The difficulty of studying post-implantation development in mammals has sparked a flurry of activity to develop in vitro models, termed embryoids, based on self-organizing pluripotent stem cells. Previous approaches to derive embryoids either lack the physiological morphology and signaling interactions, or are unconducive to model post-gastrulation development. Here, we report a bioengineering-inspired approach aimed at addressing this gap. We employ a high-throughput cell aggregation approach to simultaneously coax mouse embryonic stem cells into hundreds of uniform epiblast-like aggregates in a solid matrix-free manner. When co-cultured with mouse trophoblast stem cell aggregates, the resulting hybrid structures initiate gastrulation-like events and undergo axial morphogenesis to yield structures, termed EpiTS embryoids, with a pronounced anterior development, including brain-like regions. We identify the presence of an epithelium in EPI aggregates as the major determinant for the axial morphogenesis and anterior development seen in EpiTS embryoids. Our results demonstrate the potential of EpiTS embryoids to study peri-gastrulation development in vitro.

Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their interactome in human ESCs (hESCs) has not to date been explored. Here we mapped the OCT4 interactomes in naïve and primed hESCs, revealing extensive connections to mammalian ATP-dependent nucleosome remodeling complexes. In naïve hESCs, OCT4 is associated with both BRG1 and BRM, the two paralog ATPases of the BAF complex. Genome-wide location analyses and genetic studies reveal that these two enzymes cooperate in a functionally redundant manner in the transcriptional regulation of blastocyst-specific genes. In contrast, in primed hESCs, OCT4 cooperates with BRG1 and SOX2 to promote chromatin accessibility at ectodermal genes. This work reveals how a common transcription factor utilizes differential BAF complexes to control distinct transcriptional programs in naïve and primed hESCs.

Mutational outcomes following CRISPR-Cas9-nuclease cutting in mammalian cells have recently been shown to be predictable and, in certain cases, skewed toward single genotypes. However, the ability to control these outcomes remains limited, especially for 1-bp insertions, a common and therapeutically relevant class of repair outcomes. Here, through a small molecule screen, we identify the ATM kinase inhibitor KU-60019 as a compound capable of reproducibly increasing the fraction of 1-bp insertions relative to other Cas9 repair outcomes. Small molecule or genetic ATM inhibition increases 1-bp insertion outcome fraction across three human and mouse cell lines, two Cas9 species, and dozens of target sites, although concomitantly reducing the fraction of edited alleles. Notably, KU-60019 increases the relative frequency of 1-bp insertions to over 80% of edited alleles at several native human genomic loci and improves the efficiency of correction for pathogenic 1-bp deletion variants. The ability to increase 1-bp insertion frequency adds another dimension to precise template-free Cas9-nuclease genome editing.

The electrocardiogram (ECG) is the most commonly used exam for the evaluation of cardiovascular diseases. Here we propose that the age predicted by artificial intelligence (AI) from the raw ECG (ECG-age) can be a measure of cardiovascular health. A deep neural network is trained to predict a patient's age from the 12-lead ECG in the CODE study cohort (n = 1,558,415 patients). On a 15% hold-out split, patients with ECG-age more than 8 years greater than the chronological age have a higher mortality rate (hazard ratio (HR) 1.79, p < 0.001), whereas those with ECG-age more than 8 years smaller, have a lower mortality rate (HR 0.78, p < 0.001). Similar results are obtained in the external cohorts ELSA-Brasil (n = 14,236) and SaMi-Trop (n = 1,631). Moreover, even for apparent normal ECGs, the predicted ECG-age gap from the chronological age remains a statistically significant risk predictor. These results show that the AI-enabled analysis of the ECG can add prognostic information.

NMDA receptor (NMDAR) and GABA neuronal dysfunctions are observed in animal models of autism spectrum disorders, but how these dysfunctions impair social cognition and behavior remains unclear. We report here that NMDARs in cortical parvalbumin (Pv)-positive interneurons cooperate with gap junctions to promote high-frequency (>80 Hz) Pv neuronal burst firing and social cognition. Shank2-/- mice, displaying improved sociability upon NMDAR activation, show impaired cortical social representation and inhibitory neuronal burst firing. Cortical Shank2-/- Pv neurons show decreased NMDAR activity, which suppresses the cooperation between NMDARs and gap junctions (GJs) for normal burst firing. Shank2-/- Pv neurons show compensatory increases in GJ activity that are not sufficient for social rescue. However, optogenetic boosting of Pv neuronal bursts, requiring GJs, rescues cortical social cognition in Shank2-/- mice, similar to the NMDAR-dependent social rescue. Therefore, NMDARs and gap junctions cooperate to promote cortical Pv neuronal bursts and social cognition.

The lateral prefrontal cortex (LPFC) is disproportionately expanded in humans compared to non-human primates, although the relationship between LPFC brain structures and uniquely human cognitive skills is largely unknown. Here, we test the relationship between variability in LPFC tertiary sulcal morphology and reasoning scores in a cohort of children and adolescents. Using a data-driven approach in independent discovery and replication samples, we show that the depth of specific LPFC tertiary sulci is associated with individual differences in reasoning scores beyond age. To expedite discoveries in future neuroanatomical-behavioral studies, we share tertiary sulcal definitions with the field. These findings support a classic but largely untested theory linking the protracted development of tertiary sulci to late-developing cognitive processes.

Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

The current nucleic acid signal amplification methods for SARS-CoV-2 RNA detection heavily rely on the functions of biological enzymes which imposes stringent transportation and storage conditions, high cost and global supply shortages. Here, a non-enzymatic whole genome detection method based on a simple isothermal signal amplification approach is developed for rapid detection of SARS-CoV-2 RNA and potentially any types of nucleic acids regardless of their size. The assay, termed non-enzymatic isothermal strand displacement and amplification (NISDA), is able to quantify 10 RNA copies.µL-1. In 164 clinical oropharyngeal RNA samples, NISDA assay is 100 % specific, and it is 96.77% and 100% sensitive when setting up in the laboratory and hospital, respectively. The NISDA assay does not require RNA reverse-transcription step and is fast (<30 min), affordable, highly robust at room temperature (>1 month), isothermal (42 °C) and user-friendly, making it an excellent assay for broad-based testing.

CRISPR-Cas9 mediated genome editing offers unprecedented opportunities for treating human diseases. There are several reports that demonstrate pre-existing immune responses to Cas9 which may have implications for clinical development of CRISPR-Cas9 mediated gene therapy. Here we use 209 overlapping peptides that span the entire sequence of Staphylococcus aureus Cas9 (SaCas9) and human peripheral blood mononuclear cells (PBMCs) from a cohort of donors with a distribution of Major Histocompatibility Complex (MHC) alleles comparable to that in the North American (NA) population to identify the immunodominant regions of the SaCas9 protein. We also use an MHC Associated Peptide Proteomics (MAPPs) assay to identify SaCas9 peptides presented by MHC Class II (MHC-II) proteins on dendritic cells. Using these two data sets we identify 22 SaCas9 peptides that are both presented by MHC-II proteins and stimulate CD4+ T-cells.

