Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation.

Somatic hypermutation (SHM), initiated by activation-induced cytidine deaminase (AID), generates mutations in the antibody-coding sequence to allow affinity maturation. Why these mutations intrinsically focus on the three nonconsecutive complementarity-determining regions (CDRs) remains enigmatic. Here, we found that predisposition mutagenesis depends on the single-strand (ss) DNA substrate flexibility determined by the mesoscale sequence surrounding AID deaminase motifs. Mesoscale DNA sequences containing flexible pyrimidine-pyrimidine bases bind effectively to the positively charged surface patches of AID, resulting in preferential deamination activities. The CDR hypermutability is mimicable in in vitro deaminase assays and is evolutionarily conserved among species using SHM as a major diversification strategy. We demonstrated that mesoscale sequence alterations tune the in vivo mutability and promote mutations in an otherwise cold region in mice. Our results show a non-coding role of antibody-coding sequence in directing hypermutation, paving the way for the synthetic design of humanized animal models for optimal antibody discovery and explaining the AID mutagenesis pattern in lymphoma.

Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities.

Among arthropod vectors, ticks transmit the most diverse human and animal pathogens, leading to an increasing number of new challenges worldwide. Here we sequenced and assembled high-quality genomes of six ixodid tick species and further resequenced 678 tick specimens to understand three key aspects of ticks: genetic diversity, population structure, and pathogen distribution. We explored the genetic basis common to ticks, including heme and hemoglobin digestion, iron metabolism, and reactive oxygen species, and unveiled for the first time that genetic structure and pathogen composition in different tick species are mainly shaped by ecological and geographic factors. We further identified species-specific determinants associated with different host ranges, life cycles, and distributions. The findings of this study are an invaluable resource for research and control of ticks and tick-borne diseases.

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells.

Translation is under tight spatial and temporal controls to ensure protein production in the right time and place in cells. Methods that allow real-time, high-resolution visualization of translation in live cells are essential for understanding the spatiotemporal dynamics of translation regulation. Based on multivalent fluorescence amplification of the nascent polypeptide signal, we develop a method to image translation on individual mRNA molecules in real time in live cells, allowing direct visualization of translation events at the translation sites. Using this approach, we monitor transient changes of translation dynamics in responses to environmental stresses, capture distinct mobilities of individual polysomes in different subcellular compartments, and detect 3' UTR-dependent local translation and active transport of polysomes in dendrites of primary neurons.

Inhibition of viral suppressor of RNAi proteins by designer peptides protects from enteroviral infection in vivo.

RNA interference (RNAi) is the major antiviral mechanism in plants and invertebrates, but the absence of detectable viral (v)siRNAs in mammalian cells upon viral infection has questioned the functional relevance of this pathway in mammalian immunity. We designed a series of peptides specifically targeting enterovirus A71 (EV-A71)-encoded protein 3A, a viral suppressor of RNAi (VSR). These peptides abrogated the VSR function of EV-A71 in infected cells and resulted in the accumulation of vsiRNAs and reduced viral replication. These vsiRNAs were functional, as evidenced by RISC-loading and silencing of target RNAs. The effects of VSR-targeting peptides (VTPs) on infection with EV-A71 as well as another enterovirus, Coxsackievirus-A16, were ablated upon deletion of Dicer1 or AGO2, core components of the RNAi pathway. In vivo, VTP treatment protected mice against lethal EV-A71 challenge, with detectable vsiRNAs. Our findings provide evidence for the functional relevance of RNAi in mammalian immunity and present a therapeutic strategy for infectious disease.

Structure of the Angiotensin receptor revealed by serial femtosecond crystallography.

Angiotensin II type 1 receptor (AT(1)R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT(1)R blockers (ARBs), the structural basis for AT(1)R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high-quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT(1)R in complex with its selective antagonist ZD7155 at 2.9-Å resolution. The AT(1)R-ZD7155 complex structure revealed key structural features of AT(1)R and critical interactions for ZD7155 binding. Docking simulations of the clinically used ARBs into the AT(1)R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT(1)R structure-function relationship and structure-based drug design.

Observation of fractionally quantized anomalous Hall effect.

