Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach.

5-methylcytosine (m5C) is a prevalent RNA modification crucial for gene expression regulation. However, accurate and sensitive m5C sites identification remains challenging due to severe RNA degradation and reduced sequence complexity during bisulfite sequencing (BS-seq). Here, we report m5C-TAC-seq, a bisulfite-free approach combining TET-assisted m5C-to-f5C oxidation with selective chemical labeling, therefore enabling direct base-resolution m5C detection through pre-enrichment and C-to-T transitions at m5C sites. With m5C-TAC-seq, we comprehensively profiled the m5C methylomes in human and mouse cells, identifying a substantially larger number of confident m5C sites. Through perturbing potential m5C methyltransferases, we deciphered the responsible enzymes for most m5C sites, including the characterization of NSUN5's involvement in mRNA m5C deposition. Additionally, we characterized m5C dynamics during mESC differentiation. Notably, the mild reaction conditions and preservation of nucleotide composition in m5C-TAC-seq allow m5C detection in chromatin-associated RNAs. The accurate and robust m5C-TAC-seq will advance research into m5C methylation functional investigation.

Recognition of methamphetamine and other amines by trace amine receptor TAAR1.

Trace amine-associated receptor 1 (TAAR1), the founding member of a nine-member family of trace amine receptors, is responsible for recognizing a range of biogenic amines in the brain, including the endogenous ß-phenylethylamine (ß-PEA)1 as well as methamphetamine2, an abused substance that has posed a severe threat to human health and society3. Given its unique physiological role in the brain, TAAR1 is also an emerging target for a range of neurological disorders including schizophrenia, depression and drug addiction2,4,5. Here we report structures of human TAAR1-G-protein complexes bound to methamphetamine and ß-PEA as well as complexes bound to RO5256390, a TAAR1-selective agonist, and SEP-363856, a clinical-stage dual agonist for TAAR1 and serotonin receptor 5-HT1AR (refs. 6,7). Together with systematic mutagenesis and functional studies, the structures reveal the molecular basis of methamphetamine recognition and underlying mechanisms of ligand selectivity and polypharmacology between TAAR1 and other monoamine receptors. We identify a lid-like extracellular loop 2 helix/loop structure and a hydrogen-bonding network in the ligand-binding pockets, which may contribute to the ligand recognition in TAAR1. These findings shed light on the ligand recognition mode and activation mechanism for TAAR1 and should guide the development of next-generation therapeutics for drug addiction and various neurological disorders.

Layer Hall effect in a 2D topological axion antiferromagnet.

Whereas ferromagnets have been known and used for millennia, antiferromagnets were only discovered in the 1930s1. At large scale, because of the absence of global magnetization, antiferromagnets may seem to behave like any non-magnetic material. At the microscopic level, however, the opposite alignment of spins forms a rich internal structure. In topological antiferromagnets, this internal structure leads to the possibility that the property known as the Berry phase can acquire distinct spatial textures2,3. Here we study this possibility in an antiferromagnetic axion insulator-even-layered, two-dimensional MnBi2Te4-in which spatial degrees of freedom correspond to different layers. We observe a type of Hall effect-the layer Hall effect-in which electrons from the top and bottom layers spontaneously deflect in opposite directions. Specifically, under zero electric field, even-layered MnBi2Te4 shows no anomalous Hall effect. However, applying an electric field leads to the emergence of a large, layer-polarized anomalous Hall effect of about 0.5e2/h (where e is the electron charge and h is Planck's constant). This layer Hall effect uncovers an unusual layer-locked Berry curvature, which serves to characterize the axion insulator state. Moreover, we find that the layer-locked Berry curvature can be manipulated by the axion field formed from the dot product of the electric and magnetic field vectors. Our results offer new pathways to detect and manipulate the internal spatial structure of fully compensated topological antiferromagnets4-9. The layer-locked Berry curvature represents a first step towards spatial engineering of the Berry phase through effects such as layer-specific moiré potential.

Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding.