With the current interest in cultured meat, mammalian cell-based meat has mostly been unstructured. There is thus still a high demand for artificial steak-like meat. We demonstrate in vitro construction of engineered steak-like tissue assembled of three types of bovine cell fibers (muscle, fat, and vessel). Because actual meat is an aligned assembly of the fibers connected to the tendon for the actions of contraction and relaxation, tendon-gel integrated bioprinting was developed to construct tendon-like gels. In this study, a total of 72 fibers comprising 42 muscles, 28 adipose tissues, and 2 blood capillaries were constructed by tendon-gel integrated bioprinting and manually assembled to fabricate steak-like meat with a diameter of 5 mm and a length of 10 mm inspired by a meat cut. The developed tendon-gel integrated bioprinting here could be a promising technology for the fabrication of the desired types of steak-like cultured meats.

Melanoma cells rely on developmental programs during tumor initiation and progression. Here we show that the embryonic stem cell (ESC) factor Sall4 is re-expressed in the Tyr::NrasQ61K; Cdkn2a-/- melanoma model and that its expression is necessary for primary melanoma formation. Surprisingly, while Sall4 loss prevents tumor formation, it promotes micrometastases to distant organs in this melanoma-prone mouse model. Transcriptional profiling and in vitro assays using human melanoma cells demonstrate that SALL4 loss induces a phenotype switch and the acquisition of an invasive phenotype. We show that SALL4 negatively regulates invasiveness through interaction with the histone deacetylase (HDAC) 2 and direct co-binding to a set of invasiveness genes. Consequently, SALL4 knock down, as well as HDAC inhibition, promote the expression of an invasive signature, while inhibition of histone acetylation partially reverts the invasiveness program induced by SALL4 loss. Thus, SALL4 appears to regulate phenotype switching in melanoma through an HDAC2-mediated mechanism.

With excellent creep resistance, good high-temperature microstructural stability and good irradiation resistance, oxide dispersion strengthened (ODS) alloys are a class of important alloys that are promising for high-temperature applications. However, plagued by a nerve-wracking fact that the oxide particles tend to aggregate at grain boundary of metal matrix, their improvement effect on the mechanical properties of metal matrix tends to be limited. In this work, we employ a unique in-house synthesized oxide@W core-shell nanopowder as precursor to prepare W-based ODS alloy. After low-temperature sintering and high-energy-rate forging, high-density oxide nanoparticles are dispersed homogeneously within W grains in the prepared alloy, accompanying with the intergranular oxide particles completely disappearing. As a result, our prepared alloy achieves a great enhancement of strength and ductility at room temperature. Our strategy using core-shell powder as precursor to prepare high-performance ODS alloy has potential to be applied to other dispersion-strengthened alloy systems.

Comment in Nat Rev Clin Oncol. 2021 Oct;18(10):603. Nat Commun. 2022 Jul 8;13(1):3892. Nat Commun. 2022 Jul 8;13(1):3890.

The widespread UbiD enzyme family utilises the prFMN cofactor to achieve reversible decarboxylation of acrylic and (hetero)aromatic compounds. The reaction with acrylic compounds based on reversible 1,3-dipolar cycloaddition between substrate and prFMN occurs within the confines of the active site. In contrast, during aromatic acid decarboxylation, substantial rearrangement of the substrate aromatic moiety associated with covalent catalysis presents a molecular dynamic challenge. Here we determine the crystal structures of the multi-subunit vanillic acid decarboxylase VdcCD. We demonstrate that the small VdcD subunit acts as an allosteric activator of the UbiD-like VdcC. Comparison of distinct VdcCD structures reveals domain motion of the prFMN-binding domain directly affects active site architecture. Docking of substrate and prFMN-adduct species reveals active site reorganisation coupled to domain motion supports rearrangement of the substrate aromatic moiety. Together with kinetic solvent viscosity effects, this establishes prFMN covalent catalysis of aromatic (de)carboxylation is afforded by UbiD dynamics.

Argonaute is the primary mediator of metazoan miRNA targeting (MT). Among the currently identified >1,500 human RNA-binding proteins (RBPs), there are only a handful of RBPs known to enhance MT and several others reported to suppress MT, leaving the global impact of RBPs on MT elusive. In this study, we have systematically analyzed transcriptome-wide binding sites for 150 human RBPs and evaluated the quantitative effect of individual RBPs on MT efficacy. In contrast to previous studies, we show that most RBPs significantly affect MT and that all of those MT-regulating RBPs function as MT enhancers rather than suppressors, by making the local secondary structure of the target site accessible to Argonaute. Our findings illuminate the unappreciated regulatory impact of human RBPs on MT, and as these RBPs may play key roles in the gene regulatory network governed by metazoan miRNAs, MT should be understood in the context of co-regulating RBPs.

Reactive oxygen species (ROS) oxidize cellular nucleotide pools and cause double strand breaks (DSBs). Non-homologous end-joining (NHEJ) attaches broken chromosomal ends together in mammalian cells. Ribonucleotide insertion by DNA polymerase (pol) μ prepares breaks for end-joining and this is required for successful NHEJ in vivo. We previously showed that pol μ lacks discrimination against oxidized dGTP (8-oxo-dGTP), that can lead to mutagenesis, cancer, aging and human disease. Here we reveal the structural basis for proficient oxidized ribonucleotide (8-oxo-rGTP) incorporation during DSB repair by pol μ. Time-lapse crystallography snapshots of structural intermediates during nucleotide insertion along with computational simulations reveal substrate, metal and side chain dynamics, that allow oxidized ribonucleotides to escape polymerase discrimination checkpoints. Abundant nucleotide pools, combined with inefficient sanitization and repair, implicate pol μ mediated oxidized ribonucleotide insertion as an emerging source of widespread persistent mutagenesis and genomic instability.

Correlative imaging and quantification of intracellular nanoparticles with the underlying ultrastructure is crucial for understanding cell-nanoparticle interactions in biological research. However, correlative nanoscale imaging of whole cells still remains a daunting challenge. Here, we report a straightforward nanoscopic approach for whole-cell correlative imaging, by simultaneous ionoluminescence and ultrastructure mapping implemented with a highly focused beam of alpha particles. We demonstrate that fluorescent nanodiamonds exhibit fast, ultrabright and stable emission upon excitation by alpha particles. Thus, by using fluorescent nanodiamonds as imaging probes, our approach enables quantification and correlative localization of single nanodiamonds within a whole cell at sub-30 nm resolution. As an application example, we show that our approach, together with Monte Carlo simulations and radiobiological experiments, can be employed to provide unique insights into the mechanisms of nanodiamond radiosensitization at the single whole-cell level. These findings may benefit clinical studies of radio-enhancement effects by nanoparticles in charged-particle cancer therapy.

Vaccine-induced thrombotic thrombocytopenia with cerebral venous thrombosis is a syndrome recently described in young adults within two weeks from the first dose of the ChAdOx1 nCoV-19 vaccine. Here we report two cases of malignant middle cerebral artery (MCA) infarct and thrombocytopenia 9-10 days following ChAdOx1 nCoV-19 vaccination. The two cases arrived in our facility around the same time but from different geographical areas, potentially excluding epidemiological links; meanwhile, no abnormality was found in the respective vaccine batches. Patient 1 was a 57-year-old woman who underwent decompressive craniectomy despite two prior, successful mechanical thrombectomies. Patient 2 was a 55-year-old woman who developed a fatal bilateral malignant MCA infarct. Both patients manifested pulmonary and portal vein thrombosis and high level of antibodies to platelet factor 4-polyanion complexes. None of the patients had ever received heparin in the past before stroke onset. Our observations of rare arterial thrombosis may contribute to assessment of possible adverse effects associated with COVID-19 vaccination.