The integer quantum anomalous Hall (QAH) effect is a lattice analogue of the quantum Hall effect at zero magnetic field1-3. This phenomenon occurs in systems with topologically non-trivial bands and spontaneous time-reversal symmetry breaking. Discovery of its fractional counterpart in the presence of strong electron correlations, that is, the fractional QAH effect4-7, would open a new chapter in condensed matter physics. Here we report the direct observation of both integer and fractional QAH effects in electrical measurements on twisted bilayer MoTe2. At zero magnetic field, near filling factor ν = -1 (one hole per moiré unit cell), we see an integer QAH plateau in the Hall resistance Rxy quantized to h/e2 ± 0.1%, whereas the longitudinal resistance Rxx vanishes. Remarkably, at ν = -2/3 and -3/5, we see plateau features in Rxy at [Formula: see text] and [Formula: see text], respectively, whereas Rxx remains small. All features shift linearly versus applied magnetic field with slopes matching the corresponding Chern numbers -1, -2/3 and -3/5, precisely as expected for integer and fractional QAH states. Additionally, at zero magnetic field, Rxy is approximately 2h/e2 near half-filling (ν = -1/2) and varies linearly as ν is tuned. This behaviour resembles that of the composite Fermi liquid in the half-filled lowest Landau level of a two-dimensional electron gas at high magnetic field8-14. Direct observation of the fractional QAH and associated effects enables research in charge fractionalization and anyonic statistics at zero magnetic field.

Signatures of fractional quantum anomalous Hall states in twisted MoTe2.

The interplay between spontaneous symmetry breaking and topology can result in exotic quantum states of matter. A celebrated example is the quantum anomalous Hall (QAH) state, which exhibits an integer quantum Hall effect at zero magnetic field owing to intrinsic ferromagnetism1-3. In the presence of strong electron-electron interactions, fractional QAH (FQAH) states at zero magnetic field can emerge4-8. These states could host fractional excitations, including non-Abelian anyons-crucial building blocks for topological quantum computation9. Here we report experimental signatures of FQAH states in a twisted molybdenum ditelluride (MoTe2) bilayer. Magnetic circular dichroism measurements reveal robust ferromagnetic states at fractionally hole-filled moiré minibands. Using trion photoluminescence as a sensor10, we obtain a Landau fan diagram showing linear shifts in carrier densities corresponding to filling factor v = -2/3 and v = -3/5 ferromagnetic states with applied magnetic field. These shifts match the Streda formula dispersion of FQAH states with fractionally quantized Hall conductance of [Formula: see text] and [Formula: see text], respectively. Moreover, the v = -1 state exhibits a dispersion corresponding to Chern number -1, consistent with the predicted QAH state11-14. In comparison, several non-ferromagnetic states on the electron-doping side do not disperse, that is, they are trivial correlated insulators. The observed topological states can be electrically driven into topologically trivial states. Our findings provide evidence of the long-sought FQAH states, demonstrating MoTe2 moiré superlattices as a platform for exploring fractional excitations.

Light-induced ferromagnetism in moiré superlattices.

Many-body interactions between carriers lie at the heart of correlated physics. The ability to tune such interactions would allow the possibility to access and control complex electronic phase diagrams. Recently, two-dimensional moiré superlattices have emerged as a promising platform for quantum engineering such phenomena1-3. The power of the moiré system lies in the high tunability of its physical parameters by adjusting the layer twist angle1-3, electrical field4-6, moiré carrier filling7-11 and interlayer coupling12. Here we report that optical excitation can highly tune the spin-spin interactions between moiré-trapped carriers, resulting in ferromagnetic order in WS2 /WSe2 moiré superlattices. Near the filling factor of -1/3 (that is, one hole per three moiré unit cells), as the excitation power at the exciton resonance increases, a well-developed hysteresis loop emerges in the reflective magnetic circular dichroism signal as a function of magnetic field, a hallmark of ferromagnetism. The hysteresis loop persists down to charge neutrality, and its shape evolves as the moiré superlattice is gradually filled, indicating changes of magnetic ground state properties. The observed phenomenon points to a mechanism in which itinerant photoexcited excitons mediate exchange coupling between moiré-trapped holes. This exciton-mediated interaction can be of longer range than direct coupling between moiré-trapped holes9, and thus magnetic order arises even in the dilute hole regime. This discovery adds a dynamic tuning knob to the rich many-body Hamiltonian of moiré quantum matter13-19.

Promoting sustainable smallholder farming via multistakeholder collaboration.

