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Complex Mutation and Weak Selection together Determined the Codon Usage Bias in Bryophyte Mitochondrial Genomes

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Journal of Integrative Plant Biology 2010年第12期52卷 1100-1108页

作者： Bin Wang Jing Liu Liang Jin Xue-Ying Feng jian-qun chen State Key Laboratory of Pharmaceutical Biotechnology Department of Biology Nanjing University Nanjing 210093 China

Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usage patterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright＇s Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to fine-tune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary, complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes.

关键词： Selection Nucleotide sequence Mutation Genomes Uses Forcing Plants Planting Wells Mitochondria

Increased complexity of gene structure and base composition in vertebrates

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Journal of Genetics and Genomics 2011年第7期38卷 297-305页

作者： Ying Wu Huizhong Yuan Shengjun Tan jian-qun chen Dacheng Tian Haiwang Yang State Key Laboratory of Pharmaceutical Biotechnology Department of Biology Nanjing University Nanjing 210093 China

How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals： human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3~ UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results. We also find that GC-content increased in many gene regions （especially 5＇ UTR） in the evolution of endotherms, except in coding-exons. Analysis of individual genomes shows that 3t UTR demonstrated stronger length and GC-content correlation with intron than 5~ UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes.

关键词： GC-content Gene structure Intron UTR Vertebrate Endotherm

Uncovering the dynamic evolution of nucleotidebinding site-leucine-rich repeat(NBS-LRR) genes in Brassicaceae

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Journal of Integrative Plant Biology 2016年第2期58卷 165-177页

作者： Yan-Mei Zhang Zhu-Qing Shao Qiang Wang Yue-Yu Hang Jia-Yu Xue Bin Wang jian-qun chen State Key Laboratory of Pharmaceutical Biotechnology Center of Plant Genetics and Molecular EvolutionSchool of Life SciencesNanjing University Institute of Botany Jiangsu Province and Chinese Academy of Sciences

Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat （NBS-LRR） genes; however, the long-term evolutionary history of these resistance genes has not been fully understood, This study focuses on five Brassicaceae genomes and the Carica papaya genome to explore changes in NBS-LRR genes that have taken place in this Rosid II lineage during the past 72 million years. Various numbers of NBS-LRR genes were identified from Arabidopsis lyrata （198）, A. thaliana （165）, Brassica rapa （204）, Capsella rubella （127）, Thellungiella salsuginea （88）, and C. papaya （51）. In each genome, the identified NBS-LRR genes were found to be unevenly distributed among chromosomes and most of them were clustered together. Phylogenetic analysis revealed that, before and after Brassicaceae speciation events, both toll/interleukin-1 receptor-NBS-LRR （TNL） genes and non-toll/interleukin-1 receptor-NBS-LRR （nTNL） genes exhibited a pattern of first expansion and then contraction, suggesting that both subclasses of NBS-LRR genes were responding to pathogen pressures synchronically. Further, by examining the gain/loss of TNL and nTNL genes at different evolutionary nodes, this study revealed that both events often occurred more drastically in TNL genes. Finally, the phylogeny of nTNL genes suggested that this NBS-LRR subclass is composed of two separate ancient gene types： RPW8-NBS-LRR and Coiled-coiI-N BS-LRR.

关键词： Dynamic evolution nucleotide-binding site-leucine-rich repeat gene phylogenetic relationship plant disease resistance

The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network

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Plant Communications 2023年第1期4卷 148-166页

作者： Zhen Zeng Yang Liu Xing-Yu Feng Sai-Xi Li Xing-Mei jiang jian-qun chen Zhu-Qing Shao State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China

Arbuscular mycorrhizal symbiosis(AMS)is an ancient plant-fungus relationship that is widely distributed in terrestrial *** formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous ***,the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly *** this study,a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato,an emerging AMS *** annotation of the tomato genome was improved by a multiple-platform sequencing strategy.A total of 3,174 protein-coding genes were upregulated during AMS,42%of which were alternatively ***-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant *** additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host ***,these orthogroups were absent or not induced in monocots and/or non-AMS hosts,suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory ***,we detected 587 lncRNAs,ten miRNAs,and 146 circRNAs that responded to AMS,which were incorporated to establish a tomato AMSresponsive,competing RNA-responsive endogenous RNA(ceRNA)***,a tomato symbiotic transcriptome database(TSTD,https://***/TSTD)was constructed to serve as a resource for deep deciphering of the AMS regulatory *** results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.

