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Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias

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Science China(Life Sciences) 2022年第4期65卷 809-817页

作者： Baosheng Liao Haoyu Hu shuiming xiao Guanru Zhou Wei Sun Yang Chu Xiangxiao Meng Jianhe Wei Han Zhang Jiang Xu Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing100700China Institute of Pharmacy Hubei University of Chinese MedicineWuhan430065China Institute of Medicinal Plant Development Chinese Academy of Medical SciencesBeijing100193China Pharmacy College Chengdu University of Traditional Chinese MedicineChengdu611137China Institute of Traditional Chinese Medicine Tianjin University of Traditional Chinese MedicineTianjin301617China

Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However,the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database(GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias(Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://*** and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.

关键词： Global Pharmacopoeia Genome Database herb traditional medicine genomics

Genome-wide identification and transcriptional profiling analysis of PIN/PILS auxin transporter gene families in Panax ginseng

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Chinese Herbal Medicines 2022年第1期14卷 48-57页

作者： shuiming xiao Yang Chu Yanjun Chen Qinghe Zhao Baosheng Liao Jingjing Zhang Yuan Gao Jiang Xu Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China College of Pharmacy Hubei University of Chinese MedicineWuhan 430065China Institute of Medicinal Plant Development Chinese Academy of Medical SciencesBeijing 100193China

Objective:Plant hormones act as chemical messengers in the regulation of plant development and *** production of ginsenosides in Panax hybrid is promoted by auxins that are transported and accumulated by PIN-FORMED(PIN)and PIN-LIKES(PILS)auxin ***,genome-wide studies of PIN/PILS of ginseng are still *** current study,identification and transcriptional profiling of PIN/PILS gene families,as well as their potential relationship with ginsenoside biosynthesis in Panax ginseng were ***:PIN/PILS genes in *** was identified via in silico genome-wide analysis,followed by phylogenetic relationships,gene structure,and protein profiles ***,previously reported RNA-sequence data from various tissues and roots after infection were utilized for PIN/PILS genes expression pattern *** Pearson’s correlation analysis of specific PIN/PILS genes expression level and main ginsenoside contents were taken to reveal the potential relationship between auxin transports and ginsenoside biosynthesis in ***:A genome-wide search of *** genome for homologous auxin transporter genes identified a total of 17 PIN and 11 PILS *** alignment,putative motif organization,and sub-cellular localization indicated redundant and complementary biological functions of these PIN/PILS *** PIN/PILS genes were differentially expressed in a tissue-specific manner,and showed significant correlations with ginsenoside content *** auxin transporter genes,including both PIN and PILS subfamily members,were positively correlated with ginsenoside content(cor>0.60;P-value<0.05).The expression levels of eleven auxin transporter genes were increased dramatically in the early stage(0–0.5 DPI)after Cylindrocarpon destructans infection,accompanied with various overall expression patterns,implying the dynamic auxin transport in response to biotic ***:Based on the results,we specul

关键词： auxin genome-wide ginsenoside PILS PIN transcriptome

A Comparative Analysis of the Chloroplast Genomes of Four Salvia Medicinal Plants

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Engineering 2019年第5期5卷 907-915页

作者： Conglian Liang Lei Wang Juan Lei Baozhong Duan Weisi Ma shuiming xiao Haijun Qi Zhen Wang Yaoqi Liu xiaofeng Shen Shuai Guo Haoyu Hu Jiang Xu Shilin Chen College of Pharmacy Shandong University of Traditional Chinese Medicine(TCM)Jinan 250355China Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China State Key Laboratory of Innovative Natural Medicine and TCM Injections Jiangxi Qingfeng Pharmaceutical Co.Ltd.Ganzhou 341000China Beijing Children’s Hospital Capital Medical UniversityNational Center for Children’s HealthBeijing 100045China School of Biological Science The University of QueenslandBrisbaneQLD 4072Australia College of Pharmacy Dali UniversityDali 671000China Institute of Medicinal Plants Yunnan Academy of Agricultural SciencesKunming 650205China

