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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao key laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity Ocean University of China Marine College Shandong University Zoology Department College of ScienceKing Saud University Department of biology Bradley University laboratory for Marine biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University key laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang key laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine key laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Interannual variability of boreal summer intraseasonal oscillation over the northwestern Pacific influenced by the Pacific Meridional Mode

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Atmospheric and Oceanic Science Letters 2025年第1期18卷 6-11页

作者： Haoyu Zhou Pang-Chi Hsu Lin Chen Yitian Qian key laboratory of Meteorological Disaster Ministry of Education/Joint International Research Laboratory of Climate and Environmental Change/Collaborative Innovation Center on Forecast and Evaluation of Meteorological DisastersNanjing University of Information Science and TechnologyNanjingChina

During the boreal summer,intraseasonal oscillations exhibit significant interannual variations in intensity over two key regions:the central-western equatorial Pacific(5°S-5°N,150°E-150°W)and the subtropical Northwestern Pacific(10°-20°N,130°E-175°W).The former is well-documented and considered to be influenced by the ENSO,while the latter has received comparatively less attention and is likely influenced by the Pacific Meridional Mode(PMM),as suggested by partial correlation analysis *** elucidate the physical processes responsible for the enhanced(weakened)intraseasonal convection over the subtropical northwestern Pacific during warm(cold)PMM years,the authors employed a moisture budget *** findings reveal that during warm PMM years,there is an increase in summer-mean moisture over the subtropical northwestern *** increase interacts with intensified vertical motion perturbations in the region,leading to greater vertical moisture advection in the lower troposphere and consequently resulting in convective *** a process is pivotal in amplifying intraseasonal convection *** observational findings were further verified by model experiments forced by PMM-like sea surface temperature patterns.

关键词： Boreal summer intraseasonal oscillation Interannual variability Pacific Meridional Mode Moisture budget analysis

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Small modifications of endo-functionalized cavities lead to large changes in molecular interaction in water

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Science China Chemistry 2025年第1期 369-376页

作者： Song-Meng Wang Hao Nian Yan-Fang Wang Li-Shuo Zheng Yu-Tao Zheng Yi-Wei Dong Liping Huang Xiaoping Wang Wei Jiang Liu-Pan Yang Department of Chemistry Southern University of Science and Technology School of Chemistry and Pharmaceutical Sciences State Key Laboratory for Chemistry and Molecular Engineering of Medicinal ResourcesGuangxi Normal University School of Pharmaceutical Science Hengyang Medical School University of South China

Studying molecular recognition in aqueous environments is crucial for understanding biological processes. Herein, we present a series of N-doped endo-functionalized anthracene-based cavities by introducing inward-directed pyridine units. The subtle modifications can significantly affect the binding properties of these receptors, which is similar to the mutations in biological systems. Combining theoretical calculations and molecular recognition experiments demonstrated that these “mutations” have an impact on the hydrophobicity and charge distribution of the hosts, consequently significantly influencing molecular *** is crucial for understanding the intricate mechanisms of molecular-level interactions in biological receptors.

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Advancements and Challenges in Organic–Inorganic Composite Solid Electrolytes for All‑Solid‑State Lithium Batteries

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Nano-Micro Letters 2025年第1期17卷 46-97页

作者： Xueyan Zhang Shichao Cheng Chuankai Fu Geping Yin Liguang Wang Yongmin Wu Hua Huo State key laboratory of Space Power‑Sources School of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbin 150001People’s Republic of China College of Chemical and biological Engineering Zhejiang UniversityHangzhou 310058People’s Republic of China State key laboratory of Space Power-Sources 2965 Dongchuan RoadMinhang DistrictShanghai 200240People’s Republic of China

To address the limitations of contemporary lithium-ion batteries,particularly their low energy density and safety concerns,all-solid-state lithium batteries equipped with solid-state electrolytes have been identified as an up-and-coming *** the various SEs,organic–inorganic composite solid electrolytes(OICSEs)that combine the advantages of both polymer and inorganic materials demonstrate promising potential for large-scale ***,OICSEs still face many challenges in practical applications,such as low ionic conductivity and poor interfacial stability,which severely limit their *** review provides a comprehensive overview of recent research advancements in ***,the influence of inorganic fillers on the main functional parameters of OICSEs,including ionic conductivity,Li+transfer number,mechanical strength,electrochemical stability,electronic conductivity,and thermal stability are systematically *** lithium-ion conduction mechanism of OICSE is thoroughly analyzed and concluded from the microscopic ***,the classic inorganic filler types,including both inert and active fillers,are categorized with special emphasis on the relationship between inorganic filler structure design and the electrochemical performance of ***,the advanced characterization techniques relevant to OICSEs are summarized,and the challenges and perspectives on the future development of OICSEs are also highlighted for constructing superior ASSLBs.

关键词： Composite solid electrolytes Inorganic filler Interfacial stability Li-ion conduction mechanism Characterization techniques

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Single-cell technologies: current and near future

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Science China Life Sciences 2025年第01期 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi key laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University National key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University key laboratory of Advanced Theory and Application in Statistics and Data Science (MOE) School of StatisticsEast China Normal University

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity, tissue organization, and overall organism function(Sun et al.,2024). In 2009, single-cell RNA sequencing(sc RNA-seq) was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology, single-cell approaches have expanded to encompass other omics, such as genomics, epigenomics, proteomics,and metabolomics.

