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Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application

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Acta Pharmaceutica Sinica B 2024年第2期14卷 623-634页

作者： Jiacheng Xiong Rongrong Cui Zhaojun Li Wei Zhang Runze Zhang Zunyun Fu Xiaohong Liu Zhenghao Li Kaixian Chen Mingyue Zheng Drug Discovery and Design Center State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China College of Computer and Information Engineering Dezhou UniversityDezhou 253023China AI Department Suzhou Alphama Biotechnology Co.Ltd.Suzhou 215000China Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghai 200031China State Key Laboratory of Pharmaceutical biotechnology Nanjing UniversityNanjing 210023China

Aldehyde oxidase(AOX)is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other ***-mediated metabolism can result in unexpected outcomes,such as the production of toxic metabolites and high metabolic clearance,which can lead to the clinical failure of novel therapeutic *** models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of compounds during the early phases of drug discovery and provide valuable clues for manipulating AOX-mediated metabolism *** this study,we developed a novel graph neural network called AOMP for predicting AOX-mediated *** integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction,while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both *** significantly outperformed the benchmark methods in both cross-validation and external *** AOMP,we systematically assessed the AOX-mediated metabolism of common fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability,which were validated through in vitro ***,for the convenience of the community,we established the first online service for AOX metabolism prediction based on AOMP,which is freely available at https://***.

关键词： Drugmetabolism Aldehyde oxidase Transferlearning Graph neural network Kinase inhibitor

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Synthesis of betanin by expression of the core betalain biosynthetic pathway in carrot

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Horticultural Plant Journal 2024年第3期10卷 732-742页

作者： Bo Wang Yahui Wang Yuanjie Deng Quanhong Yao Aisheng Xiong State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China Shanghai Key Laboratory of Agricultural Genetics and Breeding Biotechnology Research Institute of Shanghai Academy of Agricultural ScienceShanghai 201106China

Betalain has received increased attention because of its high nutritional value and crucial physiological *** on the elucidation of its core biosynthetic pathway,betalain can be produced in additional plants by metabolic *** of betalain in carrot(Daucus carota L.)can improve its nutritional quality and economic value by extracting betalain from the fleshy root,non-edible part,and processing residue of *** this study,two different constructs,namely,pYB:mCD(AomelOS,BvCYP76AD1S,and BvDODA1S)and p YB:CDD(BvCYP76AD1S,BvDODA1S,and MjcDOPA5GTS),were introduced into carrot for betanin synthesis by Agrobacterium-mediated *** can be synthetized in both transgenic calli,and p YB:m CD-transgenic callus can be used to produce betacyanin by suspension ***,pYB:mCD-transgenic seedlings can synthetize betanin only by tyrosine *** p YB:CDD-transgenic lines can synthetize betanin in whole *** betanin content in fleshy root of pYB:CDD-transgenic carrot was(63.4±9)μg·g^(-1)fresh weight according to quantitative *** betanin-producing carrot plant materials can be used to synthesize betanin for industrial application or consumption as dietary sources.

关键词： Daucus carota L. Betanin Biosynthesis Metabolic engineering Biofortification

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Zwitterionic ring-opening polymerization of macrocyclic ethyleneoxy-substituted carbonate:Access to cyclic PEG-like polycarbonate

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Chinese Chemical Letters 2024年第3期35卷 282-286页

作者： Jin Huang Jinwen Li Rui Yan Yuanyuan Qu Fengzhen Guo Lei Shen Can-liang Ma Jie Sun Zhenjiang Li Kai Guo State Key Laboratory of Materials-Oriented Chemical Engineering College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjing 211816China Institute of Nanjing Advanced Biomaterials&Processing Equipment Lishui Economic Development ZoneNanjing 211299China

The innovation in polymer design to rival conventional polyethylene glycol(PEG)is an important approach to achieving a more sustainable ***,cyclic PEG-like polycarbonates having high molecular weight(4.4–49.5 kg/mol)were enabled through zwitterionic ring-opening polymerization(ZROP)of macrocyclic carbonates(MCs)mediated by N-heterocyclic carbene(NHC).The thermodynamic behavior of polymerization depends on the ring size of *** this process,the ZROP of 11-membered MC was driven by the change of enthalpy(ΔH_(p))which differed from the ZROP of 14-membered MC driven by the entropic change(ΔS_(p)).Cyclic polycarbonates depicted improved thermostability(T_(d5%)≥204℃)and higher glass transition temperatures(T_(g)>–40℃)in comparison to their linear analogues(T_(d5%)≤185℃,T_(g)~–50℃).In addition,the mechanism of ZROP of MC was addressed through computational study.A distinct mechanism of polymerization distinguishable from the well-known NHC-mediated ZROP of cyclic esters was revealed,where the zwitterion from nucleophilic addition to MC,*** intermediate,cannot be ring-opened probably due to the delocalization of negative charge on the carbonate group,but serves as an active center for the *** comparison to PEG,the attained polymer demonstrated comparable hydrophilic and biocompatible properties,as revealed by the results of contact angle and in vitro cytotoxicity studies,suggesting that cyclic polycarbonate hold the promise as the alternative of PEG.

