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

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)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** 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 *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** 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 scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** 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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Akkermansia muciniphila isolated from forest musk deer ameliorates diarrhea in mice via modification of gut microbiota

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Animal Models and Experimental Medicine 2025年第2期8卷 295-306页

作者： Yan Deng Yan Wang Ying Liu Xiaoli Yang Hai Zhang Xiaochang Xue Yi Wan Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry College of Life SciencesShaanxi Normal UniversityXi'anChina Shaanxi Institute of Microbiology Xi'anChina NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology Shaanxi Institute for Food and Drug ControlXi'anChina Department of Cell Biology National Translational Science Center for Molecular MedicineFourth Military Medical UniversityXi'anChina

Background:The forest musk deer,a rare fauna species found in China,is famous for its musk secretion which is used in selected Traditional Chinese ***,over-hunting has led to musk deer becoming an endangered species,and their survival is also greatly challenged by various high incidence and high mortality respiratory and intestinal diseases such as septic pneumonia and *** evidence has demonstrated that Akkermannia muciniphila(AKK)is a promising probiotic,and we wondered whether AKK could be used as a food additive in animal breeding pro-grammes to help prevent intestinal ***:We isolated one AKK strain from musk deer feces(AKK-D)using an im-proved enrichment medium combined with real-time *** confirmation by 16S rRNA gene sequencing,a series of in vitro tests was conducted to evaluate the probiotic effects of AKK-D by assessing its reproductive capability,simulated gas-trointestinal fluid tolerance,acid and bile salt resistance,self-aggregation ability,hy-drophobicity,antibiotic sensitivity,hemolysis,harmful metabolite production,biofilm formation ability,and bacterial adhesion to gastrointestinal ***:The AKK-D strain has a probiotic function similar to that of the standard strain in humans(AKK-H).An in vivo study found that AKK-D significantly amelio-rated symptoms in the enterotoxigenic Escherichia coli(ETEC)-induced murine diar-rhea ***-D improved organ damage,inhibited inflammatory responses,and improved intestinal barrier ***,AKK-D promoted the reconsti-tution and maintenance of the homeostasis of gut microflora,as indicated by the fact that AKK-D-treated mice showed a decrease in Bacteroidetes and an increase in the proportion of other beneficial bacteria like Muribaculaceae,Muribaculum,and unclas-sified f_Lachnospiaceae compared with the diarrhea model ***:Taken together,our data show that this novel AKK-D strain might be a potential probiotic for use in mus

关键词： Akkermansia muciniphila diarrhea enterotoxigenic Escherichia coli forest musk deer gut microbiota

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Structural analysis of a neutral polysaccharide ATP-1 from the red seaweed Asparagopsis taxiformis and its immunomodulatory effects on RAW264.7 macrophages

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Food science and Human Wellness 2025年

作者： Kun Yang Baojun Xu Wei Hu Yifan Tang Amy Hui-Mei Lin Saiyi Zhong College of Food Science and Technology， Guangdong Ocean University， Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety，Guangdong Province Engineering Laboratory for Marine Biological Products， Guangdong Provincial Engineering Technology Research Center of Seafood Guangdong Provincial Engineering Technology Research Center of Prefabricated Seafood Processing and Quality Control Food Science and Technology Program， Department of Life Sciences， BNU-HKBU United International College Singapore Institute of Food and Biotechnology Innovation (SIFBI) Shenzhen Research Institute， Guangdong Ocean University