Comment in Nat Rev Nephrol. 2021 Nov;17(11):707.

Ligand-oligonucleotide transduction provides the critical pathway to integrate non-nucleic acid molecules into nucleic acid circuits and nanomachines for a variety of strand-displacement related applications. Herein, a general platform is constructed to convert the signals of ligands into desired oligonucleotides through a precise kinetic control. In this design, the ligand-aptamer binding sequence with an engineered duplex stem is introduced between the toehold and displacement domains of the invading strand to regulate the strand-displacement reaction. Employing this platform, we achieve efficient transduction of both small molecules and proteins orthogonally, and more importantly, establish logical and cascading operations between different ligands for versatile transduction. Besides, this platform is capable of being directly coupled with the signal amplification systems to further enhance the transduction performance. This kinetically controlled platform presents unique features with designing simplicity and flexibility, expandable complexity and system compatibility, which may pave a broad road towards nucleic acid-based developments of sophisticated transduction networks.

Methane, along with other short-chain alkanes from some Archean metasedimentary rocks, has unique isotopic signatures that possibly reflect the generation of atmospheric greenhouse gas on early Earth. We find that alkane gases from the Kidd Creek mines in the Canadian Shield are microbial products in a Neoarchean ecosystem. The widely varied hydrogen and relatively uniform carbon isotopic compositions in the alkanes infer that the alkanes result from the biodegradation of sediment organic matter with serpentinization-derived hydrogen gas. This proposed process is supported by published geochemical data on the Kidd Creek gas, including the distribution of alkane abundances, stable isotope variations in alkanes, and CH2D2 signatures in methane. The recognition of Archean microbial methane in this work reveals a biochemical process of greenhouse gas generation before the Great Oxidation Event and improves the understanding of the carbon and hydrogen geochemical cycles.

Dendritic cells (DC) in the lung that induce Th17 differentiation remain incompletely understood, in part because conventional CD11b+ DCs (cDC2) are heterogeneous. Here, we report a population of cDCs that rapidly accumulates in lungs of mice following house dust extract inhalation. These cells are Ly-6C+, are developmentally and phenotypically similar to cDC2, and strongly promote Th17 differentiation ex vivo. Single cell RNA-sequencing (scRNA-Seq) of lung cDC2 indicates 5 distinct clusters. Pseudotime analysis of scRNA-Seq data and adoptive transfer experiments with purified cDC2 subpopulations suggest stepwise developmental progression of immature Ly-6C+Ly-6A/E+ cDC2 to mature Ly-6C-CD301b+ lung resident cDC2 lacking Ccr7 expression, which then further mature into CD200+ migratory cDC2 expressing Ccr7. Partially mature Ly-6C+Ly-6A/E-CD301b- cDC2, which express Il1b, promote Th17 differentiation. By contrast, CD200+ mature cDC2 strongly induce Th2, but not Th17, differentiation. Thus, Th17 and Th2 differentiation are promoted by lung cDC2 at distinct stages of maturation.

Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3' end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5' end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range.

Erratum in Nat Commun. 2021 Sep 30;12(1):5830.

Mangrove restoration has become a popular strategy to ensure the critical functions and economic benefits of this ecosystem. This study conducts a meta-analysis of the peer-reviewed literature on the outcomes of mangrove restoration. On aggregate, restored mangroves provide higher ecosystem functions than unvegetated tidal flats but lower than natural mangrove stands (respectively RR' = 0.43, 95%CIs = 0.23 to 0.63; RR' = -0.21, 95%CIs = -0.34 to -0.08), while they perform on par with naturally-regenerated mangroves and degraded mangroves. However, restoration outcomes vary widely between functions and comparative bases, and are mediated by factors such as restoration age, species, and restoration method. Furthermore, mangrove restoration offers positive benefit-cost ratios ranging from 10.50 to 6.83 under variable discount rates (-2% to 8%), suggesting that mangrove restoration is a cost-effective form of ecosystem management. Overall, the results suggest that mangrove restoration has substantial potential to contribute to multiple policy objectives related to biodiversity conservation, climate change mitigation and sustainable development.

Skeletal muscle has a remarkable ability to regenerate owing to its resident stem cells (also called satellite cells, SCs). SCs are normally quiescent; when stimulated by damage, they activate and expand to form new fibers. The mechanisms underlying SC proliferative progression remain poorly understood. Here we show that DHX36, a helicase that unwinds RNA G-quadruplex (rG4) structures, is essential for muscle regeneration by regulating SC expansion. DHX36 (initially named RHAU) is barely expressed at quiescence but is highly induced during SC activation and proliferation. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration after damage. System-wide mapping in proliferating SCs reveals DHX36 binding predominantly to rG4 structures at various regions of mRNAs, while integrated polysome profiling shows that DHX36 promotes mRNA translation via 5'-untranslated region (UTR) rG4 binding. Furthermore, we demonstrate that DHX36 specifically regulates the translation of Gnai2 mRNA by unwinding its 5' UTR rG4 structures and identify GNAI2 as a downstream effector of DHX36 for SC expansion. Altogether, our findings uncover DHX36 as an indispensable post-transcriptional regulator of SC function and muscle regeneration acting through binding and unwinding rG4 structures at 5' UTR of target mRNAs.

To realize effective van der Waals (vdW) transistors, vdW dielectrics are needed in addition to vdW channel materials. We study the dielectric properties of 32 exfoliable vdW materials using first principles methods. We calculate the static and optical dielectric constants and discover a large out-of-plane permittivity in GeClF, PbClF, LaOBr, and LaOCl, while the in-plane permittivity is high in BiOCl, PbClF, and TlF. To assess their potential as gate dielectrics, we calculate the band gap and electron affinity, and estimate the leakage current through the candidate dielectrics. We discover six monolayer dielectrics that promise to outperform bulk HfO2: HoOI, LaOBr, LaOCl, LaOI, SrI2, and YOBr with low leakage current and low equivalent oxide thickness. Of these, LaOBr and LaOCl are the most promising and our findings motivate the growth and exfoliation of rare-earth oxyhalides for their use as vdW dielectrics.

Advances in electron microscopy have enabled visualizations of the three-dimensional (3D) atom arrangements in nano-scale objects. The observations are, however, prone to electron-beam-induced object alterations, so tracking of single atoms in space and time becomes key to unravel inherent structures and properties. Here, we introduce an analytical approach to quantitatively account for atom dynamics in 3D atomic-resolution imaging. The approach is showcased for a Co-Mo-S nanocrystal by analysis of time-resolved in-line holograms achieving ~1.5 Å resolution in 3D. The analysis reveals a decay of phase image contrast towards the nanocrystal edges and meta-stable edge motifs with crystallographic dependence. These findings are explained by beam-stimulated vibrations that exceed Debye-Waller factors and cause chemical transformations at catalytically relevant edges. This ability to simultaneously probe atom vibrations and displacements enables a recovery of the pristine Co-Mo-S structure and establishes, in turn, a foundation to understand heterogeneous chemical functionality of nanostructures, surfaces and molecules.