A fundamental interest in developmental neuroscience lies in the ability to map the complete single-cell lineages within the brain. To this end, we developed a CRISPR editing-based lineage-specific tracing (CREST) method for clonal tracing in Cre mice. We then used two complementary strategies based on CREST to map single-cell lineages in developing mouse ventral midbrain (vMB). By applying snapshotting CREST (snapCREST), we constructed a spatiotemporal lineage landscape of developing vMB and identified six progenitor archetypes that could represent the principal clonal fates of individual vMB progenitors and three distinct clonal lineages in the floor plate that specified glutamatergic, dopaminergic or both neurons. We further created pandaCREST (progenitor and derivative associating CREST) to associate the transcriptomes of progenitor cells in vivo with their differentiation potentials. We identified multiple origins of dopaminergic neurons and demonstrated that a transcriptome-defined progenitor type comprises heterogeneous progenitors, each with distinct clonal fates and molecular signatures. Therefore, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.

Precision environmental health monitoring by longitudinal exposome and multi-omics profiling.

Conventional environmental health studies have primarily focused on limited environmental stressors at the population level, which lacks the power to dissect the complexity and heterogeneity of individualized environmental exposures. Here, as a pilot case study, we integrated deep-profiled longitudinal personal exposome and internal multi-omics to systematically investigate how the exposome shapes a single individual's phenome. We annotated thousands of chemical and biological components in the personal exposome cloud and found they were significantly correlated with thousands of internal biomolecules, which was further cross-validated using corresponding clinical data. Our results showed that agrochemicals and fungi predominated in the highly diverse and dynamic personal exposome, and the biomolecules and pathways related to the individual's immune system, kidney, and liver were highly associated with the personal external exposome. Overall, this data-driven longitudinal monitoring study shows the potential dynamic interactions between the personal exposome and internal multi-omics, as well as the impact of the exposome on precision health by producing abundant testable hypotheses.

Revealing the signaling of complement receptors C3aR and C5aR1 by anaphylatoxins.

The complement receptors C3aR and C5aR1, whose signaling is selectively activated by anaphylatoxins C3a and C5a, are important regulators of both innate and adaptive immune responses. Dysregulations of C3aR and C5aR1 signaling lead to multiple inflammatory disorders, including sepsis, asthma and acute respiratory distress syndrome. The mechanism underlying endogenous anaphylatoxin recognition and activation of C3aR and C5aR1 remains elusive. Here we reported the structures of C3a-bound C3aR and C5a-bound C5aR1 as well as an apo-C3aR structure. These structures, combined with mutagenesis analysis, reveal a conserved recognition pattern of anaphylatoxins to the complement receptors that is different from chemokine receptors, unique pocket topologies of C3aR and C5aR1 that mediate ligand selectivity, and a common mechanism of receptor activation. These results provide crucial insights into the molecular understanding of C3aR and C5aR1 signaling and structural templates for rational drug design for treating inflammation disorders.

Highly Potent Transparent Passive Cooling Coating via Microphase-Separated Hydrogel Combining Radiative and Evaporative Cooling.

Transparent passive cooling materials can cool targets environmentally without interfering with light transmission or visual information reception. They play a prominent role in solar cells and flexible display cooling. However, achieving potent transparent cooling remains challenging, because light transmission is accompanied by thermal energy. Here we propose to realize effective passive cooling in transparent materials via a microscale phase separation hydrogel film. The poly(N-isopropylacrylamide-co-acrylamide) hydrogel presents light transmittance of >96% and infrared emissivity as high as 95%. The microphase-separated structure affords a higher enthalpy of evaporation. The film is highly adhesive. In field applications, it reduces temperatures by 9.14 °C compared to those with uncovered photovoltaic panels and 7.68 °C compared to those for bare flexible light-emitting diode screens. Simulations indicate that energy savings of 32.76-51.65 MJ m-2 year-1 can be achieved in typical tropical monsoon climates and temperate continental climates. We expect this work to contribute to energy-efficient materials and a carbon-neutral society.