As a seaweed supplement， the powdered， entire herb of Asparagopsis taxiformis can effectively promote immune response in animals. However， the active factors responsible for this effect are currently unknown. A novel polysaccharide， ATP-1， was isolated and purified from the red alga A. taxiformis， and its structural and immunomodulatory properties were determined. ATP-1 is a neutral polysaccharide with a molecular weight of 307.978 kDa and is primarily composed of galactose (94.07%)， glucose (1.27%)， and xylose (4.66%). Scanning electron microscopy and atomic force microscopy revealed that ATP-1 had an amorphous structure and was composed of molecular chain entanglement and intramolecular hydrogen bonding interactions. The microstructure of ATP-1 exhibited asymmetric sheet–like cracks and pores. Results from immunomodulatory activity showed that ATP-1 promoted inducible nitric oxide (NO) synthase and cyclooxygenase (COX)-2 protein expression in RAW264.7 macrophages， improved macrophage phagocytic ability， and stimulated cytokine production (NO， tumor necrosis factor [TNF]-α， and interleukin [IL]-6). Quantitative proteome analysis identified 178 differentially expressed proteins (70 upregulated and 108 downregulated) that were involved in various molecular pathways， among which， TNF was one of the 20 most common and significant signaling pathways in inflammation and immunoregulation. Western blotting indicated that ATP-1 significantly upregulated the expression of IKKα， IKKβ， COX-2， and TNF-α proteins in the TNF pathway. In contrast， ATP-1 downregulated the expression of IκBα， Fas， and AIPI. Results from molecular docking suggested that hydrogen bonding predominantly contributed to the affinity between TNF-α and galactose， glucose， and xylose. These findings indicated that ATP-1 may play an immunomodulatory role by activating the TNF signaling pathway. ATP-1 enhanced macrophage phagocytic capacity and stimulated the production of cytokines NO， TNF-α， and IL-6， thereb

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Microbial resources and interactions across three-dimensional space for a freshwater ecosystem

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science of the Total Environment 2025年 980卷 179522页

作者： Chu, Dongliang Zhang, Haohong Wang, Zhi Ning, Kang Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imaging Center of AI Biology Department of Bioinformatics and Systems Biology College of Life Science and Technology Huazhong University of Science and Technology Wuhan China Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan430077 China

Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems. © 2025 The Authors

关键词： Metagenomic Three-dimensional space Genome and gene catalog Microbial refuge

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Recent Advances in Wide-Range Temperature Metal-CO_(2)Batteries:A Mini Review

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Nano-Micro Letters 2025年第4期17卷 435-453页

作者： Xuejing Zhang Ning Zhao Hanqi Zhang Yiming Fan Feng Jin Chunsheng Li Yan Sun Jiaqi Wang Ming Chen Xiaofei Hu School of Environmental and Chemical Engineering Jiangsu University of Science and TechnologyZhenjiang 212003People’s Republic of China Engineering Research Center of Energy Storage Materials and Devices Ministry of EducationSchool of ChemistryXi’an Jiaotong UniversityXi’an 710049People’s Republic of China State Key Laboratory for Strength and Vibration of Mechanical Structures Xi’an Jiaotong UniversityXi’an 710049People’s Republic of China Key Laboratory of Advanced Electrode Materials for Novel Solar Cells for Petroleum and Chemical Industry of China School of Chemistry and Life SciencesSuzhou University of Science and TechnologySuzhou 215009People’s Republic of China Department of Chemistry and Biochemistry Northern Illinois UniversityDeKalbIL 60115USA School of Chemistry and Chemical Engineering Yangzhou UniversityYangzhou 225002People’s Republic of China

The metal-carbon dioxide batteries,emerging as high-energy-density energy storage devices,enable direct CO_(2)utilization,offering promising prospects for CO_(2)capture and utilization,energy conversion,and ***,the electrochemical performance of M-CO_(2)batteries faces significant challenges,particularly at extreme *** such as high overpotential,poor charge reversibility,and cycling capacity decay arise from complex reaction interfaces,sluggish oxidation kinetics,inefficient catalysts,dendrite growth,and unstable *** significant advancements at room temperature,limited research has focused on the performance of M-CO_(2)batteries across a wide-temperature *** review examines the effects of low and high temperatures on M-CO_(2)battery components and their reaction mechanism,as well as the advancements made in extending operational ranges from room temperature to extremely low and high *** discusses strategies to enhance electrochemical performance at extreme temperatures and outlines opportunities,challenges,and future directions for the development of M-CO_(2)batteries.