The current induced motion of domain walls forms the basis of several advanced spintronic technologies. The most efficient domain wall motion is found in synthetic antiferromagnetic (SAF) structures that are composed of an upper and a lower ferromagnetic layer coupled antiferromagnetically via a thin ruthenium layer. The antiferromagnetic coupling gives rise to a giant exchange torque with which current moves domain walls at maximum velocities when the magnetic moments of the two layers are matched. Here we show that the velocity of domain walls in SAF nanowires can be reversibly tuned by several hundred m/s in a non-volatile manner by ionic liquid gating. Ionic liquid gating results in reversible changes in oxidation of the upper magnetic layer in the SAF over a wide gate-voltage window. This changes the delicate balance in the magnetic properties of the SAF and, thereby, results in large changes in the exchange coupling torque and the current-induced domain wall velocity. Furthermore, we demonstrate an example of an ionitronic-based spintronic switch as a component of a potential logic technology towards energy-efficient, all electrical, memory-in-logic.

Poly(ADP)-ribosylation (PARylation) regulates chromatin structure and recruits DNA repair proteins. Using single-molecule fluorescence microscopy to track topoisomerase I (TOP1) in live cells, we found that sustained PARylation blocked the repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) in a similar fashion as inhibition of the ubiquitin-proteasome system (UPS). PARylation of TOP1-DPC was readily revealed by inhibiting poly(ADP-ribose) glycohydrolase (PARG), indicating the otherwise transient and reversible PARylation of the DPCs. As the UPS is a key repair mechanism for TOP1-DPCs, we investigated the impact of TOP1-DPC PARylation on the proteasome and found that the proteasome is unable to associate with and digest PARylated TOP1-DPCs. In addition, PARylation recruits the deubiquitylating enzyme USP7 to reverse the ubiquitylation of PARylated TOP1-DPCs. Our work identifies PARG as repair factor for TOP1-DPCs by enabling the proteasomal digestion of TOP1-DPCs. It also suggests the potential regulatory role of PARylation for the repair of a broad range of DPCs.

Obesity is a strong risk factor for cancer progression, posing obesity-related cancer as one of the leading causes of death. Nevertheless, the molecular mechanisms that endow cancer cells with metastatic properties in patients affected by obesity remain unexplored.Here, we show that IL-6 and HGF, secreted by tumor neighboring visceral adipose stromal cells (V-ASCs), expand the metastatic colorectal (CR) cancer cell compartment (CD44v6 + ), which in turn secretes neurotrophins such as NGF and NT-3, and recruits adipose stem cells within tumor mass. Visceral adipose-derived factors promote vasculogenesis and the onset of metastatic dissemination by activation of STAT3, which inhibits miR-200a and enhances ZEB2 expression, effectively reprogramming CRC cells into a highly metastatic phenotype. Notably, obesity-associated tumor microenvironment provokes a transition in the transcriptomic expression profile of cells derived from the epithelial consensus molecular subtype (CMS2) CRC patients towards a mesenchymal subtype (CMS4). STAT3 pathway inhibition reduces ZEB2 expression and abrogates the metastatic growth sustained by adipose-released proteins. Together, our data suggest that targeting adipose factors in colorectal cancer patients with obesity may represent a therapeutic strategy for preventing metastatic disease.

2-Fluoroindoles as an important structural scaffold are widely existing in many bioactive or therapeutic agents. Despite their potential usefulness, efficient constructions of 2-fluoroindole derivatives are very sparce. The development of straightforward synthetic approaches to access 2-fluoroindoles is highly desirable for studying their fundamental properties and applications. Herein, we report an efficient and general strategy for the construction of 2-fluoroindoles in which a wide variety of 2-fluoroindoles were accessed with high efficiency and chemoselectivity. Instead of starting from indole skeletons, our strategy constructs indole scaffolds alongside the incorporation of fluorine atom on C2 position in a formal [4+1] cyclization from readily accessible ortho-vinylanilines and difluorocarbene. In our protocol, commercially accessible halodifluoroalkylative reagents provide one carbon and one fluorine atom by cleaving one C-N tertiary bond and forming one C-N bond and one C-C double bond with ortho-vinylanilines. Downstream transformations on 2-fluoroindoles lead to various valuable bioactive molecules which demonstrated significant synthetic advantages over previous reports. And mechanistic studies suggest that the reaction undergoes a cascade difluorocarbene-trapping and intramolecular Michael addition reaction followed by Csp3-F bond cleavage.

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.

Osteoporosis affects millions worldwide and is often caused by osteoclast induced bone loss. Here, we identify the cytoplasmic protein ELMO1 as an important 'signaling node' in osteoclasts. We note that ELMO1 SNPs associate with bone abnormalities in humans, and that ELMO1 deletion in mice reduces bone loss in four in vivo models: osteoprotegerin deficiency, ovariectomy, and two types of inflammatory arthritis. Our transcriptomic analyses coupled with CRISPR/Cas9 genetic deletion identify Elmo1 associated regulators of osteoclast function, including cathepsin G and myeloperoxidase. Further, we define the 'ELMO1 interactome' in osteoclasts via proteomics and reveal proteins required for bone degradation. ELMO1 also contributes to osteoclast sealing zone on bone-like surfaces and distribution of osteoclast-specific proteases. Finally, a 3D structure-based ELMO1 inhibitory peptide reduces bone resorption in wild type osteoclasts. Collectively, we identify ELMO1 as a signaling hub that regulates osteoclast function and bone loss, with relevance to osteoporosis and arthritis.

A variety of artificial cells springs from the functionalization of liposomes with proteins. However, these models suffer from low durability without repair and replenishment mechanisms, which can be partly addressed by replacing the lipids with polymers. Yet natural membranes are also dynamically remodeled in multiple cellular processes. Here, we show that synthetic amphiphile membranes also undergo fusion, mediated by the protein machinery for synaptic secretion. We integrated fusogenic SNAREs in polymer and hybrid vesicles and observed efficient membrane and content mixing. We determined bending rigidity and pore edge tension as key parameters for fusion and described its plausible progression through cryo-EM snapshots. These findings demonstrate that dynamic membrane phenomena can be reconstituted in synthetic materials, thereby providing new tools for the assembly of synthetic protocells.

High-harmonic generation is a cornerstone of nonlinear optics. It has been demonstrated in dielectrics, semiconductors, semi-metals, plasmas, and gases, but, until now, not in metals. Here we report high harmonics of 800-nm-wavelength light irradiating metallic titanium nitride film. Titanium nitride is a refractory metal known for its high melting temperature and large laser damage threshold. We show that it can withstand few-cycle light pulses with peak intensities as high as 13 TW/cm2, enabling high-harmonics generation up to photon energies of 11 eV. We measure the emitted vacuum ultraviolet radiation as a function of the crystal orientation with respect to the laser polarization and show that it is consistent with the anisotropic conduction band structure of titanium nitride. The generation of high harmonics from metals opens a link between solid and plasma harmonics. In addition, titanium nitride is a promising material for refractory plasmonic devices and could enable compact vacuum ultraviolet frequency combs.

Erratum in Nat Commun. 2021 Oct 5;12(1):5927.

