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The Clausena lansium genome provides new insights into alkaloid diversity and the evolution of the methyltransferase family

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Journal of Integrative Agriculture 2024年第10期23卷 3537-3553页

作者： Yongzan wei yi wang Fuchu Hu wei wang Changbin wei Bingqiang Xu Liqin Liu Huayang Li Can wang Hongna Zhang Zhenchang Liang Jianghui Xie State Key Laboratory of Biological Breeding of Tropical Crops Institute of Tropical Bioscience and BiotechnologyChineseAcademy of Tropical Agricultural SciencesHaikou 571101China Key Laboratory of Genetic Resources Evaluation and Utilization of Tropical Fruits and Vegetables(Co-construction by Ministryand Province) Ministry of Agriculture and Rural Affairs/Institute of Tropical Fruit TreesHainan Academy of Agricultural SciencesHaikou 571100China Beijing Key Laboratory of Grape Sciences and Enology CAS Key Laboratory of Plant ResourcesInstitute of BotanyChineseAcademy of SciencesBeijing 100093China Key Laboratory of Tropical Fruit Biology(Ministry of Agriculture and Rural Affairs) South Subtropical Crops Research InstituteChinese Academy of Tropical Agricultural SciencesZhanjiang 524091China Haikou Experimental Station Chinese Academy of Tropical Agricultural SciencesHaikou 571101China Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry Hainan UniversityHaikou 570228China Sanya Research Academy Chinese Academy of Tropical Agricultural SciencesSanya 572019China

Wampee(Clausena lansium)is an important evergreen fruit tree native to southern China that has a long history of use for medicinal ***,a chromosome-level genome of *** was constructed with a genome size of 282.9 Mb and scaffold N50 of 30.75 *** assembled genome contains 48.70%repetitive elements and 24,381 protein-coding *** genomic analysis showed that *** diverged from Aurantioideae 15.91-24.95 million years ***,some expansive and specific gene families related to methyltransferase activity and S-adenosylmethionine-dependent methyltransferase activity were also *** analysis indicated that N-methyltransferase(NMT)is mainly involved in alkaloid biosynthesis and O-methyltransferase(OMT)participates in the regulation of coumarin accumulation in *** suggested that wampee's richness in alkaloids and coumarins might be due to the gene expansions of NMT and *** tandem repeat event was one of the major reasons for the NMT ***,the reference genome of *** will facilitate the identification of some useful medicinal compounds from wampee resources and reveal their biosynthetic pathways.

关键词： Clausena lansium genome evolution methyltransferase activity alkaloid biosynthesis coumarin accumulation

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Disruption of non-classically secreted protein(MoMtp)compromised conidiation,stress homeostasis,and pathogenesis of Magnaporthe oryzae

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Journal of Integrative Agriculture 2024年第8期23卷 2686-2702页

作者： Wajjiha Batool Justice Norvienyeku wei yi Zonghua wang Shihong Zhang Lili Lin Key Laboratory for Extreme-Environmental Microbiology College of Plant ProtectionShenyang Agricultural UniversityShenyang 110866China Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops College of Life ScienceFujian Agriculture and Forestry UniversityFuzhou 350002China Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests College of Plant ProtectionHainan UniversityHaikou 570288China

Blast disease,caused by the hemibiotrophic ascomycete fungus,Magnaporthe oryzae,is a significant threat to sustainable rice production *** have shown that the blast fungus secretes vast arrays of functionally diverse proteins into the host cell for a successful disease ***,the final destinations of these effector proteins inside the host cell and their role in advancing fungal pathogenesis remain a ***,we reported that a putative mitochondrial targeting non-classically secreted protein(MoMtp)positively regulates conidiogenesis and appressorium maturation in ***,MoM TP gene deletion mutant strains triggered a hypersensitive response when inoculated on rice leaves displaying that MoMtp is essential for the virulence of *** addition,cell wall and oxidative stress results indicated that MoMtp is likely involved in the maintenance of the structural integrity of the fungus *** study also demonstrates an upregulation in the expression pattern of the MoMTP gene at all stages of infection,indicating its possible regulatory role in host invasion and the infectious development of ***,Agrobacterium infiltration and sheath inoculation confirmed that MoMtpGFP protein is predominantly localized in the host mitochondria of tobacco leaf and rice *** together,we conclude that MoMtp protein likely promotes the normal conidiation and pathogenesis of *** and might have a role in disturbing the proper functioning of the host mitochondria during pathogen invasion.

