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Neural plasticity and adult neurogenesis: the deep biology perspective

Neural Regeneration Research 2019年第2期14卷 201-205页

作者： Anna Maria Colangelo Giovanni Cirillo Lilia Alberghina Michele Papa Hans V.Westerhoff Laboratory of Neuroscience "R.Levi-Montalcini" Dept.of Biotechnology and Biosciences University of Milano-Bicocca sysbio centre of systems biology University of Milano-Bicocca NeuroMI Milan Center for Neuroscience University of Milano-Bicocca Laboratory of Morphology of Neuronal Network Department of Public Medicine University of Campania "Luigi Vanvitelli" Synthetic systems biology and Nuclear Organization University of Amsterdam Molecular Cell Physiology VU University Amsterdam and Infrastructure Systems Biology at NL (ISBE.NL) Amsterdam NL and Systems Biology School for Chemical Engineering and Analytical Science University of Manchester

The recognition that neurogenesis does not stop with adolescence has spun off research towards the reduction of brain disorders by enhancing brain regeneration. Adult neurogenesis is one of the tougher problems of developmental biology as it requires the generation of complex intracellular and pericellular anatomies, amidst the danger of neuroinflammation. We here review how a multitude of regulatory pathways optimized for early neurogenesis has to be revamped into a new choreography of time dependencies. Distinct pathways need to be regulated, ranging from neural growth factor induced differentiation to mitochondrial bioenergetics, reactive oxygen metabolism, and apoptosis. Requiring much Gibbs energy consumption, brain depends on aerobic energy metabolism, hence on mitochondrial activity. Mitochondrial fission and fusion, movement and perhaps even mitoptosis, thereby come into play. All these network processes are interlinked and involve a plethora of molecules. We recommend a deep thinking approach to adult neurobiology.

关键词： neurogenesis adult brain neuroregeneration neuron differentiation nerve growth factor energy homeostasis mitochondria deep biology systems biology

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Cooperative Virus-Virus Interactions:An Evolutionary Perspective

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BioDesign Research 2022年第1期2022卷 111-123页

作者： Ernesto Segredo-Otero Rafael Sanjuán Institute for Integrative systems biology(I2sysbio) Consejo Superior de Investigaciones Científicas-Universitat de ValènciaC/Catedrático Agustín Escardino 946980 PaternaValènciaSpain

Despite extensive evidence of virus-virus interactions,not much is known about their biological significance.Importantly,virusvirusinteractions could have evolved as a form of cooperation or simply be a by-product of other processes.Here,we review anddiscuss different types of virus-virus interactions from the point of view of social evolution,which provides a well-establishedframework for interpreting the fitness costs and benefits of such traits.We also classify interactions according to theirmechanisms of action and speculate on their evolutionary implications.As in any other biological system,the evolutionarystability of viral cooperation critically requires cheaters to be excluded from cooperative interactions.We discuss how cheaterviruses exploit cooperative traits and how viral populations are able to counteract this maladaptive process.

关键词： interpreting spite classify

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Suprabiology 2014： Promoting UK-China collaboration on systems biology and High Performance Computing

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Frontiers of Electrical and Electronic Engineering in China 2015年第1期10卷 46-53页

作者： Ettore Murabito Riccardo Colombo Chengkun Wu Malkhey Verma Samrina Rehman Jacky Snoep Shao-Liang Peng Naiyang Guan Xiangke Liao Hans V. Westerhoff Manchester Institute of Biotechnology School of Computer Science Faculty of Engineering and Physical Sciences Manchester Centre for Integrative Systems Biology The University of Manchester Manchester M139PL United Kingdom. Department of Informatics Systems and Communication University of Milan-Bicocca Milan 20126 Italy. sysbio - centre of systems biology Milan 20126 Italy. Manchester Institute of Biotechnology School of Chemical Engineering and Analytical Sciences Manchester Centre forIntegrative Systems Biology The University of Manchester Manchester M139PL United Kingdom. School of Computer Science National University of Defence Technology Changsha 410073China

In the second half of 2014 the Manchester Institute of Biotechnology, based in Manchester （UK）, hosted the first Suprabiology congress, an event attended by representa- tives of different academic institutions and industry based in both the UK and China. The congress was aimed to serve as a platform to discuss and promote potential collaborations between the UK and China on the subject of systems biology and High Performance Computing. The event, sponsored by the ＂BBSRC China Partnering Awards＂ and ISBE, was organised as a sequence of talks addressing the different aspects of systems biology that can benefit from High Performance Computing. A general discussion session followed where the scientific, techni- cal, and logistic aspects of the prospected UK-China collaborations were examined.

