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enhancing the activity and succinyl-CoA specificity of 3-ketoacyl-CoA thiolase Tfu_0875 through rational binding pocket engineering

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Synthetic and Systems Biotechnology 2024年第3期9卷 558-568页

作者： Lixia Liu shuang Liu Xiangyang Hu Shenghu Zhou Yu deng National engineering Research Center of Cereal Fermentation and Food Biomanufacturing Jiangnan University1800 Lihu RoadWuxiJiangsu214122China Jiangsu Provincial Research Center for Bioactive Product Processing Technology Jiangnan University1800 Lihu RoadWuxiJiangsu214122China

The 3-ketoacyl-CoA thiolase is the rate-limiting enzyme for linear dicarboxylic acids ***,the promiscuous substrate specificity and suboptimal catalytic performance have restricted its *** we present both biochemical and structural analyses of a high-efficiency 3-ketoacyl-CoA thiolase Tfu_***,Tfu_0875 displayed heightened activity and substrate specificity for succinyl-CoA,a key precursor in adipic acid *** enhance its performance,a deep learning approach(DLKcat)was employed to identify effective mutants,and a computational strategy,known as the greedy accumulated strategy for protein engineering(GRAPe),was used to accumulate these effective *** the mutants,Tfu_0875N249W/L163H/e217L exhibited the highest specific activity(320%of wild-type Tfu_0875),the greatest catalytic efficiency(kcat/KM=1.00 min-1mM-1),the highest succinyl-CoA specificity(KM=0.59 mM,28.1%of Tfu_0875)and dramatically reduced substrate binding energy(-30.25 kcal mol^(-1)v.s.-15.94 kcal mol^(-1)).A structural comparison between Tfu_0875N249W/L163H/e217L and the wild type Tfu_0875 revealed that the increased interaction between the enzyme and succinyl-CoA was the primary reason for the enhanced enzyme *** interaction facilitated rapid substrate anchoring and ***,a reduced binding pocket volume improved substrate specificity by enhancing the complementarity between the binding pocket and the substrate in stereo ***,our rationally designed mutant,Tfu_0875N249W/L163H/e217L,increased the adipic acid titer by 1.35-fold compared to the wild type Tfu_0875 in shake *** demonstrated enzymatic methods provide a promising enzyme variant for the adipic acid *** above effective substrate binding pocket engineering strategy can be beneficial for the production of other industrially competitive biobased chemicals when be applied to other thiolases.

关键词： Adipic acid 3-Ketoacyl-CoA thiolase Claisen condensation Deep learning GRAPe strategy

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Asymmetric Two-Component Alkenyl Catellani Reaction for the Construction of C—N Axial Chirality

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Chinese Journal of Chemistry 2024年第7期42卷 699-704页

作者： Chenggui Wu Ze-Shui Liu Yong Shang Chang Liu shuang deng Hong-Gang Cheng Hengjiang Cong Yinchun Jiao Qianghui Zhou Sauvage Center for Molecular Sciences Engineering Research Center of Organosilicon Compounds&Materials(Ministry of Education)Hubei Key Lab on Organic and Polymeric OptoElectronic MaterialsCollege of Chemistry and Molecular SciencesThe Institute for Advanced Studiesand TaiKang Center for Life and Medical SciencesWuhan UniversityWuhanHubei 430072China Key Laboratory of Xin'an Medicine Ministry of EducationAnhui University of Chinese MedicineHefeiAnhui 230038China School of Chemistry and Chemical engineering Hunan University of Science and TechnologyXiangtanHunan 411201China

Herein,we report an asymmetric two-component alkenyl Catellani reaction for the construction of C—N axial chirality through a palladium/chiral norbornene cooperative catalysis and an axial-to-axial chirality transfer *** partially aromatic iodinated 2-pyridones,quinolones,coumarin and uracil substrates react with 2,6-disubstituted aryl bromides with a tethered amide group,to afford a wide variety of polycyclic C—N atropisomers(38 examples,up to 97%e.e.).The obtained C—N axial chirality originates from the preformed transient C—C axial chirality with high *** synthetic utility of this chemistry is demonstrated by facile prepa-ration of complex quinoline and pyridine based C—N atropisomers through a N-deprotection and aromatization *** addi-tion,a remote axial-to-central diastereoinduction process dictated by C—N axial chirality is observed with excellent diastereocontrol.