关键词： plant–pathogen interactions effectors hypersensitive response pathogenesis mitochondria

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NONMONOTONE LOCAL MINIMAX METHODS FOR FINDING MULTIPLE SADDLE POINTS

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Journal of Computational Mathematics 2024年第3期42卷 851-884页

作者： wei Liu Ziqing Xie Wenfan yi South China Research Center for Applied Mathematics and Interdisciplinary Studies South China Normal UniversityGuangzhou 510631China Key Laboratory of Computing and Stochastic Mathematics(Ministry of Education) Hunan Normal UniversityChangshaHunan 410081China Hunan Provincial Key Laboratory of Intelligent Information Processing and Applied Mathematics School of MathematicsHunan UniversityChangshaHunan 410082China

In this paper,by designing a normalized nonmonotone search strategy with the BarzilaiBorwein-type step-size,a novel local minimax method(LMM),which is a globally convergent iterative method,is proposed and analyzed to find multiple(unstable)saddle points of nonconvex functionals in Hilbert *** to traditional LMMs with monotone search strategies,this approach,which does not require strict decrease of the objective functional value at each iterative step,is observed to converge faster with less ***,based on a normalized iterative scheme coupled with a local peak selection that pulls the iterative point back onto the solution submanifold,by generalizing the Zhang-Hager(ZH)search strategy in the optimization theory to the LMM framework,a kind of normalized ZH-type nonmonotone step-size search strategy is introduced,and then a novel nonmonotone LMM is *** feasibility and global convergence results are rigorously carried out under the relaxation of the monotonicity for the functional at the iterative ***,in order to speed up the convergence of the nonmonotone LMM,a globally convergent Barzilai-Borwein-type LMM(GBBLMM)is presented by explicitly constructing the Barzilai-Borwein-type step-size as a trial step-size of the normalized ZH-type nonmonotone step-size search strategy in each ***,the GBBLMM algorithm is implemented to find multiple unstable solutions of two classes of semilinear elliptic boundary value problems with variational structures:one is the semilinear elliptic equations with the homogeneous Dirichlet boundary condition and another is the linear elliptic equations with semilinear Neumann boundary *** numerical results indicate that our approach is very effective and speeds up the LMMs significantly.

关键词： Multiple saddle points Local minimax method Barzilai-Borwein gradient method Normalized nonmonotone search strategy Global convergence

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Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer

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Cancer Biology & Medicine 2024年第1期21卷 83-103页

作者： Yumei wang Haiyan wang wei Shao Yuhui Chen Yu Gui Chao Hu Xiaohong yi Lijun Huang Shasha Li Dong wang School of Basic Medical Sciences State Key Laboratory of Southwestern Chinese Medicine ResourcesChengdu University of Traditional Chinese MedicineChengdu 611137China Department of Pathology School of MedicineQinghai UniversityXining 810001China Omics Biosciences Inc Beijing 100871China Laboratory of Integrative Medicine Clinical Research Center for BreastState Key Laboratory of BiotherapyWest China HospitalSichuan University and Collaborative Innovation CenterChengdu 610041China State Key Laboratory of Southwestern Chinese Medicine Resources School of PharmacyChengdu University of Traditional Chinese MedicineChengdu 611137China Department of Endocrinology and Metabolism Guangdong Provincial Key Laboratory of Diabetology&Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity ResearchMedical Center for Comprehensive Weight ControlThe Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510630China

Objective:Epigenetic abnormalities have a critical role in breast cancer by regulating gene expression;however,the intricate interrelationships and key roles of approximately 400 epigenetic regulators in breast cancer remain *** is important to decipher the comprehensive epigenetic regulatory network in breast cancer cells to identify master epigenetic regulators and potential therapeutic ***:We employed high-throughput sequencing-based high-throughput screening(HTS^(2))to effectively detect changes in the expression of 2,986 genes following the knockdown of 400 epigenetic ***,bioinformatics analysis tools were used for the resulting gene expression signatures to investigate the epigenetic regulations in breast ***:Utilizing these gene expression signatures,we classified the epigenetic regulators into five distinct clusters,each characterized by specific *** discovered functional similarities between BAZ2B and SETMAR,as well as CLOCK and ***,we observed that CLOCK functions in a manner opposite to that of HDAC8 in downstream gene ***,we constructed an epigenetic regulatory network based on the gene expression signatures,which revealed 8 distinct modules and identified 10 master epigenetic regulators in breast ***:Our work deciphered the extensive regulation among hundreds of epigenetic *** identification of 10 master epigenetic regulators offers promising therapeutic targets for breast cancer treatment.

