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Toward fine-tuned metabolic networks in industrial microorganisms

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Synthetic and Systems Biotechnology 2020年第2期5卷 81-91页

作者： Ning Li Weizhu zeng sha Xu Jingwen Zhou Key Laboratory of Industrial Biotechnology Ministry of Education and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University1800 Lihu RoadWuxiJiangsu214122China Jiangsu Provisional Research Center for Bioactive Product Processing Technology Jiangnan University1800 Lihu RoadWuxiJiangsu214122China

There are numerous microorganisms in nature capable of synthesizing diverse useful compounds;however,these natural microorganisms are generally inefficient in the production of target products on an industrial scale,relative to either chemical synthesis or extraction *** achieve industrial production of useful compounds,these natural microorganisms must undergo a certain degree of mutation or effective fine-tuning *** review describes how to achieve an ideal metabolic fine-tuned process,including static control strategies and dynamic control *** static control strategies mainly focus on various matabolic engineering strategies,including protein engineering,upregulation/downregulation,and combinatrorial control of these metabolic engineering strategies,to enhance the flexibility of their application in fine-tuned metabolic ***,we focus on the dynamic control strategies for fine-tuned metabolic *** design principles derived would guide us to construct microbial cell factories for various useful compounds.

关键词： Fine-tuned regulation Protein engineering Upregulation Downregulation Dynamic regulation

FluxExplorer: A general platform for modeling and analyses of metabolic net-works based on stoichiometry

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Chinese Science Bulletin 2006年第6期51卷 689-696页

作者： LUO Ruoyu LIAO sha zeng shaoqun LI Yixue LUO Qingming Hubei Bioinformatics and Molecular Imaging Key Laboratory Huazhong University of Science and Technology Wuhan 430074China shanghai Center for Bioinformation Technology Shanghai 200233China These authors contributed equally to this work

Stoichiometry-based analyses of meta- bolic networks have aroused significant interest of systems biology researchers in recent years. It is necessary to develop a more convenient modeling platform on which users can reconstruct their network models using completely graphical operations, and explore them with powerful analyzing modules to get a better understanding of the properties of metabolic systems. Herein, an in silico platform, FluxExplorer, for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research. This platform integrates various analytic approaches, in- cluding flux balance analysis, minimization of meta- bolic adjustment, extreme pathways analysis, shadow prices analysis, and singular value decom- position, providing a thorough characterization of the metabolic system. Using a graphic modeling process, metabolic networks can be reconstructed and modi- fied intuitively and conveniently. The inconsistencies of a model with respect to the FBA principles can be proved automatically. In addition, this platform sup- ports systems biology markup language (SBML). FluxExplorer has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results. Generally, it is a powerful and very convenient tool for metabolic network modeling and analysis.

关键词：新陈代谢化学计量学系统生物学流量平衡分析计算模型

CoNi nanoparticles anchored inside carbon nanotube networks by transient heating:Low loading and high activity for oxygen reduction and evolution

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Journal of Energy Chemistry 2021年第3期30卷 63-71页

作者： Chengfeng Zhu Wei Yang Jiangtao Di sha zeng Jian Qiao Xiaona Wang Bo Lv Qingwen Li Key Laboratory of Multifunctional Nanomaterials and Smart Systems Advanced Materials Division.Suzhou Institute of Nano-Tech and Nano-BionicsChinese Academy of SciencesSuzhou 215123JiangsuChina School of Nano-Tech and Nano-Bionics University of Science and Technology of ChinaHefei 230026AnhuiChina Division of Nanomaterials Suzhou Institute of Nano-Tech and Nano-BionicsChinese Academy of SciencesNanchang 330200JiangxiChina School of Materials Science and Engineering and Key Laboratory of Aerospace Materials and Performance Ministry of EducationBeihang UniversityBeijing 100083China

