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Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.

Abstract The realization of high‐efficiency, reversible, stable, and safe Li‐O2 batteries is severely hindered by the large overpotential and side reactions, especially at high rate conditions. Therefore, rational design of cathode catalysts with high activity and stability is crucial to overcome the terrible issues at high current density. Herein, we report a surface engineering strategy to adjust the surface electron structure of boron (B)‐doped PtNi nanoalloy on carbon nanotubes (PtNiB@CNTs) as an efficient bifunctional cathodic catalyst for high‐rate and long‐life Li‐O2 batteries. Notably, the Li‐O2 batteries assembled with as‐prepared PtNiB@CNT catalyst exhibit ultrahigh discharge capacity of 20510 mA·h/g and extremely low overpotential of 0.48 V at a high current density of 1000 mA/g, both of which outperform the most reported Pt‐based catalysts recently. Meanwhile, our Li‐O2 batteries offer excellent rate capability and ultra‐long cycling life of up to 210 cycles at 1000 mA/g under a fixed capacity of 1000 mA·h/g, which is two times longer than those of Pt@CNTs and PtNi@CNTs. Furthermore, it is revealed that surface engineering of PtNi nanoalloy via B doping can efficiently tailor the electron structure of nanoalloy and optimize the adsorption of oxygen species, consequently delivering excellent Li‐O2 battery performance. Therefore, this strategy of regulating the nanoalloy by doping nonmetallic elements will pave an avenue for the design of high‐performance catalysts for metal‐oxygen batteries.

Rice blast, caused by rice blast fungus (Magnaporthe oryzae), is a global threat to food security, with up to 50% yield losses. Panicle blast is a severe form of rice blast, and disease responses vary between cultivars with different genotypes. Reactive oxygen species (ROS)-mediated signaling reactions and the phenylpropanoid pathway are important defense mechanisms involved in recognizing and resisting against fungal infection. To understand rice-M. oryzae interactions in resistant and susceptible cultivars, we determined dynamic changes in the activities of five defense-related enzymes in resistant cultivar jingsui 18 and susceptible cultivar jinyuan 899 infected with M. oryzae from 4 to 25 days after infection. We then performed untargeted metabolomics analyses to profile the metabolomes of the cultivars under infected and non-infected conditions. Dynamic changes in the activities of five defense-related enzymes were closely related to panicle blast resistance in rice. Metabolome data analysis identified 634 differentially accumulated metabolites (DAMs) between resistant and susceptible cultivars following infection, potentially explaining differences in disease response between varieties. The most enriched DAMs were associated with lipids and lipid-like molecules, phenylpropanoids and polyketides, organoheterocyclic compounds, organic acids and derivatives, and lignans, neolignans, and related compounds. Multiple metabolic pathways are involved in resistance to panicle blast in rice, including biosynthesis of other secondary metabolites, amino acid metabolism, lipid metabolism, phenylpropanoid biosynthesis, arachidonic acid metabolism, arginine biosynthesis, tyrosine metabolism, tryptophan metabolism, tyrosine and tryptophan biosynthesis, lysine biosynthesis, and oxidative phosphorylation.

Cross-linguistic perception is known to be molded by native and second language (L2) experiences. Yet, the role of prosodic patterns and individual characteristics on how speakers of tonal languages perceive L2 Spanish sentence modalities remains relatively underexplored. This study addresses the gap by analyzing the auditory performance of 75 Mandarin speakers with varying levels of Spanish proficiency. The experiment consisted of four parts: the first three collected sociolinguistic profiles and assessed participants' pragmatic competence and musical abilities. The last part involved an auditory gating task, where participants were asked to identify Spanish broad focus statements and information-seeking yes/no questions with different stress patterns. Results indicated that the shape of intonation contours and the position of the final stressed syllable significantly impact learners' perceptual accuracy, with effects modulated by utterance length and L2 proficiency. Moreover, individual differences in pragmatic and musical competence were found to refine auditory and cognitive processing in Mandarin learners, thereby influencing their ability to discriminate question-statement contrasts. These findings reveal the complex interplay between prosodic and individual variations in L2 speech perception, providing novel insights into how speakers of tonal languages process intonation in a non-native Romance language like Spanish.