Transforming smallholder farms is critical to global food security and environmental sustainability. The science and technology backyard (STB) platform has proved to be a viable approach in China. However, STB has traditionally focused on empowering smallholder farmers by transferring knowledge, and wide-scale adoption of more sustainable practices and technologies remains a challenge. Here, we report on a long-term project focused on technology scale-up for smallholder farmers by expanding and upgrading the original STB platform (STB 2.0). We created a formalized and standardized process by which to engage and collaborate with farmers, including integrating their feedback via equal dialogues in the process of designing and promoting technologies. Based on 288 site-year of field trials in three regions in the North China Plain over 5 y, we find that technologies cocreated through this process were more easily accepted by farmers and increased their crop yields and nitrogen factor productivity by 7.2% and 28.1% in wheat production and by 11.4% and 27.0% in maize production, respectively. In promoting these technologies more broadly, we created a "one-stop" multistakeholder program involving local government agencies, enterprises, universities, and farmers. The program was shown to be much more effective than the traditional extension methods applied at the STB, yielding substantial environmental and economic benefits. Our study contributes an important case study for technology scale-up for smallholder agriculture. The STB 2.0 platform being explored emphasizes equal dialogue with farmers, multistakeholder collaboration, and long-term investment. These lessons may provide value for the global smallholder research and practitioners.

A COBRA family protein, PtrCOB3, contributes to gelatinous layer formation of tension wood fibers in poplar.

Angiosperm trees usually develop tension wood (TW) in response to gravitational stimulation. TW comprises abundant gelatinous (G-) fibers with thick G-layers primarily composed of crystalline cellulose. Understanding the pivotal factors governing G-layer formation in TW fiber remains elusive. This study elucidates the role of a Populus trichocarpa COBRA family protein, PtrCOB3, in the G-layer formation of TW fibers. PtrCOB3 expression was upregulated, and its promoter activity was enhanced during TW formation. Comparative analysis with wild-type trees revealed that ptrcob3 mutants, mediated by Cas9/gRNA gene editing, were incapable of producing G-layers within TW fibers and showed severely impaired stem lift. Fluorescence immunolabeling data revealed a dearth of crystalline cellulose in the tertiary cell wall (TCW) of ptrcob3 TW fibers. The role of PtrCOB3 in G-layer formation is contingent upon its native promoter, as evidenced by the comparative phenotypic assessments of pCOB11::PtrCOB3, pCOB3::PtrCOB3, and pCOB3::PtrCOB11 transgenic lines in the ptrcob3 background. Overexpression of PtrCOB3 under the control of its native promoter expedited G-layer formation within TW fibers. We further identified 3 transcription factors that bind to the PtrCOB3 promoter and positively regulate its transcriptional levels. Alongside the primary TCW synthesis genes, these findings enable the construction of a 2-layer transcriptional regulatory network for the G-layer formation of TW fibers. Overall, this study uncovers mechanistic insight into TW formation, whereby a specific COB protein executes the deposition of cellulose, and consequently, G-layer formation within TW fibers.

Deficiency in the Rab25 gene leads to a decline in male fertility and testicular injury: Impact on the regulation of germ cell proliferation and apoptosis.

BACKGROUND: Rab25 is a member of the Rab family, functioning as a regulatory molecule in intracellular transport. Although its involvement in cellular functions and disease development is well-established, its precise roles in male reproductive physiology remain elusive. METHODS: To explore the specific roles of Rab25 in testicular development and spermatogenesis, we established the Rab25-/- mouse model and Rab25 knockdown germ cell line (GC-2). We compared the fertility, sperm analysis, and testicular tissues between Rab25-/- and wild-type male mice. To delve deeper into potential mechanisms, we employed immunohistochemistry, TUNEL assay, Western Blotting, CCK-8 assay, etc. to evaluate cell proliferation and apoptosis in testicular tissues and GC-2 cells. RESULTS: Our findings indicated that Rab25 was expressed in germ cells and Leydig cells in the testes. Although the weight of Rab25-/- mice testes exhibited no significant changes, fertility was compromised, with a decrease in sperm quantity and reduced motility. HE staining revealed a disorganized arrangement of germ cells and vacuolization. Additionally, chromatin marginalization and nuclear pyknosis were observed in the Rab25-/- mice. In both Rab25-/- mice testes and Rab25 knockdown GC-2 cells, we found that germ cell proliferation was reduced, while apoptosis was increased. CONCLUSIONS: In conclusion, our study proposes that Rab25 plays a vital role in spermatogenesis by regulating the proliferation and apoptosis of germ cells.

Rab25 is involved in hypospadias via the ß1 integrin/EGFR pathway.

