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A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

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Horticulture Research 2023年第8期10卷 85-96页

作者： Lan Lan Huiqi Zhao Suxia Xu Shenglong Kan Xiaoni zhang Weichao Liu Xuezhu Liao Luke RTembrock Yonglin Ren wayne Reeve Jun Yang Zhiqiang Wu Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518120China School of Medical Molecularand Forensic SciencesMurdoch University6150Western Australia90 South StreetMurdochAustralia Kunpeng Institute of Modern Agriculture at Foshan Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Sanya Institute Hainan Academy of Agricultural SciencesSanya572025China Institute of Tropical Horticulture Research Hainan Academy of Agricultural SciencesHaikou571100China Fujian Key Laboratory of Subtropical Plant Physiology&Biochemistry Fujian Institute of Subtropical BotanyXiamen361006China Key Laboratory of Horticultural Plant Biology College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China Department of Agricultural Biology Colorado State UniversityFort CollinsCO80523USA

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the ***,the absence of genome data limits our understanding of the pathways involved in bract coloration and ***,we report a chromosome-level assembly of the giga-genome of Bougainvillea×buttiana‘Mrs Butt’,a cultivar thought to be the origin of many other Bougainvillea *** assembled genome is∼5 Gb with a scaffold N50 of 151756278 bp and contains 86572 genes which have undergone recent whole-genome *** confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales,reconstructed the relationship in the Caryophyllales at whole genome level,and found discordance between species and gene trees as the result of complex introgression *** investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales *** explore the potential formation mechanism of diverse bract colors in Bougainvillea,we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars,which may limit anthocyanin *** findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color,and a higher expression level in the betalain biosynthetic pathway is required for colored *** improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.

关键词： evolutionary insight breeding

基于生物信息学与网络药理学分析薯蓣皂苷治疗阿尔茨海默病和新型冠状病毒肺炎的靶点研究

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海南医学院学报 2024年第1期30卷 39-49页

作者：张华雄张明惠李红燕新疆维吾尔自治区人民医院神经内科新疆乌鲁木齐830000 新奇康药业股份有限公司新疆乌鲁木齐830000

目的:基于生物信息学、网络药理学及分子对接技术探究薯蓣皂苷治疗阿尔茨海默病(alzheimer disease,AD)和新型冠状病毒肺炎(coronavirus disease 2019,COVID-19)的靶点。方法:利用生物信息学对AD和COVID-19的共有的差异表达基因(differe... 详细信息

目的:基于生物信息学、网络药理学及分子对接技术探究薯蓣皂苷治疗阿尔茨海默病(alzheimer disease,AD)和新型冠状病毒肺炎(coronavirus disease 2019,COVID-19)的靶点。方法:利用生物信息学对AD和COVID-19的共有的差异表达基因(differential expression gene,DEGs)进行富集分析。接着,通过转录因子(transcription Factor,TF)调控网络分析,并利用Cytoscape使其网络可视化,进一步通过DGIdb数据库预测能同时治疗AD和COVID-19的药物,与CTD数据库中AD、COVID-19相关治疗药物进行韦恩图分析,确定薯蓣皂苷作为治疗AD、COVID-19的潜在药物。使用SEA、SuperPred、SwissTargetPrediction、TCMSP对薯蓣皂苷进行靶点预测,并将其分别与AD、COVID-19的DEGs进行韦恩图交集分析,确定薯蓣皂苷治疗AD、COVID-19的靶点,对其进行基因本体论(Gene Ontology,GO)、京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)富集分析,并构建这些药物靶点的蛋白相互作用(Protein Protein Interaction,PPI)网络,筛选出关联度最高的核心靶点。利用分子对接分析薯蓣皂苷与这些核心靶点的结合情况。结果:通过富集和聚类分析,发现AD、COVID-19共有DEGs所富集的生物过程、通路、疾病均与炎症和免疫调节相关。利用这些共有DEGs与Trust数据库构建了AD和COVID-19 TFs调控网络。通过网络药理学预测到薯蓣皂苷是治疗AD和COVID-19的潜在药物,并揭示了薯蓣皂苷治疗AD的36个靶点和27个治疗COVID-19的靶点。用CytohHubba计算得分,分别选取各自关联度最高的6个的核心靶点与薯蓣皂苷进行分子对接。结论:本研究首次揭示了AD和COVID-19共有TFs调控网络,预测并验证了薯蓣皂苷是治疗AD和COVID-19的潜在药物。且通过分子对接确定了薯蓣皂苷与治疗AD和COVID-19的核心药理靶点的结合情况,为开辟临床治疗AD和COVID-19新的途径提供了理论依据。