Identification and functional analysis of circulating small extracellular vesicle lncRNA signatures in children with fulminant myocarditis.

Fulminant myocarditis (FM) is the most serious type of myocarditis. However, the molecular mechanism underlying the pathogenesis of FM has not been fully elucidated. Small extracellular vesicles (sEVs) play important roles in many diseases, but any potential role in paediatric FM has not been reported. Here, the differential signatures of lncRNAs in plasma sEVs were studied in FM children and healthy children using transcriptome sequencing followed by functional analysis. Then immune-related lncRNAs were screened to study their role in immune mechanisms, the levels and clinical relevance of core immune-related lncRNAs were verified by qRT-PCR in a large sample size. Sixty-eight lncRNAs had increased levels of plasma sEVs in children with FM and 11 had decreased levels. Functional analysis showed that the sEVs-lncRNAs with different levels were mainly related to immunity, apoptosis and protein efflux. Seventeen core immune-related sEVs-lncRNAs were screened, functional enrichment analysis showed that these lncRNAs were closely related to immune activation, immune cell migration and cytokine pathway signal transduction. The results of the study show that sEVs-lncRNAs may play an important role in the pathogenesis of fulminant myocarditis in children, especially in the mechanism of immune regulation.

The distinct initiation sites and processing activities of TTLL4 and TTLL7 in glutamylation of brain tubulin.

Mammalian brain tubulins undergo a reversible posttranslational modification-polyglutamylation-which attaches a secondary polyglutamate chain to the primary sequence of proteins. Loss of its erasers can disrupt polyglutamylation homeostasis and cause neurodegeneration. Tubulin tyrosine ligase like 4 (TTLL4) and TTLL7 were known to modify tubulins, both with preference for the ß-isoform, but differently contribute to neurodegeneration. However, differences in their biochemical properties and functions remain largely unknown. Here, using an antibody-based method, we characterized the properties of a purified recombinant TTLL4 and confirmed its sole role as an initiator, unlike TTLL7, which both initiates and elongates the side chains. Unexpectedly, TTLL4 produced stronger glutamylation immunosignals for α-isoform than ß-isoform in brain tubulins. Contrarily, the recombinant TTLL7 raised comparable glutamylation immunoreactivity for two isoforms. Given the site selectivity of the glutamylation antibody, we analyzed modification sites of two enzymes. Tandem mass spectrometry analysis revealed their incompatible site selectivity on synthetic peptides mimicking carboxyl termini of α1- and ß2-tubulins and a recombinant tubulin. Particularly, in the recombinant α1A-tubulin, a novel region was found glutamylated by TTLL4 and TTLL7, that again at distinct sites. These results pinpoint different site specificities between two enzymes. Moreover, TTLL7 exhibits less efficiency to elongate microtubules premodified by TTLL4, suggesting possible regulation of TTLL7 elongation activity by TTLL4-initiated sites. Finally, we showed that kinesin behaves differentially on microtubules modified by two enzymes. This study underpins the different reactivity, site selectivity, and function of TTLL4 and TTLL7 on brain tubulins and sheds light on their distinct role in vivo.

Unraveling the Transformation from Type-II to Z-Scheme in Perovskite-Based Heterostructures for Enhanced Photocatalytic CO2 Reduction.