关键词： Epigenetic regulators breast cancer regulatory network HTS^(2)

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A Geometric Based Connection between Fractional Calculus and Fractal Functions

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Acta Mathematica Sinica,English Series 2024年第2期40卷 537-567页

作者： Yong Shun LIANG wei yi SU School of Mathematics and Statistic Nanjing University of Science and TechnologyNanjing 210094P.R.China Department of Mathematics Nanjing UniversityNanjing 210023P.R.China

Establishing the accurate relationship between fractional calculus and fractals is an important research content of fractional calculus *** the present paper,we investigate the relationship between fractional calculus and fractal functions,based only on fractal dimension *** dimension of the Riemann-Liouville fractional integral of continuous functions seems no more than fractal dimension of functions *** fractal dimension of the Riemann-Liouville fractional differential of continuous functions seems no less than fractal dimension of functions themselves when they *** further discussion,fractal dimension of the Riemann-Liouville fractional integral is at least linearly decreasing and fractal dimension of the Riemann-Liouville fractional differential is at most linearly increasing for the Holder continuous *** about other fractional calculus,such as the Weyl-Marchaud fractional derivative and the Weyl fractional integral has also been given *** work is helpful to reveal the mechanism of fractional calculus on continuous *** the same time,it provides some theoretical basis for the rationality of the definition of fractional *** is also helpful to reveal and explain the internal relationship between fractional calculus and fractals from the perspective of geometry.

关键词： Fractional calculus fractal functions fractal dimension fractional calculus equation relationship

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Single-atom-mediated electron islands boost photocatalytic CO_(2)chemical fixation

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Science China Chemistry 2024年第7期67卷 2292-2299页

作者： Shu Shang Lei Li Xin He Hui wang Lirong Zheng wei Shao Xiaodong Zhang yi Xie Hefei National Research Center for Physical Sciences at the Microscale University of Science and Technology of ChinaHefei 230026China Institute of Energy Hefei Comprehensive National Science CenterHefei 230031China Beijing Synchrotron Radiation Facility Institute of High Energy PhysicsChinese Academy of SciencesBeijing 100049China School of Chemistry and Chemical Engineering Hefei Normal UniversityHefei 230031China

Photocatalytic cycloadditions of CO_(2)with epoxides are emerging as a significant platform for the green synthesis of valuable carbonates,where efficient catalytic systems with spatially separated charge carriers are ***,a single p-block metal atom is proposed to be a candidate for photogenerated electron localization on a metal oxide *** taking the Bi single-atom supported on ZnO nanosheet(Bi1/ZnO)as an example,we show that the Bi atom plays the role of an electron island in the sea of delocalized holes within ***,the as-formed electron island could readily promote the rate-determining ring-opening process of cycloaddition *** from the unique spatially separated electrons and holes,the Bi1/ZnO achieves a high yield of cyclic carbonates with almost 100%*** study provides a pioneering strategy for enhancing the performances of photocatalytic CO_(2)chemical fixation.

关键词： electron islands CO_(2)photofixation photogenerated charge carriers

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Improved Twin Support Vector Machine Algorithm and Applications in Classification Problems

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China Communications 2024年第5期21卷 261-279页

作者： Sun yi wang Zhouyang Beijing University of Posts and Telecommunications School of Computer Science(National Pilot Software Engineering School) Beijing University of Posts and Telecommunications International School

The distribution of data has a significant impact on the results of *** the distribution of one class is insignificant compared to the distribution of another class,data imbalance *** will result in rising outlier values and ***,the speed and performance of classification could be greatly *** the above problems,this paper starts with the motivation and mathematical representing of classification,puts forward a new classification method based on the relationship between different classification *** with the vector characteristics of the actual problem and the choice of matrix characteristics,we firstly analyze the orderly regression to introduce slack variables to solve the constraint problem of the lone *** we introduce the fuzzy factors to solve the problem of the gap between the isolated points on the basis of the support vector *** introduce the cost control to solve the problem of sample ***,based on the bi-boundary support vector machine,a twostep weight setting twin classifier is *** can help to identify multitasks with feature-selected patterns without the need for additional optimizers,which solves the problem of large-scale classification that can’t deal effectively with the very low category distribution gap.

