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Complementary sequence-mediated exon circularization

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Complementary sequence-mediated exon circularization

Zika virus spreading in South America: evolutionary analysis of emerging neutralizing resistant Phe279Ser strains

第十一次全国基因功能与表观遗传调控学术研讨会

作者： Xiao-Ou Zhang Hai-Bin Wang Yang Zhang Xuhua Lu Ling-Ling Chen Li Yang Key Laboratory of computational biology CAS-MPG Partner Institute for Computational BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences State Key Laboratory of Molecular biology Shanghai Key Laboratory of Molecular AndrologyInstitute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences Department of Orthopedic Surgery Changzheng HospitalSecond Military Medical University

Exon circularization has been identified from many loci in mammals,but the detailed mechanism of its biogenesis has remained *** using genomewide approaches and circular RNA recapitulation,we demonstrate that exon circularization is dependent on flanking intronic complementary *** sequences and their distribution exhibit rapid evolutionary changes,

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Asian Pacific Journal of Tropical Medicine 2016年第5期9卷 432-438页

作者： Marta Giovanetti Teresa Milano Luiz Carlos Alcantara Laura Carcangiu Eleonora Cella Alessia Lai Alessandra Lo Presti Stefano Pascarella Gianguglielmo Zehender Silvia Angeletti Massimo Ciccozzi Department of Infectious Parasitic and Immunomediated Diseases National Institute of HealthRomeItaly Department of biology University of Rome ‘Tor Vergata’RomeItaly Laboratory of Hematology Genetic and Computational Biology Goncalo Moniz Research Center Oswaldo Cruz Foundation (LHGB/CPq GM/FIOCRUZ)SalvadorBahiaBrazil Dipartimento di Scienze Biochimiche ‘A. Rossi Fanelli’ Universita La Sapienza00185 RomeItaly Department of Public Health and Infectious Diseases Sapienza University of RomeRomeItaly Laboratory of Infectious Diseases and Tropical Medicine University of Milan Clinical Pathology and Microbiology Laboratory University Hospital Campus Bio-Medico of RomeRomeItaly University Campus Bio-Medico RomeItaly

Objective: To investigate the genetic diversity of Zika virus(ZIKV) and the relationships existing among these circulating viruses worldwide. To evaluate the genetic polymorphisms harboured from ZIKV that can have an influence on the virus circulation. Methods: Three different ZIKV dataset were built. The first dataset included 63 E gene sequences, the second one 22 NS3 sequences and the third dataset was composed of 108 NS5 gene sequences. Phylogenetic and selective pressure analysis was performed. The edited nucleic acid alignment from the Envelope dataset was used to generate a conceptual translation to the corresponding peptide sequences through UGene software. Results: The phylogeographic reconstruction was able to discriminate unambiguously that the Brazilian strains are belonged to the Asian lineage. The structural analysis reveals instead the presence of the Ser residue in the Brazilian sequences(however already observed in other previously reported ZIKV infections) that could suggest the presence of a neutralization-resistant population of viruses. Conclusions: Phylogenetic, evolutionary and selective pressure analysis contributed to improve the knowledge on the circulation of ZIKV.

关键词： Zika virus Phylogeny Evolution

Systematics of the avian family Alaudidae using multilocus and genomic data

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Avian Research 2023年第2期14卷 137-152页

作者： Per Alstrom Zeinolabedin Mohammadi Erik D.Enbody Martin Irestedt Derek Engelbrecht Pierre-Andre Crochet Alban Guillaumet Loïs Rancilhac B.Irene Tieleman Urban Olsson Paul F.Donald Martin Stervander Animal Ecology Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityNorbyvagen 18DSE-75236UppsalaSweden Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing100101China Department of biology Faculty of SciencesGolestan UniversityGorganGolestanIran Department of Medical Biochemistry and Microbiology Uppsala University75123UppsalaSweden Department of Biomolecular Engineering University of CaliforniaSanta Cruz95060Santa CruzCAUSA Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryP.O.Box 50007SE-10405StockholmSweden Department of Biodiversity University of LimpopoPrivate Bag X1106Sovenga0727South Africa CEFE CNRSUniv MontpellierEPHEIRDMontpellierFrance Department of Biological&Environmental Sciences Troy UniversityTroyAL36082USA Groningen Institute for evolutionary Life Sciences University of GroningenNijenborgh 79747 AGGroningenthe Netherlands Department of Biological and Environmental Sciences University of GothenburgP.O.Box 463SE-40530GothenburgSweden Gothenburg Global Biodiversity Centre P.O.Box 461SE-40530GothenburgSweden BirdLife International The David Attenborough BuildingPembroke StCambridgeCB23QZUK Department of Zoology University of CambridgeDowning StreetCambridgeCB23EJUK Bird Group Natural History MuseumAkeman StreetTringHertfordshireHP236APUnited Kingdom