关键词：生物信息学网络药理学薯蓣皂苷阿尔茨海默病新型冠状病毒肺炎

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Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

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National Science Review 2019年第4期6卷 810-824页

作者： Elaine A.Ostrander Guo-Dong Wang Greger Larson Bridgett M.von Holdt Brian W.Davis Vidhya Jagannathan Christophe Hitte Robert K.wayne Ya-Ping zhang National Human Genome Research Institute National Institutes of Health State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Palaeogenomics and Bio-Archaeology Research Network School of Archaeology University of Oxford Department of Ecology and Evolutionary Biology Princeton University College of Veterinary Medicine and Biomedical Sciences Texas A&M University Institute of Genetics Vetsuisse Faculty University of Bern IGDR CNRS University of Rennes Department of Ecology and Evolutionary Biology University of CaliforniaLos Angeles the Dog10K Consortium

Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10 K Consortium(http://***10 ***) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 *** effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.

关键词： genomics genome-wide association studies(GWAS) breed selection variation evolution

基于网络药理学及实验验证探讨敦煌医方小补肝汤抗运动性疲劳的作用机制

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中药药理与临床 2024年第6期40卷 25-32页

作者：芦文娟张禄璐梁永林霍敏峰张李香甘肃中医药大学基础医学院兰州730030 敦煌医学与转化教育部重点实验室兰州730030

目的:运用网络药理学及实验验证的方法探讨小补肝汤干预运动性疲劳的有效成分及可能作用机制。方法:在中药系统药理学分析平台(TCMSP)检索小补肝汤的活性成分;通过人类基因组数据库(Genecards)、药物数据库(Drugbank)、在线人类孟德尔遗... 详细信息

目的:运用网络药理学及实验验证的方法探讨小补肝汤干预运动性疲劳的有效成分及可能作用机制。方法:在中药系统药理学分析平台(TCMSP)检索小补肝汤的活性成分;通过人类基因组数据库(Genecards)、药物数据库(Drugbank)、在线人类孟德尔遗传(OMIM)、遗传药理学与药物基因组学数据库(PharmGkb),获取疾病的靶标基因;利用Venny2.1.0在线工具绘制药物与疾病靶点的韦恩图,获得交集靶点,将其导入STRING数据库,构建蛋白相互作用(PPI)网络图,通过Bioconductor等在线软件进行基因组数据的高通量分析,得到基因本体(GO)生物功能注释图和京都基因与基因组百科全书(KEGG)富集通路图,预测作用通路,并采用动物实验验证网络药理学预测结果。结果:通过筛选得到小补肝汤36种活性成分,药物-疾病共同靶点244个;通过构建药物-成分-靶点-疾病调控网络,筛选出豆甾醇(Stigmasterol)、海风藤酮(Kadsurenone)、β-谷固醇(Beta-sitosterol)、山蒟酮C(Hancinone C)及黄杉素(Taxifolin)等核心成分;通过蛋白互作网络的构建,筛选出AKT1、GNAQ及PTGS2等11个关键靶点;GO富集分析得出生物学过程BP 3675个,包括对药物的反应、对氧含量的反应、对缺氧的反应等;细胞组分379个,包括膜筏、膜微区、线粒体外膜等;分子功能624个,包括DNA-结合转录因子结合、泛素蛋白连接酶结合及G蛋白偶联胺受体活性等;KEGG富集分析得出涉及的信号通路主要有钙信号通路(GNAQ-PLCB2-IP3R1-CAM)、cAMP信号通路和甲状腺激素信号等通路。动物实验结果显示,与正常对照组比较,模型对照组负重游泳力竭时间显著减少,血清中乳酸(LD)、尿素氮(BUN)的含量显著升高,肝糖原与肌糖原的含量显著降低(P<0.01),骨骼肌组织病理可见骨骼肌细胞排列紊乱不均,有较多炎症细胞弥漫浸润,骨骼肌组织GNAQ、PLCB2、IP3RI、CAM蛋白表达显著上调(P<0.01);与模型对照组比较,各给药组小鼠负重游泳力竭时间显著增加(P<0.01),血清中LD、BUN的含量明显降低(P<0.05),肝糖原与肌糖原的含量明显升高(P<0.05),各给药组小鼠骨骼肌纤维排列有所改善,炎性细胞浸润明显减少,骨骼肌组织GNAQ、PLCB2、IP3RI、CAM蛋白表达明显下调(P<0.05)。结论:小补肝汤能下调运动性疲劳小鼠骨骼肌组织中GNAQ、PLCB2、IP3RI、CAM蛋白表达,从而调节胞内钙离子浓度,减轻因钙超载导致的细胞线粒体、肌浆网功能破坏而引起的疲劳。