Carboxylic acids are readily available, structurally diverse and shelf-stable; therefore, converting them to the isoelectronic boronic acids, which play pivotal roles in different settings, would be highly enabling. In contrast to the well-recognised decarboxylative borylation, the chemical space of carboxylic-to-boronic acid transformation via deoxygenation remains underexplored due to the thermodynamic and kinetic inertness of carboxylic C-O bonds. Herein, we report a deoxygenative borylation reaction of free carboxylic acids or their sodium salts to synthesise alkylboronates under metal-free conditions. Promoted by a uniquely Lewis acidic and strongly reducing diboron reagent, bis(catecholato)diboron (B2cat2), a library of aromatic carboxylic acids are converted to the benzylboronates. By leveraging the same borylative manifold, a facile triboration process with aliphatic carboxylic acids is also realised, diversifying the pool of available 1,1,2-alkyl(trisboronates) that were otherwise difficult to access. Detailed mechanistic studies reveal a stepwise C-O cleavage profile, which could inspire and encourage future endeavours on more appealing reductive functionalisation of oxygenated feedstocks.

Glycans are fundamental cellular building blocks, involved in many organismal functions. Advances in glycomics are elucidating the essential roles of glycans. Still, it remains challenging to properly analyze large glycomics datasets, since the abundance of each glycan is dependent on many other glycans that share many intermediate biosynthetic steps. Furthermore, the overlap of measured glycans can be low across samples. We address these challenges with GlyCompare, a glycomic data analysis approach that accounts for shared biosynthetic steps for all measured glycans to correct for sparsity and non-independence in glycomics, which enables direct comparison of different glycoprofiles and increases statistical power. Using GlyCompare, we study diverse N-glycan profiles from glycoengineered erythropoietin. We obtain biologically meaningful clustering of mutant cell glycoprofiles and identify knockout-specific effects of fucosyltransferase mutants on tetra-antennary structures. We further analyze human milk oligosaccharide profiles and find mother's fucosyltransferase-dependent secretor-status indirectly impact the sialylation. Finally, we apply our method on mucin-type O-glycans, gangliosides, and site-specific compositional glycosylation data to reveal tissues and disease-specific glycan presentations. Our substructure-oriented approach will enable researchers to take full advantage of the growing power and size of glycomics data.

Epicardial formation is necessary for normal myocardial morphogenesis. Here, we show that differentiating hiPSC-derived lateral plate mesoderm with BMP4, RA and VEGF (BVR) can generate a premature form of epicardial cells (termed pre-epicardial cells, PECs) expressing WT1, TBX18, SEMA3D, and SCX within 7 days. BVR stimulation after Wnt inhibition of LPM demonstrates co-differentiation and spatial organization of PECs and cardiomyocytes (CMs) in a single 2D culture. Co-culture consolidates CMs into dense aggregates, which then form a connected beating syncytium with enhanced contractility and calcium handling; while PECs become more mature with significant upregulation of UPK1B, ITGA4, and ALDH1A2 expressions. Our study also demonstrates that PECs secrete IGF2 and stimulate CM proliferation in co-culture. Three-dimensional PEC-CM spheroid co-cultures form outer smooth muscle cell layers on cardiac micro-tissues with organized internal luminal structures. These characteristics suggest PECs could play a key role in enhancing tissue organization within engineered cardiac constructs in vitro.

RAS proteins are GTPases that lie upstream of a signaling network impacting cell fate determination. How cells integrate RAS activity to balance proliferation and cellular senescence is still incompletely characterized. Here, we identify ZNF768 as a phosphoprotein destabilized upon RAS activation. We report that ZNF768 depletion impairs proliferation and induces senescence by modulating the expression of key cell cycle effectors and established p53 targets. ZNF768 levels decrease in response to replicative-, stress- and oncogene-induced senescence. Interestingly, ZNF768 overexpression contributes to bypass RAS-induced senescence by repressing the p53 pathway. Furthermore, we show that ZNF768 interacts with and represses p53 phosphorylation and activity. Cancer genomics and immunohistochemical analyses reveal that ZNF768 is often amplified and/or overexpressed in tumors, suggesting that cells could use ZNF768 to bypass senescence, sustain proliferation and promote malignant transformation. Thus, we identify ZNF768 as a protein linking oncogenic signaling to the control of cell fate decision and proliferation.

Rhodopsin (RHO) gene mutations are a common cause of autosomal dominant retinitis pigmentosa (ADRP). The need to suppress toxic protein expression together with mutational heterogeneity pose challenges for treatment development. Mirtrons are atypical RNA interference effectors that are spliced from transcripts as short introns. Here, we develop a novel mirtron-based knockdown/replacement gene therapy for the mutation-independent treatment of RHO-related ADRP, and demonstrate efficacy in a relevant mammalian model. Splicing and potency of rhodopsin-targeting candidate mirtrons are initially determined, and a mirtron-resistant codon-modified version of the rhodopsin coding sequence is validated in vitro. These elements are then combined within a single adeno-associated virus (AAV) and delivered subretinally in a RhoP23H knock-in mouse model of ADRP. This results in significant mouse-to-human rhodopsin RNA replacement and is associated with a slowing of retinal degeneration. This provides proof of principle that synthetic mirtrons delivered by AAV are capable of reducing disease severity in vivo.

The polyadenosine tail (poly[A]-tail) is a universal modification of eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). In budding yeast, Pap1-synthesized mRNA poly(A) tails enhance export and translation, whereas Trf4/5-mediated polyadenylation of ncRNAs facilitates degradation by the exosome. Using direct RNA sequencing, we decipher the extent of poly(A) tail dynamics in yeast defective in all relevant exonucleases, deadenylases, and poly(A) polymerases. Predominantly ncRNA poly(A) tails are 20-60 adenosines long. Poly(A) tails of newly transcribed mRNAs are 50 adenosine long on average, with an upper limit of 200. Exonucleolysis by Trf5-assisted nuclear exosome and cytoplasmic deadenylases trim the tails to 40 adenosines on average. Surprisingly, PAN2/3 and CCR4-NOT deadenylase complexes have a large pool of non-overlapping substrates mainly defined by expression level. Finally, we demonstrate that mRNA poly(A) tail length strongly responds to growth conditions, such as heat and nutrient deprivation.

Plants use nitrate, ammonium, and organic nitrogen in the soil as nitrogen sources. Since the elevated CO2 environment predicted for the near future will reduce nitrate utilization by C3 species, ammonium is attracting great interest. However, abundant ammonium nutrition impairs growth, i.e., ammonium toxicity, the primary cause of which remains to be determined. Here, we show that ammonium assimilation by GLUTAMINE SYNTHETASE 2 (GLN2) localized in the plastid rather than ammonium accumulation is a primary cause for toxicity, which challenges the textbook knowledge. With exposure to toxic levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within cells, thereby elevating shoot acidity and stimulating expression of acidic stress-responsive genes. Application of an alkaline ammonia solution to the ammonium medium efficiently alleviated the ammonium toxicity with a concomitant reduction in shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is acidic stress.

