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Whole-genome sequencing in medicinal plants:current progress and prospect

Science China(Life Sciences) 2024年第2期67卷 258-273页

作者： Yifei Pei Liang Leng Wei Sun Baocai Liu Xue Feng Xiwen Li shilin chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Agricultural Bioresource Fujian Academy of Agricultural SciencesFuzhou 350003China

Advancements in genomics have dramatically accelerated the research on medicinal plants,and the development of herbgenomics has promoted the“Project of 1K Medicinal Plant Genome”to decipher their genetic code.However,it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity.Whole genomes of 123 medicinal plants were published until September 2022.These published genome sequences were investigated in this review,covering their classification,research teams,ploidy,medicinal functions,and sequencing strategies.More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes.Diploid species account for a majority of sequenced medicinal plants.The whole genomes of plants in the Poaceae family are the most studied.Almost 40%of the published papers studied species with tonifying,replenishing,and heat-cleaning medicinal effects.Medicinal plants are still in the process of domestication as compared with crops,thereby resulting in unclear genetic backgrounds and the lack of pure lines,thus making their genomes more difficult to complete.In addition,there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome.Herein,a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants.Moreover,whole genome-based biological studies of medicinal plants,including breeding and biosynthesis,were reviewed.We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

关键词： herbgenomics whole genome high throughput sequencing research strategy model species application

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Biosynthesis of natural products from medicinal plants:Challenges,progress and prospects

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Chinese Herbal Medicines 2024年第1期16卷 1-2页

作者： shilin chen Academician of Chinese Academy of Engineering chengdu University of Traditional Chinese Medicine Chengdu 611137China

Medicinal plants play a crucial role in traditional Chinese medicine and modern pharmaceuticals,serving as valuable resources for natural products used for plant-based medicines and new drugs.Nevertheless,the conventional techniques for acquiring natural products have been unable to meet the increasing requirements of drug research and development.Chemical synthesis of natural products are usually complex process and might bring the risk of causing environmental problems.The extraction of natural products from medicinal plants are difficult and impractical,resulting in inefficient outputs.The creative methods and strategies are imperative to be developed to enhance the production of natural product from medicinal plants.Therefore,focusing on the biosynthetic pathways,metabolic engineering,and synthetic biology of natural products provides the avenues for obtaining abundant natural product resources.

关键词： medicinal abundant natural

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Finite Element Simulations of the Localized Failure and Fracture Propagation in Cohesive Materials with Friction

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Computer Modeling in Engineering & Sciences 2024年第7期140卷 997-1015页

作者： chengbao Hu shilin Gong Bin chen Zhongling Zong Xingwang Bao Xiaojian Ru Department of Civil Engineering Hangzhou City UniversityHangzhou310015China Zhejiang Engineering Research Center of Intelligent Urban Infrastructure Hangzhou310015China Key Laboratory of Safe Construction and Intelligent Maintenance for Urban Shield Tunnels of Zhejiang Province Hangzhou310015China School of Civil and Ocean Engineering Jiangsu Ocean UniversityLianyungang222005China Institute of Municipal Engineering Hangzhou Shangcheng District Municipal Engineering Group Co.Ltd.Hangzhou310016China

Strain localization frequently occurs in cohesive materials with friction(e.g.,composites,soils,rocks)and is widely recognized as a fundamental cause of progressive structural failure.Nonetheless,achieving high-fidelity simulation for this issue,particularly concerning strong discontinuities and tension-compression-shear behaviors within localized zones,remains significantly constrained.In response,this study introduces an integrated algorithmwithin the finite element framework,merging a coupled cohesive zone model(CZM)with the nonlinear augmented finite elementmethod(N-AFEM).The coupledCZMcomprehensively describes tension-compression and compressionshear failure behaviors in cohesive,frictional materials,while the N-AFEM allows nonlinear coupled intraelement discontinuities without necessitating extra nodes or nodal DoFs.Following CZM validation using existing experimental data,this integrated algorithm was utilized to analyze soil slope failure mechanisms involving a specific tensile strength and to assess the impact of mechanical parameters(e.g.,tensile strength,weighting factor,modulus)in soils.