关键词： System biology High Performance Computing Flux Balance Analysis Nonnegative Matrix Factorization Biochemical Network

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Engineering a Circular Riboregulator in Escherichia coli

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BioDesign Research 2020年第1期2020卷 9-17页

作者： William Rostain Shensi Shen Teresa Cordero Guillermo Rodrigo Alfonso Jaramillo Warwick Integrative Synthetic biology centre(WISB)and School of Life Sciences University of WarwickCV47AL CoventryUK Institute of systems and Synthetic biology CNRS-Universitéd’Évry Val-d’Essonne91000ÉvryFrance Instituto de Biología Molecular y Celular de Plantas CSIC-Universidad Politécnica de Valencia46022 ValenciaSpain Institute for Integrative systems biology(I2sysbio) CSIC-Universitat de València46980 PaternaSpain

RNAs of different shapes and sizes,natural or synthetic,can regulate gene expression in prokaryotes and eukaryotes.Circular RNAs have recently appeared to be more widespread than previously thought,but their role in prokaryotes remains elusive.Here,by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme,we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli.We showed that the resulting riboregulator can trans-activate gene expression by interacting with a cis-repressed messenger RNA.We characterized the system with a fluorescent reporter and with an antibiotic resistance marker,and we modeled this novel posttranscriptional mechanism.This first reported example of a circular RNA regulating gene expression in E.coli adds to an increasing repertoire of RNA synthetic biology parts,and it highlights that topological molecules can play a role in the case of prokaryotic regulation.

关键词： mechanism circular sizes

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Engineering of a Promoter Repressed by a Light-Regulated Transcription Factor in Escherichia coli

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BioDesign Research 2021年第1期2021卷 59-69页

作者： Daniel Camsund Alfonso Jaramillo Peter Lindblad Microbial Chemistry Department of Chemistry-ÅngströmUppsala UniversityUppsalaSweden Molecular systems biology Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden Warwick Integrative Synthetic biology centre(WISB)and School of Life Sciences University of WarwickCoventryUK Génomique Métabolique GenoscopeInstitut François JacobCEACNRSUniv EvryUniversitéParis-SaclayEvryFrance Institute for Integrative systems biology(I2sysbio) CSIC–Universitat de València46980 PaternaSpain

Light-regulated gene expression systems allow controlling gene expression in space and time with high accuracy.Contrary to previous synthetic light sensors that incorporate two-component systems which require localization at the plasma membrane,soluble one-component repression systems provide several advantageous characteristics.Firstly,they are soluble and able to diffuse across the cytoplasm.Secondly,they are smaller and of lower complexity,enabling less taxing expression and optimization of fewer parts.Thirdly,repression through steric hindrance is a widespread regulation mechanism that does not require specific interaction with host factors,potentially enabling implementation in different organisms.Herein,we present the design of the synthetic promoter P_(EL)that in combination with the light-regulated dimer EL222 constitutes a onecomponent repression system.Inspired by previously engineered synthetic promoters and the Escherichia coli lacZYA promoter,we designed P_(EL)with two EL222 operators positioned to hinder RNA polymerase binding when EL222 is bound.P_(EL)is repressed by EL222 under conditions of white light with a light-regulated repression ratio of five.Further,alternating conditions of darkness and light in cycles as short as one hour showed that repression is reversible.The design of the P_(EL)EL222 system herein presented could aid the design and implementation of analogous one-component optogenetic repression systems.Finally,we compare the P_(EL)-EL222 system with similar systems and suggest general improvements that could optimize and extend the functionality of EL222-based as well as other one-component repression systems.

关键词： pressed system analogous

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Abscisic Acid Connects Phytohormone Signaling with RNA Metabolic Pathways and Promotes an Antiviral Response that Is Evaded by a Self- Controlled RNA Virus

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Plant Communications 2020年第5期1卷 111-128页

作者： Fabio Pasin Hongying Shan Beatriz García Maren Müller David San León Márta Ludman David H.Fresno Károly Fátyol Sergi Munné-Bosch Guillermo Rodrigo Juan Antonio García Centro Nacional de Biotecnología(CNB-CSIC) 28049 MadridSpain Agricultural Biotechnology Research Center Academia Sinica11529 TaipeiTaiwan Departamento de Biologı´a Evolutiva Ecologı´a y Ciencias AmbientalesFacultad de Biologı´aUniversidad de Barcelona08028 BarcelonaSpain Agricultural Biotechnology Institute National Agricultural Research and Innovation Centre2100 Godoll}oHungary Institute for Integrative systems biology(I2sysbio) CSIC-University of Valencia46980 PaternaSpain Present address:College of Horticulture and Gardening Tianjin Agricultural University300384 TianjinChina

A complex network of cellular receptors,RNA targeting pathways,and small-molecule signaling provides robust plant immunity and tolerance to viruses.To maximize their fitness,viruses must evolve control mechanisms to balance host immune evasion and plant-damaging effects.The genus Potyvirus comprises plant viruses characterized by RNA genomes that encode large polyproteins led by the P1 protease.A P1 autoinhibitory domain controls polyprotein processing,the release of a downstream functional RNAsilencing suppressor,and viral replication.Here,we show that P1Pro,a plum pox virus clone that lacks the P1 autoinhibitory domain,triggers complex reprogramming of the host transcriptome and high levels of abscisic acid(ABA)accumulation.A meta-analysis highlighted ABA connections with host pathways known to control RNA stability,turnover,maturation,and translation.Transcriptomic changes triggered by P1Pro infection or ABA showed similarities in host RNA abundance and diversity.Genetic and hormone treatment assays showed that ABA promotes plant resistance to potyviral infection.Finally,quantitative mathematical modeling of viral replication in the presence of defense pathways supported self-control of polyprotein processing kinetics as a viral mechanism that attenuates the magnitude of the host antiviral response.Overall,our findings indicate that ABA is an active player in plant antiviral immunity,which is nonetheless evaded by a self-controlled RNA virus.