Summary: The commercial mass production of bifunctional oxygen catalysts with high activity and stability is critical for constructing high-performance lithium-oxygen (Li-O2) batteries, but remains challenging. Herein, we describe a protocol for the scalable fabrication of a 2D bifunctional electrocatalyst of Pt/RuO2/graphene by spatial confinement strategy and elaborately evaluate its oxygen reduction/evolution reactions for advanced Li-O2 batteries. We then detail the synthesis steps for preparing materials followed by assembly and evaluation of the three-electrode systems and coin-type Li-O2 batteries.For complete details on the use and execution of this protocol, please refer to Li et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Piriformospora indica, a plant root-colonizing basidiomycete fungus, exhibits strong growth-promoting activity in symbiosis with a broad range of plants. Here, we report the potential of P. indica to improve growth, yield, and disease resistance in wheat in the field. In the present study, P. indica successfully colonized wheat through chlamydospores and formed dense mycelial networks that covered roots. Plants subjected to the seed soaking (SS) treatment with P. indica chlamydospore suspensions enhanced tillering 2.28-fold compared to the non-inoculated wheat in the tillering stage. In addition, P. indica colonization promoted vegetative growth significantly during the three-leaf, tillering, and jointing stages. Moreover, the P. indica-SS-treatment enhanced wheat yield by 16.37 ± 1.63%, by increasing grains per ear and panicle weight and decreased damage to wheat shoot and root architecture markedly, with high field control effects against Fusarium pseudograminearum (81.59 ± 1.32%), Bipolaris sorokiniana (82.19 ± 1.59%), and Rhizoctonia cerealis (75.98 ± 1.36%). Most of the primary metabolites, such as amino acids, nucleotides, and lipids, involved in vegetative reproduction were increased in P. indica-SS-treatment plants, whereas secondary metabolites, such as terpenoids, polyketides, and alkaloids, decreased following P. indica inoculation. The up-regulated processes of protein, carbohydrate, and lipid metabolism indicated that P. indica colonization increased growth, yield, and disease resistance via the acceleration of plant primary metabolism. In conclusion, P. indica improved morphological, physiological, and metabolic substance levels, and further promoted its growth, yield, and disease resistance in wheat.

Chronic obstructive pulmonary disease (COPD) is a lung inflammatory disease that is associated with environmental allergic component exposure. Cigarette smoke is an environmental toxicant that induces lung malfunction leading to various pulmonary diseases. Astaxanthin (AST) is a carotenoid that shows antioxidant and anti-inflammatory activities which might be a promising candidate for COPD therapy. In this study, we released that AST could attenuate cigarette smoke-induced DNA damage and apoptosis in vivo and in vitro. AST administration ameliorated cigarette smoke extract (CSE)-induced activation of Caspase-3 and apoptosis. Pretreated mice with AST significantly decrease CSE-induced DNA damage which shows lower nuclear γ-H2AX level. AST treatment also dramatically reduces the production of intracellular reactive oxygen species (ROS) by suppressing the expression of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase enzyme 4 (NOX4) and dual oxidase 1 (DUOX1). Taken together, this study suggested that AST can decrease CSE-induced DNA damage and apoptosis by inhibiting NOX4/DUOX1 expression that promotes ROS generation. AST may be a potential protective agent against CSE-associated lung disease that is worth in-depth investigation.