关键词： M-CO_(2)batteries Wide-range temperature Electrolytes Interfaces Electrode reactions

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Highly anticipated natural diterpenoids as an important source of new drugs in 2013-2023

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Chinese Chemical Letters 2025年第1期36卷 119-136页

作者： Yingjie Wang Peng Tang Wenchao Tu Qi Gao Cuizhu Wang Luying Tan Lixin Zhao Hongye Han Liefeng Ma Kouharu Otsuki Weilie Xiao Wenli Wang Jinping Liu Yong Li Zhajun Zhan Wei Li Xianli Zhou Ning Li School of Traditional Chinese Materia Medica Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning provinceKey Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang CityShenyang Pharmaceutical UniversityShenyang 110016China Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of EducationYunnan Characteristic Plant Extraction LaboratoryYunnan Key Laboratory of Research and Development for Natural ProductsSchool of Pharmacy and School of Chemical Science and TechnologyState Key Laboratory for Conservation and Utilization of Bio-Resources in YunnanYunnan UniversityKunming 650091China School of Pharmacy Nantong UniversityNantong 226001China School of Pharmaceutical Sciences Jilin UniversityChangchun 130021China State Key Laboratory of Bioactive Substance and Function of Natural Medicines Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China College of Pharmaceutical Sciences Zhejiang University of TechnologyHangzhou 310014China Faculty of Pharmaceutical Sciences Toho UniversityFunabashiChiba 274-8510Japan School of Life Science and Engineering Southwest Jiaotong UniversityChengdu 610031China

This review covers the structures of diterpenoids,including chain(72),monocyclic(9),labdane-type(67),clerodane-type(127)abietane-type(716),ent-kaurane-type(89),grayanane-type(331),ingenanetype(55),tigliane-type(154),daphnane-type(237),and aconitine-type diterpene alkaloids(265)with rich biological activities reported in *** the drugs in clinical use or under clinical investigation of diterpenoids and leading compounds were summarized.

关键词： Natural diterpenoids Structures Bioactivities Druggability Leading compounds New drugs

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Visual Attention Graph

arXiv

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arXiv 2025年

作者： Yang, Kai-Fu Li, Yong-Jie MOE Key Laboratory for NeuroInformation School of Life Science and Technology University of Electronic Science and Technology of China Sichuan Chengdu610054 China University of Electronic Science and Technology of China Zhejiang Huzhou313001 China

Visual attention plays a critical role when our visual system executes active visual tasks by interacting with the physical scene. However, how to encode the visual object relationship in the psychological world of our brain deserves to be explored. In the field of computer vision, predicting visual fixations or scanpaths is a usual way to explore the visual attention and behaviors of human observers when viewing a scene. Most existing methods encode visual attention using individual fixations or scanpaths based on the raw gaze shift data collected from human observers. This may not capture the common attention pattern well, because without considering the semantic information of the viewed scene, raw gaze shift data alone contain high inter- and intra-observer variability. To address this issue, we propose a new attention representation, called Attention Graph, to simultaneously code the visual saliency and scanpath in a graph-based representation and better reveal the common attention behavior of human observers. In the attention graph, the semantic-based scanpath is defined by the path on the graph, while saliency of objects can be obtained by computing fixation density on each node. Systemic experiments demonstrate that the proposed attention graph combined with our new evaluation metrics provides a better benchmark for evaluating attention prediction methods. Meanwhile, extra experiments demonstrate the promising potentials of the proposed attention graph in assessing human cognitive states, such as autism spectrum disorder screening and age classification. © 2025, CC BY-NC-ND.

关键词： Diseases

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Quantitative evaluation of intensity fidelity of superresolution reconstruction for structured illumination microscopy

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Journal of Innovative Optical Health sciences 2025年第1期18卷 153-163页

作者： Yujun Tang Linbo Wang Gang Wen Hui Li School of Biomedical Engineering(Suzhou)Division of Life Sciences and Medicine University of Science and Technology of China Suzhou 230041 P.R.China Jiangsu Key Laboratory of Medical Optics Suzhou Institute of Biomedical Engineering and Technology Chinese Academy of Sciences Suzhou 215163P.R.China Laboratory of Advanced Theranostic Materials and Technology Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo 315201 P.R.China

Super-resolution structured illumination microscopy(SR-SIM)relies heavily on post-processing reconstruction to obtain high-quality SR images from raw *** many SIM reconstruction algorithms have been developed to recover fine cellular structures with high fidelity even from the noisy data,whether the pixel intensities of reconstructed SR images are still proportional to the original fluorescence intensity has been less *** linearity between the intensity before and after reconstruction is de fined as the intensity ***,we proposed a method to evaluate the reconstructed SR image intensity fidelity at different spatial *** the proposed metric,we systematically investigated the impact of the key factors on the intensity fidelity in the standard Wiener-SIM reconstructions with simulated data,then evaluated the intensity fidelity of the SR images reconstructed by representative open-source *** work provides a reference for SR-SIM image intensity fidelity improvement.

