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Complicated evolutionary patterns of microRNAs in vertebrates

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Science China(Life Sciences) 2008年第6期51卷 552-559页

作者： WANG XiaoWo, ZHANG XueGong & LI YanDa moe key laboratory of bioinformatics and bioinformatics division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China moe key laboratory of bioinformatics and bioinformatics division TNLIST / Department of Automation Tsinghua University Beijing China

MicroRNAs (miRNAs) are a class of ～22 nt long endogenous non-coding RNAs that play important regulatory roles in diverse organisms. Up to now, little is known about the evolutionary properties of these crucial regulators. Most miRNAs were thought to be phylogenetically conserved, but recently, a number of poorly-conserved miRNAs have been reported and miRNA innovation is shown to be an ongoing process. In this work, through the characterization of an miRNA super family, we studied the evolutionary patterns of miRNAs in vertebrates. Recently generated miRNAs seem to evolve rapidly during a certain period following their emergence. Multiple lineage-specific expansions were observed. Homolgous premiRNAs may produce mature products from the opposite stem arms following tandem duplications, which may have important contribution to miRNA innovation. Our observations of miRNAs' complicated evolutionary patterns support the notion that these key regulatory molecules may play very active roles in evolution.

关键词： microRNA evolution miRNA:miRNA* interconversion lineage specific duplication

Interplant communication:an emerging battlefield in plant-aphid-virus interactions

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Science China(Life Sciences) 2024年第5期67卷 1069-1071页

作者： Yunjing Wang Qian Gong Yule Liu moe key laboratory of bioinformatics and Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China

Plants constantly face threats from various organisms,including pathogens and herbivores.Among the pathogens,plant viruses are obligate intracellular parasites that infect plants and cause serious crop yield losses.

关键词： plant Plants communication

NeoHunter:Flexible software for systematically detecting neoantigens from sequencing data

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Quantitative Biology 2024年第1期12卷 70-84页

作者： Tianxing Ma Zetong Zhao Haochen Li Lei Wei Xuegong Zhang moe key Lab of bioinformatics Bioinformatics Division of BNRIST and Department of AutomationTsinghua UniversityBeijingChina School of Medicine Tsinghua UniversityBeijingChina School of Life Sciences Tsinghua UniversityBeijingChina

Complicated molecular alterations in tumors generate various mutant peptides.Some of these mutant peptides can be presented to the cell surface and then elicit immune responses,and such mutant peptides are called neoantigens.Accurate detection of neoantigens could help to design personalized cancer vaccines.Although some computational frameworks for neoantigen detection have been proposed,most of them can only detect SNV-and indel-derived neoantigens.In addition,current frameworks adopt oversimplified neoantigen prioritization strategies.These factors hinder the comprehensive and effective detection of neoantigens.We developed NeoHunter,flexible software to systematically detect and prioritize neoantigens from sequencing data in different formats.NeoHunter can detect not only SNV-and indel-derived neoantigens but also gene fusion-and aberrant splicing-derived neoantigens.NeoHunter supports both direct and indirect immunogenicity evaluation strategies to prioritize candidate neoantigens.These strategies utilize binding characteristics,existing biological big data,and T-cell receptor specificity to ensure accurate detection and prioritization.We applied NeoHunter to the TESLA dataset,cohorts of melanoma and non-small cell lung cancer patients.NeoHunter achieved high performance across the TESLA cancer patients and detected 79%(27 out of 34)of validated neoantigens in total.SNV-and indel-derived neoantigens accounted for 90%of the top 100 candidate neoantigens while neoantigens from aberrant splicing accounted for 9%.Gene fusion-derived neoantigens were detected in one patient.NeoHunter is a powerful tool to‘catch all’neoantigens and is available for free academic use on Github(XuegongLab/NeoHunter).