Abstract Background Mesenchymal stem cells (MSCs) have shown immense therapeutic potential for various brain diseases. Intrathecal administration of MSCs may enhance their recruitment to lesions in the central nervous system, but any impact on cerebrospinal fluid (CSF) flow remains unclear. Methods Rats with or without middle cerebral artery occlusion (MCAO) received intrathecal injections of 2D cultured MSCs, 3D cultured MSCs or an equal volume of artificial cerebrospinal fluid (ACSF). Ventricle volume was assessed by MRI on Days 2 and 14 post-MCAO surgery. A beam walking test was used to assess fine motor coordination and balance. Aggregation of MSCs was evaluated in CSF and frozen brain tissue. Differential expression of cell adhesion molecules was evaluated by RNA-Seq, flow cytometry and immunofluorescence analyses. The influence of VCAM-1 blockade in mediating the aggregation of 2D MSCs was investigated in vitro by counting cells that passed through a strainer and in vivo by evaluating ventricular dilation. Results MSC expanded in 2D culture formed aggregates in the CSF and caused ventricular enlargement in both MCAO and normal rats. Aggregates were associated with impaired motor function. 2D MSCs expressed higher levels of integrin α4 and VCAM-1 than 3D MSCs. Blockade of VCAM-1 in 2D MSCs reduced their aggregation in vitro and reduced lateral ventricular enlargement after intrathecal infusion. 3D MSCs exhibited lower cell aggregation and reduced cerebral ventricular dilation after intrathecal transplantation Conclusions The aggregation of 2D MSCs, mediated by the interaction of integrin α4 and VCAM-1, is a potential risk for obstruction of CSF flow after intrathecal transplantation.

The role of human activity in shaping the terrestrial environment has been a core scientific issue of interest across various disciplines. However, it remains unclear whether there are significant differences in the patterns of the anthropogenic impact on the terrestrial environment in terms of spatial and temporal dimensions, and we are yet to identify the underlying factors that have driven it. Here, we present an analysis of sporopollen and geochemical proxies from a section of the Anjiangbei site (AJB) on the Yunnan Plateau, spanning the Ming–Qing period, in order to explore the spatio-temporal variation in the anthropogenic impact on the terrestrial environment in the Lake Dian basin. Integrating the reported multidisciplinary evidence, we aim to reveal the influencing factors of anthropogenic impact. Our results show that there were remarkable differences in anthropogenic impact on the terrestrial environment in the Lake Dian basin between the Late Bronze Age and the Ming–Qing period. Changes in crop vegetation and the forest were all affected by human activity in the Lake Dian basin during the two periods, and were more evident during the Ming–Qing period. The heavy metal pollution in the soil was obvious during the Ming–Qing period. The increase in the intensity of human activity, especially the rise in population, could be attributed to changes in the hydrological environment in the Lake Dian basin during the Late Bronze Age and to geopolitical change during the Ming–Qing period. This study reveals the different patterns in human impact on the terrestrial environment in the Lake Dian basin during the Late Bronze Age and the Ming–Qing period, providing new evidence to enable a deeper understanding of past human–environment interactions on the Yunnan Plateau.

Background: Metastatic castration-resistant prostate cancer (mCRPC) is a highly aggressive stage of prostate cancer, and non-mutational epigenetic reprogramming plays a critical role in its progression. Super enhancers (SE), epigenetic elements, are involved in multiple tumor-promoting signaling pathways. However, the SE-mediated mechanism in mCRPC remains unclear.Methods: SE-associated genes and transcription factors were identified from a cell line (C4-2B) of mCRPC by the CUT&Tag assay. Differentially expressed genes (DEGs) between mCRPC and primary prostate cancer (PCa) samples in the GSE35988 dataset were identified. What’s more, a recurrence risk prediction model was constructed based on the overlapping genes (termed SE-associated DEGs). To confirm the key SE-associated DEGs, BET inhibitor JQ1 was applied to cells to block SE-mediated transcription. Finally, single-cell analysis was performed to visualize cell subpopulations expressing the key SE-associated DEGs.Results: Nine human TFs, 867 SE-associated genes and 5417 DEGs were identified. 142 overlapping SE-associated DEGs showed excellent performance in recurrence prediction. Time-dependent receiver operating characteristic (ROC) curve analysis showed strong predictive power at 1 year (0.80), 3 years (0.85), and 5 years (0.88). The efficacy of his performance has also been validated in external datasets. In addition, FKBP5 activity was significantly inhibited by JQ1.Conclusion: We present a landscape of SE and their associated genes in mCPRC, and discuss the potential clinical implications of these findings in terms of their translation to the clinic.