The ability to create perovskite-based heterostructures with desirable charge transfer characteristics represents an important endeavor to render a set of perovskite materials and devices with tunable optoelectronic properties. However, due to similar material selection and band alignment in type-II and Z-scheme heterostructures, it remains challenging to obtain perovskite-based heterostructures with a favorable electron transfer pathway for photocatalysis. Herein, we report a robust tailoring of effective charge transfer pathway in perovskite-based heterostructures via a type-II to Z-scheme transformation for highly efficient and selective photocatalytic CO2 reduction. Specifically, CsPbBr3/TiO2 and CsPbBr3/Au/TiO2 heterostructures are synthesized and then investigated by ultrafast spectroscopy. Moreover, taking CsPbBr3/TiO2 and CsPbBr3/Au/TiO2 as examples, operando experiments and theoretical calculations confirm that the type-II heterostructure could be readily transformed into a Z-scheme heterostructure through establishing a low-resistance Ohmic contact, which indicates that a fast electron transfer pathway is crucial in Z-scheme construction, as further demonstrated by CsPbBr3/Ag/TiO2 and CsPbBr3/MoS2 heterostructures. In contrast to pristine CsPbBr3 and CsPbBr3/TiO2, the CsPbBr3/Au/TiO2 heterostructure exhibits 5.4- and 3.0-fold enhancement of electron consumption rate in photocatalytic CO2 reduction. DFT calculations and in situ diffuse reflectance infrared Fourier transform spectroscopy unveil that the superior CO selectivity is attributed to the lower energy of *CO desorption than that of hydrogenation to *HCO. This meticulous design sheds light on the modification of perovskite-based multifunctional materials and enlightens conscious optimization of semiconductor-based heterostructures with desirable charge transfer for catalysis and optoelectronic applications.

NR0B1 augments sorafenib resistance in hepatocellular carcinoma through promoting autophagy and inhibiting apoptosis.

NR0B1 is frequently activated in hepatocellular carcinoma (HCC). However, the role of NR0B1 is controversial in HCC. In this study, we observed that NR0B1 was an independent poor prognostic factor, negatively correlated with the overall survival of HCC and the relapse-free survival of patients treated with sorafenib. Meanwhile, NR0B1 promoted the proliferation, migration, and invasion of HCC cells, inhibited sorafenib-induced apoptosis, and elevated the IC50 of sorafenib in HCC cells. NR0B1 was further displayed to increase sorafenib-induced autophagic vesicles and activate Beclin1/LC3-II-dependent autophagy pathway. Finally, NR0B1 was revealed to transcriptionally suppress GSK3ß that restrains AMPK/mTOR-driven autophagy and increases BAX-mediated apoptosis. Collectively, our study uncovered that the ectopic expression of NR0B1 augmented sorafenib-resistance in HCC cells by activating autophagy and inhibiting apoptosis. Our findings supported that NR0B1 was a detrimental factor for HCC prognosis.

An Orthogonal CRISPR/dCas12a System for RNA Imaging in Live Cells.

CRISPR/Cas technology has made great progress in the field of live-cell imaging beyond genome editing. However, effective and easy-to-use CRISPR systems for labeling multiple RNAs of interest are still needed. Here, we engineered a CRISPR/dCas12a system that enables the specific recognition of the target RNA under the guidance of a PAM-presenting oligonucleotide (PAMmer) to mimic the PAM recognition mechanism for DNA substrates. We demonstrated the feasibility and specificity of this system for specifically visualizing endogenous mRNA. By leveraging dCas12a-mediated precursor CRISPR RNA (pre-crRNA) processing and the orthogonality of dCas12a from different bacteria, we further demonstrated the proposed system as a simple and versatile molecular toolkit for multiplexed imaging of different types of RNA transcripts in live cells with high specificity. This programmable dCas12a system not only broadens the RNA imaging toolbox but also facilitates diverse applications for RNA manipulation.

Advances in common in vitro cellular models of pulmonary fibrosis.

The development of in vitro models is essential for a comprehensive understanding and investigation of pulmonary fibrosis (PF) at both cellular and molecular levels. This study presents a literature review and an analysis of various cellular models used in scientific studies, specifically focusing on their applications in elucidating the pathogenesis of PF. Our study highlights the importance of taking a comprehensive approach to studing PF, emphasizing the necessity of considering multiple cell types and organs and integrating diverse analytical perspectives. Notably, primary cells demonstrate remarkable cell growth characteristics and gene expression profiles; however, their limited availability, maintenance challenges, inability for continuous propagation and susceptibility to phenotypic changes over time significantly limit their utility in scientific investigation. By contrast, immortalized cell lines are easily accessible, cultured and continuously propagated, although they may have some phenotypic differences from primary cells. Furthermore, in vitro coculture models offer a more practical and precise method to explore complex interactions among cells, tissues and organs. Consequently, when developing models of PF, researchers should thoroughly assess the advantages, limitations and relevant mechanisms of different cell models to ensure their selection is consistent with the research objectives.

pH-Controllable Redox Responsive Amphiphilic Viologens for Switchable Emulsions.