关键词： Alkenyl Catellani reaction Asymmetric catalysis Atropisomerism Axial-to-axial chirality transfer Heterocycles

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Oriented mesoporous nanofibers show nature's wisdom

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National Science Review 2024年第06期11卷 90-91页

作者： Yonghui deng Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Collaborative Innovation Center of Chemistry for Energy Material (iChEM) Fudan University State Key Lab of Transducer Technology Shanghai Institute of Microsystem and Information Technology Chinese Academy of Sciences

electrodes assembled with conventional nanoparticulate materials in electrochemical energy devices usually have a random and torturous porous system. To meet ever-increasing demands for higher volumetric energy density at packagelevel, packing more active materials in a limited volume becomes increasingly difficult since transportation of reactants(e.g. electrolyte) and charges through high-tortuosity channels/pathways in thick electrodes meets large impedance[1].

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WRKY11 up-regulated dirigent expression to enhance lignin/lignans accumulation in Lilium regale Wilson during response to Fusarium wilt

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Journal of Integrative Agriculture 2024年第8期23卷 2703-2722页

作者： Jie deng Zi’e Wang Wenyun Li Xiaohua Chen Diqiu Liu Faculty of Life Science and Technology Kunming University of Science and TechnologyKunming 650500China

Lilium are highly economically valuable ornamental plants that are susceptible to Fusarium wilt caused by Fusarium *** regale Wilson,a wild lily native to China,is highly resistant to *** this study,a WRKY transcription factor,WRKY11,was isolated from ***,and its function during the interaction between *** and *** was *** ectopic expression of LrWRKY11 in tobacco increased the resistance to F oxysporum,moreover,the transcriptome sequencing and UHPLC-MS/MS analysis indicated that the methyl salicylate and methyl jasmonate levels rose in LrWRKY11 transgenic tobacco,meanwhile,the expression of lignin/lignans biosynthesis-related genes including a dirigent(DiR)was *** lignin/lignans contents in LrWRKY11-transgenic tobacco also significantly increased compared with the wild-type *** addition,the resistance of *** scales in which LrWRKY11 expression was silenced by RNAi evidently decreased,and additionally,the expression of lignin/lignans biosynthesis-related genes including LrDIR1 was significantly ***,LrDIR1 and its promoter(PLrDIR1)sequence containing the W-box element were isolated from *** interaction assay indicated that LrWRKY11 specifically bound to the W-box element in PLrDIR1 and activated LrDIR1 ***,β-glucuronidase activity in the transgenic tobacco co-expressing LrWRKY11/PLrDIR1-β-glucuronidase was higher than that in transgenic tobacco expressing PLrDIR1-β-glucuronidase ***,the ectopic expression of LrDIR1 in tobacco enhanced the resistance to *** and increased the lignin/lignans *** brief,this study revealed that LrWRKY11 positively regulated *** resistance to *** through interaction with salicylic acid/jasmonic acid signaling pathways and modulating LrDIR1 expression to accumulate lignin/lignans.

关键词： Lilium regale Fusarium oxysporum WRKY transcription factor dirigent

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effects of hydroxyproline supplementation in low fish meal diets on collagen synthesis, myofiber development and muscular texture of juvenile Pacific white shrimp(Litopenaeus vannamei)

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Animal Nutrition 2024年第2期17卷 428-437页

作者： Menglin Shi Haoming Li Tianyu Chen Bocheng Huang Xiaoyue Li Xiaohui Dong Shuyan Chi Qihui Yang Hongyu Liu Junming deng Beiping Tan shuang Zhang Shiwei Xie Laboratory of Aquatic Nutrition and Feed College of Fisheries Guangdong Ocean University Aquatic Animals Precision Nutrition and High-efficiency Feed engineering Research Centre of Guangdong Province Key Laboratory of Aquatic Livestock and Poultry Feed Science and Technology in South China Ministry of Agriculture Guangdong Provincial Key Lab of Aquatic Animals Disease Control and Healthy Culture

This experiment aimed to evaluate the impact of dietary hydroxyproline(Hyp) supplementation on the muscle quality of juvenile Pacific white shrimp(Litopenaeus vannamei) fed a low fishmeal diet. Six formulated diets included one high fishmeal(HF; 25% fishmeal content) and five low fishmeal diets(10%fishmeal content) with 0%, 0.2%, 0.4%, 0.6% and 0.8% Hyp(LF0, LF2, LF4, LF6 and LF8, respectively). each diet was assigned to four replicates, and 40 shrimp(0.32 ± 0.00 g) per replicate were fed four times a day for 8 weeks. Dietary Hyp supplementation had little effects on growth performance, but increased the contents of Hyp, prolyl 4-hydroxylases(P4Hs), and collagen. The meat yield, springiness, hardness,chewiness, and cohesiveness of muscle were the highest in the LF4 group among the low fishmeal groups(P eezing loss of muscle were the lowest in the LF4 group(P etary supplementation with 0.4% Hyp increased the myofiber density and decreased the myofiber diameter of muscle(P ementation of Hyp in the diet up-regulated the mRNA expression of smyhc5,smyhc15, col1a1, col1a2, igf-1f, tgf-β and tor and down-regulated the mRNA expression of smyhc1, smyhc2,smyhc6a(P ementation of Hyp in the diet up-regulated the protein expression of P-4e-BP1,P-AKT, AKT and P-AKT/AKT(P ese results suggested that the addition of 0.4% Hyp to low fishmeal diets improved the muscle quality of L. vannamei.