Abstract Solid‐state Li–air batteries with ultrahigh energy density and safety are promising for long‐range electric vehicles and special electronics. However, the challenging issues of developing Li–air battery‐oriented solid‐state electrolytes (SSEs) with high ionic conductivity, interfacial compatibility, and stability to boost reversibility, increase stable triple‐phase boundaries, and protect the Li anode in an open system substantially impede their applications. Herein, we systematically summarize the recent progress achieved in terms of SSEs for Li–air batteries, and describe in detail the basic characteristics of SSE|air cathode interfaces and SSE|Li anode interfaces. First, the major characteristics of SSEs in Li–air batteries in terms of ionic/electronic conductivity, chemical/electrochemical/thermal stability, mechanical strength, and interfacial compatibility are briefly introduced according to three types of SSEs: inorganic, organic, and hybrid SSEs. Second, key strategies of integrating catalytic sites, porous structures, and electronic conductors with SSEs to enhance triple‐phase boundaries at the SSE|air cathode for improving Coulombic efficiency are described in detail. Moreover, the protection of Li metal from H2O, CO2, O2, and redox mediators at the SSE|Li anode to ensure safety is elaborately overviewed. Finally, future opportunities and perspectives on three important topics of three‐dimensional structural integration, external field assistance, and operando characterizations are proposed for advanced solid‐state Li–air batteries.

Rice (Oryza sativa L.) is one of the world’s most crucial food crops, as it currently supports more than half of the world’s population. However, the presence of sheath blight (SB) caused by Rhizoctonia solani has become a significant issue for rice agriculture. This disease is responsible for causing severe yield losses each year and is a threat to global food security. The breeding of SB-resistant rice varieties requires a thorough understanding of the molecular mechanisms involved and the exploration of immune genes in rice. To this end, we conducted a screening of rice cultivars for resistance to SB and compared the transcriptome based on RNA-seq between the most tolerant and susceptible cultivars. Our study revealed significant transcriptomic differences between the tolerant cultivar ZhengDao 22 (ZD) and the most susceptible cultivar XinZhi No.1 (XZ) in response to R. solani invasion. Specifically, the tolerant cultivar showed 7066 differentially expressed genes (DEGs), while the susceptible cultivar showed only 60 DEGs. In further analysis, we observed clear differences in gene category between up- and down-regulated expression of genes (uDEGs and dDEGs) based on Gene Ontology (GO) classes in response to infection in the tolerant cultivar ZD, and then identified uDEGs related to cell surface pattern recognition receptors, the Ca2+ ion signaling pathway, and the Mitogen-Activated Protein Kinase (MAPK) cascade that play a positive role against R. solani. In addition, DEGs of the jasmonic acid and ethylene signaling pathways were mainly positively regulated, whereas DEGs of the auxin signaling pathway were mainly negatively regulated. Transcription factors were involved in the immune response as either positive or negative regulators of the response to this pathogen. Furthermore, our results showed that chloroplasts play a crucial role and that reduced photosynthetic capacity is a critical feature of this response. The results of this research have important implications for better characterization of the molecular mechanism of SB resistance and for the development of resistant cultivars through molecular breeding methods.