The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Australia.A decade-old molecular phylogeny,comprising~80%of the species,revealed multiple cases of parallel evolution and large variation in rates of morphological evolution,which had misled taxonomists into creating many non-monophyletic ***,we reconstruct the phylogeny of the larks,using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species(in total 133 taxa;not all loci available for all species).We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling(in total 51 samples of 44 taxa across 40 species).Our results confirm the previous findings of rampant morphological convergence and divergence,and reveal new cases of paraphyletic *** propose a new subfamily classification,and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the *** study supports recently proposed species splits as well as some recent lumps,while also questioning some of the *** comprehensive phylogeny will form an important basis for future studies,such as comparative studies of lark natural history,ecology,evolution and conservation.

关键词： Phylogeny Phylogenomics Multispecies coalescent Lark Paraphyly Taxonomy Subfamily description

Anomalous Sorption Kinetics of Self-Interacting Particles by a Spherical Trap

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Communications in computational Physics 2022年第3期31卷 707-738页

作者： Antonio Raudino Antonio Grassi Giuseppe Lombardo Giovanni Russo Clarissa Astuto Mario Corti Department of Chemical Sciences University of CataniaViale A.Doria 6-95125CataniaItaly Department of Mathematics University of CataniaViale A.Doria 6-95125 CataniaItaly Applied Mathematics and computational Science King Abdullah University of Science and Technology(KAUST)4700ThuwalSaudi Arabia CNR-IPCF Viale F.Stagno d’Alcontres 3798158 MessinaItaly

In this paper we propose a computational framework for the investigation of the correlated motion between positive and negative ions exposed to the attraction of a bubble surface that mimics the(oscillating)cell *** we aim to investigate the role of surface traps with substances freely diffusing around the *** physical system we want to model is an anchored gas drop submitted to a diffusive flowof charged surfactants(ions).When the diffusing surfactantsmeet the surface of the bubble,they are reversibly adsorbed and their local concentration is accurately *** correlated diffusion of surfactants is described by a Poisson-Nernst-Planck(PNP)system,in which the drift term is given by the gradient of a potential which includes both the effect of the bubble and the Coulomb interaction between the *** latter term is obtained from the solution of a self-consistent Poisson *** very short Debye lengths one can adopt the so called Quasi-Neutral limit which drastically simplifies the system,thus allowing for much faster numerical *** paper has four main *** first one is to present a PNP model that describes ion charges in presence of a *** second one is to provide benchmark tests for the validation of simplified multiscale models under current development[1].The third one is to explore the relevance of the term describing the interaction among the apolar tails of the *** last one is to quantitatively explore the validity of the Quasi-Neutral limit by comparison with detailed numerical simulation for smaller and smaller Debye *** order to reach these goals,we propose a simple and efficient Alternate Direction Implicit method for the numerical solution of the non-linear PNP system,which guarantees second order accuracy both in space and time,without requiring solution of nonlinear equation at each time *** semi-implicit scheme for a simplified PNP system near quasi neutrality is also p

关键词： Spherycal trap quasi-neutrality finite differences Coulomb potential Poisson-Nernst-Planck system ADI discretization semi-implicit scheme

Genetic dissection of growth trajectories in forest trees:From FunMap to FunGraph

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Forestry Research 2021年第1期1卷 173-182页

作者： Li Feng Peng Jiang Caifeng Li Jinshuai Zhao Ang Dong Dengcheng Yang Rongling Wu center for computational biology College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China center for Statistical Genetics Departments of Public Health Sciences and StatisticsThe Pennsylvania State UniversityHersheyPA 17033USA

Growth is the developmental process involving important genetic *** mapping(FunMap)has been used as an approach to map quantitative trait loci(QTLs)governing growth trajectories by incorporating growth *** is based on reductionism thinking,with a power to identify a small set of significant QTLs from the whole pool of genome-wide ***,increasing evidence shows that a complex trait is controlled by all genes the organism may possibly ***,we describe and demonstrate a different mapping approach that encapsulates all markers into genetic interaction *** approach,symbolized as FunGraph,combines functional mapping,evolutionary game theory,and prey-predator theory into mathematical graphs,allowing the observed genetic effect of a locus to be decomposed into its independent component(resulting from this locus’intrinsic capacity)and dependent component(due to extrinsic regulation by other loci).Using FunGraph,we can visualize and trace the roadmap of how each locus interact with every other locus to impact *** a population-based association study of Euphrates poplar,we use FunGraph to identify the previously neglected genetic interaction effects that contribute to the genetic architecture of juvenile stem *** could open up a novel gateway to comprehend the global genetic control mechanisms of complex traits.

