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Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

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Zoological Research 2021年第6期42卷 692-709页

作者： mao-sen ye Jin-Yan Zhang Dan-Dan Yu Min Xu Ling Xu Long-Bao Lv Qi-Yun Zhu Yu Fan Yong-Gang Yao Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences&Yunnan Province KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common DiseasesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650204China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China National Resource Center for Non-Human Primates National Research Facility for Phenotypic&Genetic Analysis of Model Animals Primate Facility) Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650107China 4 State Key Laboratory of Veterinary Etiological BiologyLanzhou Veterinary Research InstituteChinese Academy of Agricultural SciencesLanzhouGansu 730046China

The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical *** reference genome annotation for both mRNA and long non-coding RNA(lncRNA)is crucial for developing animal models using this *** the current study,we collected a total of 234 high-quality RNA sequencing(RNA-seq)datasets and two long-read isoform sequencing(ISO-seq)datasets and improved the annotation of our previously assembled high-quality chromosomelevel tree shrew *** obtained a total of 3514 newly annotated coding genes and 50576 lncRNA *** also characterized the tissuespecific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated *** identified 144 tree shrew-specific gene families,including interleukin 6(IL6)and STT3 oligosaccharyltransferase complex catalytic subunit B(STT3B),which underwent significant changes in *** of the overall expression patterns in tissues and pathways across four species(human,rhesus monkey,tree shrew,and mouse)indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome ***,the newly annotated purine rich element binding protein A(PURA)gene and the STT3B gene family showed dysregulation upon viral *** updated version of the tree shrew genome annotation(KIZ version 3:TS_3.0)is available at http://*** and provides an essential reference for basic and biomedical studies using tree shrew animal models.

关键词： Tree shrew Genome annotation Transcriptome Gene family Virus infection

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GSNOR negatively regulates the NLRP3 inflammasome via S-nitrosation of MAPK14

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Cellular & Molecular Immunology 2024年第6期21卷 561-574页

作者： Qianjin Liu Lijin Jiao mao-sen ye Zhiyu Ma Jinsong Yu Ling-Yan Su Wei-Yin Zou Lu-Xiu Yang Chang Chen Yong-Gang Yao Key Laboratory of Genetic Evolution&Animal Models and Key Laboratory of Animal Models&Human Disease Mechanisms of Yunnan ProvinceKunming Institute of ZoologyChinese Academy of Sciences650201KunmingYunnanChina Kunming College of Life Science University of Chinese Academy of Sciences650204KunmingYunnanChina Key Laboratory of Biomacromolecules(CAS) National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences100101BeijingChina KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of Sciences650201KunmingYunnanChina National Research Facility for Phenotypic&Genetic Analysis of Model Animals(Primate Facility) National Resource Center for Non-Human PrimatesKunming Institute of ZoologyChinese Academy of Sciences650201KunmingChina

Hyperactivation of the NLRP3 inflammasome has been implicated in the pathogenesis of numerous ***,the precise molecular mechanisms that modulate the transcriptional regulation of NLRP3 remain largely *** this study,we demonstrated that S-nitrosoglutathione reductase(GSNOR)deficiency in macrophages leads to significant increases in the Nlrp3 and Il-1βexpression levels and interleukin-1β(IL-1β)secretion in response to NLRP3 inflammasome ***,in vivo experiments utilizing Gsnor^(−/−)mice revealed increased disease severity in both lipopolysaccharide(LPS)-induced septic shock and dextran sodium sulfate(DSS)-induced colitis ***,we showed that both LPS-induced septic shock and DSS-induced colitis were ameliorated in Gsnor^(−/−)Nlrp3^(−/−)double-knockout(DKO)***,GSNOR deficiency increases the S-nitrosation of mitogen-activated protein kinase 14(MAPK14)at the Cys211 residue and augments MAPK14 kinase activity,thereby promoting Nlrp3 and Il-1βtranscription and stimulating NLRP3 inflammasome *** findings suggested that GSNOR is a regulator of the NLRP3 inflammasome and that reducing the level of S-nitrosylated MAPK14 may constitute an effective strategy for alleviating diseases associated with NLRP3-mediated inflammation.

