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Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories

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Synthetic and Systems Biotechnology 2023年第3期8卷 498-508页

作者： Yalun Wu qianqian yuan Yongfu Yang Defei Liu Shihui Yang Hongwu Ma State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan430062HubeiChina Biodesign Center Key Laboratory of Systems Microbial BiotechnologyTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China Hubei Key Laboratory of Applied Mathematics Faculty of Mathematics and StatisticsHubei UniversityWuhan430062HubeiChina Artificial Intelligence and Knowledge Engineering Lab School of Computer Science and Information EngineeringHubei UniversityWuhan430062HubeiChina

High-quality genome-scale metabolic models(GEMs)could play critical roles on rational design of microbial cell factories in the classical Design-Build-Test-Learn cycle of synthetic biology *** of the constant establishment and update of GEMs for model microorganisms such as Escherichia coli and Saccharomyces cerevisiae,high-quality GEMs for non-model industrial microorganisms are still *** mobilis *** ZM4 is a non-model ethanologenic microorganism with many excellent industrial characteristics that has been developing as microbial cell factories for biochemical *** five GEMs of *** have been constructed,these models are either generating ATP incorrectly,or lacking information of plasmid genes,or not providing standard format *** this study,a high-quality GEM iZM516 of *** ZM4 was *** information from the improved genome annotation,literature,datasets of Biolog Phenotype Microarray studies,and recently updated Gene-Protein-Reaction information was combined for the curation of ***,516 genes,1389 reactions,1437 metabolites,and 3 cell compartments are included in iZM516,which also had the highest MEMOTE score of 91%among all published GEMs of *** growth was then predicted by iZM516,which had 79.4%agreement with the experimental results of the substrate *** addition,the potential endogenous succinate synthesis pathway of *** ZM4 was proposed through simulation and analysis using ***,metabolic engineering strategies to produce succinate and 1,4-butanediol(1,4-BDO)were designed and then simulated under anaerobic condition using *** results indicated that 1.68 mol/mol succinate and 1.07 mol/mol 1,4-BDO can be achieved through combinational metabolic engineering strategies,which was comparable to that of the model species *** study thus not only established a high-quality GEM iZM516 to help understand and design microbial cell fac

关键词： Genome-scale metabolic models(GEMSs) Non-model industrial microorganism Zymomonas mobilis Biolog phenotype microarray Succinate 1,4-Butanediol

Friction Characteristics of Space Lubricating Oil No.4129 in Rolling and Sliding Contact

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China Petroleum Processing & Petrochemical Technology 2014年第2期16卷 79-83页

作者： Wang Yanshuang Cao Jiawei Li Hang Li Pu yuan qianqian Henan University of Science and Technology

The friction coefficients between the surfaces of a ball and a disc lubricated by a space lubricating oil No.4129 were measured at various operating conditions on a ball-disc friction test rig. Friction characteristic curves were obtained under sliding and rolling movements at point contact. A new model for calculation of the friction coefficient was presented. The results show that the bigger the load is, the larger the friction coefficient becomes. The rolling speed ranging from 1 m/s to10 m/s has an important effect on the friction coefficient. The friction coefficient increases with the increase in sliding speed and the decrease in rolling speed. The linear variation region of the friction coefficient versus the sliding speed at high rolling speed is wider than that at low rolling speed. The model for calculation of the friction coefficient is accurate for engineering use.

关键词： lubricating oil friction coefficient rolling and sliding contact friction characteristic

Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501

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Synthetic and Systems Biotechnology 2023年第4期8卷 688-696页

作者： qianqian yuan Fan Wei Xiaogui Deng Aonan Li Zhenkun Shi Zhitao Mao Feiran Li Hongwu Ma Biodesign Center Key Laboratory of Engineering Biology for Low-carbon ManufacturingTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China University of Chinese Academy of Sciences Beijing100049China National Technology Innovation Center of Synthetic Biology Tianjin300308China School of Biological Engineering Tianjin University of Science and TechnologyTianjinChina Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhen518055China

Pseudomonas stutzeri A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial *** a prominent strain in the fields of agriculture and bioengineering,there is still a lack of comprehensive understanding regarding its metabolic capabilities,specifically in terms of central metabolism and substrate ***,further exploration and extensive studies are required to gain a detailed insight into these *** study reconstructed a genome-scale metabolic network model for *** A1501 and conducted extensive curations,including correcting energy generation cycles,respiratory chains,and biomass *** final model,iQY1018,was successfully developed,covering more genes and reactions and having higher prediction accuracy compared with the previously published model *** substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model *** model prediction accuracy of substrate utilization for *** A1501 reached 90%.The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived *** work provides an updated,high-quality model of *** A1501for further research and will further enhance our understanding of the metabolic capabilities.

