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The global integrative network:integration of signaling and metabolic pathways

aBIOTECH 2022年第4期3卷 281-291页

作者： Yuying Lin Shen Yan Xiao Chang xiaoquan qi Xu Chi Department of Dermatology Xuan Wu HospitalBeijing100053China Agricultural Information Institute Chinese Academy of Agricultural ScienceBeijing100081China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing100093China The Innovative Academy of Seed Design Chinese Academy of SciencesBeijing100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China

The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes.The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis.However,current databases use distinct structures to present signaling and metabolic pathways,which leads to the chaos in the integrated networks.Moreover,for the metabolic pathways,the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes,which hinders the topological analysis of the integrated networks.Here,we propose a novel“meta-pathway”structure,which uses the uniformed structure to display the signaling and metabolic pathways,and resolves the difficulty in linking the metabolic enzymes to the reactions topologically.We compiled a comprehensive collection of global integrative networks(GINs)by merging the meta-pathways of 7077 species.We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species—human,mouse,Arabidopsis,and rice.Almost all of the nodes were assembled into one major network for each of the four species,which provided opportunities for robust crosstalk and topological analysis,and knowledge graph construction.

关键词： Signaling pathways Metabolic pathways Integration Crosstalk of pathways

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Mining plant metabolomes:Methods,applications,and perspectives

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Plant Communications 2021年第5期2卷 92-105页

作者： Aimin Ma xiaoquan qi Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China Innovation Academy for Seed Design Chinese Academy of SciencesBeijing 100049China

Plants produce a variety of metabolites that are essential for plant growth and human health.To fully understand the diversity of metabolites in certain plants,lots of methods have been developed for metabolites detection and data processing.In the data-processing procedure,how to effectively reduce false-positive peaks,analyze large-scale metabolic data,and annotate plant metabolites remains challenging.In this review,we introduce and discuss some prominent methods that could be exploited to solve these problems,including a five-step filtering method for reducing false-positive signals in LC-MS analysis,QPMASS for analyzing ultra-large GC-MS data,and MetDNA for annotating metabolites.The main applications of plant metabolomics in species discrimination,metabolic pathway dissection,population genetic studies,and some other aspects are also highlighted.To further promote the development of plant metabolomics,more effective and integrated methods/platforms for metabolite detection and comprehensive databases for metabolite identification are highly needed.With the improvement of these technologies and the development of genomics and transcriptomics,plant metabolomics will be widely used in many fields.

关键词： plant metabolomics metabolites data-processing methods application

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Functional diversity and metabolic engineering of plantspecialized metabolites

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Life Metabolism 2022年第2期1卷 109-121页

作者： Shaoqun Zhou Yongshuo Ma Yi Shang xiaoquan qi Sanwen Huang Jiayang Li Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China Department of Chemical Engineering Massachusetts Institute of TechnologyCambridgeMA 02142USA Yunnan Key Laboratory of Potato Biology The CAAS-YNNU-YINMORE Joint Academy of Potato SciencesYunnan Normal UniversityKunmingYunan 650500China Key Laboratory of Plant Molecular Physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China State Key Laboratory of Plant Genomics National Center for Plant Gene ResearchInstitute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China

Plants are talented biochemists that produce a broad diversity of small molecules.These so-called specialized metabolites(SMs)play critical roles in the adaptive evolution of plants to defend against biotic and abiotic stresses,attract pollinators,and modulate soil microbiota for their own benefits.Many plant SMs have been used as nutrition and flavor compounds in our daily food,as well as drugs for treatment of human diseases.Current multi-omics tools have significantly accelerated the process of biosynthetic pathway elucidation in plants through correlation analyses,genetic mapping,and de novo biosynthetic gene cluster predictions.Understanding the biosynthesis of plant SMs has enabled reconstitution of naturally occurring specialized metabolic pathways in microbial hosts,providing a sustainable supply of these high-value molecules.In this review,we illustrate the general functions of several typical plant SMs in natural ecosystems and for human societies.We then provide an overview of current methods elucidating the biosynthetic pathways of plant SMs,and synthetic biology strategies that optimize the efficiency of heterologous biosynthetic pathways in microbial hosts.Moving forward,dissection of the functions and application of plant SMs by using current multidiscipline approaches would be greatly benefit to the scientific community and human societies.