BACKGROUND: Hypospadias is a common congenital abnormality of the penile. Abnormal regulation of critical genes involved in urethral development leads to hypospadias. We used the Rab25-/- mice and foreskin fibroblasts transfected with lentivirus in vitro and in vivo to investigate the role of Rab25 in hypospadias. METHODS: The expression levels of various molecules in tissue samples and foreskin fibroblasts were confirmed using molecular biology methods (western blotting, PCR, immunohistochemistry, etc.). A scanning electron microscope (SEM) was used to visualize the external morphology of genital tubercles (GTs) of gestation day (GD) 18.5 male wild-type (WT) and Rab25-/- mice. RESULTS: An expanded distal cleft and V-shaped urethral opening were observed in GD 18.5 Rab25-/- mice. We demonstrated that Rab25 mediated hypospadias through the ß1 integrin/EGFR pathway. In addition, silencing Rab25 inhibited cell proliferation and migration and promoted apoptosis in the foreskin fibroblasts; Ki-67- and TUNEL-positive cells were mainly concentrated near the urethral seam. CONCLUSION: These findings suggest that Rab25 plays an essential role in hypospadias by activation of ß1 integrin/EGFR pathway, and Rab25 is a critical mediator of urethral seam formation in GD18.5 male fetal mice.

Cholesteric cellulose liquid crystal ink for three-dimensional structural coloration.

SignificanceWe propose a printable structural color ink composed of cholesteric cellulose liquid crystals together with gelatin and a thermal-responsive hydrogel. The ink is endowed with vivid structural colors and printability due to its constituents. Based on this, we print a series of graphics and three-dimensional (3D) objects with vivid color appearances. Moreover, the printed objects possess dual thermal responsiveness, which results in visible color change around body temperature. These performances, together with the biocompatibility of the constituents, indicate that the present ink represents a leap forward to the next-generation 3D printing and would unlock a wide range of real-life applications.

Interplay between quantum anomalous Hall effect and magnetic skyrmions.

SignificanceQuantum anomalous Hall effect (QAHE) and magnetic skyrmion (SK), as two typical topological states in momentum (K) and real (R) spaces, attract much interest in condensed matter physics. However, the interplay between these two states remains to be explored. We propose that the interplay between QAHE and SK may generate an RK joint topological skyrmion (RK-SK), characterized by the SK surrounded by nontrivial chiral boundary states (CBSs). Furthermore, the emerging external field-tunable CBS in RK-SK could create additional degrees of freedom for SK manipulations, beyond the traditional SK. Meanwhile, external field can realize a rare topological phase transition between K and R spaces. Our work opens avenues for exploring unconventional quantum states and topological phase transitions in different spaces.

Direct Visualization of Dark Interlayer Exciton Transport in Moiré Superlattices.

Moiré superlattices have emerged as an unprecedented manipulation tool for engineering correlated quantum phenomena in van der Waals heterostructures. With moiré potentials as a naturally configurable solid-state that sustains high exciton density, interlayer excitons in transition metal dichalcogenide heterostructures are expected to achieve high-temperature exciton condensation. However, the exciton degeneracy state is usually optically inactive due to the finite momentum of interlayer excitons. Experimental observation of dark interlayer excitons in moiré potentials remains challenging. Here we directly visualize the dark interlayer exciton transport in WS2/h-BN/WSe2 heterostructures using femtosecond transient absorption microscopy. We observe a transition from classical free exciton gas to quantum degeneracy by imaging temperature-dependent exciton transport. Below a critical degeneracy temperature, exciton diffusion rates exhibit an accelerating downward trend, which can be explained well by a nonlinear quantum diffusion model. These results open the door to quantum information processing and high-precision metrology in moiré superlattices.

Highly Tunable Interlayer Coupling and Electronic Structures of Few-Layer Graphene with Pressure.

The interlayer electronic coupling is responsible for the electronic structure evolution from monolayer graphene to graphite and for the moiré potential in twisted bilayer graphene. Here we demonstrate that the interlayer transfer integral (hopping parameter) increases nearly 40% with a quite moderate pressure of ∼3.5 GPa, manifested by the resonance peak shift in the infrared spectra of all 2-10 L graphene. A simple model based on the Morse potential enabled us to establish the relationship between the transfer integral and pressure. Our work provides fundamental insights into the dependence of the electronic coupling on the interlayer distance.

STRN3 promotes tumour growth in hepatocellular carcinoma by inhibiting the hippo pathway.