关键词： cancer vaccine molecular alteration neoantigen neoantigen prioritization

Perspective on new cell-free DNA technologies for early cancer detection

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Cancer Biology & Medicine 2024年第2期21卷 139-143页

作者： Jie Li Xun Lan Department of Basic Medical Sciences School of MedicineTsinghua UniversityBeijing 100084China moe key laboratory of bioinformatics Tsinghua UniversityBeijing 100084China Tsinghua-Peking Joint Center for Life Sciences Tsinghua UniversityBeijing 100084China

High cancer heterogeneity and aggressiveness are major factors contributing to the poor prognosis of patients with advanced cancer~(1-5).Early detection of cancer can significantly improve the prognosis of patients with early-stage cancer after standard treatment.Although traditional cancer detection technologies,such as endoscopy for gastrointestinal cancer,mammography for breast cancer。

关键词： prognosis cancer patients

scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

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Journal of Genetics and Genomics 2024年第4期51卷 462-465页

作者： Zijing Gao Xiaoyang Chen Zhen Li Xuejian Cui Qun Jiang keyi Li Shengquan Chen Rui Jiang Ministry of Education key laboratory of bioinformatics Bioinformatics Division at the Beijing National Research Center for Information Science and TechnologyCenter for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China School of Mathematical Sciences and LPMC Nankai UniversityTianjin 300071China

Recent advances in single-cell sequencing technologies provide significant implications for understanding cellular heterogeneity,developmental biology,and disease mechanisms.To fully exploit the potential of these data,numerous tools have been proposed for upstream and downstream analyses.In the the single-cell RNA sequencing(scRNA-seq)community,scRNA-tools(Zappia et al.,2018)was proposed to help researchers navigate the plethora of tools by category.Since its inception,scRNA-tools has been widely used and its updated version further reveals trends in the field with over 1000 collected tools(Zappia and Theis,2021),providing a valuable guidance in selecting tools for analyses.

关键词： analytic selecting Tools

Optimizing magnetoelastic properties by machine learning and high-throughput micromagnetic simulation

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Rare Metals 2024年第5期43卷 2251-2262页

作者： Jian-Hu Gong Zheng-Ming Zhang Cheng-Liang Zhang Peng-Qiang Hu Chao Zhou Dun-Hui Wang Sen Yang division of Microelectronic Materials and Devices Hangzhou Dianzi University School of Physics MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter and State Key Laboratory for Mechanical Behavior of Materials Xi'an Jiaotong University National laboratory of Solid State Microstructures Nanjing University

Magnetoelastic couplings in giant magnetostrictive materials （GMMs） attract significant interests due to their extensive applications in the fields of spintronics and energy harvesting devices.Understanding the role of the selection of materials and the response to external fields is essential for attaining desired functionality of a GMM.Herein,machine learning （ML） models are conducted to predict saturation magnetostrictions （λs） in RFe2-type （R=rare earth） GMMs with different compositions.According to ML-predicted composition–λsrelations,it is discovered that the values ofλshigher than1100×10–6are almost situated in the composition space surrounded by 0.26≤x≤0.60 and 1.90≤y≤2.00 for the ternary compounds of TbxDy1-xFey.Assisted by ML predictions,the compositions are further narrowed down to the space surrounded by 0.26≤x≤0.32 and 1.92≤y≤1.97 for the excellent piezomagnetic （PM） performance in the TbxDy1-xFey-based PM device through our developed high-throughput （HTP） micromagnetic simulation（MMS） algorithm.Accordingly,high sensitivities up to10.22–13.61 m T·MPa–1are observed in the optimized range within which the available experimental data fall well.This work not only provides valuable insights toward understanding the mechanism of magnetoelastic couplings,but also paves the way for designing and optimizing highperformance magnetostrictive materials and PM sensing devices.

关键词： Magnetostriction Piezomagnetic effect Machine learning Micromagnetic simulation

Probing valence quark width of the proton in deeply virtual Compton scattering at high energies

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Chinese Physics C 2024年第5期48卷 235-243页

作者：向文昌曹德文周代翠 Physics division Guangzhou Maritime UniversityGuangzhou 510725China key laboratory of Quark and Lepton Physics(moe) and Institute of Particle PhysicsCentral China Normal UniversityWuhan 430079China