关键词： FEM analysis strong discontinuity nonlinear soil rupture cohesive zone model tension-compression-shear coupling

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Tetrabromobisphenol A exerts thyroid disrupting effects but has little overt impact on postnatal brain development and neurobehaviors in mice

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Journal of Environmental Sciences 2024年第8期142卷 1-10页

作者： shilin Song Yuanyuan Li Lin Lv Mengqi Dong Zhanfen Qin State Key Laboratory of Environmental Chemistry and Ecotoxicology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China College of Resources and Environment University of Chinese Academy of SciencesBeijing 100049China School of Environment Tsinghua UniversityBeijing 100084China

Tetrabromobisphenol A(TBBPA)is a widely used brominated flame retardant.There is evidence showing that TBBPA can exert thyroid disrupting effects in mammals,but different results were also reported,along with inconsistent reports regarding its neurotoxicity.Here,we investigated thyroid disrupting effects and neurotoxicity of TBBPA(5,50,500μg/(kg·day))to male mice following maternal and direct exposure through drinking water,with the antithyroid drug propylthiouracil(PTU)as the positive control.On postnatal day(PND)15,we expectedly observed severe thyroid compensatory hyperplasia and cerebellar developmental retardation in PTU-treated pups.The highest dose of TBBPA also caused thyroid histological alteration but had no effects on cerebellar development in terms of Purkinje cell morphology and the thickness of the internal granular layer and the molecular layer of the cerebellum.During puberty and adulthood,the thyroid morphological alterations became more pronounced in the TBBPA-treated animals,accompanied by decreased serum thyroid hormone levels.Furthermore,the 50 and 500μg/(kg·day)TBBPA groups showed a significant decrease in the serum level of serotonin,a neurotransmitter associated with anxiety behaviors.Correspondingly,the highest dose group displayed anxiety-like behaviors in the elevated plus-maze test on PND 35,but this neurobehavioral alteration disappeared on PND 56.Moreover,no changes in neurobehavioral parameters tested were found in TBBPAtreated animals at puberty and adulthood.Altogether,all observations show that TBBPA can exert thyroid disrupting effects but has little overt impact on brain development and neurobehaviors in mice,suggesting that thyroid disruption does not necessarily cause overtly adverse neurodevelopmental outcomes.

关键词： Tetrabromobisphenol A Thyroid disruption Brain development Neurobehavior Cerebellum

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Uncovering the electrooxidation behavior of 5-hydroxymethylfurfural on Ni/Co electrodes

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Journal of Energy Chemistry 2024年第5期92卷 1-7页

作者： shilin Fan Bin Zhu Xiao Yu Yang Gao Weiping Xie Yong Yang Jian Zhang Chunlin chen Ningbo Institute of Materials Technology&Engineering Chinese Academy of SciencesNingbo 315201ZhejiangChina University of Chinese Academy of Sciences Beijing 100049China

Biomass,derived from plant photosynthesis that captures carbon dioxide to form carbohydrates,offers vast renewable reserves.The electrooxidation of biomass,coupled with the hydrogen evolution reaction,enables the simultaneous production of biomass-based plastic monomers and green hydrogen,attracting significant scholarly interest.However,ambiguity remains regarding the adsorption mechanism at the catalyst surface(Langmuir-Hinshelwood or Eley-Rideal)and the adsorbed substrate groups.To address this,we prepared a Ni/Co electrode for the electrooxidation of 5-hydroxymethylfurfural(HMF)into 2,5-furandicarboxylic acid(FDCA)through a corrosion reaction and electro-reduction pathway.HMF conversion reached 100.00%,FDCA yield reached 96.82%,and Faradic efficiency(FE)reached 92.14%.Meaningfully,utilizing in-situ spectroscopy and electrochemical methods,this work provided valuable insights into active sites and catalyst surface adsorption.

关键词： Electrocatalysis Electrochemistry 2,5-Furandicarboxylicacid 5-Hydroxymethylfurfural Biomass

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Boron nitride microribbons strengthened and toughened alumina composite ceramics with excellent mechanical,dielectric,and thermal conductivity properties

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Journal of Advanced Ceramics 2024年第4期13卷 496-506页

作者： Jilin Wang Dongping Lu Weiping Xuan Yuchun Ji Ruiqi chen Shaofei Li Wenbiao Li Wenzhuo chen shilin Tang Guoyuan Zheng Fei Long Guangxi Key Laboratory of Optical and Electronic Materials and Devices Collaborative Innovation Center for Exploration of Nonferrous Metal Deposits and Efficient Utilization of ResourcesSchool of Materials Science and EngineeringGuilin University of TechnologyGuilin 541004China Key Laboratory of New Processing Technology for Nonferrous Metals and Materials of Ministry of Education Guilin University of TechnologyGuilin 541004China School of Materials Science and Engineering Peking UniversityBeijing 100871China Department of Civil and Environmental Engineering The Hong Kong Polytechnic UniversityKowloon 999077Hong KongChina