Abstract Background We show previously that three-dimensional (3D) spheroid cultured mesenchymal stem cells (MSCs) exhibit reduced cell size thus devoid of lung entrapment following intravenous (IV) infusion. In this study, we determined the therapeutic effect of 3D-cultured MSCs on ischemic stroke and investigated the mechanisms involved. Methods Rats underwent middle cerebral artery occlusion (MCAO) and reperfusion. 1 × 106 of 3D- or 2D-cultured MSCs, which were pre-labeled with GFP, were injected through the tail vain three and seven days after MCAO. Two days after infusion, MSC engraftment into the ischemic brain tissues was assessed by histological analysis for GFP-expressing cells, and infarct volume was determined by MRI. Microglia in the lesion were sorted and subjected to gene expressional analysis by RNA-seq. Results We found that infusion of 3D-cultured MSCs significantly reduced the infarct volume of the brain with increased engraftment of the cells into the ischemic tissue, compared to 2D-cultured MSCs. Accordingly, in the brain lesion of 3D MSC-treated animals, there were significantly reduced numbers of amoeboid microglia and decreased levels of proinflammatory cytokines, indicating attenuated activation of the microglia. RNA-seq of microglia derived from the lesions suggested that 3D-cultured MSCs decreased the response of microglia to the ischemic insult. Interestingly, we observed a decreased expression of mincle, a damage-associated molecular patterns (DAMPs) receptor, which induces the production of proinflammatory cytokines, suggestive of a potential mechanism in 3D MSC-mediated enhanced repair to ischemic stroke. Conclusions Our data indicate that 3D-cultured MSCs exhibit enhanced repair to ischemic stroke, probably through a suppression to ischemia-induced microglial activation.

Abstract Background The exact animal origin of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) remains obscure and understanding its host range is vital for preventing interspecies transmission. Methods Herein, we applied single‐cell sequencing to multiple tissues of 20 species (30 data sets) and integrated them with public resources (45 data sets covering 26 species) to expand the virus receptor distribution investigation. While the binding affinity between virus and receptor is essential for viral infectivity, understanding the receptor distribution could predict the permissive organs and tissues when infection occurs. Results Based on the transcriptomic data, the expression profiles of receptor or associated entry factors for viruses capable of causing respiratory, blood, and brain diseases were described in detail. Conserved cellular connectomes and regulomes were also identified, revealing fundamental cell‐cell and gene‐gene cross‐talks from reptiles to humans. Conclusions Overall, our study provides a resource of the single‐cell atlas of the animal kingdom which could help to identify the potential host range and tissue tropism of viruses and reveal the host‐virus co‐evolution.

Abstract Ustilaginoidea virens, the causal agent of rice false smut, is an economically important filamentous fungal pathogen. A high-quality reference genome of U. virens promotes understanding of molecular mechanisms underlying its virulence and pathogenicity. Here, we report the first chromosome-level assembly of U. virens genome consisting of seven chromosomes ranging from 2.4 to 7.5 Mb. The assembly has dramatic improvements over previous assemblies, including considerably longer contigs, higher proportion of repetitive elements and more functionally annotated genes. Phylogenetic analyses revealed an extremely low intraspecific sequence divergence in U. virens. By contrast, intraspecific genome comparisons uncovered dynamic genomic alterations including massive structural variations and widespread lineage-specific regions (LSRs) among U. virens strains, which were mainly generated by recent burst of retrotransposons. Genomic plasticity created by structural variations and LSRs might drive rapid evolution of U. virens. High-quality mitochondrial genomes of eight U. virens strains exhibit size variations from 94 to 102 kb. Consistently, U. virens contains conserved lengths of exons and highly dynamic mobile introns, which contribute to intraspecific size variations due to gain/loss of homing endonuclease genes. This study highlights unique characteristics in nuclear and mitochondrial genomic divergence and provides new insights into genomic and mitochondrial evolution of U. virens.

Abstract Background Immune cells play important roles in mediating immune response and host defense against invading pathogens. However, insights into the molecular mechanisms governing circulating immune cell diversity among multiple species are limited. Methods In this study, we compared the single‐cell transcriptomes of immune cells from 12 species. Distinct molecular profiles were characterized for different immune cell types, including T cells, B cells, natural killer cells, monocytes, and dendritic cells. Results Our data revealed the heterogeneity and compositions of circulating immune cells among 12 different species. Additionally, we explored the conserved and divergent cellular crosstalks and genetic regulatory networks among vertebrate immune cells. Notably, the ligand and receptor pair VIM‐CD44 was highly conserved among the immune cells. Conclusions This study is the first to provide a comprehensive analysis of the cross‐species single‐cell transcriptome atlas for peripheral blood mononuclear cells (PBMCs). This research should advance our understanding of the cellular taxonomy and fundamental functions of PBMCs, with important implications in evolutionary biology, developmental biology, and immune system disorders.