关键词： Zwitterionic ring-opening polymerization Cyclic polycarbonate Macrocycles Tetrahedral intermediate NHC carbene

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The biological functions and metabolic pathways of valine in swine

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Journal of Animal Science and biotechnology 2024年第1期15卷 20-34页

作者： Chuni Wang Yao Peng Yiru Zhang Juan Xu Sheng Jiang Leli Wang Yulong Yin Institute of Subtropical Agriculture Chinese Academy of SciencesChangshaChina Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation College of Life SciencesHunan Normal UniversityChangshaChina Tianjin Institute of Industrial biotechnology Chinese Academy of SciencesTianjinChina

Valine is an essential amino acid and a type of branched-chain amino acid. Due to the involvement of branchedchain amino acids in various metabolic pathways, there has been a surge of interests in valine nutrition and its role in animal physiology. In pigs, the interactions between valine and other branched-chain amino acids or aromatic amino acids are complex. In this review, we delve into the interaction mechanism, metabolic pathways, and biological functions of valine. Appropriate valine supplementation not only enhances growth and reproductive performances, but also modulates gut microbiota and immune functions. Based on past observations and interpretations, we provide recommended feed levels of valine for weaned piglets, growing pigs, gilts, lactating sows, barrows and entire males. The summarized valine nutrient requirements for pigs at different stages offer valuable insights for future research and practical applications in animal husbandry.

关键词： Additional dosage Biological function Metabolic pathway Pig Valine

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Taxonomy and phylogeny of the section Chaetoceros(Chaetocerotaceae,Bacillariophyta),with description of two new species

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Journal of Oceanology and Limnology 2024年第4期42卷 1286-1311页

作者： Xudan LU Mengyi ZHAI Nina LUNDHOLM Yang LI Guangdong Provincial Key Laboratory of biotechnology for Plant Development Guangzhou Key Laboratory of Subtropical Biodiversity and BiomonitoringCollege of Life ScienceSouth China Normal UniversityGuangzhou 510631China Natural History Museum of Denmark University of CopenhagenCopenhagen K 1353Denmark

Chaetoceros Ehrenberg is one of the most diverse genera of planktonic *** species in section Chaetoceros are characterized by cells and setae having numerous chloroplasts and being widely ***,the delimitations of some species are problematic because of limited morphological information in the classical *** strains of the section Chaetoceros were established,morphological features were studied using light and electron microscopy,and the hypervariable D 1-D 3 region of the nuclear ribosomal large subunit gene was sequenced to address phylogenetic *** species belonging to the section Chaetoceros were recorded,including two new species,*** *** *** *** hainanensis was characterized by straight chains,narrowly lanceolate to hexagonal apertures,sibling setae diverging in nearly right angles,stipule-shaped spines on terminal setae and arrowhead-shaped spines on intercalary *** had short straight chains,narrowly lanceolate apertures,arrowhead-shaped spines and circular poroids arranged in a grid pattern on terminal and intercalary *** phylogenetic analyses revealed six groups formed by 19 species within the section Chaetoceros,which was found to be *** subdivision of the section is still not well *** morphological characters within each group varied considerably and molecular information on more species are needed to enrich the phylogenetic profiling.

关键词： morphology large subunit ribosomal RNA encoding gene(LSU) section Chaetoceros Chaetoceros hainanensis Chaetoceros tridiscus

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Woody plant cell walls:Fundamentals and utilization

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Molecular Plant 2024年第1期17卷 112-140页