关键词： abscisic acid antiviral immune evasion mathematical modeling viral polyprotein processing Potyvirus RNA metabolism

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The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

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Horticulture Research 2023年第5期10卷 207-219页

作者： Xiaoya Shi Shuo Cao Xu Wang Siyang Huang Yue Wang Zhongjie Liu Wenwen Liu Xiangpeng Leng Yanling Peng Nan Wang Yiwen Wang Zhiyao Ma Xiaodong Xu Fan Zhang Hui Xue Haixia Zhong Yi Wang Kekun Zhang Amandine Velt Komlan Avia Daniela Holtgräwe Jérôme Grimplet JoséTomás Matus Doreen Ware Xinyu Wu Haibo Wang Chonghuai Liu Yuling Fang Camille Rustenholz Zongming Cheng Hua Xiao Yongfeng Zhou College of Horticulture Qingdao Agricultural UniversityQingdao 266109China State Key Laboratory of Tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Key Laboratory of Horticultural Plant biology Ministry of Education College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070China School of Agriculture and Food Science University College DublinBelfieldDublin 4Ireland National Demonstration Center for Experimental Plant Science Education College of AgricultureGuangxi UniversityNanning 530004China State Key Laboratory of Resource Insects Southwest UniversityChongqing 400715China Institute of Horticulture Crops Xinjiang Academy of Agricultural SciencesUrumqi 830091China Beijing Key Laboratory of Grape Science and Enology Institute of BotanyChinese Academy of SciencesXiangshanBeijing 100093China College of Enology Northwest A&F UniversityYangling 712100China SVQV INRAE-University of Strasbourg68000 ColmarFrance Genetics and Genomics of Plants CeBiTec&Faculty of BiologyBielefeld University33615 BielefeldGermany Unidad de Hortofruticultura Centro de Investigación y Tecnología Agroalimentaria de Aragón(CITA)50059 ZaragozaSpain Institute for Integrative systems biology(I2sysbio) Systems Biotech ProgramUniversitat de València-CSICPaterna46908ValenciaSpain Cold Spring Harbor Laboratory Cold Spring HarborNY 11724USA USDA ARS NEA Robert W.Holley Center for Agriculture and Health Agricultural Research ServiceIthacaNY 14853USA Fruit Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(Germplasm Resources Utilization)Ministry of Agriculture/Key Laboratory of Mineral Nutrition and Fertilizers Efficient Utilization of Deciduous Fruit TreeLiaoning ProvinceXingch

Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

关键词： breeding crops cultivar

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Biodesign Research to Advance the Principles and Applications of Biosystems Design

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BioDesign Research 2019年第1期2019卷 1-4页

作者： Xiaohan Yang Lei S.Qi Alfonso Jaramillo Zong-Ming(Max)Cheng Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Bioengineering Stanford UniversityStanfordCA 94305USA Department of Chemical and systems biology Stanford UniversityStanfordCA 94305USA Stanford ChEM-H Stanford UniversityStanfordCA 94305USA Warwick Integrative Synthetic biology centre(WISB)and School of Life Sciences University of WarwickCV47AL CoventryUK ISSB CNRSUniv EvryCEAUniversitéParis-Saclay91025 EvryFrance Institute for Integrative systems biology(I2sysbio) University of Valencia-CSIC46980 PaternaSpain Department of Plant Sciences University of TennesseeKnoxvilleTN 37996USA Nanjing Agricultural University NanjingJiangsu ProvinceChina

Over the course of civilization,humans have increasingly expanded their freedom to live a better life.In comparison with the primitive society,our modern society has many more choices of life-supporting resources,such as yearround food supply,permanent shelters,diverse energy sources,and effective preventive and curing medicine.However,our society is currently still heavily relying on the resources provided by Mother Nature,which cannot meet the future global needs in terms of both quantity and quality under the pressure of population growth,natural resource reduction,and environmental deterioration.For example,the food sources originating from plants,animals,or microbes do not have the nutrition balance for optimal human health[1–3].Climate change and environmental deterioration threaten the food security[4–6].Increasingly,infectious diseases(e.g.,HIV/AIDS),genetic diseases(e.g.,cancer),and improper lifestyle-related disorders(e.g.,obesity)become more prevalent and remain challenging to be prevented,controlled,and cured.Conventional medical technologies and modern medicine development are also meeting the ceiling.

关键词： expanded supporting deterioration

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