Aluminum oxide(Al_(2)O_(3))ceramics have been widely utilized as circuit substrates owing to their exceptional performance.In this study,boron nitride microribbon(BNMR)/Al_(2)O_(3)composite ceramics are prepared using spark plasma sintering(SPS).This study examines the effect of varying the amount of toughened phase BNMR on the density,mechanical properties,dielectric constant,and thermal conductivity of BNMR/Al_(2)O_(3)composite ceramics while also exploring the mechanisms behind the toughening and increased thermal conductivity of the fabricated ceramics.The results showed that for a BNMR content of 5 wt%,BNMR/Al_(2)O_(3)composite ceramics displayed more enhanced characteristics than pure Al_(2)O_(3)ceramics.In particular,the relative density,hardness,fracture toughness,and bending strength were 99.95%±0.025%,34.11±1.5 GPa,5.42±0.21 MPa·m1/2,and 375±2.5 MPa,respectively.These values represent increases of 0.76%,70%,35%,and 25%,respectively,compared with the corresponding values for pure Al_(2)O_(3)ceramics.Furthermore,during the SPS process,BNMRs are subjected to high temperatures and pressures,resulting in the bending and deformation of the Al_(2)O_(3)matrix;this leads to the formation of special thermal pathways within it.The dielectric constant of the composite ceramics decreased by 25.6%,whereas the thermal conductivity increased by 45.6%compared with that of the pure Al_(2)O_(3)ceramics.The results of this study provide valuable insights into ways of enhancing the performance of Al_(2)O_(3)-based ceramic substrates by incorporating novel BNMRs as a second phase.These improvements are significant for potential applications in circuit substrates and related fields that require high-performance materials with improved mechanical properties and thermal conductivities.

关键词： boron nitride microribbons/aluminum oxide(BNMRs/Al_(2)O_(3))composite ceramics boron nitride microribbon(BNMR) spark plasma sintering(SPS) strengthening and toughening thermal conductivity

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Strategies on biosynthesis and production of bioactive compounds in medicinal plants

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Chinese Herbal Medicines 2024年第1期16卷 13-26页

作者： Miaoxian Guo Haizhou Lv Hongyu chen Shuting Dong Jianhong Zhang Wanjing Liu Liu He Yimian Ma Hua Yu shilin chen Hongmei Luo Key Lab of Chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of ChinaInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Engineering Research Center of Chinese Medicine Resource Ministry of EducationBeijing 100193China Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou 311121China chengdu University of Traditional Chinese Medicine Chengdu 611137China

Medicinal plants are a valuable source of essential medicines and herbal products for healthcare and disease therapy.Compared with chemical synthesis and extraction,the biosynthesis of natural products is a very promising alternative for the successful conservation of medicinal plants,and its rapid development will greatly facilitate the conservation and sustainable utilization of medicinal plants.Here,we summarize the advances in strategies and methods concerning the biosynthesis and production of natural products of medicinal plants.The strategies and methods mainly include genetic engineering,plant cell culture engineering,metabolic engineering,and synthetic biology based on multiple“OMICS”technologies,with paradigms for the biosynthesis of terpenoids and alkaloids.We also highlight the biosynthetic approaches and discuss progress in the production of some valuable natural products,exemplifying compounds such as vindoline(alkaloid),artemisinin and paclitaxel(terpenoids),to illustrate the power of biotechnology in medicinal plants.

关键词： biosynthetic strategies biotechnology natural products medicinal plants synthetic biology

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QL1706 (anti-PD-1 IgG4/CTLA-4 antibody) plus chemotherapy with or without bevacizumab in advanced non-small cell lung cancer: a multi-cohort, phase II study

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Signal Transduction and Targeted Therapy 2024年第2期9卷 797-806页

作者： Yan Huang Yunpeng Yang Yuanyuan Zhao Hongyun Zhao Ningning Zhou Yaxiong Zhang Likun chen Ting Zhou Gang chen Ting Wu Lu Lu shilin Xue Xiaoyan Kang Li Zhang Wenfeng Fang Department of Medical Oncology Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineNo.651 Dongfeng East RoadGuangzhouGuangdong 510060China Department of Medicine Qilu Pharmaceutical Co.Ltd.JinanChina

First-line chemoimmunotherapy(with or without bevacizumab)has improved outcomes in advanced non-small cell lung cancer(NSCLC).Here,this open-label,multi-cohort phase II study(NCT05329025)was done to investigate the safety and efficacy of QL1706(a single bifunctional MabPair product against PD-1 and CTLA-4)and chemotherapy with or without bevacizumab in this population.Patients were enrolled into five different cohorts based on genotype(cohorts 1-4,epidermal growth factor receptor[EGFR]wild-type;cohort 5,EGFR-mutant and progressed on EGFR-tyrosine kinase inhibitors[TKIs]).Between June 11,2021 and December 29,2021,91 patients were enrolled.Most frequent treatment-related adverse events(TRAEs)included decreased appetite(60[65.9%]),anemia(60[65.9%]),infusion-related reactions(48[52.7%]),and pruritus(44[48.4%]).Grade≥3 TRAEs occurred in 30(33.0%)patients.Twenty-seven(45%)patients with wild-type EGFR achieved partial response(PR)(objective response rate[ORR]=45%)and had a median progression-free survival(mPFS)of 6.8 months(95%CI:5.2-9.7).For 31 patients harboring mutated EGFR,17(54.8%)achieved PR(ORR=54.8%),with an mPFS of 8.5 months(95%CI:5.72-not evaluable).Overall,QL1706 plus chemotherapy,regardless of having bevacizumab,was generally tolerable and had promising antitumor activity for EGFR wild-type advanced NSCLC in first-line setting.Moreover,QL1706 plus chemotherapy and bevacizumab showed favorable antitumor activity for patients who had EGFR mutated NSCLC but failed in TKI therapy,demonstrating a potential for treating this population.