关键词：小补肝汤网络药理学运动性疲劳鸟嘌呤核苷酸结合蛋白q肽钙离子

Long-term simulation of growth stage-based irrigation scheduling in maize under various water constraints in Colorado, USA

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Frontiers of Agricultural Science and Engineering 2017年第2期4卷 172-184页

作者： Quanxiao FANG Liwang MA Lajpat Rai AHUJA Thomas James TROUT Robert wayne MALONE Huihui zhang Dongwei GUI Qiang YU Agronomy College Qingdao Agricultural University State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau Northwest A&F University USDA-ARS Rangeland Resources and Systems Research Unit USDA-ARS Agricultural Water Management and Systems Research Unit USDA-ARS National Laboratory for Agriculture and the Environment State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences

Due to varying crop responses to water stress at different growth stages, scheduling irrigation is a challenge for farmers, especially when water availability varies on a monthly, seasonal and yearly basis. The objective of this study was to optimize irrigation between the vegetative(V) and reproductive(R) phases of maize under different available water levels in Colorado. Longterm(1992–2013) scenarios simulated with the calibrated Root Zone Water Quality Model were designed to meet40%–100% of crop evapotranspiration(ET) requirements at V and R phases, subject to seasonal water availabilities(300, 400, 500 mm, and no water limit), with and without monthly limits(total of 112 scenarios). The most suitable irrigation between V and R phases of maize was identified as 60/100, 80/100, and 100/100 of crop ET requirement for the 300, 400, 500 mm water available, respectively, based on the simulations from 1992 to 2013. When a monthly water limit was imposed, the corresponding suitable irrigation targets between V and R stages were 60/100,100/100, and 100/100 of crop ET requirement for the above three seasonal water availabilities, *** targets for producing higher crop yield with reduced risk of poor yield were discussed for projected five-year water availabilities.

关键词： RZWQM ET-based irrigation schedule maize water constrains

Eigenvalue approximation from below using non-conforming finite elements

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Science China Mathematics 2010年第1期53卷 137-150页

作者： YANG YiDu 1 ,zhang ZhiMin 2 & LIN FuBiao 11 School of Mathematics and Computer Science,Guizhou Normal University,Guiyang 550001,China 2 Department of Mathematics,wayne State University,Detroit,MI 48202,USA School of Mathematics and Computer Science Guizhou Normal University Department of Mathematics Wayne State University

This is a survey article about using non-conforming finite elements in solving eigenvalue problems of elliptic operators,with emphasis on obtaining lower bounds. In addition,this article also contains some new materials for eigenvalue approximations of the Laplace operator,which include:1) the proof of the fact that the non-conforming Crouzeix-Raviart element approximates eigenvalues associated with smooth eigenfunctions from below;2) the proof of the fact that the non-conforming EQ rot1 element approximates eigenvalues from below on polygonal domains that can be decomposed into rectangular elements;3) the explanation of the phenomena that numerical eigenvalues λ 1,h and λ 3,h of the non-conforming Q rot1 element approximate the true eigenvalues from below for the L-shaped domain. Finally,we list several unsolved problems.