关键词： GSNOR S-nitrosation NLRP3 inflammasome MAPK14 Septic shock Colitis

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Chromosomal level assembly and population sequencing of the Chinese tree shrew genome

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Zoological Research 2019年第6期40卷 506-521页

作者： Yu Fan mao-sen ye Jin-Yan Zhang Ling Xu Dan-Dan Yu Tian-Le Gu Yu-Lin Yao Jia-Qi Chen Long-Bao Lv Ping Zheng Dong-Dong Wu Guo-Jie Zhang Yong-Gang Yao Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming Yunnan 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming Yunnan 650204China Kunming Primate Research Center of the Chinese Academy of Sciences Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China KIZ–CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Yunnan Key Laboratory of Animal Reproduction Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China

Chinese tree shrews (Tupaia belangeri chinensis) have become an increasingly important experimental animal in biomedical research due to their close relationship to primates. An accurately sequenced and assembled genome is essential for understanding the genetic features and biology of this animal. In this study, we used long-read single-molecule sequencing and high-throughput chromosome conformation capture (Hi-C) technology to obtain a high-qualitychromosome-scale scaffolding of the Chinese tree shrew genome. The new reference genome (KIZ version 2: TS_2.0) resolved problems in presently available tree shrew genomes and enabled accurate identification of large and complex repeat regions, gene structures, and species-specific genomic structural variants. In addition, by sequencing the genomes of six Chinese tree shrew individuals, we produced a comprehensive map of 12.8 M single nucleotide polymorphisms and confirmed that the major histocompatibility complex (MHC) loci and immunoglobulin gene family exhibited high nucleotide diversity in the tree shrew genome. We updated the tree shrew genome database (TreeshrewDB v2.0: http://***) to include the genome annotation information and genetic variations. The new high-quality reference genome of the Chinese tree shrew and the updated TreeshrewDB will facilitate the use of this animal in many different fields of research.

关键词： Tupaia belangeri Chromosomal level assembly genome Population sequencing Database

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Metal-organic framework(MOF)-derived selenidation strategy to prepare porous(Zn,Cu)CoSex micro/nanostructures for sodium-ion batteries

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Rare Metals 2022年第12期41卷 4104-4115页

作者： ye-mao Lin Hao-sen Fan Cai-Zhen Zhu Jian Xu College of Chemistry and Environmental Engineering Shenzhen UniversityShenzhen 518060China College of Materials Science and Metallurgy Engineering Guizhou UniversityGuiyang 550025China

Owning to the wide distribution,low cost,and similar chemical-electrochemical properties with lithium,sodium-ion batteries(SIBs) have attracted much attention during recent years and may have the potential to replace the commercial lithium-ion ***,facile and simple bottom-up approach has been rationally applied to fabricate carbon-encapsulated ZnSe@CoSe_(2)micro spheres and Cu_(2)Se@CoSe_(2)*** as-prepared ZnSe@-CoSe_(2)microspheres and Cu_(2)Se@CoSe_(2)nanocubes composites inherited the original structure of ZnCo-MOF and CuCo-MOF,***,both ZnSe@CoSe_(2)micro spheres and Cu_(2)Se@CoSe_(2)nanocubes delivered excellent electrochemical performance when presented as anode materials for *** ZnSe@CoSe2micro spheres and Cu_(2)Se@CoSe_(2)nanocubes electrode could display a long-term cycling stability with a reversible capacity of 525 and 423 mAh·g^(-1)at the current density of 1 A·g^(-1)after 500 cycles,***,even at a high current density of 5 A·g^(-1),ZnSe@CoSe_(2)microsphere could still maintain 520 mAh·g^(-1)after 500 cycles,demonstrating remarkable capacity and excellent cycling *** high performances were beneficial from the unique hollow and porous structure of ZnSe@CoSe_(2)microspheres and Cu_(2)Se@CoSe_(2)nanocubes derived from the precursor which facilitate the transport of sodium ions,contributing to high capacity,improved excellent cycle stability and rate capability.

关键词： Metal selenides Prussian blue analogue Sodium-ion batteries Metal-organic frameworks(MOF)

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Effect of cholesterol metabolism on hepatolithiasis

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World Journal of Gastroenterology 2025年第1期31卷 157-162页

作者： Lin Zheng Zi-Yu ye Jun-Ji Ma Department of Gastroenterology The Second Hospital of Hebei Medical UniversityHebei Key Laboratory of GastroenterologyHebei Institute of GastroenterologyHebei Clinical Research Center for Digestive DiseasesNo.215 Heping West RoadShijiazhuang 050000Hebei ProvinceChina

Surgical intervention is currently the primary treatment for hepatolithiasis;how-ever,some patients still experience residual stones and high recurrence rates after *** metabolism seems to play an important role in hepatoli-thiasis pathogenesis.A high cholesterol diet is one of the significant reasons for the increasing incidence of ***,regular diet and appropriate medical intervention are crucial measures to prevent hepatolithiasis and reduce recurrence rate after *** dietary cholesterol and drugs that increase cholesterol stone solubility are key therapeutic approaches in treating *** article discusses the cholesterol metabolic pathways related to the pathogenesis of hepatolithiasis,as well as food intake and targeted therapeutic drugs.