We use the refined hot spot model to study the valence quark shape of the proton with the deeply virtual Compton scattering at high energies in the color glass condensate framework.To investigate the individual valence quark shape,a novel treatment of the valence quark width is employed.We calculate the cross-sections for coherent and incoherent deeply virtual Compton scattering using,for the first time,different widths(Bu and Bd)for the profile density distributions of the up and down quarks instead of using the same width as in the literature.We find that the cross-sections calculated with Bu≥Bd at each collision energy are consistent with each other,which is in agreement with theoretical expectations,whereas those computed with Bu

关键词： gluon saturation physics color glass condensate proton shape fluctuations

Novel concept of nano-additive design:PTFE@silica Janus nanoparticles for water lubrication

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Friction 2024年第2期12卷 258-270页

作者： Yanfei LIU Hailing HE Meng YANG Ruize ZHANG Shengtao YU Tiantian YANG Wenzhong WANG Fuxin LIANG School of Mechanical Engineering Beijing Institute of TechnologyBeijing 100081China Institute of Polymer Science&Engineering Department of Chemical EngineeringTsinghua UniversityBeijing 100084China moe key laboratory of bioinformatics Center for Plant BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China College of Biological Sciences China Agricultural UniversityBeijing 100193China

Polytetrafluoroethylene(PTFE)has been widely used as a lubrication additive for reducing friction and wear;however,the hydrophobic nature of PTFE restricts its application in eco-friendly water-based lubrication systems.In this study,for the first time,we designed novel PTFE@silica Janus nanoparticles(JNs)to meet the requirement for additives in water-based lubricants,which have excellent dispersion stability in water attributed to the unique amphiphilic structure.By introducing the lubrication of the aqueous dispersion of the JNs with a concentration of 0.5 wt%,the coefficient of friction(COF)and wear volume were reduced by 63.8%and 94.2%,respectively,comparing to those with the lubrication of pure water.Meanwhile,the JNs suspension also exhibits better lubrication and wear-resistance performances comparing to commercial silica and PTFE suspensions.The excellent tribological behaviors of PTFE@silica JNs as nano-additives could be attributed to the synergetic effect of the two components,where the PTFE provided lubrication through the formed tribofilms on the friction pairs,and the rigid silica further enhanced the wear-resistance performance.Most importantly,the unique structure of JNs makes it possible to use PTFE as an additive in water-lubrication systems.Our study shed light on the design and application of novel JNs nanomaterials as additives to meet the requirements of future industrial applications.

关键词： Janus nanoparticles(JNs) polytetrafluoroethylene(PTFE) nano-additives friction lubrication

Plant virology in the 21st century in China:Recent advances and future directions

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Journal of Integrative Plant Biology 2024年第3期66卷 579-622页

作者： Jianguo Wu Yongliang Zhang Fangfang Li Xiaoming Zhang Jian Ye Taiyun Wei Zhenghe Li Xiaorong Tao Feng Cui Xianbing Wang Lili Zhang Fei Yan Shifang Li Yule Liu Dawei Li Xueping Zhou Yi Li State key laboratory for Ecological Pest Control of Fujian and Taiwan Crops Vector-borne Virus Research CenterCollege of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou 350002China State key laboratory of Plant Environmental Resilience and Ministry of Agriculture key laboratory of Soil Microbiology College of Biological SciencesChina Agricultural UniversityBeijing 100193China State key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China State key laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China State key laboratory of Plant Genomics Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China State key laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Department of Plant Pathology The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjing 210095China State key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Institute of Plant VirologyNingbo UniversityNingbo 315211China moe key laboratory of bioinformatics Center for Plant BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China State key laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China

Plant viruses are a group of intracellular pathogens that persistently threaten global food security.Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years,including basic research and technologies for preventing and controlling plant viral diseases.Here,we review these milestones and advances,including the identification of new crop-infecting viruses,dissection of pathogenic mechanisms of multiple viruses,examination of multilayered interactions among viruses,their host plants,and virus-transmitting arthropod vectors,and in-depth interrogation of plantencoded resistance and susceptibility determinants.Notably,various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants.We also recommend future plant virology studies in China.

关键词： China emerging plant viruses plant virology plant resistance/susceptibility to viral infection plant-virus transmission vector interactions plant virus-based vectors viral pathogenesis