Transitional metal alloy and compounds have been developed as the low cost and efficient bifunctional electrocatalysts for oxygen reduction reaction(ORR)and oxygen evolution reaction(OER).However,a high mass loading of these catalysts is commonly needed to achieve acceptable catalytic performance,which could cause such problems as battery weight gain,mass transport blocking,and catalyst *** report herein the preparation of fine CoNi nanoparticles(5-6 nm)anchored inside a nitrogendoped defective carbon nanotube network(CoNi@N-DCNT)by a transient Joule heating *** utilized as an electrocatalyst for oxygen reduction and evolution in alkaline media,the CoNi@N-DCNT film catalyst with a very low mass loading of 0.06 mg cm^(-2) showed excellent bifunctional catalytic *** ORR,the onset potential(Eonset)and the half-wave potential(E_(1/2))were 0.92 V versus reversible hydrogen electrode(***)and 0.83 V(***),*** OER,the potential at the current density(J)of 10 mA cm^(-2)(E_(10))was 1.53 V,resulting in an overpotential of 300 mV much lower than that of the commercial RuO_(2) catalyst(320 mV).The potential gap between E_(1/2) and E_(10) was as small as 0.7 *** the low mass loading,the mass activity at E_(10) reached at 123.2 A g^(-1),much larger than that of the RuO_(2) catalyst and literature results of transitional metal-based bifunctional ***,the CoNi@N-DCNT film catalyst showed very good long-term stability during the ORR and OER *** excellent bifunctional catalytic performance could be attributed to the synergistic effect of the bimetal alloy.

关键词： Transient Joule heating method Carbon nanotubes Nano alloy Low loading Bifunctional catalyst

Polar-coded forward error correction for MLC NAND flash memory

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Science China(Information Sciences) 2018年第10期61卷 224-239页

作者： haochuan SONG Jen-Chien FU Shih-Jia zeng Jin sha Zaichen ZhaNG Xiaohu YOU Chuan ZhaNG Lab of Efficient Architectures for Digital-communication(LEADS) National Mobile Communications Research Laboratory Southeast University Quantum Information Center of Southeast University National Mobile Communications Research Laboratory Southeast University Lite-On Technology Corporation School of Electronic Science and Engineering Nanjing University

With the ever-growing storage density, high-speed, and low-cost data access, flash memory has inevitably become popular. Multi-level cell(MLC) NAND flash memory, which can well balance the data density and memory stability, has occupied the largest market share of flash memory. With the aggressive memory scaling, however, the reliability decays sharply owing to multiple interferences. Therefore, the control system should be embedded with a suitable error correction code(ECC) to guarantee the data integrity and accuracy. We proposed the pre-check scheme which is a multi-strategy polar code scheme to strike a balance between reasonable frame error rate(FER) and decoding latency. Three decoders namely binaryinput, quantized-soft, and pure-soft decoders are embedded in this scheme. Since the calculation of soft loglikelihood ratio(LLR) inputs needs multiple sensing operations and optional quantization boundaries, a 2-bit quantized hard-decision decoder is proposed to outperform the hard-decoded LDPC bit-flipping decoder with fewer sensing operations. We notice that polar codes have much lower computational complexity compared with LDPC codes. The stepwise maximum mutual information(SMMI) scheme is also proposed to obtain overlapped boundaries without exhausting search. The mapping scheme using Gray code is employed and proved to achieve better raw error performance compared with other alternatives. hardware architectures are also given in this paper.

关键词： polar coding non-volatile memory error correcting code NAND flash memory

Origins of high ductility exhibited by an extruded magnesium alloy Mg-1.8Zn-0.2Ca:Experiments and crystal plasticity modeling

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Journal of Materials Science & Technology 2021年第25期84卷 27-42页

作者： Jie Wang Gaoming Zhu Leyun Wang Evgenii Vasilev Jun-Sang Park Gang sha Xiaoqin zeng Marko Knezevic National Engineering Research Center of Light Alloy Net Forming Shanghai Jiao Tong UniversityShanghai200240China Department of Mechanical Engineering University of New HampshireDurhamNH03824USA Advanced Photon Source Argonne National LaboratoryLemontIL60439USA School of Materials Science and Engineering Nanjing University of Science and TechnologyNanjing210094China State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong UniversityShanghai200240China

Low ductility and strength are major bottlenecks against Mg alloys’wide *** this work,we systematically design the composition and fabrication process for a low-alloyed Mg-Zn-Ca alloy,showing that it can be extruded at low temperatures(~250℃)and high speeds(~2 mm/s).After the extrusion,this alloy exhibits a substantially weakened basal texture,relatively small grain size,very high tensile elongation(~30%),and good *** origin of the considerably improved ductility was studied using a combination of three-dimensional atom probe tomography(3D-APT),transmission electron microscopy(TEM),electron backscattered diffraction(EBSD)in conjunction with surface slip trace analysis,in-situ synchrotron X-ray diffraction,and elasto-plastic self-consistent(EPSC)***-segregation of Zn and Ca atoms at a grain boundary is observed and associated with texture weakening and grain boundary mediated plasticity,both improving the *** basal slip and prismatic slip are identified as the dominant deformation systems in the alloy,the ratio between their slip resistances is substantially reduced relative to pure Mg and most other Mg alloys,significantly contributing to the improved ductility of the *** Mg-Zn-Ca alloy exhibiting excellent mechanical properties and low fabrication cost is a promising candidate for industrial productions.