关键词： tomato RNAome landscape arbuscular mycorrhizal symbiosis evolution ceRNA network

An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion

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Molecular Plant 2021年第12期14卷 2015-2031页

作者： Yang Liu Zhen Zeng Yan-Mei Zhang Qian Li Xing-Mei jiang Zhen jiang Ji-Hong Tang Dijun chen Qiang Wang jian-qun chen Zhu-Qing Shao State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China jiangsu Key Laboratory for the Research and Utilization of Plant Resources Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjing 210014China

Nucleotide-binding leucine-rich-repeat(NLR)genes comprise the largest family of plant disease-resis-tance *** NLR genes are phylogenetically divided into the TNL,CNL,and RNL *** copy numbers and subclass composition vary tremendously across angiosperm ***,the evolutionary associations between genomic NLR content and ecological adaptation,or between NLR content and signal transduction components,are poorly characterized because of limited genome *** this study,we established an angiosperm NLR atlas(ANNA,https://***/ANNA/)that includes NLR genes from over 300 angiosperm *** ANNA,we revealed that NLR copy numbers differ up to 66-fold among closely related species owing to rapid gene loss and ***,NLR contraction was associated with adaptations to aquatic,parasitic,and carnivorous *** convergent NLR reduction in aquatic plants resembles the lack of NLR expansion during the long-term evolution of green algae before the colonization of land.A co-evolutionary pattern between NLR subclasses and plant immune pathway components was also identified,suggesting that immune pathway deficiencies may drive TNL ***,we identified a conserved TNL lineage that may function independently of the EDS1-SAG101-NRG1 ***,these findings provide new insights into the evolution of NLR genes in the context of ecological adaptation and genome content variation.

关键词： NLR genes plant disease resistance EDS1 gene family gene family evolution angiosperms

Phylogeny of Dioscorea sect. Stenophora based on chloroplast matK, rbcL and trnL-F sequences

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植物分类学报 2008年第3期46卷 315-321页

作者： Xing GAO Yu-Ping ZHU Bao-cheng WU Ya-Mei ZHAO jian-qun chen Yue-Yu HANG Instimte of Botany Jiangsu Province and Chinese Academy of Sciences Jiangsu Province Key Laboratory for Plant Ex Situ Conservation Nanj ing 210014 China Department of Biology Nanjing University Nanjing 210093 China

Seventeen species, one subspecies and one variety of Dioscorea sect. Stenophora Uline were investi-gated for their phylogenetic relationships based on a sequence analysis of chloroplast matK and rbcL genes and trnL-F intergenic spacer by maximum parsimony and maximum likelihood methods. The results showed that: (a) sect. Stenophora was a strongly supported monophyletic group; (b) D. rockii, D. membranacea, D. banzhuana, and D. simulans formed a moderately supported monophyletic group, and D. prazeri was weakly supported to be sister to this group; (c) D. althaeoides and D. nipponica ssp. nipponica formed a moderately supported clade, and D. nipponica ssp. rosthornii was not a member of this clade; (d) D. zingiberensis and D. sinoparviflora showed a moderate to strong sister relationship; and (e) D. collettii var. hypoglauca and D. collettii var. collettii were sister to each other, but with only weak support.

关键词：系统演化叶绿体序列薯蓣属

Artesunate enhances T-cell-mediated antitumoractivity through augmenting T-cell function andreversing immune escape of HepG2 cells

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Artesunate enhances T-cell-mediated antitumoractivity throug...