Herbgenomics is an emerging field of traditional Chinese medicine(TCM)research and *** combining TCM research with genomics,herbgenomics can help to establish the scientific validity of TCM and bring it into wider usage within the field of *** Linn.(***.)is a large genus of Labiatae that includes important medicinal *** this herbgenomics study,the complete chloroplast(cp)genomes of two Salvia spp.—namely,*** and ***,which are used as a surrogate for ***—were sequenced and compared with those of two other reported Salvia spp.—namely,*** and *** genome organization,gene number,type,and repeat sequences were *** annotation results showed that both Salvia plants contain 114 unique genes,including 80 protein-coding,30 transfer RNA(tRNA),and four ribosomal RNA(rRNA)*** sequence analysis revealed 21 forward and 22 palindromic sequences in both Salvia cp genomes,and 17 and 21 tandem repeats in *** and ***,respectively.A synteny comparison of the Salvia *** genomes showed a high degree of sequence similarity in the coding regions and a relatively high divergence of the intergenic *** alignment and single-nucleotide polymorphism(SNP)analyses found some candidate fragments to identify Salvia spp.,such as the intergenic region of the trnV–ndhC,trnQ–rps16,atpI–atpH,psbA–ycf3,ycf1,rpoC2,ndhF,matK,rpoB,rpoA,and accD *** of the results—including the repeat sequences and SNP sites,the inverted repeat(IR)region border,and the phylogenetic analysis—showed that *** and *** are extremely similar from a genetic *** cp genome sequences of the two Salvia *** here will pave the way for breeding,species identification,phylogenetic evolution,and cp genetic engineering studies of Salvia medicinal plants.

关键词： Salvia Chloroplast genome Comparative analysis

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分数阶流行病模型的近似解析解

江西师范大学学报（自然科学版） 2015年第5期39卷 526-530页

作者：肖水明杨兰惠周家兴南昌大学理学院数学系江西南昌330031 南昌大学软件学院江西南昌330047

在经典的SIR,SIRS,SIS流行病模型基础上引入关于时间的分数阶导数,并利用同伦摄动方法分别求出这3个模型的近似解析解,而且应用数值实验结果印证了FDEs的记忆特征.改进和推广了一些已有的成果,且对深入研究分数阶流行病模型有很好的启... 详细信息

在经典的SIR,SIRS,SIS流行病模型基础上引入关于时间的分数阶导数,并利用同伦摄动方法分别求出这3个模型的近似解析解,而且应用数值实验结果印证了FDEs的记忆特征.改进和推广了一些已有的成果,且对深入研究分数阶流行病模型有很好的启示作用.

关键词：分数阶微分方程流行病模型同伦摄动方法近似解析解

微生物诱导碳酸钙沉积固化建筑渣土抗风蚀扬尘影响因素的试验研究

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工业建筑 2022年第11期52卷 71-78页

作者：刘忠肖水明刘飞飞龙文梁张敏霞深圳市市政工程总公司广东深圳518000 河南理工大学土木工程学院河南焦作454150

为研究钙源、胶结液浓度、菌液浓度、温度和胶结液pH值等对微生物诱导碳酸钙沉积(MICP)固化渣土抗风蚀和扬尘的影响,开展了单因素正交MICP固化建筑渣土试验和风洞试验,同时辅以X射线三维显微镜和X射线衍射等微观手段。试验结果表明:以... 详细信息

为研究钙源、胶结液浓度、菌液浓度、温度和胶结液pH值等对微生物诱导碳酸钙沉积(MICP)固化渣土抗风蚀和扬尘的影响,开展了单因素正交MICP固化建筑渣土试验和风洞试验,同时辅以X射线三维显微镜和X射线衍射等微观手段。试验结果表明:以氯化钙为钙源,胶结液浓度为0.5 mol/L,菌液浓度(OD600值)为4.0,温度为20~40℃,中性或弱碱性环境下MICP固化建筑渣土抗风蚀效果教佳;MICP固化建筑渣土的易溶盐含量和pH值最大增幅分别为0.92%和0.20,MICP固化建筑渣土兼具环境友好的特性。

关键词：微生物诱导生成碳酸钙建筑渣土抑尘影响因素微观机理

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人参内生菌的研究进展

世界科学技术-中医药现代化 2022年第8期24卷 2938-2946页

作者：凡贞洁徐静雅侯典云胡灏禹肖水明徐江中国中医科学院中药研究所北京100700 河南科技大学农学院洛阳471000

内生菌由细菌、真菌、古菌和原生生物组成,它们生活在植物的活体组织中,具有丰富的次级代谢产物多样性。人参内生菌在人参的生长发育、次级代谢产物的生成和环境适应等方面均有重要的促进作用,对人参的产量和品质有较大影响。随着人们... 详细信息

内生菌由细菌、真菌、古菌和原生生物组成,它们生活在植物的活体组织中,具有丰富的次级代谢产物多样性。人参内生菌在人参的生长发育、次级代谢产物的生成和环境适应等方面均有重要的促进作用,对人参的产量和品质有较大影响。随着人们在微生物领域研究的深入,高通量测序技术已经成为研究植物内生菌的重要方法。文章主要从人参内生菌分离与鉴定研究方法、人参内生菌的多样性、人参内生菌及其次级代谢产物的活性、人参内生菌对宿主的影响等4个方面对人参内生菌近年来的研究进展进行讨论,并对其发展方向提出展望,以期为药用植物内生菌研究和品质改良提供新思路、新方法。