关键词： non-conforming element eigenvalue lower bound

Enhancing cartilage repair with optimized supramolecular hydrogel-based scaffold and pulsed electromagnetic field

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Bioactive Materials 2023年第4期22卷 312-324页

作者： Yucong Li Linlong Li Ye Li Lu Feng Bin Wang Ming Wang Haixing Wang Meiling Zhu Yongkang Yang Erik IWaldorff Nianli zhang Ingmar Viohl Sien Lin Liming Bian wayne Yuk-Wai Lee Gang Li Department of Orthopaedics&Traumatology Stem Cells and Regenerative Medicine LaboratoryLi Ka Shing Institute of Health SciencesThe Chinese University of Hong KongPrince of Wales HospitalShatinHong Kong Special Administrative Region Research&Clinical Affairs Orthofix Medical Inc.LewisvilleTXUSA Department of Rehabilitation Sciences Hong Kong Polytechnic UniversityHong Kong Special Administrative Region Innovation Centre for Advanced Interdisciplinary Medicine Key Laboratory of Biological Targeting DiagnosisTherapy and Rehabilitation of Guangdong Higher Education InstitutesThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina The Eighth Affiliated Hospital Sun Yat-Sen UniversityShenzhenPR China School of Biomedical Sciences and Engineering National Engineering Research Center for Tissue Restoration and ReconstructionKey Laboratory of Biomedical Materials and Engineering of the Ministry of EducationSouth China University of TechnologyGuangzhouPR China Department of Orthopaedics and Traumatology SH Ho Scoliosis Research LaboratoryJoint Scoliosis Research Center of the Chinese University of Hong Kong and Nanjing UniversityThe Chinese University of Hong KongHong Kong Special Administrative Region

Functional tissue engineering strategies provide innovative approach for the repair and regeneration of damaged *** is widely used because it could provide rapid defect filling and proper structure support,and is biocompatible for cell aggregation and matrix *** have been made to seek suitable scaffolds for cartilage tissue *** Alg-DA/Ac-β-CD/gelatin hydrogel was designed with the features of physical and chemical multiple crosslinking and self-healing *** time,swelling ratio,biodegradability and biocompatibility of the hydrogels were systematically characterized,and the injectable self-healing adhesive hydrogel were demonstrated to exhibit ideal properties for cartilage ***,the new hydrogel design introduces a pre-gel state before photo-crosslinking,where increased viscosity and decreased fluidity allow the gel to remain in a semi-solid *** granted multiple administration routes to the hydrogels,which brings hydrogels the ability to adapt to complex clinical *** electromagnetic fields(PEMF)have been recognized as a promising solution to various health problems owing to their noninvasive properties and therapeutic *** treatment offers a better clinical outcome with fewer,if any,side effects,and wildly used in musculoskeletal tissue *** we propose PEMF as an effective biophysical stimulation to be 4th key element in cartilage tissue *** this study,the as-prepared Alg-DA/Ac-β-CD/gelatin hydrogels were utilized in the rat osteochondral defect model,and the potential application of PEMF in cartilage tissue engineering were *** treatment were proven to enhance the quality of engineered chondrogenic constructs in vitro,and facilitate chondrogenesis and cartilage repair in *** of the results suggested that with the injectable self-healing adhesive hydrogel and PEMF treatment,this newly proposed tissue engineering strategy r

关键词： Supramolecular hydrogels Pulsed electromagnetic field Cartilage tissue engineering Mesenchymal stem cells Chondrogenesis

Surrogate markers and predictors of endogenous insulin secretion in children and adolescents with type 1 diabetes

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World Journal of Pediatrics 2021年第1期17卷 99-105页

作者： Jin-Na Yuan Jian-Wei zhang wayne S.Cutfield Guan-Ping Dong You-Jun Jiang Wei Wu Ke Huang Xiao-Chun Chen Yan Zheng Bi-Hong Liu Jose G.B.Derraik Jun-Fen Fu Department of Endocrinology National Clinical Research Center for Child HealthThe Children's HospitalZhejiang University School of MedicineHangzhou 310003China Department of Pediatrics Shaoxing Women and Children's HospitalShaoxingChina Liggins Institute University of AucklandAucklandNew Zealand A Better Start-National Science Challenge University of AucklandAucklandNew Zealand Department of Women’s and Children’s Health Uppsala UniversityUppsalaSweden