Quantum public-key crypto via EPR pairs

2018年浙江省检验医学学术年会

作者：祝宇翀 Jun-Quan Liu Peng Qian jian-qun chen 杭州金域医学检验所有限公司 Department of Gastroenterology Affiliated Hospital of Xuzhou Medical University

Objective:To explore the effect and mechanism of artesunate T cell-mediated antitumor immune responses against hepatoma carcinoma cells (HepG2) in ***:Human cd T cells or HepG2 were respectively treated with artesunate,Results:The results showed that the cytotoxicity effect of cd T cells pretreated with artesunate on HepG2 cells was augmented via elevating the expression of GraB in cd T cells.

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 58-63页

作者： Xiang-qun Fu Hong-Wei Li jian-Hong Shi Tan Li Wan-Su Bao Henan Key Laboratory of Quantum Information and Cryptography Information Engineering University Synergetic Innovation Center of Quantum Information and Quantum Physics University of Science and Technology of China

With the development of quantum computing technology, quantum public-key cryptography is gradually becoming an alternative to the existing classical public-key cryptography. This paper designs a quantum trapdoor one-way function via EPR pairs and quantum measurements. Based on this, a new quantum public-key cryptosystem is presented, which offers forward security,and can resist the chosen-plaintext attack and chosen-ciphertext attack. Compared with the existing quantum public-key cryptos,eavesdropping can be automatically detected in this new quantum public-key cryptosystem under a necessary condition, which is also detailed in the paper.

关键词： quantum public-key crypto trapdoor one-way function EPR pairs

生长抑素对溃疡性结肠炎模型大鼠肠道炎性损伤的治疗作用

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世界华人消化杂志 2009年第17期17卷 1726-1731页

作者：刘元山陈剑群朱炳喜徐州医学院附属医院消化内科江苏省徐州市221002

目的:观察生长抑素(奥曲肽)对溃疡性结肠炎(ulcerative colitis,UC)大鼠模型的作用,初步探讨其可能机制.方法:♂SD大鼠随机分为正常对照组、奥曲肽对照组、模型组、治疗组,每组7只.模型组、治疗组大鼠用三硝基苯磺酸(TNBS)/乙醇溶液灌... 详细信息

目的:观察生长抑素(奥曲肽)对溃疡性结肠炎(ulcerative colitis,UC)大鼠模型的作用,初步探讨其可能机制.方法:♂SD大鼠随机分为正常对照组、奥曲肽对照组、模型组、治疗组,每组7只.模型组、治疗组大鼠用三硝基苯磺酸(TNBS)/乙醇溶液灌肠复制UC模型.观察各组实验大鼠体质量变化、大体及组织病理学改变.采用酶联免疫吸附法检测细胞因子(IL-6、IL-10、TNF-α)的含量、蛋白质印迹杂交法检测结肠组织NF-κBp65蛋白的表达.结果:生长抑素可以缓解大鼠体质量的减轻,减少腹泻及便血的发生,并且能够显著改善结肠组织大体和组织学评分.与正常组比较,模型组大鼠结肠黏膜IL-6、TNF-α表达明显升高(188.27±11.65ng/Lvs102.13±7.12ng/L,87.39±6.74ng/Lvs121.51±8.56ng/L,均P<0.01);IL-10表达明显下降(71.40±8.28ng/Lvs202.97±12.26ng/L,P<0.01);与模型组比较,治疗组大鼠结肠黏膜IL-6、TNF-α表达均明显降低(142.03±12.68ng/L,90.87±9.26ng/L,均P<0.01),IL-10表达明显升高(124.07±10.05ng/L,P<0.01).模型组结肠组织中NF-κB的蛋白含量明显高于治疗组(1059.60±96.35vs471.23±11.61,P<0.01).结论:生长抑素对TNBS诱导的大鼠溃疡性结肠炎具有显著治疗作用,其作用机制可能是通过影响炎症反应的信号通路NF-κB的活化,进而下调促炎细胞因子及上调抗炎细胞因子的产生和表达.

关键词：溃疡性结肠炎生长抑素核因子-κB 肿瘤坏死因子白介素-6 白介素-10