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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 ***,it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic *** genomes of 123 medicinal plants were published until September *** published genome sequences were investigated in this review,covering their classification,research teams,ploidy,medicinal functions,and sequencing *** than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant *** species account for a majority of sequenced medicinal *** whole genomes of plants in the Poaceae family are the most *** 40%of the published papers studied species with tonifying,replenishing,and heat-cleaning 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 *** addition,there is still no clear routine framework for a medicinal plant to obtain a high-quality whole ***,a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal ***,whole genome-based biological studies of medicinal plants,including breeding and biosynthesis,were *** 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 ***,the conventional techniques for acquiring natural products have been unable to meet the increasing requirements of drug research and *** synthesis of natural products are usually complex process and might bring the risk of causing environmental *** extraction of natural products from medicinal plants are difficult and impractical,resulting in inefficient *** creative methods and strategies are imperative to be developed to enhance the production of natural product from medicinal ***,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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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 ***,traditional approaches to GPCR ligand discovery are time-consuming and *** 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 *** this study,we provide guidelines for effectively utilizing AI methods for GPCR ligand discovery,including data collation and representation,model selection,and specific ***,the online resources that are instrumental in GPCR ligand discovery were summarized,including databases and repositories that contain valuable GPCR-related information and ligand ***,GPCR and ligand representation schemes that can convert data into computer-readable formats were ***,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 ***,an AI-driven multi-omics integration strategy for GPCR ligand discovery that combines information from various omics disciplines was ***,the challenges and future directions of the application of AI in GPCR research were *** 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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Minimizing interfacial energy losses in inverted perovskite solar cells by a dipolar stereochemical 2D perovskite interface

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Journal of Energy Chemistry 2024年第3期90卷 496-503,I0011页

作者： Junjie Qian Jingjing He Qihang Zhang chenyue Zhu shilin chen Zhanpeng Wei Xuesong Leng Ziren Zhou Benben Shen Yu Peng Qiang Niu Shuang Yang Yu Hou Key Laboratory for Ultrafine Materials of Ministry of Education Shanghai Engineering Research Center of Hierarchical NanomaterialsSchool of Materials Science and EngineeringEast China University of Science and TechnologyShanghai 200237China National Enterprise Technology Center Inner Mongolia Erdos Electric Power and Metallurgy Group Company LimitedOrdos 016064Inner MongoliaChina

Inverted perovskite solar cells(PSCs) have attracted broad research and industrial interest owing to their suppressed hysteresis,cost-effectiveness,and ***,the issue of non-radiative recombination losses at the n-type interface between the perovskite and fullerene has impeded further improvement of photovoltaic ***,we modify the n-type interface of FAPbI_(3) perovskite films by constructing a stereochemical two-dimensional(2D) perovskite interlayer,in which the organic cations comprise both pyridine and ammonium *** pyridine N donor can create stable bonding with the surface-uncoordinated Pb on the perovskite,thereby passivating the shallow-level defects and enhancing the air stability of the ***,the pyridine N donor also offers a positive polar interface to decrease the surface work function of the perovskite film,enabling n-type ***,we employ a p-i-n photovoltaic(PV) device with the positive dipole interlayer at perovskite/fullerene contact and achieve remarkable photoelectric conversion efficiency(PCE) of 22.0%.

关键词： Perovskite solar cells Dipole interlayer Stereochemistry Non-radiative recombination

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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 *** 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 ***,we summarize the advances in strategies and methods concerning the biosynthesis and production of natural products of medicinal *** 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 *** 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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金钱白花蛇三指蛋白的表达和纯化

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中华中医药杂志 2024年第5期39卷 2155-2160页

作者：廖雪娇徐江陈士林山东中医药大学济南250355 中国中医科学院中药研究所北京100700 成都中医药大学成都611137

目的:银环蛇幼蛇的干燥体是常用的药用动物金钱白花蛇的主要来源,具有祛风通络、定惊止痉的功效。银环蛇毒性大,且毒腺分泌的蛇毒是复杂的具有药用活性的多肽和蛋白质混合物。在了解银环蛇毒素中的三指蛋白家族后,发现其潜在的药用价值... 详细信息

目的:银环蛇幼蛇的干燥体是常用的药用动物金钱白花蛇的主要来源,具有祛风通络、定惊止痉的功效。银环蛇毒性大,且毒腺分泌的蛇毒是复杂的具有药用活性的多肽和蛋白质混合物。在了解银环蛇毒素中的三指蛋白家族后,发现其潜在的药用价值,便于探索更好的纯化方法,得到高纯度的三指蛋白。方法:通过质粒的转入,三指蛋白能在大肠杆菌中被诱导表达;将菌液超声破碎后离心,SDS-PAGE验证证明三指蛋白在适宜的温度下能可溶性表达;将上清液上样于纯化柱中,梯度洗脱,得到含有杂质的蛋白;透析、超滤浓缩洗去杂质,得到高纯度的三指蛋白。结果:所建立的三指蛋白诱导表达纯化体系,具有良好的重复性和准确性,应用该方法对三指蛋白进行诱导表达和纯化,测得三指蛋白表达和纯化的SDS-PAGE验证图可得清晰的目的条带;通过透析和超滤浓缩除去杂质蛋白,可显著提高三指蛋白的浓度。结论:本研究所建立的三指蛋白诱导表达和纯化体系操作简便,可获得高浓度和高纯度的三指蛋白,为大批量的生产三指蛋白提供科学有效的依据,同时可为后续三指蛋白相互作用研究提供物质基础。

关键词：金钱白花蛇(银环蛇) 三指蛋白表达纯化相互作用

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Progress and prediction of multicomponent quantification in complex systems with practical LC-UV methods