关键词： fuzzy ordered regression(OR) relaxing variables twin support vector machine

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Identification of residues in Lassa virus glycoprotein 1 involved in receptor switch

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Virologica Sinica 2024年第4期39卷 600-608页

作者： Jiao Guo yi Wan Yang Liu Xiaoying Jia Siqi Dong Gengfu Xiao wei wang State Key Laboratory of Virology Wuhan Institute of VirologyCenter for Biosafety Mega-ScienceChinese Academy of SciencesWuhan 430071China University of the Chinese Academy of Sciences Beijing 100049China The Xi'an Key Laboratory of Pathogenic Microorganism and Tumor Immunity School of Basic MedicineXi'an Medical UniversityXi'an 710021China

Lassa virus(LASV)is an enveloped,negative-sense RNA virus that causes Lassa hemorrhagic *** entry of LASV requires the viral glycoprotein 1(GP1)to undergo a receptor switch from its primary receptor alpha-dystroglycan(α-DG)to its endosomal receptor lysosome-associated membrane protein 1(LAMP1).A conserved histidine triad in LASV GP1 has been reported to be responsible for receptor *** test the hypothesis that other non-conserved residues also contribute to receptor switch,we constructed a series of mutant LASV GP1 proteins and tested them for binding to *** residues,L84,K88,L107,and H170,were identified as critical for receptor *** any of the four residues with the corresponding lymphocytic choriomeningitis virus(LCMV)residue(L84 N,K88E,L10F,and H170S)reduced the binding affinity of LASV GP1 for ***,all mutations caused decreases in glycoprotein precursor(GPC)-mediated membrane fusion at both pH 4.5 and *** infectivity of pseudotyped viruses bearing either GPCL84N or GPCK88E decreased sharply in multiple cell types,while L107F and H170S had only mild effects on *** biolayer light interferometry assay,we found that all four mutants had decreased binding affinity to LAMP1,in the order of binding affinity being L84 N>L107F>K88E>*** four amino acid loci identified for the first time in this study have important reference significance for the in-depth investigation of the mechanism of receptor switching and immune escape of LASV occurrence and the development of reserve anti-LASV infection drugs.

关键词： Lassa virus(LASV) Lysosome-associated membrane protein 1 (LAMP1) Glycoprotein Receptor switch Membrane fusion

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Application of Global Dynamic Reconfiguration in Artificial Neural Network System based on Field Programmable Gate Array

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Semiconductor Photonics and Technology 2008年第3期14卷 174-178,195页

作者： LI wei wang wei MA yi-mei wang Jin-hai School of Information and Communication Engineering Tianjin Polytechnic University Tianjin 300160 CHN

Presented is a global dynamic reconfiguration design of an artificial neural network based on field programmable gate array(FPGA). Discussed are the dynamic reconfiguration principles and methods. Proposed is a global dynamic reconfiguration scheme using Xilinx FPGA and platform flash. Using the revision capabilities of Xilinx XCF32P platform flash, an artificial neural network based on Xilinx XC2V30P Virtex-Ⅱ can be reconfigured dynamically from back propagation(BP) learning algorithms to BP network testing algorithms. The experimental results indicate that the scheme is feasible, and that, using dynamic reconfiguration technology, FPGA resource utilization can be reduced remarkably.

关键词： FPGA dynamic reconfiguration platform flash global reconfiguratiom artificial neural network

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A Rapid and Effective HPLC Method for Identification of Bovis Calculus in Chinese Patent Medicines

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Chinese Herbal Medicines 2013年第3期5卷 224-233页

作者： XIA Jing XIA Li wang wei-yi SHA yi-wei wang Ke JI Shen Shanghai Institute for Food and Drug Control Guangdong Food and Drug Vocational College Key Laboratory of Marine Biogenetic Resources Third Institute of OceanographyState Oceanic Administration (SOA) Shanghai Chongming Institute for Food and Drug Control

Objective Due to the limited resource and the large demand,many kinds of Bovis Calculus(BC) including artificial Bovis Calculus(ABC),in vivo cultured Bovis Calculus(in vivo CBC),and in vitro cultured Bovis Calculus(in vitro CBC)were used in Chinese patent medicines(CPMs).Previous studies have shown that the chemical constituents of ABC and their properties were different from other *** two types of CBC with much higher price than ABC were approximately equivalent with natural Bovis Calculus in quality and clinical *** aim of the study is to establish a rapid and effective method for the identification of BC in *** An HPLC method with the higher specificity for analyzing bilirubin was established to distinguish ABC from other three kinds of BC by comparing the change of bilirubin content with the addition of EDTA-2Na as the extraction solvent and *** The bilirubin content in CPMs containing ABC was basically unchanged,while that in CPMs containing other kinds of BC showed significant *** proposed method was employed to analyze a variety of CPMs containing Bovis Calculus(CPMBCs) and proven to be *** An effective analytical method is established for the quality control of CPMBCs and further ensures the safety and efficacy of these drugs in clinical practice.

关键词： artificial Bovis Calculus bilirubin Bovis Calculus Chinese patent medicines cultured Bovis Calculus EDTA-2Na solution

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