关键词： Structured illumination microscopy super-resolution image reconstruction intensity fidelity spectrum optimization

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Advances in nanocarriers for targeted drug delivery and controlled drug release

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Chinese Journal of Natural Medicines 2025年第5期23.0卷 513-528页

作者： Wang, Yuqian Huang, Renqi Feng, Shufan Mo, Ran State Key Laboratory of Natural Medicines Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases Center of Advanced Pharmaceuticals and Biomaterials School of Life Science and Technology China Pharmaceutical University Nanjing 211198 China

Nanocarrier-based drug delivery systems (nDDSs) present significant opportunities for improving disease treatment, offering advantages in drug encapsulation, solubilization, stability enhancement, and optimized pharmacokinetics and biodistribution. nDDSs, comprising lipid, polymeric, protein, and inorganic nanovehicles, can be guided by or respond to biological cues for precise disease treatment and management. Equipping nanocarriers with tissue/cell-targeted ligands enables effective navigation in complex environments, while functionalization with stimuli-responsive moieties facilitates site-specific controlled release. These strategies enhance drug delivery efficiency, augment therapeutic efficacy, and reduce side effects. This article reviews recent strategies and ongoing advancements in nDDSs for targeted drug delivery and controlled release, examining lesion-targeted nanomedicines through surface modification with small molecules, peptides, antibodies, carbohydrates, or cell membranes, and controlled-release nanocarriers responding to endogenous signals such as pH, redox conditions, enzymes, or external triggers like light, temperature, and magnetism. The article also discusses perspectives on future developments. © 2025 China Pharmaceutical University

关键词： Controlled release Drug delivery Nanocarrier Stimuli responsiveness Tissue targeting

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A high-resolution 20K SNP array for comprehensive genotyping and genetic mapping in Nicotiana tabacum L.

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The Crop Journal 2025年第2期13卷 630-635页

作者： Shizhou Yu Zhixiao Yang Jie Zhang Linggai Cao Jie Liu Peng Lu Jiemeng Tao Jufen Wan Qingdong Zeng Tenghang Xu Peijian Cao Jingjing Jin Xueliang Ren Molecular Genetics Key Laboratory of China Tobacco Guizhou Academy of Tobacco ScienceGuiyang 550081GuizhouChina Beijing Life Science Academy Beijing 102200China China Tobacco Gene Research Center Zhengzhou Tobacco Research Institute of CNTCZhengzhou 450001HenanChina State Key Laboratory for Crop Stress Resistance and High-Efficiency Production Northwest A&F UniversityYangling 712100ShaanxiChina College of Agronomy and Biotechnology Hebei Normal University of Science and TechnologyQinhuangdao 066004HebeiChina

Nicotiana tabacum(2n=4x=48),an economically important non-food crop and a model plant for genetic studies,faces challenges in efficient genotyping of novel *** address this,we developed the Ta-LD-SC,a 20K SNP Affymetrix Axiom array,based on resequencing data from 150 tobacco accessions.A total of 20,213 unique SNPs were carefully selected,achieving coverage of over 90%of the tobacco genome(Nitab4.5 and NtaSR1)with a uniform probe distribution,limiting density to no more than 5 SNPs per 200 *** array underwent extensive validation using 866 tobacco accessions(NP panel)and 288 F2 individuals from a cross between K326 and Oxford 26(GP panel).Performance metrics demonstrated its robustness,with high SNP call rates(93.6%-99.8%),a low technical error rate(<1%),and a superior PolyHighResolution SNP rate(79.79%)compared to other crop SNP *** structure analysis of the NP panel revealed two major introductions of foreign germplasm that have significantly influenced the genetic diversity of Chinese tobacco *** the array,a genome-wide association study(GWAS)identified 62 genes linked to eight agronomic traits,and a high-density genetic map encompassing 4553 SNPs across 6606.08 cM was *** Ta-LD-SC array provides a valuable tool for rapid,high-quality genotyping offering supporting marker annotations that may benefit genetic research and breeding of tobacco.

关键词： Cultivated tobacco SNP array Population structure Differentiation patterns Breeding and genetic improvement

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