Ustilaginoidea virens, the causal agent of rice false smut (RFS), has become one of the most devastating rice pathogens worldwide. As a group of essential virulence factors, the effectors in the filamentous fungus might play central roles in the interaction between plants and pathogens. However, little is known about the roles of individual effectors in U. virens virulence. In this study, we identified and characterized a small secreted cysteine-rich effector, SCRE2, in U. virens. SCRE2 was first confirmed as an effector through yeast secretion, protein localization and translocation assays, as well as its expression pattern during U. virens infection. Transient expression of SCRE2 in Nicotiana benthamiana suppressed necrosis-like defense symptoms triggered by the mammalian BAX and oomycete elicitin INF1 proteins. The ability of SCRE2 to inhibit immunity-associated responses in N. benthamiana, including elicitor-triggered cell death and oxidative burst, is further defined to a small peptide region SCRE268-85 through expressing a series of truncated proteins. Convincingly, ectopic expression of SCRE2 in the transgenic rice cells significantly inhibited pathogen-associated molecular pattern-triggered immunity including flg22- and chitin-induced defense gene expression and oxidative burst. Furthermore, the scre2 knockout mutant generated by the CRISPR/Cas9 system greatly attenuated in U. virens virulence to rice. Collectively, this study indicates that the effector SCRE2 is able to inhibit plant immunity and is required for full virulence of U. virens.

Background: In China, over 80% of all work-related deaths in the mining industry occur in coal mines and human factors constitute 85% of the direct causes of coal mine accidents, which indicates that significant shortcomings cur-rently exist in the safety behavior management of Chinese coal mine workers. We aimed to verify the impact of human psychological behavior in coal mine accidents systematically through experimental study, theoretical analysis and man-agement application. Methods: Four test instruments (Sensory and cognitive capacity test, Sixteen-Personal Factor Questionnaire, Symp-tom Checklist 90 Questionnaire and the supervisors’ evaluation) were employed from November 2013 to June 2014 to identify unsafe behavior factors, the self-established Questionnaire of Safety Behavior Norms (QSBN) was also used to propose the safety behavior countermeasures of coal mine employees. Results: The mental health of most coal mine workers’ is relatively poor. The sensory and cognitive capacity of those in different work posts varies greatly, as does the sense of responsibility. Workers are susceptible to external influ-ences, and score low in site management. When the 16-PF and SCL-90 sensory and cognitive assessments were com-bined, the psychological index predictive power was greatest for estimating sense of efficiency and degree of satisfac-tion in internal evaluations, while at the same time lowest for estimating control of introversion-extroversion and stress character. Conclusion: The psychological indicators can predict part of employee safety behavior, and assist a coal mine enter-prise to recruit staff, develop occupational safety norms and improve the working environment.

Terrain plays a critical role in the selection of cropland. As a physical and geographical element of the landscape, terrain is an important limiting factor in land use change and has a strong influence on human activities. The objectives of this study are to investigate the topographic characteristics of cropland-related transformations in China during the first decade of the 21st century and to explore the implications of land use change as it relates to securing a national food supply. A 2010 satellite-based land use dataset and the DEM data were used to conduct spatial statistical analysis using altitude, slope, and fragmentation data. The results showed the following. (1) As the urbanization and industrialization of China occur, and China attempts to replace this occupied cropland with newly reclaimed cropland, the topography of the most recently reclaimed cropland has been more poorly suited to farming than the topography of the occupied cropland it replaces in most provinces. (2) The area of occupied cropland was much larger than of those reclaimed; the qualities of occupied and reclaimed cropland were significantly different. (3) Land reclamation mainly occurred in northern China, instead of in southern China, which has a higher level of economic development. Our findings imply that the potential area available for cropland production may be limited.