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Exploring marine endosymbiosis systems with omics techniques

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Science China(Life Sciences) 2021年第6期64卷 1013-1016页

作者： yisi hu Shuyan Sun huizhong Fan Wenliang Zhou Fuwen Wei CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)Guangzhou 511458China University of Chinese Academy of Sciences Beijing 100049China

Endosymbiosis is the phenomenon where one organism lives inside another,usually in a mutualistic *** this system,the hosts provide shelter and nutrients to the endosymbionts,who could affect the hosts in a physiologic... 详细信息

关键词： evolutionary marine mutual

Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals

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The Innovation 2023年第3期4卷 91-101页

作者： yisi hu Shenli Yuan Xin Du Jiang Liu Wenliang Zhou Fuwen Wei CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)Guangzhou 511458China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China

DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes,including gene expression regulation,transposable element repression,and genomic ***,most studies on DNA methylation have been conducted in humans and other model species,whereas the dynamics of DNA methylation across mammals remain poorly explored,limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA ***,we generated and gathered comparative epigenomic data from 13 mammalian species,including two marsupial species,to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait *** found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning,indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape *** a broader view,we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary *** analyzing the features of known and newly identified potential imprints in all studied mammals,we found that genomic imprinting may function in embryonic development through the binding of specific transcription *** findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution,suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory.

关键词： imprinting evolution mammals

The metabolic adaptation in wild vertebrates via omics approaches

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Life Metabolism 2022年第3期1卷 234-241页

作者： Xin Du yisi hu Guangping huang Fuwen Wei Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)GuangzhouGuangdong 511458China

Metabolism is the basis for sustaining life and essential to the adaptive evolution of *** the development of high-throughput sequencing technology,genetic mechanisms of adaptive evolution,including metabolic adaptation,have been extensively resolved by omics approaches,but a deep understanding of genetic and epigenetic metabolic adaptation is still *** metabolic adaptations from genetic and epigenetic perspectives in wild vertebrates is vital to understanding species evolution,especially for the early stages of adaptative ***,we summarize the advances in our understanding of metabolic adaptations via omics approaches in wild vertebrates based on three types of cases:extreme environment,periodically changing environment,and changes of species *** conclude that the understanding of the formation of metabolic adaptations at the genetic level alone can well identify the adaptive genetic variation that has developed during evolution,but cannot resolve the potential impact of metabolic adaptations on the adaptative evolution in the ***,it seems imperative to include epigenomics and metabolomics in the study of adaptation,and that in the future genomic and epigenetic data should be integrated to understand the formation of metabolic adaptation of wild vertebrate organisms.

关键词： adaptative evolution metabolic adaptation comparative genomics multi-omics epigenetics

Toward the generation of pure coral genomes with experimental and bioinformatic improvements

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The Innovation 2024年第4期5卷 30-32页

作者： yisi hu Zhiwei Zhang Shuyan Sun Youfang Sun hui huang Wenliang Zhou Fuwen Wei Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)Guangzhou 511458China Jiangxi Provincial Key Laboratory of Conservation Biology College of ForestryJiangxi Agricultural UniversityNanchang 330029China Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Tropical Marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China

Stony corals,the primary architects of coral reef ecosystems,are largely underrepresented in omics studies despite their *** presence of endosymbiotic Symbiodiniaceae algae complicates the extraction of pure coral DNA,posing a challenge for genomic ***,we devised a comprehensive methodological framework that incorporates various experimental treatments to achieve 99%purity in coral DNA extraction and a robust bioinformatics pipeline to guarantee the assembly of high-quality,contamination-free coral *** of our framework using Acropora millepora samples demonstrated its efficacy and superiority in obtaining high-quality pure coral genomes using easily accessible adult *** integrated framework serves as a critical foundation for largescale genome-enabled research on stony corals,providing insight into coral evolution and conservation.

关键词： coral guarantee purity

Regional scientific research benefits threatened-species conservation

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National Science Review 2019年第6期6卷 1076-1079页

作者： yisi hu Zhenhua Luo Colin A.Chapman Stuart L.Pimm Samuel T.Turvey Michael J.Lawes Carlos A.Peres Tien Ming Lee Pengfei Fan School of Life Sciences Sun Yat-Sen University School of Life Sciences Central China Normal University Department of Anthropology and School of Environment Mc Gill University School of Life Sciences University of Kwa Zulu-Natal The College of Life Sciences Northwest University Nicholas School of the Environment Duke University

Although conventional wisdom considers knowledge of threatened species’ ecology and status essential for conservation, few studies demonstrate this in a quantitative way across many species and within the same political entity. Here,we evaluated the impacts of scientific research against conservation interventions(including funding) and specieslevel correlates, accounting for phylogenetic relatedness, on the conservation

关键词： China Regional scientific research benefits threatened-species conservation

基于加权效用函数的LoRa扩频因子和码率分配

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电子测量技术 2023年第20期46卷 74-80页

作者：谢桂辉肖华煦王景双胡轶斯中国地质大学(武汉)自动化学院武汉430074 中山智联未来科技有限公司中山528437

针对大规模LoRa网络数据包到达率下降、能耗急剧增加的问题,提出了基于加权效用函数的LoRa扩频因子和码率分配方法。首先,建立扩频因子和码率对数据包到达率和能耗的耦合影响关系;然后,基于赏罚机制建立数据包到达率和能耗的效用函数,... 详细信息