A pH and redox dual responsive amphiphilic viologen is synthesized, which can be reversibly transformed among the zwitterionic (SVa), monovalent anionic (SV+), and divalent anionic (SVH2+) forms upon pH variation, exhibiting pH-controllable redox responsive properties. Switchable Pickering emulsions with different droplet size and viscosity are prepared by the mixture of hydrophilic silica nanoparticles and the viologens (SV+ or SVH2+) at acidic conditions, while such combination yielded an oil-in-dispersion emulsion at neutral pH value. Not only can rapid reversible demulsification/stabilization of the Pickering emulsions be achieved by redox reactions, but the rate of redox-demulsification can also be controlled by pH trigger. The dual-responsive amphiphilic viologens have potential applications in developing intelligent colloid materials and molecular logic systems.

Self-Healing Behavior of the Metal Halide Perovskites and Photovoltaics.

Perovskite solar cells have achieved rapid progress in the new-generation photovoltaic field, but the commercialization lags behind owing to the device stability issue under operational conditions. Ultimately, the instability issue is attributed to the soft lattice of ionic perovskite crystal. In brief, metal halide perovskite materials are susceptible to structural instability processes, including phase segregation, component loss, lattice distortion, and fatigue failure under harsh external stimuli such as high humidity, strong irradiation, wide thermal cycles, and large stress. Developing self-healing perovskites to further improve the unsatisfactory operational stability of their photoelectric devices under harsh stimuli has become a cutting-edge hotspot in this field. This self-healing behavior needs to be studied more comprehensively. Therefore, the self-healing behavior of the metal halide perovskites and photovoltaics is classified and summarized in this review. By discussing recent advances, underlying mechanisms, strategies, and existing challenges, this review provides perspectives on self-healing of perovskite solar cells in the future.

A Rapid, Scalable Laser-Scribing Process to Prepare Si/Graphene Composites for Lithium-Ion Batteries.

Silicon has gained significant attention as a lithium-ion battery anode material due to its high theoretical capacity compared to conventional graphite. Unfortunately, silicon anodes suffer from poor cycling performance caused by their extreme volume change during lithiation and de-lithiation. Compositing silicon particles with 2D carbon materials, such as graphene, can help mitigate this problem. However, an unaddressed challenge remains: a simple, inexpensive synthesis of Si/graphene composites. Here, a one-step laser-scribing method is proposed as a straightforward, rapid (≈3 min), scalable, and less-energy-consuming (≈5 W for a few minutes under air) process to prepare Si/laser-scribed graphene (LSG) composites. In this research, two types of Si particles, Si nanoparticles (SiNPs) and Si microparticles (SiMPs), are used. The rate performance is improved after laser scribing: SiNP/LSG retains 827.6 mAh g-1 at 2.0 A gSi+C -1, while SiNP/GO (before laser scribing) retains only 463.8 mAh g-1. This can be attributed to the fast ion transport within the well-exfoliated 3D graphene network formed by laser scribing. The cyclability is also improved: SiNP/LSG retains 88.3% capacity after 100 cycles at 2.0 A gSi+C -1, while SiNP/GO retains only 57.0%. The same trend is found for SiMPs: the SiMP/LSG shows better rate and cycling performance than SiMP/GO composites.

An efficient genetic transformation system mediated by Rhizobium rhizogenes in fruit trees based on the transgenic hairy root to shoot conversion.