关键词： bevacizumab chemotherapy phase

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Synergistic Co-doping effect of CNTs and PVP in Na_(4)MnCr(PO_(4))3 cathode as a strategy for improving the electrochemical performance of SIBs

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Chinese Chemical Letters 2024年第2期35卷 539-543页

作者： Ruoyu chen Denys S.Butenko shilin Li Xinyu Zhang Guangshe Li Igor V.Zatovsky Wei Han College of Physics State Key Laboratory of Inorganic Synthesis and Preparative ChemistryInternational Center of Future ScienceJilin UniversityChangchun 130012China Academy for Advanced Interdisciplinary Studies Southern University of Science and TechnologyShenzhen 518055China State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of ChemistryJilin UniversityChangchun 130012China F.D.Ovcharenko Institute of Biocolloidal Chemistry NAS UkraineKyiv 03142Ukraine

In order to solve the contradiction between the rapidly growing energy demand and the excessive exploitation of fossil fuels,it is urgent to research and develops more environmentally friendly and efficient energy storage technologies.Therefore,the development of high-performance cathode materials to enhance the energy density of SIB is currently one of the most important topics of scientific research.Advanced high-voltage and low-cost cathode material for SIBs,a composite of carbon-coated Na_(4)MnCr(PO_(4))_(3)(NASICON-type),polyvinylpyrrolidone(PVP),and modified carbon nanotubes(CNTs)is prepared by sol-gel and freeze-drying method.Due to the high conductivity of CNTs,the conductivity of the composite is significantly improved,and its initial capacity is increased to 114 mAh/g at 0.5 C and 96 mAh/g at 5 C(Mn^(2+)/Mn^(4+)conversion for voltage windows 1.4-4.3 V).Moreover,the multi-electrons transfer of Cr^(3+)/Cr^(4+) and Mn^(2+)/Mn^(4+) can provide a high capacity of 165 mAh/g at 0.1 C and 102 mAh/g at 5 C in the high voltage window of 1.4-4.6 V.Furthermore,PVP can effectively inhibit the Jahn-Teller effect caused by Mn ion,making the composite have more excellent high-rate performance and stability.In addition,GITT,EIS and CV curves were drawn to better reveal the excellent kinetic properties of Na_(4)MnCr(PO_(4))_(3)@C@PVP@CNT cathode,and the mechanism of its performance improvement is deeply studied and discussed.Accordingly,the co-doping of CNTs and PVP is a simple way to high conductivity and fast charging of cathode materials for SIBs.

关键词： Sodium-ion batteries Na_(4)MnCr(PO_(4))_(3) Carbon nanotubes Polyvinylpyrrolidone Synergistic effect

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人工智能加速GPCR配体的发现

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Engineering 2024年第1期32卷 18-28页

作者： Wei chen Chi Song Liang Leng Sanyin Zhang shilin chen State Key Laboratory of Southwestern Chinese Medicine Resources Innovative Institute of Chinese Medicine and PharmacyChengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China

G protein-coupled receptors(GPCRs)are crucial players in various physiological processes,making them attractive candidates for drug discovery.However,traditional approaches to GPCR ligand discovery are time-consuming and resource-intensive.The emergence of artificial intelligence(AI)methods has revolutionized the field of GPCR ligand discovery and has provided valuable tools for accelerating the identification and optimization of GPCR ligands.In this study,we provide guidelines for effectively utilizing AI methods for GPCR ligand discovery,including data collation and representation,model selection,and specific applications.First,the online resources that are instrumental in GPCR ligand discovery were summarized,including databases and repositories that contain valuable GPCR-related information and ligand data.Next,GPCR and ligand representation schemes that can convert data into computer-readable formats were introduced.Subsequently,the key applications of AI methods in the different stages of GPCR drug discovery were discussed,ranging from GPCR function prediction to ligand design and agonist identification.Furthermore,an AI-driven multi-omics integration strategy for GPCR ligand discovery that combines information from various omics disciplines was proposed.Finally,the challenges and future directions of the application of AI in GPCR research were deliberated.In conclusion,continued advancements in AI techniques coupled with interdisciplina ry collaborations will offer great potential for improving the efficiency of GPCR ligand discovery.

关键词： G protein-coupled receptor Ligand Artificial intelligence Multi-omics Drug discovery

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