关键词： Hepatolithiasis Cholesterol metabolism High-fat diet 3-hydroxy-3-methylglutaryl-coenzyme A reductase Interlobular bile duct

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Three-dimensional fracture of UO2 ceramic pellets by phase field modeling

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 169-180页

作者： Wei Xiong Xuan ye Hongzhang Cheng Xiaoming Liu Institute of Nuclear and New Energy Technology Collaborative Innovation Center of Advanced Nuclear Energy Technology Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education Tsinghua University State Key Laboratory of Nonlinear Mechanics Institute of Mechanics Chinese Academy of Sciences School of Engineering Science University of Chinese Academy of Sciences

Fracture is the primary failure type for the UO2ceramic pellets,which are operated under irradiation and thermal processes,and physically confined by the *** this work,by combining closely coupled physical processes of heat conduction,heat transfer,and mechanical deformation with the cohesive phase field framework,we proposed a high-precision modeling of quasistatic cracking of three-dimensional （3D） UO2ceramic fuel pellets under high temperature and *** simulation results agree well with the experimental results,indicating that the proposed method has the potential to capture 3D crack modes in the interested time ***,we studied the relation of the 3D fracture patterns of fuel pellets with the peak power *** was found that the power level plays a critical role in determining the competition between radial and circumferential cracks,as well as transverse penetrating cracks.

关键词： phase field method nuclear fuel pellet coupled thermo-mechanical model thermal fracture

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Prussian Blue Analogue‑Templated Nanocomposites for Alkali‑Ion Batteries:Progress and Perspective

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Nano-Micro Letters 2025年第1期17卷 216-261页

作者： Jian‑En Zhou Yilin Li Xiaoming Lin Jiaye ye Key Laboratory of Theoretical Chemistry of Environment Ministry of EducationSchool of ChemistrySouth China Normal UniversityGuangzhou 510006People’s Republic of China School of Chemistry and Physics Faculty of ScienceQueensland University of Technology2 George StreetBrisbaneQLD 4000Australia Centre for Materials Science Queensland University of Technology2 George StreetBrisbaneQLD 4000Australia

Lithium-ion batteries(LIBs)have dominated the portable electronic and electrochemical energy markets since their commercialisation,whose high cost and lithium scarcity have prompted the development of other alkali-ion batteries(AIBs)including sodium-ion batteries(SIBs)and potassium-ion batteries(PIBs).Owing to larger ion sizes of Na^(+)and K^(+)compared with Li^(+),nanocomposites with excellent crystallinity orientation and well-developed porosity show unprecedented potential for advanced lithium/sodium/potassium *** enticing open rigid framework structures,Prussian blue analogues(PBAs)remain promising self-sacrificial templates for the preparation of various nanocomposites,whose appeal originates from the well-retained porous structures and exceptional electrochemical activities after thermal *** review focuses on the recent progress of PBA-derived nanocomposites from their fabrication,lithium/sodium/potassium storage mechanism,and applications in AIBs(LIBs,SIBs,and PIBs).To distinguish various PBA derivatives,the working mechanism and applications of PBA-templated metal oxides,metal chalcogenides,metal phosphides,and other nanocomposites are systematically evaluated,facilitating the establishment of a structure–activity correlation for these *** on the fruitful achievements of PBA-derived nanocomposites,perspectives for their future development are envisioned,aiming to narrow down the gap between laboratory study and industrial reality.

关键词： Prussian blue analogues Self-sacrificial template Lithium-ion batteries Sodium-ion batteries Potassium-ion batteries

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Real-time recognition of human lower-limb locomotion based on exponential coordinates of relative rotations

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Science China(Technological Sciences) 2021年第7期64卷 1423-1435页

作者： XU sen DING ye State Key Laboratory of Mechanical System and Vibration School of Mechanical EngineeringShanghai Jiao Tong UniversityShanghai200240China

This paper proposes a data-driven method using a parametric representation of relative rotations to classify human lower-limb locomotion, which is designed for wearable robots. Three Inertial measurement units(IMUs) are mounted on the subject's waist,left knee, and right knee, respectively. Features for classification comprise relative rotations, angular velocities, and waist acceleration. Those relative rotations are represented by the exponential coordinates. The rotation matrices are normalized by Karcher mean and then the Support Vector Machine(SVM) method is used to train the data. Experiments are conducted with a time-window size of less than 40 ms. Three SVM classifiers telling 3, 5 and 6 rough lower-limb locomotion types respectively are trained, and the average accuracies are all over 98%. With the combination of those rough SVM classifiers, an easy SVMbased ensembled-system is proposed to classify 16 fine locomotion types, achieving the average accuracy of 98.22%, and its latency is 18 ms when deployed to an onboard computer.