关键词： Mg-Zn-Ca alloy Ductility Deformation mechanisms Crystal plasticity modeling Grain boundary mediated plasticity

Highly sensitive detection of melamine based on reversed phase liquid chromatography mass spectrometry

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Chinese Science Bulletin 2009年第5期54卷 732-737页

作者： WU QingQing FAN KeXin sha Wei RUAN HongQiang zeng Rong SHIEH ChiaHui Key Laboratory of Systems Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China shanghai KeyTag Bioscience Inc. Shanghai 200233 China

In this work, we developed a highly sensitive method to detect melamine based on reversed phase liquid chromatography mass spectrometry. A mass spectrometry compatible ion pair, heptafluorobu-tyric acid(HFBA), was used to separate melamine by reversed phase liquid chromatography prior to electrospray mass spectrometry. The incorporation of isotope internal standard and multiple reaction monitoring improved the accuracy and linearity of quantification. Based on this strategy, the method limit of quantification was 0.1 ng/g. The limits of quantification were 8 ng/g for liquid milk and 15 ng/g for dry milk powder. This method provided a reproducible and stable approach to sensitive detection and quantification of melamine.

关键词：反相流相色谱质谱分析法离子对多反应监测模式三聚氰胺

Enhanced cobalamin biosynthesis in Ensifer adhaerens by regulation of key genes with gradient promoters

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Synthetic and Systems Biotechnology 2022年第3期7卷 941-948页

作者： sha Xu Zhiqiang Xiao Shiqin Yu Weizhu zeng Yongming Zhu Jingwen Zhou National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University1800 Lihu RoadWuxiJiangsu214122China School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of EducationJiangnan University1800 Lihu RoadWuxiJiangsu214122China Science Center for Future Foods Jiangnan University1800 Lihu RoadWuxiJiangsu214122China Jiangsu Provisional Research Center for Bioactive Product Processing Technology Jiangnan University1800 Lihu RoadWuxiJiangsu214122China Hunan Hongying Biotechnology Co.Ltd. 10 Hongying RoadJinshiHunan415400China

Cobalamin is an essential human vitamin widely used in the pharmaceutical,food,and feed additive industries and currently produced by bacteria or *** adhaerens HY-1 is an industrial strain that also produces *** production outputs are poor and the specific synthesis pathways require *** this study,the whole genome sequence of *** HY-1 was generated and annotated,and genes associated with cobalamin biosynthesis were ***,three genes,CobSV,CobQ,and CobW were identified as the most efficient ones for enhancing cobalamin *** transcriptome sequencing of *** HY-1 cells at different growth stages,65 endogenous promoters with different gradient strengths were *** combined expression of different strength promoters and key genes,a high cobalamin-producing recombinant strain,‘hmm’(genotype:PmetH-CobSV-PibpA-CobQ-Pmdh-CobW),was *** production was 143.8 mg/L in shaking flasks,which was 41.0%higher than the original *** production was further enhanced to 171.2 mg/L using fed-batch ***,our data and novel approach provide important references for the analysis of cobalamin synthesis and other metabolites in complex metabolic pathways.

关键词： Ensifer adhaerens Cobalamin Genome sequence Transcriptome sequence Promoter Overexpression Combinations

High responsivity and fast response 8×8β-Ga_(2)O_(3)solar-blind ultraviolet imaging photodetector array

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Science China(Technological Sciences) 2023年第11期66卷 3259-3266页