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ImSpiRE: image feature-aided spatial resolution enhancement method

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Science China Life Sciences 2025年第1期 272-283页

作者： Yuwei Hua Yizhi Zhang Zhenming Guo Shan Bian Yong Zhang State key laboratory of Cardiovascular Diseases and Medical Innovation Center Institute for Regenerative MedicineDepartment of NeurosurgeryShanghai East HospitalShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji University

The resolution of most spatially resolved transcriptomic technologies usually cannot attain the single-cell level, limiting their applications in biological discoveries. Here, we introduce ImSpiRE, an image feature-aided spatial resolution enhancement method for in situ capturing spatial transcriptome. Taking the information stored in histological images, ImSpiRE solves an optimal transport problem to redistribute the expression profiles of spots to construct new transcriptional profiles with enhanced resolution, together with extending the gene expression profiles into unmeasured regions. Applications to multiple datasets confirm that ImSpiRE can enhance spatial resolution to the subspot level while contributing to the discovery of tissue domains, signaling communication patterns, and spatiotemporal characterization.

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Fine-tuning the spatial allocation of phytohormones for smart canopy, smart breeding, and smart agriculture

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Science China Life Sciences 2025年第1期 309-310页

作者： Tao Zhou Lin Li National key laboratory of Crop Genetic Improvement Huazhong Agricultural University HuBei HongShan laboratory

The dual challenges of global climate change and population growth have increased demand for higher crop yields per unit area. The innovative technology of smart agriculture aims to synergize breeding, cultivation, and production through the application of biological and informatics technologies. Historically, the “Green Revolution” introduced semidwarf varieties of certain key crops by utilizing mutations affecting gibberellin pathways, which significantly increased planting densities and yields.

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Passive activity enhances residual control ability in patients with complete spinal cord injury

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Neural Regeneration Research 2025年第8期20卷 2337-2347页

作者： Yanqing Xiao Mingming Gao Zejia He Jia Zheng Hongming Bai Jia-Sheng Rao Guiyun Song Wei Song Xiaoguang Li Beijing key laboratory for Biomaterials and Neural Regeneration Beijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringBeihang UniversityBeijingChina Department of Rehabilitation Evaluation China Rehabilitation Research CenterBeijingChina Cardiac Center Beijing Children’s HospitalCapital Medical UniversityBeijingChina The State key laboratory of Virtual Reality technology and Systems Beihang UniversityBeijingChina Department of Rehabilitation Engineering China Rehabilitation Science InstituteBeijingChina

Patients with complete spinal cord injury retain the potential for volitional muscle activity in muscles located below the spinal injury ***,because of prolonged inactivity,initial attempts to activate these muscles may not effectively engage any of the remaining neurons in the descending pathway.A previous study unexpectedly found that a brief clinical round of passive activity significantly increased volitional muscle activation,as measured by surface *** this study,we further explored the effect of passive activity on surface electromyographic signals during volitional control tasks among individuals with complete spinal cord *** patients with chronic complete thoracic spinal cord injury were *** electromyography data from eight major leg muscles were acquired and compared before and after the passive activity *** results indicated that the passive activity led to an increased number of activated volitional muscles and an increased frequency of *** the cumulative root mean square of surface electromyography amplitude for volitional control of movement showed a slight increase after passive activity,the difference was not statistically *** findings suggest that brief passive activity may enhance the ability to initiate volitional muscle activity during surface electromyography tasks and underscore the potential of passive activity for improving residual motor control among patients with motor complete spinal cord injury.

关键词： complete spinal cord injury cycle training epidural electrical stimulation motor training passive activity physiological state spinal cord circuit surface electromyography volitional control task

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A surface engineering strategy for the stabilization of zinc metal anodes with montmorillonite layers toward long-life rechargeable aqueous zinc ion batteries

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Journal of Energy Chemistry 2025年第1期100卷 94-105页

作者： Wenbo Wang Ruifeng Xu Xu Zhang Peiyu Wang Bao Yang Bingjun Yang Juan Yang Kailimai Su Pengjun Ma Yanan Deng Xianfeng Fan Wanjun Chen key laboratory for Electronic Materials College of Electrical Engineering Northwest Minzu University Resource Chemistry and Energy Materials Research Center State Key Laboratory of Solid Lubrication Lanzhou Institute of Chemical Physics Chinese Academy of Sciences University of Chinese Academy of Sciences Institute for Materials and Processes School of Engineering University of Edinburgh

Rechargeable aqueous zinc-ion batteries （AZIBs） exhibit appreciable potential in the domain of electrochemical energy ***,there are serious challenges for AZIBs,for instance zinc dendrite growth,hydrogen evolution reaction （HER）,and corrosion side ***,we propose a surface engineering modification strategy for coating the montmorillonite （MMT） layer onto the surface of the Zn anode to tackle these issues,thereby achieving high cycling stability for rechargeable *** results reveal that the MMT layer on the surface of the Zn anode is able to provide ordered zincophilic channels for zinc ions migration,facilitating the reaction kinetics of zinc *** functional theory（DFT） calculations and water contact angle （CA） tests prove that MMT@Zn anode exhibits superior adsorption capacity for Zn2+and better hydrophobicity than the bare Zn anode,thereby achieving excellent cycling ***,the MMT@Zn||MMT@Zn symmetric cell holds the stable cycling over 5600 h at 0.5 mA cm-2and 0.125 m A h cm-2,even exceeding 1800 h long cycling under harsh conditions of 5 m A cm-2and 1.25 m A h *** MMT@Zn||V2O5full cell reaches over 3000 cycles at 2 A g-1with excellent rate ***,this surface engineering modification strategy for enhancing the electrochemical performance of AZIBs represents a promising application.

关键词： Surface engineering strategy Montmorillonite layer Protection mechanism of Zn anode Cycling stability Aqueous zinc ion batteries

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