Genetic transformation is a critical tool for gene editing and genetic improvement of plants. Although many model plants and crops can be genetically manipulated, genetic transformation systems for fruit trees are either lacking or perform poorly. We used Rhizobium rhizogenes to transfer the target gene into the hairy roots of Malus domestica and Actinidia chinensis. Transgenic roots were generated within 3 weeks, with a transgenic efficiency of 78.8%. Root to shoot conversion of transgenic hairy roots was achieved within 11 weeks, with a regeneration efficiency of 3.3%. Finally, the regulatory genes involved in stem cell activity were used to improve shoot regeneration efficiency. MdWOX5 exhibited the most significant effects, as it led to an improved regeneration efficiency of 20.6% and a reduced regeneration time of 9 weeks. Phenotypes of the overexpression of RUBY system mediated red roots and overexpression of MdRGF5 mediated longer root hairs were observed within 3 weeks, suggesting that the method can be used to quickly screen genes that influence root phenotype scores through root performance, such as root colour, root hair, and lateral root. Obtaining whole plants of the RUBY system and MdRGF5 overexpression lines highlights the convenience of this technology for studying gene functions in whole plants. Overall, we developed an optimized method to improve the transformation efficiency and stability of transformants in fruit trees.

miR-155 facilitates the synergistic replication between avian leukosis virus subgroup J and reticuloendotheliosis virus by targeting a dual pathway.

IMPORTANCE: The synergy of two oncogenic retroviruses is an essential phenomenon in nature. The synergistic replication of ALV-J and REV in poultry flocks increases immunosuppression and pathogenicity, extends the tumor spectrum, and accelerates viral evolution, causing substantial economic losses to the poultry industry. However, the mechanism of synergistic replication between ALV-J and REV is still incompletely elusive. We observed that microRNA-155 targets a dual pathway, PRKCI-MAPK8 and TIMP3-MMP2, interacting with the U3 region of ALV-J and REV, enabling synergistic replication. This work gives us new targets to modulate ALV-J and REV's synergistic replication, guiding future research on the mechanism.

Axion optical induction of antiferromagnetic order.

Using circularly polarized light to control quantum matter is a highly intriguing topic in physics, chemistry and biology. Previous studies have demonstrated helicity-dependent optical control of chirality and magnetization, with important implications in asymmetric synthesis in chemistry; homochirality in biomolecules; and ferromagnetic spintronics. We report the surprising observation of helicity-dependent optical control of fully compensated antiferromagnetic order in two-dimensional even-layered MnBi2Te4, a topological axion insulator with neither chirality nor magnetization. To understand this control, we study an antiferromagnetic circular dichroism, which appears only in reflection but is absent in transmission. We show that the optical control and circular dichroism both arise from the optical axion electrodynamics. Our axion induction provides the possibility to optically control a family of [Formula: see text]-symmetric antiferromagnets ([Formula: see text], inversion; [Formula: see text], time-reversal) such as Cr2O3, even-layered CrI3 and possibly the pseudo-gap state in cuprates. In MnBi2Te4, this further opens the door for optical writing of a dissipationless circuit formed by topological edge states.

Perovskite photodetector-based laser absorption spectroscopy for gas detection.

A gas detection method based on CH3NH3PbI3 (MAPbI3) and poly (3,4-ethylenedioxythiophene): poly (4-styrene sulfonate) (PEDOT:PSS) composite photodetectors (PDs) is proposed. The operation of the PD primarily relies on the photoelectric effect within the visible light band. Our study involves constructing a gas detection system based on tunable diode laser spectroscopy (TDLAS) and MAPbI3/PEDOT:PSS PD, and O2 was selected as the target analyte. The system has achieved a minimum detection limit (MDL) of 0.12% and a normalized noise equivalent absorption coefficient (NNEA) of 8.83 × 10-11 cm-1⋅W⋅Hz-1/2. Furthermore, the Allan deviation analysis results indicate that the system can obtain sensitivity levels as low as 0.058% over an averaging time of 328 seconds. This marks the first use of MAPbI3/PEDOT:PSS PD in gas detection based on TDLAS. Despite the detector's performance leaves much to be desired, this innovation offers a new approach to developing spectral based gas detection system.