作者： Wei Li Ying-Chung Jimmy Lin Ying-Lan Chen Chenguang Zhou Shuang Li Nette De Ridder Dyoni M.Oliveira Lanjun Zhange Baocai Zhang Jack P.Wang Changzheng Xu Xiaokang Fu Keming Luo Ai-Min Wu Taku Demura Meng-Zhu Lu Yihua Zhou Laigeng Li Toshiaki Umezawa Wout Boerjan Vincent L.Chiang State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040China Department of Life Science National Taiwan UniversityTaipeiTaiwanChina Department of biotechnology and Bioindustry Sciences College of Bioscience and BiotechnologyNational Cheng Kung UniversityTainanTaiwanChina Department of Plant biotechnology and Bioinformatics Ghent UniversityTechnologiepark 719052 GhentBelgium VIB Center for Plant Systems Biology Technologiepark 719052 GhentBelgium State Key Laboratory of Plant Genomics Insttute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Forest biotechnology Group Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC 27695USA Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation Integrative Science Center of Germplasm CreationSchool of Life SciencesSouthwest UniversityChongqing 400715China Guangdong Key Laboratory for Innovative Developmentand Utilization of Forest Plant Germplasm College of Forestry and Landscape ArchitecturesSouth China Agricultural UniversityGuangzhou510642China Center for Digital Green-innovation Nara Institute of Science and TechnologykomaNara 630-0192Japan State Key Laboratory of Subtropical Siviculture College of Forestry and BiotechnologyZhejang A&F UniversityHangzhou 311300China CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences300 Fenglin RoadShanghai 200032China Laboratoryof MetabolicScienceofForest Plants and Microorganisms Rsearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto 611-0011 Japan

Cell walls in plants,particularly forest trees,are the major carbon sink of the terrestrial *** and biosynthetic features of plant cell walls were revealed early on,focusing mostly on herbaceous model *** developments in genomics,transcriptomics,epigenomics,transgenesis,and associated analytical techniques are enabling novel insights into formation of woody cell ***,we review multilevel regulation of cell wall biosynthesis in forest tree *** highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic *** outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.

关键词： regulation of cell wall formation biosynthesis of cell wall components lignin cellulose hemicellulose cell wall utilization

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Gut microbiota: a potential target for hyperuricemia and gout

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Food Science and Human Wellness 2024年

作者： Feiyan Zhao Shuying Yang Laiyu Kwok Hongbin Li Heping Zhang Zhihong Sun Inner Mongolia Key Laboratory of Dairy biotechnology and Engineering Key Laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs Key Laboratory of Dairy biotechnology and Engineering Ministry of Education Inner Mongolia Agricultural University Department of Rheumatology and Immunology The Affiliated Hospital of Inner Mongolia Medical University Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases

Modern lifestyle and diet have increased the incidence rate of uric acid (UA) metabolism-related diseases like hyperuricemia (HUA) and gout， posing heavy economic burden to individual patients and their families and the society. Uric acid metabolism is a complex physiological process involving the kidney， intestine， and other organs. A number of factors together regulate UA metabolism， including genetics， diet， hormones， and the gut microbiota. This review summaries the gut microbiota features in subjects with HUA and gout， and the therapeutic effects of implementing microecological therapies (probiotics， prebiotics， or fecal microbiota transplant) that target modulate the gut microbiota and its downstream metabolism on the disease. Current evidence shows that these strategies are safe and promising in alleviate inflammation， reduce UA， and restoring a healthy gut microbiota in subjects with UA metabolism-related diseases. However， most clinical data are generated by animal studies. Therefore， we propose that vigorous human intervention trials should be conducted in the future to evaluate the therapeutic effects of microecological therapies in managing HUA and gout.

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Using NH_(2)-MIL-125(Ti)for efficient removal of Cr(Ⅵ)and Rh B from aqueous solutions:Competitive and cooperative behavior in the binary system

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Journal of Environmental Sciences 2024年第2期136卷 437-450页

作者： Lei Zheng Lixia Sun Jiangbo Qiu Junling Song Luyi Zou Yue Teng Yongzhong Zong Hongyan Yu School of Environmental and Civil Engineering Jiangnan UniversityWuxi 214122China School of Chemical and Material Engineering Jiangnan UniversityWuxi 214122China Kunming South Water Co. Ltd.Kunming 650501China Jiangsu Key Laboratory of Anaerobic biotechnology Jiangnan UniversityWuxi 214122China

The coexistence of inorganic and organic contaminants is a challenge for real-life water treatment ***,in this research,we used NH_2-MIL-125(Ti)to evaluate the single adsorption of hexavalent chromium(Cr(Ⅵ))or Rhodamine B(RhB)in an aqueous solution and further investigate simultaneous adsorption experiments to compare the adsorption behavior *** main influencing factors,for example,reaction time,initial concentration,reaction temperature,and pH were studied in *** all reaction systems,the pseudo-second-order kinetic and Langmuir isotherm models were well illuminated the adsorption progress of Cr(Ⅵ)and *** studies showed that the adsorption process was spontaneous and *** compared to the single system,the adsorption capacity of Cr(Ⅵ)in the binary system gradually decreased as the additive amount of RhB increased,whereas the adsorption capacity of RhB in the binary system was expanded *** the binary reaction system contained 100 mg/L Cr(Ⅵ),the removal rate of RhB increased to 97.58%.The formation of Cr(Ⅵ)-RhB and Cr(Ⅲ)-RhB complexes was the cause that provided facilitation for the adsorption of *** findings prove that the interactions during the water treatment process between contaminants may obtain additional benefits,contributing to a better adsorption capacity of co-existing contaminant.