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Journal of Pharmaceutical Analysis 2023年第2期13卷 142-155页

作者： Xi chen Zhao Yang Yang Xu Zhe Liu Yanfang Liu Yuntao Dai shilin chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing100700China Key Lab of Separation Science for Analytical Chemistry Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu611137China

Complex systems exist widely,including medicines from natural products,functional foods,and biological *** biological activity of complex systems is often the result of the synergistic effect of multiple *** the quality evaluation of complex samples,multicomponent quantitative analysis(MCQA)is usually *** overcome the difficulty in obtaining standard products,scholars have proposed achieving MCQA through the“single standard to determine multiple components(SSDMC)”*** method has been used in the determination of multicomponent content in natural source drugs and the analysis of impurities in chemical drugs and has been included in the Chinese *** on a convenient(ultra)high-performance liquid chromatography method,how can the repeatability and robustness of the MCQA method be improved?How can the chromatography conditions be optimized to improve the number of quantitative components?How can computer software technology be introduced to improve the efficiency of multicomponent analysis(MCA)?These are the key problems that remain to be solved in practical ***,this review article summarizes the calculation methods of relative correction factors in the SSDMC approach in the past five years,as well as the method robustness and accuracy ***,it also summarizes methods to improve peak capacity and quantitative accuracy in MCA,including column selection and twodimensional chromatographic analysis ***,computer software technologies for predicting chromatographic conditions and analytical parameters are introduced,which provides an idea for intelligent method development in *** paper aims to provide methodological ideas for the improvement of complex system analysis,especially MCQA.

关键词： Multicomponent quantification analysis Single standard to determine multiple components Predictive software

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低速双燃料柴油机奥托循环下的增压器配机

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柴油机 2024年第3期46卷 8-13页

作者：陈世林邓高雄徐赵刚刘聪王璞上海中船三井造船柴油机有限公司上海201306

基于奥托循环的燃烧特点与需求,从柴油机空燃比和增压器特性两方面对低速双燃料柴油机奥托循环下的增压器配机进行分析。柴油机100%负荷处的压比流量应处于增压器的压力流量特性图的中心位置,在高负荷区域预估的增压器效率、扫气压力、... 详细信息

基于奥托循环的燃烧特点与需求,从柴油机空燃比和增压器特性两方面对低速双燃料柴油机奥托循环下的增压器配机进行分析。柴油机100%负荷处的压比流量应处于增压器的压力流量特性图的中心位置,在高负荷区域预估的增压器效率、扫气压力、扫气量尽可能稍大于设计要求,尽可能采用最小喷嘴环设计,增压器压气机工作线应处于高效区域。在此基础上对X92DF柴油机开展配机策划和试验验证。试验结果表明:该柴油机各项性能满足设计要求,增压器达到预期效果。

关键词：低速双燃料柴油机奥托循环空燃比增压器配机废气旁通

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Cannabis sativa: origin and history, glandular trichome development, and cannabinoid biosynthesis

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Horticulture Research 2023年第9期10卷 306-320页

作者： Ziyan Xie Yaolei Mi Lingzhe Kong Maolun Gao Shanshan chen Weiqiang chen Xiangxiao Meng Wei Sun shilin chen Zhichao Xu Key Laboratory of Saline-alkali Vegetation Ecology Restoration(Northeast Forestry University) Ministry of EducationHarbin 150040China College of Life Science Northeast Forestry UniversityHarbin 150040China Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China

Is Cannabis a boon or bane?Cannabis sativa has long been a versatile crop for fiber extraction(industrial hemp),traditional Chinese medicine(hemp seeds),and recreational drugs(marijuana).Cannabis faced global prohibition in the twentieth century because of the psychoactive properties of △^(9)-tetrahydrocannabinol;however,recently,the perspective has changed with the recognition of additional therapeutic values,particularly the pharmacological potential of cannabidiol.A comprehensive understanding of the underlying mechanism of cannabinoid biosynthesis is necessary to cultivate and promote globally the medicinal application of Cannabis ***,we comprehensively review the historical usage of Cannabis,biosynthesis of trichome-specific cannabinoids,regulatory network of trichome development,and synthetic biology of *** review provides valuable insights into the efficient biosynthesis and green production of cannabinoids,and the development and utilization of novel Cannabis varieties.

关键词： comprehensive versatile globally

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DNA barcoding in herbal medicine: Retrospective and prospective

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Journal of Pharmaceutical Analysis 2023年第5期13卷 431-441页

作者： shilin chen Xianmei Yin Jianping Han Wei Sun Hui Yao Jingyuan Song Xiwen Li Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu611137China Key Laboratoryof Beijing for Identification and Safety Evaluation of Chinese Medicine Instituteof Chinese Materia MedicaChina Academyof Chinese Medical SciencesBeijing100700China State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese MedicineChengdu611137China Institute of Medicinal Plant Development Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing100193China

DNA barcoding has been widely used for herb identification in recent decades,enabling safety and innovation in the field of herbal *** this article,we summarize recent progress in DNA bar-coding for herbal medicine to provide ideas for the further development and application of this *** importantly,the standard DNA barcode has been extended in two ***,while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples,super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic ***,mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal *** addition,some mo-lecular techniques,such as high-throughput sequencing and isothermal amplification,are combined with DNA barcodes for species identification,which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding ***,standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference se-quences for species identification,which increases the accuracy and credibility of species discrimination based on DNA *** summary,DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.

关键词： Herbal identification Super-barcode Mini-barcode Meta-barcoding Cutting-edgebarcoding

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