关键词： locomotion recognition exponential coordinate relative rotation support vector machine

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Netrin-1 signaling pathway mechanisms in neurodegenerative diseases

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Neural Regeneration Research 2025年第4期20卷 960-972页

作者： Kedong Zhu Hualong Wang Keqiang ye Guiqin Chen Zhaohui Zhang Department of Neurology Renmin Hospital of Wuhan UniversityWuhanHubei ProvinceChina Department of Neurology The First Hospital of Hebei Medical UniversityBrain Aging and Cognitive Neuroscience Laboratory of Heibei ProvinceShijiazhuangHebei ProvinceChina Faculty of Life and Health Sciences Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong ProvinceChina

Netrin-1 and its receptors play crucial roles in inducing axonal growth and neuronal migration during neuronal *** profound impacts then extend into adulthood to encompass the maintenance of neuronal survival and synaptic *** amounts of evidence highlight several key points:(1)Diminished Netrin-1 levels exacerbate pathological progression in animal models of Alzheimer’s disease and Parkinson’s disease,and potentially,similar alterations occur in humans.(2)Genetic mutations of Netrin-1 receptors increase an individuals’susceptibility to neurodegenerative disorders.(3)Therapeutic approaches targeting Netrin-1 and its receptors offer the benefits of enhancing memory and motor function.(4)Netrin-1 and its receptors show genetic and epigenetic alterations in a variety of *** findings provide compelling evidence that Netrin-1 and its receptors are crucial targets in neurodegenerative *** a comprehensive review of Netrin-1 signaling pathways,our objective is to uncover potential therapeutic avenues for neurodegenerative disorders.

关键词： Alzheimer’s disease axon guidance colorectal cancer Netrin-1 receptors Netrin-1 signaling pathways Netrin-1 neurodegenerative diseases neuron survival Parkinson’s disease UNC5C

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The burden of upper motor neuron involvement is correlated with the bilateral limb involvement interval in patients with amyotrophic lateral sclerosis:a retrospective observational study

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Neural Regeneration Research 2025年第5期20卷 1505-1512页

作者： Jieying Wu Shan ye Xiangyi Liu Yingsheng Xu Dongsheng Fan Department of Neurology Peking University Third HospitalBeijingChina Beijing Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases BeijingChina Key Laboratory for Neuroscience National Health Commission/Ministry of EducationPeking UniversityBeijingChina

Amyotrophic lateral sclerosis is a rare neurodegenerative disease characterized by the involvement of both upper and lower motor *** bilateral limb involvement significantly affects patients'daily lives and may lead them to be confined to ***,the effect of upper and lower motor neuron impairment and other risk factors on bilateral limb involvement is *** address this issue,we retrospectively collected data from 586 amyotrophic lateral sclerosis patients with limb onset diagnosed at Peking University Third Hospital between January 2020 and May 2022.A univariate analysis revealed no significant differences in the time intervals of spread in different directions between individuals with upper motor neuron-dominant amyotrophic lateral sclerosis and those with classic amyotrophic lateral *** used causal directed acyclic graphs for risk factor determination and Cox proportional hazards models to investigate the association between the duration of bilateral limb involvement and clinical baseline characteristics in amyotrophic lateral sclerosis *** factor analyses revealed that higher upper motor neuron scores(hazard ratio[HR]=1.05,95%confidence interval[CI]=1.01–1.09,P=0.018),onset in the left limb(HR=0.72,95%CI=0.58–0.89,P=0.002),and a horizontal pattern of progression(HR=0.46,95%CI=0.37–0.58,P<0.001)were risk factors for a shorter interval until bilateral limb *** results demonstrated that a greater degree of upper motor neuron involvement might cause contralateral limb involvement to progress more quickly in limb-onset amyotrophic lateral sclerosis *** findings may improve the management of amyotrophic lateral sclerosis patients with limb onset and the prediction of patient prognosis.

关键词： amyotrophic lateral sclerosis bilateral limb involvement Cox proportional hazards regression model horizontal spread restricted cubic spline analysis time interval upper motor neuron vertical spread

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