关键词： forest mapping neglected

Topology inference of uncertain complex dynamical networks and its applications in hidden nodes detection

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Science China(Technological Sciences) 2016年第8期59卷 1232-1243页

作者： WANG YingFei WU XiaoQun FENG Hui LU JunAn LU JinHu School of Mathematics and Statistics Wuhan University Wuhan 430072 China computational Science Hubei Key Laboratory Wuhan University Wuhan 430072 China Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China

一个复杂动态网络的拓扑的结构在决定网络起一个重要作用进化机制和功能的行为，因此认出并且推断网络结构具有理论、实际的意义。尽管各种各样的途径被建议了估计网络拓扑学，许多很好没在网络个人之中被建立到网络动力学和传播延期的... 详细信息

一个复杂动态网络的拓扑的结构在决定网络起一个重要作用进化机制和功能的行为，因此认出并且推断网络结构具有理论、实际的意义。尽管各种各样的途径被建议了估计网络拓扑学，许多很好没在网络个人之中被建立到网络动力学和传播延期的普遍存在的吵闹的性质。这份报纸集中于不明确的复杂动态网络的拓扑学推理。一个辅助网络被构造，一个适应计划被建议追踪拓扑的参数。考虑网络模型应当包含实际随机的不安，是引人注目的，并且吵闹的观察作为构造辅助网络的控制输入被拿。特别地，控制技术能进一步被采用找到隐藏的消息提供者(或潜伏的变量) 在网络。数字例子被提供说明建议计划的有效性。另外，联合力量并且在鉴定性能上联合延期的影响被估计。建议计划向工程师提供一条方便途径推断一般复杂动态网络的拓扑学并且找到隐藏的消息提供者，和评估能进一步便于的详细表演实际电路设计。

关键词：网络拓扑结构动态网络隐节点应用检测传输延迟辅助网络耦合强度

3D assessment of intervertebral disc degeneration in zebrafish identifies changes in bone density that prime disc disease

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Bone Research 2021年第4期9卷 521-536页

作者： Erika Kague Francesco Turci Elis Newman Yushi Yang Kate Robson Brown Mona S.Aglan Ghada A.Otaify Sarnia A.Temtamy Victor L.Ruiz-Perez Stephen Cross C.Patrick Royall P.Eckhard Witten Chrissy L.Hammond School of Physiology Pharmacology and NeuroscienceBiomedical SciencesUniversity of BristolBristolUK School of Physics HH Wills Physics LaboratoryUniversity of BristolBristolUK Centre for Nanoscience and Quantum Information University of BristolBristolUK Bristol Centre for Functional Nanomaterials University of BristolBristolUK Department of Anthropology and Archaeology University of BristolBristolUK Department of Mechanical Engineering University of BristolBristolUK Clinical Genetics Department Human Genetics and Genome Research DivisionCenter of Excellence for Human GeneticsNational Research CentreCairoEgypt lnstituto de Investigaciones Biomedicas de Madridand Ciber de Enfermedades Raras(CIBERER)MadridSpain Wolfson Bioimaging Facility Biomedical SciencesUniversity of BristolBristolUK School of Chemistry University of BristolBristolUK evolutionary Developmental biology Department of BiologyGhent UniversityGhentBelgium

Back pain is a common condition with a high social impact and represents a global health *** disc disease(IVDD)is one of the major causes of back pain;no therapeutics are currently available to reverse this *** impact of bone mineral density(BMD)on IVDD has been controversial,with some studies suggesting osteoporosis as causative for IVDD and others suggesting it as protective for *** studies to evaluate the influence of genetic components of BMD in IVDD could highlight opportunities for drug development and *** taking a holistic 3D approach,we established an aging zebrafish model for spontaneous *** BMD in aging,detected by automated computational analysis,is caused by bone deformities at the ***,aged zebrafish spines showed changes in bone morphology,microstructure,mineral heterogeneity,and increased fragility that resembled *** of the discs recapitulated IVDD symptoms found in humans:the intervertebral ligament(equivalent to the annulus fibrosus)showed disorganized collagen fibers and herniation,while the disc center(nucleus pulposus equivalent)showed dehydration and cellular *** manipulated BMD in young zebrafish by mutating sp7 and cathepsin K,leading to low and high BMD,***,we detected IVDD in both groups,demonstrating that low BMD does not protect against IVDD,and we found a strong correlation between high BMD and *** learning was applied to high-resolution synchrotron\iCJ image data to analyze osteocyte 3D lacunar distribution and morphology,revealing a role of sp7 in controlling the osteocyte lacunar 3D *** findings suggest potential avenues through which bone quality can be targeted to identify beneficial therapeutics for IVDD.