针对大规模LoRa网络数据包到达率下降、能耗急剧增加的问题,提出了基于加权效用函数的LoRa扩频因子和码率分配方法。首先,建立扩频因子和码率对数据包到达率和能耗的耦合影响关系;然后,基于赏罚机制建立数据包到达率和能耗的效用函数,并以它们的加权值为目标函数,利用贪心算法进行扩频因子和码率联合分配;最后,通过遍历搜索的方法确定最优的权重系数。仿真结果表明,相比目前最新的CA-ADR算法,所提算法的网络平均数据包到达率提高了21.2%,网络平均能效提高165%。本文算法有效提高了LoRa网络的通信可靠性和终端设备的生命周期,在智慧城市、智慧农业等众多场景具有较高的应用价值。

关键词： LoRa 数据包到达率效用函数扩频因子码率

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造礁石珊瑚演化发育生物学研究进展

中国科学:生命科学 2024年第5期54卷 805-818页

作者：张志伟周文良张晶晶胡怡思魏辅文南方海洋科学与工程广东省实验室(广州) 海洋生物演化与保护生物学研究中心广州大学生命科学学院江西农业大学林学院

造礁石珊瑚是海洋中的关键动物类群.在漫长的演化过程中,造礁石珊瑚获得与虫黄藻细胞内共生、生物矿化造礁等重要功能性状,是珊瑚礁生态系统的框架生物,在维持生态系统生物多样性及生态调节功能等方面发挥关键作用.同时,以造礁石珊瑚为... 详细信息

造礁石珊瑚是海洋中的关键动物类群.在漫长的演化过程中,造礁石珊瑚获得与虫黄藻细胞内共生、生物矿化造礁等重要功能性状,是珊瑚礁生态系统的框架生物,在维持生态系统生物多样性及生态调节功能等方面发挥关键作用.同时,以造礁石珊瑚为代表的刺胞动物是双侧动物最近缘的分支,在系统发育演化上占据非常关键的地位,其胚层、体轴以及多种功能细胞的发育调控等相关研究结果,对探讨双侧动物相应性状的演化起源具有极其重要的指导意义.本文梳理造礁石珊瑚在演化发育生物学领域的研究进展,重点关注其重要细胞类群、胚层和体轴、繁殖策略及其细胞内共生和生物矿化等关键性状的演化起源和发育调控机制等.同时,本文提出几个未来造礁石珊瑚演化发育研究值得重点关注的方向,包括关键功能性状的分子基础、生殖细胞发育和性别决定、干细胞与再生能力等.

关键词：造礁石珊瑚演化发育生物学繁殖策略细胞内共生生物矿化

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考虑舵面效能柔性飞机阵风减缓控制系统

北京航空航天大学学报 2025年第1期51卷 248-256页

作者：刘易斯杨佑绪刘燚成志勇余灵富南昌航空大学飞行器工程学院南昌330063 北京机电工程研究所北京100083

舵面效能损耗会直接影响柔性飞机阵风减缓效果,考虑舵面效能损耗是主动阵风减缓控制系统设计的关键。针对柔性飞机遭遇阵风干扰问题,以某大展弦比柔性飞机模型为对象,建立包含刚体运动和弹性模态的柔性飞机结构动力学模型,考虑舵面作动... 详细信息

舵面效能损耗会直接影响柔性飞机阵风减缓效果,考虑舵面效能损耗是主动阵风减缓控制系统设计的关键。针对柔性飞机遭遇阵风干扰问题,以某大展弦比柔性飞机模型为对象,建立包含刚体运动和弹性模态的柔性飞机结构动力学模型,考虑舵面作动器存在舵面效能损耗的情况,设计一种自适应观测器实时在线估计舵面作动器效能因子,重构和求解自适应主动容错H_(∞)控制器,实现柔性飞机阵风载荷减缓。离散和连续阵风激励下的柔性飞机开/闭环时域响应仿真表明:在舵面无效能损耗情况下,H_(∞)控制与比例-积分-微分(PID)控制均能达到较好的减缓效果,H_(∞)控制相较于PID控制响应时间更快;在舵面存在效能损耗情况下,自适应观测器在4 s内能够完成效能因子评估,基于该效能因子设计的H_(∞)控制器能够达到与理想情况相当的阵风减缓效果。

关键词：气动伺服弹性阵风响应阵风减缓控制系统自适应观测器主动容错控制系统

Identification of a New Peptide Deformylase Gene From Enterococcus faecium and Establishment of a New Screening Model Targeted on PDF for Novel Antibiotics

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Biomedical and Environmental Sciences 2004年第3期17卷 350-358页

作者： XIAN-BINGTANG Shu-yisi YUE-QINZHANG TheNationalKeyLaboratoryforScreeningNewMicrobialDrugs InstituteofMedicinalBiotechnologyChineseAcademyofMedicalSciencesandPekingUnionMedicalCollegeBeifing100050China InstituteofMedicinalBiotechnology ChineseAcademyofMediicalSciences＆PekingUnionMedicalCollegeNo.1TiantanXiliBeijing100050China

Objective To identify a new peptide deformylase (PDF) gene (Genebank Accession AY238515) from Enterococcus faecium and to establish a new screening model targeted on PDF. Methods A new PDF gene was identified by BLAST analysis and PCR and was subsequently over-expressed in the prokaryotic expression host *** Bl21(DE3). Over-expressed protein was purified for enzymatic assay by metal affinity chromatography and a new screening model was established for novel antibiotics. Result A new PDF gene of Enterococcus faecium was identified successfully. Ten positive samples were picked up from 8000 compound library and the microbial fermentation broth samples. Conclusion A new PDF of gene Enterococcus faecium was first identified and the model had a high efficacy. Positive samples screened may be antibacterial agents of broad spectrum.

关键词： Enterococcus faecium Peptide deformylase (PDF) Antibacterial gents of broad spectrum