关键词： Hydroxyproline Collagen Muscle quality Litopenaeus vannamei

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Performance of physical-informed neural network (PINN) for the key parameter inference in Langmuir turbulence parameterization scheme

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Acta Oceanologica Sinica 2024年第5期43卷 121-132页

作者： Fangrui Xiu Zengan deng School of Marine Science and Technology Tianjin UniversityTianjin 300072China

The Stokes production coefficient(e_(6))constitutes a critical parameter within the Mellor-Yamada type(MY-type)Langmuir turbulence(LT)parameterization schemes,significantly affecting the simulation of turbulent kinetic energy,turbulent length scale,and vertical diffusivity coefficient for turbulent kinetic energy in the upper ***,the accurate determination of its value remains a pressing scientific *** study adopted an innovative approach by leveraging deep learning technology to address this challenge of inferring the e_(6).Through the integration of the information of the turbulent length scale equation into a physical-informed neural network(PINN),we achieved an accurate and physically meaningful inference of e_(6).Multiple cases were examined to assess the feasibility of PINN in this task,revealing that under optimal settings,the average mean squared error of the e_(6) inference was only 0.01,attesting to the effectiveness of *** optimal hyperparameter combination was identified using the Tanh activation function,along with a spatiotemporal sampling interval of 1 s and 0.1 *** resulted in a substantial reduction in the average bias of the e_(6) inference,ranging from O(10^(1))to O(10^(2))times compared with other *** study underscores the potential application of PINN in intricate marine environments,offering a novel and efficient method for optimizing MY-type LT parameterization schemes.

关键词： Langmuir turbulence physical-informed neural network parameter inference

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Characteristics of the crack tip field in high-speed railway tunnel linings under train-induced aerodynamic shockwaves

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Underground Space 2024年第5期18卷 199-217页

作者： Yi-Kang Liu Yu-Ling Wang e deng Yi-Qing Ni Wei-Chao Yang Wai-Kei Ao School of Civil engineering Central South UniversityChangsha 410075China National Rail Transit electrification and Automation engineering Technology Research Center(Hong Kong Branch) The Hong Kong Polytechnic UniversityHong Kong 999077China Department of Civil and environmental engineering The Hong Kong Polytechnic UniversityHong Kong 999077China The Hong Kong Polytechnic University Shenzhen Research Institute Shenzhen 518057China National engineering Research Center of High-speed Railway Construction Technology Changsha 410075China

High-speed railway tunnels in various countries have continuously reported accidents of vault falling concrete *** the concrete block falling occurs,serious consequences follow,and traffic safety may be *** aerodynamic shockwave evolves from the initial compression wave may be an important inducement causing the tunnel lining cracks to grow and form falling concrete blocks.A joint calculation framework is established based on ANSYS Fluent,ABAQUS,and FRANC3D for calculating the crack tip field under the aerodynamic *** intensification effect of aerodynamic shockwaves in the crack is revealed,and the evolution characteristics of the crack tip field and the influence factors of stress intensity factor(SIF)are *** show that(1)the aerodynamic shockwave intensifies after entering the crack,resulting in more significant pressure in the crack than the input *** maximum pressure of the inclined and longitudinal cracks is higher than the corresponding values of the circumferential crack,respectively.(2)The maximum SIF of the circumferential,inclined,and longitudinal crack appears at 0.5,0.68,and 0.78 times the crack front *** maximum SIF of the circumferential crack is higher than that of the inclined and longitudinal *** possibility of crack growth of the circumferential crack is the highest under aerodynamic shockwaves.(3)The influence of train speed on the SIF of the circumferential crack is more than 40%.When the train speed,crack depth,and crack length change,the change of pressure in the crack is the direct cause of the change of SIF.

关键词： Falling concrete blocks Tunnel lining cracks Aerodynamic shockwave Intensification effect Crack tip field Stress intensity factor

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Microbes in mass extinction: an accomplice or a savior?