关键词： intervertebral degeneration protective

Integrating Systemic Risk and Risk Analysis Using Copulas

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International Journal of Disaster Risk Science 2018年第4期9卷 561-567页

作者： Stefan Hochrainer-Stigler Georg Pflug Ulf Dieckmann Elena Rovenskaya Stefan Thurner Sebastian Poledna Gergely Boza Joanne Linnerooth-Bayer Ake Brannstrom International Institute for Applied Systems Analysis(IIASA) 2361 LaxenburgAustria Department of Statistics and Operations Research University of Vienna1010 ViennaAustria Complexity Science Hub 1080 ViennaAustria Faculty of computational Mathematics and Cybernetics Lomonosov Moscow State UniversityMoscowRussia 119234 Medical University of Vienna 1090 ViennaAustria Santa Fe Institute Santa FeNM 87501USA evolutionary Systems Research Group MTA-oK-BLI Centre for Ecological ResearchHungarian Academy of SciencesTihany 8237Hungary Department of Mathematics and Mathematical Statistics Umea University90187 UmeaSweden

Systemic risk research is gaining traction across diverse disciplinary research communities, but has as yet not been strongly linked to traditional, well-established risk analysis research. This is due in part to the fact that systemic risk research focuses on the connection of elements within a system, while risk analysis research focuses more on individual risk to single elements. We therefore investigate how current systemic risk research can be related to traditional risk analysis approaches from a conceptual as well as an empirical point of view. Based on Sklar's Theorem, which provides a one-to-one relationship between multivariate distributions and copulas, we suggest a reframing of the concept of copulas based on a network perspective. This provides a promising way forward for integrating individual risk(in the form of probability distributions) and systemic risk(in the form of copulasdescribing the dependencies among such distributions)across research domains. Copulas can link continuous node states, characterizing individual risks, with a gradual dependency of the coupling strength between nodes on their states, characterizing systemic risk. When copulas are used for describing such refined coupling between nodes,they can provide a more accurate quantification of a system's network structure. This enables more realistic systemic risk assessments, and is especially useful when extreme events(that occur at low probabilities, but have high impacts) affect a system's nodes. In this way, copulas can be informative in measuring and quantifying changes in systemic risk and therefore be helpful in its management. We discuss the advantages and limitations of copulas for integrative risk analyses from the perspectives of modeling, measurement, and management.

关键词： Copulas Individual risk Risk analysis Systemic risk

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结构稳定性:概念、方法和应用

生物多样性 2020年第11期28卷 1345-1361页

作者：宋础良 Department of Civil and Environmental Engineering Massachusetts Institute of TechnologyCambridgeMA 02139USA Department of biology McGill UniversityMontrealH3A1B1Canada Department of Ecology and evolutionary biology University of TorontoTorontoOntario M5S 3B2Canada

群落内物种间相互作用的结构是高度组织化的。群落结构对多物种共存的影响机制是群落生态学的核心科学问题之一。目前生态学界在这一问题上存在多种不同的观点。一个可能的原因是,由于环境因子的复杂性,大部分研究忽略了环境因子对群落... 详细信息

群落内物种间相互作用的结构是高度组织化的。群落结构对多物种共存的影响机制是群落生态学的核心科学问题之一。目前生态学界在这一问题上存在多种不同的观点。一个可能的原因是,由于环境因子的复杂性,大部分研究忽略了环境因子对群落结构和物种共存的重要影响。在这一背景下,近期发展起来的结构稳定性理论系统地联系了群落结构、环境因子和物种共存,并在此基础上建立了一个和经验数据紧密结合的理论框架。本文首先简要回顾了当前关于群落结构研究的争鸣,然后介绍了结构稳定性的理论框架和计算方法,最后详细介绍了结构稳定性理论在不同生态群落和不同生态学问题中的应用。在全球气候变化的背景下,结构稳定性理论提供了一种新的视角来理解群落层面的生物多样性维持机制。

关键词：群落结构物种共存结构稳定性环境梯度环境胁迫