关键词： plant specialized metabolites metabolic engineering

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Recent advances in multifunctional shape memory photonic crystals and practical applications

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Nano Research 2024年第1期17卷 79-96页

作者： Yong qi Shufen Zhang State Key Laboratory of Fine Chemicals Frontier Science Center for Smart MaterialsDalian University of TechnologyDalian 116024China

Shape memory photonic crystals(SMPCs)are smart composite materials with changeable structural color integrated by shape memory polymer and photonic crystals.SMPC can produce one or more temporary shapes through nanoscale deformation,memorizing current states.SMPC can be recovered to their original shapes or some intermediate states under external stimuli,accompanied by the variation of structural color.As porous carriers with built-in sensing properties,SMPCs promoted the interdisciplinary development of nanophotonic technology in materials science,environmental engineering,biomedicine,chemical engineering,and mechanics.Herein,the recent progress on multifunctional SMPCs and practical applications,including traditional and cold programmable SMPCs,is summarized and discussed.The primary concern is shape programming at the nanoscale that has demonstrated numerous attractive functions,including smart sensing,ink-free printing,solvent detection,reprogrammable gradient wetting,and controllable bubble transportation,under variations of the surface nanostructure.It aims to figure out the nanoscale shape memory effects on structural color conversion and additional performance,inspiring the fabrication of the next generation of SMPCs.Finally,perspectives on future research directions and applications are also presented.It is believed that multifunctional SMPCs are powerful nanophotonic tools for the interdisciplinary development of numerous disciplines in the future.

关键词： photonic crystal shape memory structural color cold programmable shape recovery

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Geometric Constraints for Global Regularity of 3D Shear Thickening Fluids

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Acta Mathematicae Applicatae Sinica 2024年第1期40卷 205-210页

作者： Jia-qi Yang Research&Development Institute of Northwestern Polytechnical University in Shenzhen Shenzhen518063China Key Laboratory for Mechanics in Fluid Solid Coupling Systems Institute of MechanicsChinese Academy of SciencesBeijing100190China

We consider the relation between the direction of the vorticity and the global regularity of 3D shear thickening fluids.It is showed that a weak solution to the non-Newtonian incompressible fluid in the whole space is... 详细信息

关键词： direction of the vorticity non-Newtonian fluid global regularity

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Plant metabolomics and metabolic biology

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Journal of Integrative Plant Biology 2014年第9期56卷 814-815页

作者： xiaoquan qi Dabing Zhang Institute of Botany the Chinese Academy of Sciences Shanghai Jiaotong University

Plants produce a large array of specialized metabolites（natural products）that not only are essential for growth and development,but also play important roles in adaptation to the variable stressful environments.Also,many plant metabolites are essential nutrient elements for humans and serve as natural drugs.However,study of the biosynthesis of natural products is still in its infancy,because more than 90%of plant metabolites are unknown and only a small number of genes/ enzymes involved in metabolism are identified in the model plants Arabidopsis and rice.

关键词： specialized nutrient adaptation biosynthesis environments genomics mutant anthocyanin biologic transcripts

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Understanding the spatial interaction of ultrasounds based on three-dimensional dual-frequency ultrasonic field numerical simulation

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China Foundry 2024年第1期21卷 29-43页

作者： Zhao-yang Yin qi-chi Le Yan-chao Jiang Da-zhi Zhao qi-yu Liao qi Zou Key Lab of Electromagnetic Processing of Materials Ministry of EducationNortheastern UniversityShenyang 110819China School of Materials Science and Engineering Northeastern UniversityShenyang 110819China

A transient 3D model was established to investigate the effect of spatial interaction of ultrasounds on the dual-frequency ultrasonic field in magnesium alloy melt.The effects of insertion depth and tip shape of the ultrasonic rods,input pressures and their ratio on the acoustic field distribution were discussed in detail.Additionally,the spacing,angle,and insertion depth of two ultrasonic rods significantly affect the interaction between distinct ultrasounds.As a result,various acoustic pressure distributions and cavitation regions are obtained.The spherical rods mitigate the longitudinal and transversal attenuation of acoustic pressure and expand the cavitation volume by 53.7%and 31.7%,respectively,compared to the plate and conical rods.Increasing the input pressure will enlarge the cavitation region but has no effect on the acoustic pressure distribution pattern.The acoustic pressure ratio significantly affects the pressure distribution and the cavitation region,and the best cavitation effect is obtained at the ratio of 2:1(P15:P20).