HCC is a globally high-incidence malignant tumour, and its pathogenesis is still unclear. Recently, STRN3 has been found to be elevated in various tumours, but its expression and biological functions in HCC have not been studied. In the study, clinical correlation analysis was performed on 371 liver cancer patients from TCGA database and liver cancer tissues and normal tissues from the GEO database. qRT-PCR and western blotting were used to detect relevant proteins in cells, and CCK8 and colony formation experiments were performed to analyse cell proliferation ability. Transwell and wound healing experiments were performed to detect cell invasion ability, and flow cytometry was used to detect cell apoptosis. Single-cell sequencing data and multiple immunofluorescence were analysed for the expression abundance and distribution of certain proteins. Immunohistochemistry was used to assess the expression of STRN3 in patients' tumour and adjacent non-cancerous tissues. The results indicated STRN3 was highly expressed in liver tumour tissues and was closely associated with poor prognosis. Knockdown of STRN3 could significantly inhibit cell proliferation and migration ability. At the same time, we found that STRN3 could inhibit the Hippo pathway and promote the entry of YAP protein into the nucleus. Our study first found that STRN3 could promote tumour growth by inhibiting the Hippo pathway. The study of STRN3 can promote the understanding and treatment of the occurrence and development of HCC.

ATM-mediated double-strand break repair is required for meiotic genome stability at high temperature.

In eukaryotes, meiotic recombination maintains genome stability and creates genetic diversity. The conserved Ataxia-Telangiectasia Mutated (ATM) kinase regulates multiple processes in meiotic homologous recombination, including DNA double-strand break (DSB) formation and repair, synaptonemal complex organization, and crossover formation and distribution. However, its function in plant meiotic recombination under stressful environmental conditions remains poorly understood. In this study, we demonstrate that ATM is required for the maintenance of meiotic genome stability under heat stress in Arabidopsis thaliana. Using cytogenetic approaches we determined that ATM does not mediate reduced DSB formation but does ensure successful DSB repair, and thus meiotic chromosome integrity, under heat stress. Further genetic analysis suggested that ATM mediates DSB repair at high temperature by acting downstream of the MRE11-RAD50-NBS1 (MRN) complex, and acts in a RAD51-independent but chromosome axis-dependent manner. This study extends our understanding on the role of ATM in DSB repair and the protection of genome stability in plants under high temperature stress.

Genome-wide identification of Gα family in grass carp (Ctenopharyngodon idella) and reproductive regulation functional characteristics of Cignaq.

BACKGROUND: The Gα family plays a crucial role in the complex reproductive regulatory network of teleosts. However, the characterization and function of Gα family members, especially Gαq, remain poorly understood in teleosts. To analyze the characterization, expression, and function of grass carp (Ctenopharyngodon idella) Gαq, we identified the Gα family members in grass carp genome, and analyzed the expression, distribution, and signal transduction of Gαq/gnaq. We also explored the role of Gαq in the reproductive regulation of grass carp. RESULTS: Our results showed that the grass carp genome contains 27 Gα genes with 46 isoforms, which are divided into four subfamilies: Gαs, Gαi/o, Gαq/11, and Gα12/13. The expression level of Cignaq in the testis was the highest and significantly higher than in other tissues, followed by the hypothalamus and brain. The luteinizing hormone receptor (LHR) was mainly localized to the nucleus in grass carp oocytes, with signals also present in follicular cells. In contrast, Gαq signal was mainly found in the cytoplasm of oocytes, with no signal in follicular cells. In the testis, Gαq and LHR were co-localized in the cytoplasm. Furthermore, the grass carp Gαq recombinant protein significantly promoted Cipgr expression. CONCLUSIONS: These results provided preliminary evidence for understanding the role of Gαq in the reproductive regulation of teleosts.

Evaluation of cfDNA fragmentation characteristics in plasma for the diagnosis of lung cancer: A prospective cohort study.

Lung cancer is one of the most prevalent cancers worldwide, yet only approximately 16% of patients are diagnosed in early stage, highlighting the urgent need for novel, highly accurate detection models. In our study, patients with suspected lung cancer or lung disease, as identified through radiographic imaging, along with healthy individuals, were consecutively recruited from Beijing Chest Hospital. Circulating free DNA (cfDNA) was extracted from plasma samples, and low-depth whole-genome sequencing was performed to identify fragmentomic features for model construction. A total of 265 participants were prospectively enrolled, comprising 124 lung cancer patients and 141 noncancer individuals. The model we developed was based on four cfDNA fragmentation characteristics, including 20-bp breakpoint nucleotides motif, fragmentation size coverage, fragmentation size distribution, and copy number variation. In an independent test cohort, the model achieved an area under the curve (AUC) of 0.861 (95% CI: 0.781-0.942) and demonstrated a sensitivity of 70% (95% CI: 53.5%-83.4%) at a specificity of 89.4% (95% CI: 76.9%-96.5%). Notably, the model was also effective in detecting early-stage cancer, with an AUC of 0.808 (95% CI: 0.69-0.925). In summary, our lung cancer detection model shows strong screening capabilities by leveraging four cfDNA fragmentation characteristics, exhibiting robust performance in early cancer diagnosis.