Pain is a central feature of soft tissue trauma, which under certain contexts, results in aberrant osteochondral differentiation of tissue-specific stem cells. Here, the role of sensory nerve fibers in this abnormal cell fate decision is investigated using a severe extremity injury model in mice. Soft tissue trauma results in NGF (Nerve growth factor) expression, particularly within perivascular cell types. Consequently, NGF-responsive axonal invasion occurs which precedes osteocartilaginous differentiation. Surgical denervation impedes axonal ingrowth, with significant delays in cartilage and bone formation. Likewise, either deletion of Ngf or two complementary methods to inhibit its receptor TrkA (Tropomyosin receptor kinase A) lead to similar delays in axonal invasion and osteochondral differentiation. Mechanistically, single-cell sequencing suggests a shift from TGFβ to FGF signaling activation among pre-chondrogenic cells after denervation. Finally, analysis of human pathologic specimens and databases confirms the relevance of NGF-TrkA signaling in human disease. In sum, NGF-mediated TrkA-expressing axonal ingrowth drives abnormal osteochondral differentiation after soft tissue trauma. NGF-TrkA signaling inhibition may have dual therapeutic use in soft tissue trauma, both as an analgesic and negative regulator of aberrant stem cell differentiation.

We have shown that calcium-activated potassium (KCa)-channels regulate fundamental progenitor-cell functions, including proliferation, but their contribution to cell-therapy effectiveness is unknown. Here, we test the participation of KCa-channels in human heart explant-derived cell (EDC) physiology and therapeutic potential. TRAM34-sensitive KCa3.1-channels, encoded by the KCNN4 gene, are exclusively expressed in therapeutically bioactive EDC subfractions and maintain a strongly polarized resting potential; whereas therapeutically inert EDCs lack KCa3.1 channels and exhibit depolarized resting potentials. Somatic gene transfer of KCNN4 results in membrane hyperpolarization and increases intracellular [Ca2+], which boosts cell-proliferation and the production of pro-healing cytokines/nanoparticles. Intramyocardial injection of EDCs after KCNN4-gene overexpression markedly increases the salutary effects of EDCs on cardiac function, viable myocardium and peri-infarct neovascularization in a well-established murine model of ischemic cardiomyopathy. Thus, electrophysiological engineering provides a potentially valuable strategy to improve the therapeutic value of progenitor cells for cardioprotection and possibly other indications.

Age-related clonal hematopoiesis (ARCH) is characterized by age-associated accumulation of somatic mutations in hematopoietic stem cells (HSCs) or their pluripotent descendants. HSCs harboring driver mutations will be positively selected and cells carrying these mutations will rise in frequency. While ARCH is a known risk factor for blood malignancies, such as Acute Myeloid Leukemia (AML), why some people who harbor ARCH driver mutations do not progress to AML remains unclear. Here, we model the interaction of positive and negative selection in deeply sequenced blood samples from individuals who subsequently progressed to AML, compared to healthy controls, using deep learning and population genetics. Our modeling allows us to discriminate amongst evolutionary classes with high accuracy and captures signatures of purifying selection in most individuals. Purifying selection, acting on benign or mildly damaging passenger mutations, appears to play a critical role in preventing disease-predisposing clones from rising to dominance and is associated with longer disease-free survival. Through exploring a range of evolutionary models, we show how different classes of selection shape clonal dynamics and health outcomes thus enabling us to better identify individuals at a high risk of malignancy.

Erratum in Nat Commun. 2021 Dec 8;12(1):7263.

C9ORF72 hexanucleotide GGGGCC repeat expansion is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat-containing RNA mediates toxicity through nuclear granules and dipeptide repeat (DPR) proteins produced by repeat-associated non-AUG translation. However, it remains unclear how the intron-localized repeats are exported and translated in the cytoplasm. We use single molecule imaging approach to examine the molecular identity and spatiotemporal dynamics of the repeat RNA. We demonstrate that the spliced intron with G-rich repeats is stabilized in a circular form due to defective lariat debranching. The spliced circular intron, instead of pre-mRNA, serves as the translation template. The NXF1-NXT1 pathway plays an important role in the nuclear export of the circular intron and modulates toxic DPR production. This study reveals an uncharacterized disease-causing RNA species mediated by repeat expansion and demonstrates the importance of RNA spatial localization to understand disease etiology.

The mammalian sensory neocortex consists of hierarchically organized areas reciprocally connected via feedforward (FF) and feedback (FB) circuits. Several theories of hierarchical computation ascribe the bulk of the computational work of the cortex to looped FF-FB circuits between pairs of cortical areas. However, whether such corticocortical loops exist remains unclear. In higher mammals, individual FF-projection neurons send afferents almost exclusively to a single higher-level area. However, it is unclear whether FB-projection neurons show similar area-specificity, and whether they influence FF-projection neurons directly or indirectly. Using viral-mediated monosynaptic circuit tracing in macaque primary visual cortex (V1), we show that V1 neurons sending FF projections to area V2 receive monosynaptic FB inputs from V2, but not other V1-projecting areas. We also find monosynaptic FB-to-FB neuron contacts as a second motif of FB connectivity. Our results support the existence of FF-FB loops in primate cortex, and suggest that FB can rapidly and selectively influence the activity of incoming FF signals.

Erratum in Nat Commun. 2022 May 31;13(1):3129.

Human pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins. The splicing activity was assayed with a model HNRNPH1 pre-mRNA containing short 56-nucleotide intron. We identify a known alternative splicing regulator SPF45 (RBM17) as a constitutive splicing factor that is required to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells reveals that SPF45 is essential in the efficient splicing of many short introns. To initiate the spliceosome assembly on a short intron with the truncated poly-pyrimidine tract, the U2AF-homology motif (UHM) of SPF45 competes out that of U2AF65 (U2AF2) for binding to the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.

Efficient and precise base editors (BEs) for C-to-G transversion are highly desirable. However, the sequence context affecting editing outcome largely remains unclear. Here we report engineered C-to-G BEs of high efficiency and fidelity, with the sequence context predictable via machine-learning methods. By changing the species origin and relative position of uracil-DNA glycosylase and deaminase, together with codon optimization, we obtain optimized C-to-G BEs (OPTI-CGBEs) for efficient C-to-G transversion. The motif preference of OPTI-CGBEs for editing 100 endogenous sites is determined in HEK293T cells. Using a sgRNA library comprising 41,388 sequences, we develop a deep-learning model that accurately predicts the OPTI-CGBE editing outcome for targeted sites with specific sequence context. These OPTI-CGBEs are further shown to be capable of efficient base editing in mouse embryos for generating Tyr-edited offspring. Thus, these engineered CGBEs are useful for efficient and precise base editing, with outcome predictable based on sequence context of targeted sites.

White matter structural connections are likely to support flow of functional activation or functional connectivity. While the relationship between structural and functional connectivity profiles, here called SC-FC coupling, has been studied on a whole-brain, global level, few studies have investigated this relationship at a regional scale. Here we quantify regional SC-FC coupling in healthy young adults using diffusion-weighted MRI and resting-state functional MRI data from the Human Connectome Project and study how SC-FC coupling may be heritable and varies between individuals. We show that regional SC-FC coupling strength varies widely across brain regions, but was strongest in highly structurally connected visual and subcortical areas. We also show interindividual regional differences based on age, sex and composite cognitive scores, and that SC-FC coupling was highly heritable within certain networks. These results suggest regional structure-function coupling is an idiosyncratic feature of brain organisation that may be influenced by genetic factors.