关键词： network prediction metabolism

Estimating the quarantine failure rate for COVID-19

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Infectious Disease Modelling 2021年第1期6卷 924-929页

作者： Meili Li qianqian yuan Pian Chen Baojun Song Junling Ma College of Science Donghua UniversityShanghai201620China Department of Applied Mathematics and Statistics Montclair State UniversityMontclairNJ07043USA Department of Mathematics and Statistics University of VictoriaVictoriaBCV8W 2Y2Canada

Quarantine is a crucial control measure in reducing imported COVID-19 cases and community ***,some quarantined COVID-19 patients may show symptoms after finishing quarantine due to a long median incubation period,potentially causing community *** assess the recommended 14-day quarantine policy,we develop a formula to estimate the quarantine failure rate from the incubation period distribution and the epidemic *** found that the quarantine failure rate increases with the exponential growth rate of the epidemic *** apply our formula to United States,Canada,and Hubei Province,*** the lockdown of Wuhan City,the quarantine failure rate in Hubei Province is about 4.1%.If the epidemic curve flattens or slowly decreases,the failure rate is less than 2.8%.The failure rate in US may be as high as 8.3%-11.5%due to a shorter 10-day quarantine period,while the failure rate in Canada may be between 2.5%and 3.9%.A 21-day quarantine period may reduce the failure rate to 0.3%-0.5%.

关键词： Quarantine Incubation period Exponential growth rate Epidemic curve

Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework

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Research 2023年第3期2023卷 117-128页

作者： Zhenkun Shi Rui Deng qianqian yuan Zhitao Mao Ruoyu Wang Haoran Li Xiaoping Liao Hongwu Ma Biodesign Center Key Laboratory of Engineering Biology for Low-carbon ManufacturingTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences300308TianjinChina National Center of Technology Innovation for Synthetic Biology 300308TianjinChina College of Biotechnology Tianjin University of Science&TechnologyTianjinChina Haihe Laboratory of Synthetic Biology 300308.TianjinChina

Enzyme commission(EC)numbers,which associate a protein sequence with the biochemical reactions it catalyzes,are essential for the accurate understanding of enzyme functions and cellular *** ab initio computational approaches were proposed to predict EC numbers for given input protein ***,the prediction performance(accuracy,recall,and precision),usability,and efficiency of existing methods decreased seriously when dealing with recently discovered proteins,thus still having much room to be ***,we report HDMLF,a hierarchical dual-core multitask learning framework for accurately predicting EC numbers based on novel deep learning *** is composed of an embedding core and a learning core;the embedding core adopts the latest protein language model for protein sequence embedding,and the learning core conducts the EC number ***,HDMLF is designed on the basis of a gated recurrent unit framework to perform EC number prediction in the multi-objective hierarchy,multitasking ***,we introduced an attention layer to optimize the EC prediction and employed a greedy strategy to integrate and fine-tune the final *** analyses against 4 representative methods demonstrate that HDMLF stably delivers the highest performance,which improves accuracy and F1 score by 60%and 40%over the state of the art,*** additional case study of tyrB predicted to compensate for the loss of aspartate aminotransferase aspC,as reported in a previous experimental study,shows that our model can also be used to uncover the enzyme ***,we established a web platform,namely,ECRECer(https://***),using an entirely could-based serverless architecture and provided an offline bundle to improve usability.

关键词： server prediction entirely

ECMpy 2.0:A Python package for automated construction and analysis of enzyme-constrained models

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Synthetic and Systems Biotechnology 2024年第3期9卷 494-502页

作者： Zhitao Mao Jinhui Niu Jianxiao Zhao yuanyuan Huang Ke Wu Liyuan Yun Jirun Guan qianqian yuan Xiaoping Liao Zhiwen Wang Hongwu Ma Biodesign Center Key Laboratory of Engineering Biology for Low-carbon ManufacturingTianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China National Center of Technology Innovation for Synthetic Biology Tianjin300308China Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) Tianjin UniversityTianjin300072China College of Biotechnology Tianjin University of Science and TechnologyTianjin300457China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina Tianjin Agricultural College Tianjin300384China Haihe Laboratory of Synthetic Biology Tianjin300308China

Genome-scale metabolic models(GEMs)have been widely employed to predict microorganism ***,GEMs only consider stoichiometric constraints,leading to a linear increase in simulated growth and product yields as substrate uptake rates *** divergence from experimental measurements prompted the creation of enzyme-constrained models(ecModels)for various species,successfully enhancing chemical *** upon studies that allocate macromolecule resources,we developed a Python-based workflow(ECMpy)that constructs an enzyme-constrained *** involves directly imposing an enzyme amount constraint in GEM and accounting for protein subunit composition in ***,this procedure de-mands manual collection of enzyme kinetic parameter information and subunit composition details,making it rather *** this work,we’ve enhanced the ECMpy toolbox to version 2.0,broadening its scope to automatically generate ecGEMs for a wider array of *** 2.0 automates the retrieval of enzyme kinetic parameters and employs machine learning for predicting these parameters,which significantly enhances parameter ***,ECMpy 2.0 introduces common analytical and visualization features for ecModels,rendering computational results more user ***,ECMpy 2.0 seamlessly integrates three published algorithms that exploit ecModels to uncover potential targets for metabolic *** 2.0 is available at https://***/tibbdc/ECMpy or as a pip package(https://***/project/ECMpy/).