Background No studies have examined endogenous insulin secretion in pediatric patients with type 1 diabetes in China using the gold-standard mixed-meal tolerance *** the latter is labor-intensive,we examined simpler surrogate markers of endogenous insulin secretion in Chinese youth,as previously reported for a European *** Participants were 57 children and adolescents with type 1 diabetes aged 4.4-16.8 years(56% females).We per-formed 120-minute mixed-meal tolerance tests with serum C-peptide(CP)measurements every 30 *** insulin deficiency(SID)was defined as CP peak<0.2 nmol/*** CP and creatinine levels were measured at 0 and 120 *** Twenty-five(44%)patients had *** CP levels missed one case(96% sensitivity)with no false posi-tives(100% specificity).While the 120-minute urine CP/creatinine had 100% sensitivity,it yielded markedly lower speci-ficity(63%).Every 1-year increase in diabetes duration and 1-year decrease in age at diagnosis were associated with 37%(P<0.001)and 20%(P=0.005)reductions in serum CP area-under-the-curve,***,86% of children aged<5 years had SID compared to none among patients aged ≥11 *** Simple fasting CP measurements could be used to detect most SID cases in Chinese youth with type 1 *** CP is a far more reliable measure of endogenous insulin secretion than the more commonly used insulin ***,it could more precisely determine insulin secretory capacity to target those who could benefit,if treatments to preserve residual insulin secretion are developed.

关键词： Endogenous insulin secretion Mixed-meal tolerance test(MMTT) Type 1 diabetes mellitus

O-alg-THAM/gel hydrogels functionalized with engineered microspheres based on mesenchymal stem cell secretion recruit endogenous stem cells for cartilage repair

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Bioactive Materials 2023年第10期28卷 255-272页

作者： Yucong Li Linlong Li Ming Wang Boguang Yang Baozhen Huang Shanshan Bai Xiaoting zhang Nan Hou Haixing Wang Zhengmeng Yang Chong Tang Ye Li wayne Yuk-Wai Lee Lu Feng Micky D.Tortorella Gang Li Stem Cells and Regenerative Medicine Laboratory Li Ka Shing Institute of Health SciencesThe Chinese University of Hong KongPrince of Wales HospitalShatinHong Kong Special Administrative Region of China Musculoskeletal Research Laboratory Department of Orthopaedics&TraumatologyFaculty of MedicineThe Chinese University of Hong KongPrince of Wales HospitalShatinHong Kong Special Administrative Region of China The CUHK-ACC Space Medicine Centre on Health Maintenance of Musculoskeletal System The Chinese University of Hong Kong Shenzhen Research InstituteShenzhenPR China Department of Orthopaedics Peking University Shougang HospitalBeijingPR China Department of Rehabilitation Sciences Hong Kong Polytechnic UniversityHong Kong Special Administrative Region of China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhouChina

Lacking self-repair abilities,injuries to articular cartilage can lead to cartilage degeneration and ultimately result in *** engineering based on functional bioactive scaffolds are emerging as promising approaches for articular cartilage regeneration and *** the use of cell-laden scaffolds prior to implantation can regenerate and repair cartilage lesions to some extent,these approaches are still restricted by limited cell sources,excessive costs,risks of disease transmission and complex manufacturing *** approaches through the recruitment of endogenous cells offer great promise for in situ articular cartilage *** this study,we propose an endogenous stem cell recruitment strategy for cartilage *** on an injectable,adhesive and self-healable o-alg-THAM/gel hydrogel system as scaffolds and a biophysio-enhanced bioactive microspheres engineered based on hBMSCs secretion during chondrogenic differentiation as bioactive supplement,the as proposed functional material effectively and specifically recruit endogenous stem cells for cartilage repair,providing new insights into in situ articular cartilage regeneration.

关键词： Bioactive hydrogels Solidified secretome Adhesive hydrogels Acellular functional scaffold Cartilage repair