Accurate and imperceptible monitoring of electrophysiological signals is of primary importance for wearable healthcare. Stiff and bulky pregelled electrodes are now commonly used in clinical diagnosis, causing severe discomfort to users for long-time using as well as artifact signals in motion. Here, we report a ~100 nm ultra-thin dry epidermal electrode that is able to conformably adhere to skin and accurately measure electrophysiological signals. It showed low sheet resistance (~24 Ω/sq, 4142 S/cm), high transparency, and mechano-electrical stability. The enhanced optoelectronic performance was due to the synergistic effect between graphene and poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS), which induced a high degree of molecular ordering on PEDOT and charge transfer on graphene by strong π-π interaction. Together with ultra-thin nature, this dry epidermal electrode is able to accurately monitor electrophysiological signals such as facial skin and brain activity with low-motion artifact, enabling human-machine interfacing and long-time mental/physical health monitoring.

Biobased poly(γ-methyl-α-methylene-γ-butyrolactone) (PMMBL), an acrylic polymer bearing a cyclic lactone ring, has attracted increasing interest because it not only is biorenewable but also exhibits superior properties to petroleum-based linear analog poly(methyl methacrylate) (PMMA). However, such property enhancement has been limited to resistance to heat and solvent, and mechanically both types of polymers are equally brittle. Here we report the expeditious synthesis of well-defined PMMBL-based ABA tri-block copolymers (tri-BCPs)-enabled by dual-initiating and living frustrated Lewis pairs (FLPs)-which are thermoplastic elastomers showing much superior mechanical properties, especially at high working temperatures (80-130 °C), to those of PMMA-based tri-BCPs. The FLPs consist of a bulky organoaluminum Lewis acid and a series of newly designed bis(imino)phosphine superbases bridged by an alkyl linker, which promote living polymerization of MMBL. Uniquely, such bisphosphine superbases initiate the chain growth from both P-sites concurrently, enabling the accelerated synthesis of tri-BCPs in a one-pot, two-step procedure. The results from mechanistic studies, including the single crystal structure of the dually initiated active species, detailed polymerizations, and kinetic studies confirm the livingness of the polymerization and support the proposed polymerization mechanism featuring the dual initiation and subsequent chain growth from both P-sites of the superbase di-initiator.

Chronically elevated intraocular pressure (IOP) is the major risk factor of primary open-angle glaucoma, a leading cause of blindness. Dysfunction of the trabecular meshwork (TM), which controls the outflow of aqueous humor (AqH) from the anterior chamber, is the major cause of elevated IOP. Here, we demonstrate that mice deficient in the Krüppel-like zinc finger transcriptional factor GLI-similar-1 (GLIS1) develop chronically elevated IOP. Magnetic resonance imaging and histopathological analysis reveal that deficiency in GLIS1 expression induces progressive degeneration of the TM, leading to inefficient AqH drainage from the anterior chamber and elevated IOP. Transcriptome and cistrome analyses identified several glaucoma- and extracellular matrix-associated genes as direct transcriptional targets of GLIS1. We also identified a significant association between GLIS1 variant rs941125 and glaucoma in humans (P = 4.73 × 10-6), further supporting a role for GLIS1 into glaucoma etiology. Our study identifies GLIS1 as a critical regulator of TM function and maintenance, AqH dynamics, and IOP.

Precise control of mammalian gene expression is facilitated through epigenetic mechanisms and nuclear organization. In particular, insulated chromosome structures are important for regulatory control, but the phenotypic consequences of their boundary disruption on developmental processes are complex and remain insufficiently understood. Here, we generated deeply sequenced Hi-C data for human pluripotent stem cells (hPSCs) that allowed us to identify CTCF loop domains that have highly conserved boundary CTCF sites and show a notable enrichment of individual developmental regulators. Importantly, perturbation of such a boundary in hPSCs interfered with proper differentiation through deregulated distal enhancer-promoter activity. Finally, we found that germline variations affecting such boundaries are subject to purifying selection and are underrepresented in the human population. Taken together, our findings highlight the importance of developmental gene isolation through chromosomal folding structures as a mechanism to ensure their proper expression.

The carriers' transportation between layers of two-dimensional (2D) perovskites is inhibited by dielectric confinement. Here, for the first time, we employ a femtosecond laser to introduce ultrafast shock pressure in the range of 0~15.45 GPa to reduce dielectric confinement by modulating the structure and exciton dynamics in a perovskite single crystal (PSCs), e.g. (F-PEA)2PbI4 (4-fluorophenethylammonium, F-PEA). The density functional theory (DFT) simulation and experimental results show that the inorganic framework distortion results in a bandgap reduction. It was found that the exciton-optical phonon coupling and free excitons (FEs) binding energy are minimized at 2.75 GPa shock pressure due to a reduction in dielectric confinement. The stability testing under various harsh light and humid thermal conditions shows that femtosecond laser shocking improves the stability of (F-PEA)2PbI4 PSCs. Femtosecond laser shock processing provides a new approach for regulating the structure and enhancing halide perovskite properties.

Comment on doi: 10.1038/ncomms10870.

Complement is an enzymatic humoral pattern-recognition defence system of the body. Non-specific deposition of blood biomolecules on nanomedicines triggers complement activation through the alternative pathway, but complement-triggering mechanisms of nanomaterials with dimensions comparable to or smaller than many globular blood proteins are unknown. Here we study this using a library of <6 nm poly(amido amine) dendrimers bearing different end-terminal functional groups. Dendrimers are not sensed by C1q and mannan-binding lectin, and hence do not trigger complement activation through these pattern-recognition molecules. While, pyrrolidone- and carboxylic acid-terminated dendrimers fully evade complement response, and independent of factor H modulation, binding of amine-terminated dendrimers to a subset of natural IgM glycoforms triggers complement activation through lectin pathway-IgM axis. These findings contribute to mechanistic understanding of complement surveillance of dendrimeric materials, and provide opportunities for dendrimer-driven engineering of complement-safe nanomedicines and medical devices.

Blue organic light-emitting diodes require high triplet interlayer materials, which induce large energetic barriers at the interfaces resulting in high device voltages and reduced efficiencies. Here, we alleviate this issue by designing a low triplet energy hole transporting interlayer with high mobility, combined with an interface exciplex that confines excitons at the emissive layer/electron transporting material interface. As a result, blue thermally activated delay fluorescent organic light-emitting diodes with a below-bandgap turn-on voltage of 2.5 V and an external quantum efficiency (EQE) of 41.2% were successfully fabricated. These devices also showed suppressed efficiency roll-off maintaining an EQE of 34.8% at 1000 cd m-2. Our approach paves the way for further progress through exploring alternative device engineering approaches instead of only focusing on the demanding synthesis of organic compounds with complex structures.

Circulating phosphate levels are tightly controlled within a narrow range in mammals. By using a novel small-molecule inhibitor, we show that the enzymatic activity of inositol hexakisphosphate kinases (IP6K) is essential for phosphate regulation in vivo. IP6K inhibition suppressed XPR1, a phosphate exporter, thereby decreasing cellular phosphate export, which resulted in increased intracellular ATP levels. The in vivo inhibition of IP6K decreased plasma phosphate levels without inhibiting gut intake or kidney reuptake of phosphate, demonstrating a pivotal role of IP6K-regulated cellular phosphate export on circulating phosphate levels. IP6K inhibition-induced decrease in intracellular inositol pyrophosphate, an enzymatic product of IP6K, was correlated with phosphate changes. Chronic IP6K inhibition alleviated hyperphosphataemia, increased kidney ATP, and improved kidney functions in chronic kidney disease rats. Our results demonstrate that the enzymatic activity of IP6K regulates circulating phosphate and intracellular ATP and suggest that IP6K inhibition is a potential novel treatment strategy against hyperphosphataemia.