关键词： Enzyme-constrained model Python package Automated construction Multiple analysis functions

A self-monitoring microneedle patch for light-controlled synergistic treatment of melanoma

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Bioactive Materials 2023年第9期27卷 58-71页

作者： Chenyuan Wang Yongnian Zeng Kai-Feng Chen Jiawei Lin qianqian yuan Xue Jiang Gaosong Wu Fubing Wang Yong-Guang Jia Wei Li Department of Thyroid and Breast Surgery Zhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China School of Materials Science and Engineering South China University of TechnologyGuangzhouGuangdong510641China TaiKang Center for Life and Medical Sciences Wuhan UniversityWuhanChina Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center Zhongnan Hospital of Wuhan UniversityWuhanChina Wuhan Research Center for Infectious Diseases and Cancer Chinese Academy of Medical SciencesWuhanChina

Melanoma is the most aggressive and malignant form of skin *** melanoma treatment methods generally suffer from frequent drug administration as well as difficulty in direct monitoring of drug ***,a self-monitoring microneedle(MN)-based drug delivery system,which integrates a dissolving MN patch with aggregation-induced emission(AIE)-active PATC microparticles,is designed to achieve light-controlled pulsatile chemo-photothermal synergistic therapy of *** PATC polymeric particles,termed D/I@PATC,encapsulate both of chemotherapeutic drug doxorubicin(DOX)and the photothermal agent indocyanine green(ICG).Upon light illumination,PATC gradually dissociates into smaller particles,causing the release of encapsulated DOX and subsequent fluorescence intensity change of PATC particles,thereby not only enabling direct observation of the drug release process under light stimuli,but also facilitating verification of drug release by fluorescence recovery after light ***,encapsulation of ICG in PATC particles displays significant improvement of its photothermal stability both in vitro and in *** a tumor-bearing mouse,the application of one D/I@PATC MN patch combining with two cycles of light irradiation showed excellent controllable chemo-photothermal efficacy and exhibited~97%melanoma inhibition rate without inducing any evident systemic toxicity,suggesting a great potential for skin cancer treatment in clinics.

关键词： Microneedle Controlled release Melanoma AIE Photothermal therapy Chemotherapy

负游隙对特大型双排四点接触球轴承载荷分布的影响

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机械工程学报 2012年第21期48卷 110-115页

作者：王燕霜袁倩倩河南科技大学机电工程学院洛阳471003

给出负游隙双排四点接触球轴承接触载荷分布的计算模型。采用Newton–Raphson法计算了某型号双排四点接触球轴承在联合载荷时不同负游隙下的接触载荷分布情况,分析负游隙与轴承接触载荷分布的关系,并与经验公式的计算结果进行对比。结... 详细信息

给出负游隙双排四点接触球轴承接触载荷分布的计算模型。采用Newton–Raphson法计算了某型号双排四点接触球轴承在联合载荷时不同负游隙下的接触载荷分布情况,分析负游隙与轴承接触载荷分布的关系,并与经验公式的计算结果进行对比。结果表明:计算模型正确合理。随着负游隙绝对值增大,发生4点接触的钢球数越多,直到所有钢球都发生4点接触;轴承中最大接触载荷随负游隙绝对值的增大先减小后增大。双排四点接触球轴承上排钢球与滚道接触的最大接触载荷比下排球与滚道接触的最大接触载荷大。

关键词：变桨轴承双排球轴承负游隙四点接触

特大型四点接触球轴承沟曲率半径系数的设计方法

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机械工程学报 2015年第21期51卷 80-86页

作者：王燕霜袁倩倩天津职业技术师范大学机械工程学院天津300222 河南科技大学机电工程学院洛阳471003

沟曲率半径系数是轴承设计中一个重要的设计参数,对轴承的承载能力和疲劳寿命有较大影响。目前为止,特大型四点接触球轴承沟曲率半径系数的设计依靠经验取值,缺乏设计依据,由此设计出来的轴承不能保证满足承载能力的要求。给出了特大型... 详细信息

沟曲率半径系数是轴承设计中一个重要的设计参数,对轴承的承载能力和疲劳寿命有较大影响。目前为止,特大型四点接触球轴承沟曲率半径系数的设计依靠经验取值,缺乏设计依据,由此设计出来的轴承不能保证满足承载能力的要求。给出了特大型四点接触球轴承精确静承载曲线的绘制方法,提出了根据特大型四点接触球轴承精确静承载曲线设计轴承沟曲率半径系数的方法并给出了相应的设计流程,同时还给出了此类轴承疲劳寿命的计算方法。给出的沟曲率半径系数设计方法能够精确设计特大型四点接触球轴承的沟曲率半径系数,设计出的轴承一定满足轴承承载能力的要求及较高疲劳寿命的要求。此外,该设计方法可提高轴承的设计效率,并为轴承沟曲率半径系数设计方法的发展提供理论基础。

关键词：沟曲率半径系数特大型轴承四点接触球轴承静承载能力