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National Science Review 2024年第1期11卷 12-15页

作者： Genming Luo deng Liu Hao Yang State Key Laboratory of Geobiology and environmental Geology China University of Geosciences (Wuhan)

Microbes include various types of organisms that are invisible to the naked eye,e.g. bacteria, archaea and microeukaryotes. Although the precise number remains largely unknown, microbes are recognized as the unseen majority of our biosphere [1]. As a group of organisms classified by body size, microbes cover a considerable spectrum of metabolisms,

关键词： AFTeRMATH

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Depositional model of the Member deng-2 marginal microbial mound-bank complex of the dengying Formation in the southwestern Sichuan Basin, SW China: Implications for the ediacaran microbial mound construction and hydrocarbon exploration

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Petroleum Science 2024年第2期21卷 806-822页

作者： Jin-Min Song Xin Jin Zhong Luo Shu-Gen Liu Shao-Bo Liu Xing-Zhi Ma Zhi-Wu Li Xue-Song Lu Ling-Li Zhao Ke-Ran Li Jia-Xin Ren Li-Zhou Tian Hao-shuang deng State Key Laboratory of Oil and Gas Reservoir Geology and exploitation Chengdu University of TechnologyChengdu610059SichuanChina PetroChina Research Institute of Petroleum exploration and Development Beijing100083China Xihua University Chengdu610039SichuanChina

Recent advances in hydrocarbon exploration have been made in the Member deng-2 marginal microbial mound-bank complex reservoirs of the dengying Formation in the western Sichuan Basin, SW China,where the depositional process is regarded confusing. The microfacies, construction types, and depositional model of the Member deng-2 marginal microbial mound-bank complex have been investigated using unmanned aerial vehicle photography, outcrop section investigation, thin section identification,and seismic reflections in the southwestern Sichuan Basin. The microbialite lithologic textures in this region include thrombolite, dendrolite, stromatolite, fenestral stromatolite, spongiostromata stone,oncolite, aggregated grainstone, and botryoidal grapestone. Based on the comprehensive analysis of“depositional fabrics-lithology-microfacies”, an association between a fore mound, mound framework,and back mound subfacies has been proposed based on water depth, current direction, energy level and lithologic assemblages. The microfacies of the mound base, mound core, mound flank, mound cap, and mound flat could be recognized among the mound framework subfacies. Two construction types of marginal microbial mound-bank complex have been determined based on deposition location, mound scale, migration direction, and sedimentary facies association. Type Jinkouhe microbial mound constructions(TJMMCs) develop along the windward margin owing to their proximity to the seaward subfacies fore mound, with a northeastwardly migrated microbial mound on top of the mud mound,exhibiting the characteristics of large-sized mounds and small-sized banks in the surrounding area. Type e'bian microbial mound constructions(TeMMCs) primarily occur on the leeward margin, resulting from the presence of onshore back mound subfacies, with the smaller southwestward migrated microbial mounds existing on a thicker microbial flat. The platform margin microbial mound depositional model can be correlated with certain late

关键词： Sichuan Basin The Member deng-2 Marginal microbial mound-bank complex Depositional model exploration implications

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Disinfection Byproducts and Their Precursors in Drinking Water Sources:Origins,Influencing Factors,and environmental Insights

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engineering 2024年第5期36卷 36-50页

作者： Rong Xiao Yang deng Zuxin Xu Wenhai Chu State Key Laboratory of Pollution Control and Resource Reuse College of Environmental Science and EngineeringTongji UniversityShanghai 200092China Ministry of education Key Laboratory of the Yangtze River Water environment Tongji UniversityShanghai 200092China Department of earth and environmental Studies Montclair State UniversityMontclairNJ 07043USA

Tracing the contamination origins in water sources and identifying the impacts of natural and human processes are essential for ecological safety and public ***,current analysis approaches are not ideal,as they tend to be laborious,time-consuming,or technically *** byproducts(DBPs)are a family of well-known secondary pollutants formed by the reactions of chemical disinfectants with DBP precursors during water disinfection *** DBP precursors have various origins(e.g.,natural,domestic,industrial,and agricultural sources),and since the formation of DBPs from different precursors in the presence of specific disinfectants is distinctive,we argue that DBPs and DBP precursors can serve as alternative indicators to assess the contamination in water sources and identify pollution *** providing a retrospective of the origins of DBPs and DBP precursors,as well as the specific formation patterns of DBPs from different precursors,this article presents an overview of the impacts of various natural and anthropogenic factors on DBPs and DBP precursors in drinking water *** practice,the DBPs(i.e.,their concentration and speciation)originally present in source water and the DBP precursors determined using DBP formation potential tests—in which water samples are dosed with a stoichiometric excess of specific disinfectants in order to maximize DBP formation under certain reaction conditions—can be considered as alternative *** jointly used with other water quality parameters(e.g.,dissolved organic carbon,dissolved organic nitrogen,fluorescence,and molecular weight distribution)and specific contaminants of emerging concern(e.g.,certain pharmaceuticals and personal care products),DBPs and DBP precursors in drinking water sources can provide a more comprehensive picture of water pollution for better managing water resources and ensuring human health.

关键词： Disinfection byproducts Disinfection byproduct precursors Drinking water sources Contamination indicator Natural factors Human factors

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