Atomic diffusion has been recognized as a particularly powerful tool in the synthesis of heterostructures. However, controlled atomic diffusion is very difficult to achieve in the fabrication of individual nanostructures. Here, an electrically driven in situ solid-solid diffusion reaction inside a TEM is reported for the controlled fabrication of two different hetero-nanostructures in the Ag-Te system. Remarkably, the morphology and structure of the as-formed heterostructures are strongly dependent on the path of atomic diffusion. Our experiments revealed that the surface diffusion of Te atoms to Ag nanowires leads to a core-shell structure, while the bulk diffusion of Ag atoms give rise to a Ag2Te-Te segmented heterostructure. Heat released by Joule heating caused the surface diffusion process to be replaced by bulk diffusion and thereby determined the structure of the final product. Our experimental results provide an insight into solid-state diffusion reactions under an electric field and also propose a new process for the fabrication of complex nanostructures.

Comment in Nat Commun. 2021 Aug 10;12(1):4834.

The malaria parasite Plasmodium falciparum replicates inside erythrocytes in the blood of infected humans. During each replication cycle, a small proportion of parasites commits to sexual development and differentiates into gametocytes, which are essential for parasite transmission via the mosquito vector. Detailed molecular investigation of gametocyte biology and transmission has been hampered by difficulties in generating large numbers of these highly specialised cells. Here, we engineer P. falciparum NF54 inducible gametocyte producer (iGP) lines for the routine mass production of synchronous gametocytes via conditional overexpression of the sexual commitment factor GDV1. NF54/iGP lines consistently achieve sexual commitment rates of 75% and produce viable gametocytes that are transmissible by mosquitoes. We also demonstrate that further genetic engineering of NF54/iGP parasites is a valuable tool for the targeted exploration of gametocyte biology. In summary, we believe the iGP approach developed here will greatly expedite basic and applied malaria transmission stage research.

The ability to maintain a sequence of items in memory is a fundamental cognitive function. In the rodent hippocampus, the representation of sequentially organized spatial locations is reflected by the phase of action potentials relative to the theta oscillation (phase precession). We investigated whether the timing of neuronal activity relative to the theta brain oscillation also reflects sequence order in the medial temporal lobe of humans. We used a task in which human participants learned a fixed sequence of pictures and recorded single neuron and local field potential activity with implanted electrodes. We report that spikes for three consecutive items in the sequence (the preferred stimulus for each cell, as well as the stimuli immediately preceding and following it) were phase-locked at distinct phases of the theta oscillation. Consistent with phase precession, spikes were fired at progressively earlier phases as the sequence advanced. These findings generalize previous findings in the rodent hippocampus to the human temporal lobe and suggest that encoding stimulus information at distinct oscillatory phases may play a role in maintaining sequential order in memory.

Plants respond to warm temperature by increased elongation growth of organs to enhance cooling capacity. Phytohormones, such as auxin and brassinosteroids, regulate this growth process. However, our view on the players involved in warm temperature-mediated growth remains fragmentary. Here, we show that warm temperature leads to an increased expression of JOXs and ST2A, genes controlling jasmonate catabolism. This leads to an elevated 12HSO4-JA level and consequently to a reduced level of bioactive jasmonates. Ultimately this results in more JAZ proteins, which facilitates plant growth under warm temperature conditions. Taken together, understanding the conserved role of jasmonate signalling during thermomorphogenesis contributes to ensuring food security under a changing climate.

Glutamoptosis is the induction of apoptotic cell death as a consequence of the aberrant activation of glutaminolysis and mTORC1 signaling during nutritional imbalance in proliferating cells. The role of the bioenergetic sensor AMPK during glutamoptosis is not defined yet. Here, we show that AMPK reactivation blocks both the glutamine-dependent activation of mTORC1 and glutamoptosis in vitro and in vivo. We also show that glutamine is used for asparagine synthesis and the GABA shunt to produce ATP and to inhibit AMPK, independently of glutaminolysis. Overall, our results indicate that glutamine metabolism is connected with mTORC1 activation through two parallel pathways: an acute alpha-ketoglutarate-dependent pathway; and a secondary ATP/AMPK-dependent pathway. This dual metabolic connection between glutamine and mTORC1 must be considered for the future design of therapeutic strategies to prevent cell growth in diseases such as cancer.

During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.

As conductors in electronic applications shrink, microscopic conduction processes lead to strong deviations from Ohm's law. Depending on the length scales of momentum conserving (lMC) and relaxing (lMR) electron scattering, and the device size (d), current flows may shift from ohmic to ballistic to hydrodynamic regimes. So far, an in situ methodology to obtain these parameters within a micro/nanodevice is critically lacking. In this context, we exploit Sondheimer oscillations, semi-classical magnetoresistance oscillations due to helical electronic motion, as a method to obtain lMR even when lMR ≫ d. We extract lMR from the Sondheimer amplitude in WP2, at temperatures up to T ~ 40 K, a range most relevant for hydrodynamic transport phenomena. Our data on μm-sized devices are in excellent agreement with experimental reports of the bulk lMR and confirm that WP2 can be microfabricated without degradation. These results conclusively establish Sondheimer oscillations as a quantitative probe of lMR in micro-devices.

Selective cleavage of C-C bonds is very important in organic chemistry, but remains challenging because of their inert chemical nature. Herein, we report that Zn/NC-X catalysts, in which Zn2+ coordinate with N species on microporous N-doped carbon (NC) and X denotes the pyrolysis temperature, can effectively catalyze aerobic oxidative cleavage of C(CO)-C bonds and quantitatively convert acetophenone to methyl benzoate with a yield of 99% at 100 °C. The Zn/NC-950 can be applied for a wide scope of acetophenone derivatives as well as more challenging alkyl ketones. Detail mechanistic investigations reveal that the catalytic performance of Zn/NC-950 can be attributed to the coordination between Zn2+ and N species to change the electronic state of the metal, synergetic effect of the Zn single sites with their surrounding N atoms, as well as the microporous structure with the high surface area and structural defects of the NC.

Sutures separate the flat bones of the skull and enable coordinated growth of the brain and overlying cranium. The coronal suture is most commonly fused in monogenic craniosynostosis, yet the unique aspects of its development remain incompletely understood. To uncover the cellular diversity within the murine embryonic coronal suture, we generated single-cell transcriptomes and performed extensive expression validation. We find distinct pre-osteoblast signatures between the bone fronts and periosteum, a ligament-like population above the suture that persists into adulthood, and a chondrogenic-like population in the dura mater underlying the suture. Lineage tracing reveals an embryonic Six2+ osteoprogenitor population that contributes to the postnatal suture mesenchyme, with these progenitors being preferentially affected in a Twist1+/-; Tcf12+/- mouse model of Saethre-Chotzen Syndrome. This single-cell atlas provides a resource for understanding the development of the coronal suture and the mechanisms for its loss in craniosynostosis.

Comment on Nat Commun. 2020 Sep 25;11(1):4858. Nat Commun. 2021 Aug 10;12(1):4833.