关键词： dual-frequency ultrasonic numerical model acoustic pressure spatial interaction magnesium alloy

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Adaptive sampling for corrugated plate digitization using a laser displacement sensor

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Science China(Technological Sciences) 2024年第5期67卷 1510-1523页

作者： WU ChengXing qi qi CHEN BaiJin YANG JiXiang DING Han State Key Laboratory of Intelligent Manufacturing Equipment and Technology School of Mechanical Science and EngineeringHuazhong University of Science and TechnologyWuhan430074China State Key Laboratory of Intelligent Manufacturing Equipment and Technology School of Materials Science and EngineeringHuazhong University of Science and TechnologyWuhan430074China

The surface quality of a corrugated plate directly determines the heat transfer property of the thermal power mechanical apparatus.Traditional detection methods are impractical for real-world production,being slow and destructive.In contrast,the point laser displacement sensor,employing the optical triangle method,emerges as a promising device for assessing parts with variable curvature and highly reflective surfaces.Despite its benefits,high-density sampling by an innate frequency introduces challenges such as data redundancy and a poor signal-to-noise ratio,potentially affecting the efficiency and precision of subsequent data processing.To address these challenges,adjustable frequency data sampling has been developed for this sensor,allowing adaptive sampling for corrugated plate digitization.The process begins with surface digitization to extract discrete points,which are transformed into intersection curves using the B-spline fitting technique.Subsequently,dominant points are identified,considering multigeometric constraints for curvature and arch height.Finally,the sampling signal is adjusted based on the distribution information of dominant points.Comparative results indicate that the proposed method effectively minimizes redundant sampling without compromising the accurate capture of essential geometric features.

关键词： corrugated plate laser displacement sensor adaptive sampling dominant point curvature arch height

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A systematic COSMO-RS study on mutual solubility of ionic liquids and C6-hydrocarbons

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Green Chemical Engineering 2024年第1期5卷 97-107页

作者： Chuxin qi Zhen Song Hongye Cheng Lifang Chen Zhiwen qi State Key Laboratory of Chemical Engineering School of Chemical EngineeringEast China University of Science and Technology130 Meilong RoadShanghai200237China

When considering the usage of ionic liquids(ILs)for reactions and separations involving non-polar or weak-polar hydrocarbons,the knowledge of the mutual solubility behaviors of ILs and hydrocarbons is of the utmost importance.In this work,taking four typical C6-hydrocarbons namely benzene,cyclohexene,cyclohexane,and hexane as representatives,the mutual solubility of ILs and non-polar or weak-polar hydrocarbons are systematically studied based on the COSMO-RS model.The reliability of COSMO-RS for these systems is first evaluated by comparing experimental and predicted hydrocarbon-in-IL activity coefficient at infinite dilution and binary/ternary liquid-liquid equilibria of related systems.Then,the mutual solubility of the four hydrocarbons and13,650 ILs(composed by 210 cations and 65 anions)are predicted.The effect of different IL structural characteristics including alkyl chain length,cation family/symmetry/functional group,and anion on the IL-hydrocarbon mutual solubility behaviors are further analyzed by the analyses of interaction energy and screen charge distribution.The mutual solubility databases and the structural effects identified thereon could provide useful guidance for IL selection in related applications.

关键词： C6-hydrocarbons Ionic liquids Mutual solubility COSMO-RS Structural effect analysis

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Deciphering and integrating invariants for neural operator learning with various physical mechanisms

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National Science Review 2024年第4期11卷 111-122页

作者： Rui Zhang qi Meng Zhi-Ming Ma Academy of Mathematics and Systems Science Chinese Academy of Sciences(CAS) Microsoft Research

Neural operators have been explored as surrogate models for simulating physical systems to overcome the limitations of traditional partial differential equation(PDE) solvers. However, most existing operator learning methods assume that the data originate from a single physical mechanism, limiting their applicability and performance in more realistic scenarios. To this end, we propose the physical invariant attention neural operator(PIANO) to decipher and integrate the physical invariants for operator learning from the PDE series with various physical mechanisms. PIANO employs self-supervised learning to extract physical knowledge and attention mechanisms to integrate them into dynamic convolutional layers.Compared to existing techniques, PIANO can reduce the relative error by 13.6%–82.2% on PDE forecasting tasks across varying coefficients, forces or boundary conditions. Additionally, varied downstream tasks reveal that the PI embeddings deciphered by PIANO align well with the underlying invariants in the PDE systems, verifying the physical significance of PIANO.

关键词： neural operator PDE solver contrastive learning physical invariants

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