关键词： Adsorption Heavy metal ion Organic dye Simultaneous removal Mechanism studies

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Efficient degradation of aqueous dichloromethane by an enhanced microbial electrolysis cell:Degradation kinetics,microbial community and metabolic mechanisms

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Journal of Environmental Sciences 2024年第5期139卷 150-159页

作者： Meng Wu Di Zhao Bing Gu ZiruWang Jun Hu Zhiliang Yu Jianming Yu College of Environment College of Biotechnology and BioengineeringCollaborative Innovation Center of Yangtze River Delta Region Green PharmaceuticalsZhejiang University of TechnologyHangzhou 310014China Shentuo Environment(Hangzhou)Co.Ltd. Hangzhou 311121China Zhejiang Tianyi Environmental Co.Ltd. Hangzhou 310000China

Dichloromethane(DCM)has been listed as a toxic and harmful water pollutant,and its re moval needs *** electrolysis cells(MECs)are viewed as a promising alterna tive for pollutant removal,which can be strengthened from two aspects:microbial inocula tion and *** this study,the MEC for DCM degradation was inoculated with the ac tive sludge enhanced by Methylobacterium rhodesianum H13(strain H13)and then acclimated in the form of a microbial fuel cell(MFC).Both the introduction of strain H13 and the initi ation in MFC form significantly promoted DCM *** degradation kinetics were fitted by the Haldane model,with V_(max),K_(h),K_(i)and v_(max)values of 103.2 mg/L/hr,97.8 mg/L268.3 mg/L and 44.7 mg/L/hr/cm^(2),*** cyclic voltammogram implies that DCM redox reactions became easier with the setup of MEC,and the electrochemical impedance spectrogram shows that the acclimated and enriched microbes reduced the charge transfe resistance from the electrode to the *** the biofilm,the dominant genera shifted from Geobacter to Hyphomicrobium in acclimation ***,Methylobacterium played an increasingly important *** metabolism mainly occurred through the hydrolytic glutathione S-transferase pathway,given that the gene dcmA was identified rather than the dhlA and P450/*** exogenous electrons facilitated the reduction of GSSG,directly o indirectly accelerating the GSH-catalyzed *** study provides support fo the construction of an efficient and stable MEC for DCM removal in water environment.

关键词： Dichloromethane Microbial electrolysis cells Metabolic pathways Electron transfer Degradation kinetics

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Prevotella and succinate treatments altered gut microbiota,increased laying performance,and suppressed hepatic lipid accumulation in laying hens

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Journal of Animal Science and biotechnology 2024年第2期15卷 844-861页

作者： Min Liu Zeyue Kang Xikang Cao Hongchao Jiao Xiaojuan Wang Jingpeng Zhao Hai Lin College of Animal Science and Technology Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and PreventionKey Laboratory of Efficient Utilization of Non‑Grain Feed Resources(Co‑Construction by Ministry and Province)Ministry of Agriculture and Rural AffairsShandong Agricultural UniversityTai’an 271018China

Background This work aimed to investigate the potential benefits of administering Prevotella and its primary metabolite succinate on performance,hepatic lipid accumulation and gut microbiota in laying *** One hundred and fifty 58-week-old Hyline Brown laying hens,with laying rate below 80%and plasma triglyceride(TG)exceeding 5 mmol/L,were used in this *** hens were randomly allocated into 5 groups and subjected to one of the following treatments:fed with a basal diet(negative control,NC),oral gavage of 3 mL/hen saline every other day(positive control,PC),gavage of 3 mL/hen Prevotella melaninogenica(10^(7)CFU/mL,PM)or 3 mL/hen Prevotella copri(10^(7)CFU/mL,***)every other day,and basal diet supplemented with 0.25%sodium succinate(Succinate).The results showed that PM and *** treatments significantly improved laying rate compared to the PC(P0.05).PM treatment increased(P<0.05)the mRNA levels of genes PGC-1βand APB-5B at week 4,and ACC and CPT-1 at week *** results indicated enhanced antioxidant activities at week 8,as evidenced by reduced hepatic malondialdehyde(MDA)level and improved antioxidant enzymes activities in PM and Succinate groups(P<0.05).Supplementing with Prevotella or succinate can alter the cecal ***,the abundance of Prevotella in the Succinate group was significantly higher than that in the other 4 groups at the family and genus levels(P<0.05).Conclusions Oral intake of Prevotella and dietary supplementation of succinate can ameliorate lipid metabolism of laying *** beneficial effect of Prevotella is consistent across different *** finding highlights that succinate,the primary metaboli

关键词： Fatty liver Gut microbiota Laying hen Prevotella Succinate

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