作者： SHEN GaoHui LIU zeng TANG Kai sha ShuLin LI Lei TAN Chee-Keong GUO YuFeng TANG WeiHua Innovation Center of Gallium Oxide Semiconductor(IC-GAO) College of Integrated Circuit Science and EngineeringNanjing University of Posts and TelecommunicationsNanjing 210023China National and Local Joint Engineering Laboratory for RF Integration and Micro-Assembly Technologies Nanjing University of Posts and TelecommunicationsNanjing 210023China Key Laboratory of Aerospace Information Materials and Physics(NUAA) MIITNanjing 211106China College of Physics MIIT Key Laboratory of Aerospace Information Materials and PhysicsKey Laboratory for Intelligent Nano Materials and DevicesNanjing University of Aeronautics and AstronauticsNanjing 211106China Advanced Materials Thrust Function HubThe Hong Kong University of Science and Technology(Guangzhou)Nansha 511458China Department of Electronic and Computer Engineering School of EngineeringThe Hong Kong University of Science and TechnologyHong Kong 999077China

In this work,an 8×8 Ga_(2)O_(3)solar-blind ultraviolet photodetector array is introduced for image sensing *** 2-in wafer-scaled Ga_(2)O_(3)thin film was grown by metalorganic chemical vapor deposition technique;and the photodetector array was fabricated through ultraviolet photolithography,lift-off,and electron-beam *** addition to the high solar-blind/visible rejection ratio of 104,every photodetector cell in the array has high performance and fast response speed,such as responsivity of 49.4 A W^(-1),specific detectivity of 6.8×10^(14)Jones,external quantum efficiency of 1.9×10^(4)%,linear dynamic range of 117.8 d B,and response time of 41 ms,respectively,indicating the high photo-response performance of the ***,the photodetector array displayed uniform responsivity with a standard deviation of~6%,and presented a sensing image of low chromatic aberration,owing to the high resolution of the photodetector *** a word,this work may contribute to developing Ga_(2)O_(3)-based optoelectronic device applications.

关键词： Ga_(2)O_(3) photodetector array imaging photo-response

Resource prediction and assessment based on 3D/4D big data modeling and deep integration in key ore districts of North China

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Science China Earth Sciences 2021年第9期64卷 1590-1606页

作者： Gongwen WANG Zhiqiang ZhaNG Ruixi LI Junjian LI Deming sha Qingdong zeng Zhenshan PANG Dapeng LI Leilei HUANG School of Earth Sciences and Resources China University of Geosciences(Beijing)Beijing100083China Tianjin Geological Survey Center of China Geological Survey Tianjin300170China Shenyang Geological Survey Center of China Geological Survey Shenyang110000China Key Laboratory of Mineral Resources Institute of Geology and GeophysicsChinese Academy of SciencesBeijing100029China Institutions of Earth Science Chinese Academy of SciencesBeijing100029China College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijing100049China Development Research Center of China Geological Survey Beijing100037China shandong Academy of Geological Sciences Jinan250013China

The North China district has been subjected to significant research with regard to the ore-forming dynamics,processes,and quantitative forecasting of gold deposits;it accounts for the highest number of gold reserves and annual products in *** on the top-level design of geoscience theory and the method adopted by the National Key R&D Project(deep process and metallogenic mechanism of North China Craton(NCC)metallogenic system),this paper systematically collects and constructs the geoscience data(district,camp,and deposit scales)in four key gold districts of North China(Jiaojia-Sanshandao,Southern Zhaoping,Wulong,and Qingchengzi).The settings associated with the geological dynamics of gold deposits were quantitatively and synthetically analyzed,namely:NCC destruction,metallogenic events,genetic models,and exploration ***-dimensional(3D)and four-dimensional(4D)geological modeling was performed using the big data on the districts,while the district-scale 3D exploration criteria were integrated to construct a quantitative exploration *** them,FLAC3D modelling and the Geo Cube software(version 3.0)were used to implement the numerical simulation of the 3D geological models and the constraints of the fluid saturation parameters of the Jiaojia fault to reconstruct the 4D fault structure models of the Jiaojia fault(with a depth of 5000 m).Using Geo Cube3.0,multiple integration modules(general weights of evidence(Wof E),Boost Wof E,Fuzzy Wof E,Logistic Regression,Information Entropy,and Random Forest)and exploration criteria were integrated,while the C-V fractal classification of A,B and C targets in four districts was carried *** research results are summarized in the following four areas:(1)Four gold districts in the study area have more than three targets(the depth is 3000 m),and the class A,B and C targets exhibit a good spatial correlation with gold bodies that are controlled by mining engineering at depths greater than 1000 m.(2)The Boost Wof

关键词： Geoscience big data 3D/4D modeling Weights of evidence Random forest Target optimization and resources assessment Gold district in North China

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