关键词：人参内生菌多样性次级代谢产物生物学活性

苦瓜全粉和苦瓜乙醇提取物健康功效的体外评估

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基因组学与应用生物学 2019年第11期38卷 5113-5119页

作者：黄鲁燕何欣欣薛正晟徐佳肖水明王凌华上海交通大学生命科学技术学院微生物代谢国家重点实验室

本研究的目的是运用体外模型评估苦瓜全粉和苦瓜乙醇提取物的健康功效。苦瓜全粉和苦瓜乙醇提取物以7.5 mg/mL和15 mg/mL的剂量与新鲜粪便样品进行体外厌氧培养。通过454焦磷酸测序技术分析粪便菌群组成的变化,同时测定发酵上清中短链... 详细信息

本研究的目的是运用体外模型评估苦瓜全粉和苦瓜乙醇提取物的健康功效。苦瓜全粉和苦瓜乙醇提取物以7.5 mg/mL和15 mg/mL的剂量与新鲜粪便样品进行体外厌氧培养。通过454焦磷酸测序技术分析粪便菌群组成的变化,同时测定发酵上清中短链脂肪酸的含量以及对Caco-2单层细胞跨膜电阻的影响。结果显示,苦瓜全粉(15 mg/mL)可以明显地扶植Faecalibacterium属细菌,同时抑制Bilophila和Desulfovibrio属细菌的增殖;同等剂量的苦瓜全粉发酵上清中短链脂肪酸的含量明显高于苦瓜乙醇提取物发酵上清;源自苦瓜乙醇提取物(15 mg/mL)的发酵上清对Caco-2单层细胞跨膜电阻的增强作用要大于苦瓜全粉(15 mg/mL)。本研究探究了体外苦瓜全粉和苦瓜乙醇提取物不同的生理功效,为以后苦瓜制品的选择提供了初步证据。

关键词：苦瓜全粉苦瓜乙醇提取物短链脂肪酸肠道菌群 Caco-2单层细胞跨膜电阻

A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome

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A gut microbiota-targeted dietary intervention for ameliorat...

第十四届全国中药和天然药物学术研讨会

作者： shuiming xiao Na Fei xiaoyan Pang Jian Shen Linghua Wang Baorang Zhang Menghui Zhang xiaojun Zhang Chenhong Zhang Min Li Lifeng Sun Zhengsheng Xue Jingjing Wang Jie Feng Feiyari Yan Naisi Zhao Jiaqi Liu Wenmin Long Liping Zhao Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences

＜正＞Chronic inflammation induced by endotoxin from a dysbiotic gut microbiota contributes to the development of obesity-related metabolic *** of gut microbiota by a diet to balance its composition becomes a promising strategy to help manage obesity.A dietary scheme based on whole grains,traditional Chinese medicinal foods,and prebiotics

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培土清心方对特应性皮炎儿童肠道菌群的影响

中国皮肤性病学杂志 2020年第6期34卷 688-691页

作者：裴悦肖水明莫秀梅刘俊峰梁家芬张瑜王楚阳黄志海李红毅广州中医药大学第二附属医院皮肤科广东广州510120 中国中医科学院中药研究所北京100700

目的通过高通量测序手段检测比较特应性皮炎(AD)患儿与健康对照儿童肠道菌群结构差异,并对比培土清心方干预前后对AD患儿的临床疗效及肠道菌群的改变情况,初步探索培土清心方对肠道菌群的影响。方法共纳入60例受试者(实验组、健康对照组... 详细信息

目的通过高通量测序手段检测比较特应性皮炎(AD)患儿与健康对照儿童肠道菌群结构差异,并对比培土清心方干预前后对AD患儿的临床疗效及肠道菌群的改变情况,初步探索培土清心方对肠道菌群的影响。方法共纳入60例受试者(实验组、健康对照组各30例),实验组分别在口服培土清心方0周(AD.0W)、4周(AD.4W)进行SCORAD评分并采集粪便样品,对照组在0周时采集粪便样品,统一对粪便样品进行16S rRNA基因测序检测。结果实验组用药4周(AD.4W)SCORD评分降低,差异有统计学意义(PAD.4W组>健康对照组(P>0.05)。②差异菌门水平:Firmicutes(厚壁菌门)相对丰度:AD.0W组0.05);Bacteroidetes(拟杆菌门)相对丰度:AD.4W组0.05);Faecalibacterium(柔嫩梭菌属)相对丰度:AD.0W组

关键词：特应性皮炎肠道菌群培土清心方 16S rRNA基因测序检测