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Study of the potential mechanism of acupuncture treatment for functional dyspepsia based on association rule mining and bioinformatics/network pharmacology approach

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Gastroenterology & Hepatology research 2023年第2期5卷 6-15页

作者： An-Lan Zhao Ling-Yong Xiao Hong-Yue Niu Lian Liu Xiao-Yu Dai Department of Acupuncture First Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjin 300193China National Clinical research Center for Chinese Medicine Acupuncture and Moxibustion Tianjin 300381Chian College of Acupuncture and Massage Tianjin University of Traditional Chinese MedicineTianjin 300000China

Objective:To explore the main acupoint prescription and mechanism of acupuncture in treating Functional dyspepsia(FD)by analyzing the clinical randomized controlled trial literature on acupoints and targets of acupuncture in the treatment of FD combined with association rule mining and bioinformatics/network pharmacology ***:Search relevant clinical randomized controlled trial literature on acupoints and therapeutic targets of acupuncture in the treatment of FD from eight databases from their inception to June 18th,*** obtained acupuncture selection points,meridian,and therapeutic targets and established acupoints database for acupuncture treatment of ***-related targets were collected from GeneCards,DisGeNET,OMIM,and DrugBank *** obtained the potential targets of acupuncture on FD by taking the intersection of acupuncture for FD therapeutic targets and FD-related *** performed the protein-protein interaction network,Gene Ontology(GO)analysis,and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment ***:In this study,26 Randomized Controlled Trials related to acupuncture treatment of FD were *** obtained 29 acupoints,17 acupuncture for FD therapeutic targets,and 10 intersection *** necrosis factor(TNF),Interleukin(IL)-1,and Neuropeptide Y(NPY)are key targets of acupuncture in the treatment of ***:ST36-CV12-PC6-LR3 is the main acupoint prescription for *** may affect Neuroactive ligand-receptor interaction,Gastric acid secretion,and IL-17,TNF signaling pathways by regulating related key targets,and play a synergistic role in the treatment of FD by inhibiting gastric acid secretion,alleviating inflammatory response,regulating the brain-gut axis,improving mood and other aspects.

关键词： acupuncture functional dyspepsia network acupuncture mechanism

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Cloning and bioinformatics Analysis of FaPHYC Gene in Tall Fescue (Festuca arundinacea)

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Agricultural Biotechnology 2019年第5期8卷 1-5页

作者： Lu CAI Xiaoxia LIU Degang ZHAO Xiaoli WANG Xi CHEN Biological Technology Institute of Guizhou Province Guiyang 550000China Institute of Prataculture Guizhou Academy of Agricultural SciencesGuiyang 550006China The National-Local Joint Engineering research Center of Karst Region Plant Resources Utilization & Breeding of Guizhou Province Guizhou UniversityGuiyang 550025China

The cDNA of PHYC gene of tall fescue ( Festuca arundinacea ) was cloned by RT-PCR,named *** sequence was analyzed by bioinformatic software,and the results showed that the full-length cDNA(3816 bp) was obtained with an open reading frame predicated to be 3 411 bp,which encoded 1 136 amino *** BLASTP analysis,the N-terminal of FaPHYC was composed of GAF and pPhytochrome domains,and its C-terminal included two repeated PAS domains,one histidine kinase A domain and one histidine kinase-like ATPase *** phylogenetic analysis showed that FaPHYC was closely related to PHYCs from other Gramineae *** qRT-PCR results showed that FaPHYC expression was regulated by drought stress,heat stress,salt stress and nitrogen *** real-time quantitative PCR assay showed the expression of FaPHYC in tall fescue seedlings was continuously up-regulated during the light period and down-regulated in the *** results suggest that FaPHYC is photoperiod sensitive and plays a functional role in flowering regulation by photoperiod in tall *** FaPHYC gene was cloned and reported from tall fescue for the first time,which lays a foundation for the investigation of the stress mechanism of FaPHYC in tall fescue plant.

关键词： Festuca arundinacea FaPHYC gene Gene cloning bioinformatics analysis

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PPPM (Predictive, Preventive and Personalized Medicine) as a New Model of the National and International Healthcare Services and Thus a Promising Strategy to Prevent a Disease: From Basics to Practice

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International Journal of Clinical Medicine 2014年第14期5卷 855-870页

作者： I. A. Sadkovsky O. Golubnitschaja M. A. Mandrik M. A. Studneva H. Abe H. Schroeder E. N. Antonova F. Betsou T. A. Bodrova K. Payne S. V. Suchkov Department of Medicine Genetics and Comparative Pathology University of Alabama at Birmingham (UAB) Birmingham USA European Association for Predictive Preventive and Personalized Medicine (EPMA) Brussels EU Rheinische Friedrich-Wilhelms-University of Bonn Bonn Germany I.M. Sechenov First Moscow State Medical University Moscow Russia I.M. Sechenov First Moscow State Medical University Moscow Russia A.I. Evdokimov Moscow State Medical & Dental University Moscow Russia United Cultural Convention (UCC) Cambridge UK Institute of Population Health and Health Economics University of Manchester Manchester UK International Society for Personalized Medicine (ISPM) Tokyo Japan National research University “Higher School of Economics” Moscow Russia Université du Luxembourg and IBBL (Integrated BioBank of Luxembourg) Luxembourg EU

Nowadays the system of public health is constructed in such a manner so that its main objective is the recovery of an already sick person, while prediction and prevention receive little attention. Meanwhile the development of these aspects of medicine can lead to the ability to control morbidity among the population, to identify chronic and genetic diseases in the early stages of development, and thus to prevent their further progression. This will reduce traditionally high costs of sick people treatment and the number of disabled population, and improve the quality and duration of life. The elaboration of new fields of science that are working on the study and interpretation of data obtained during laboratory and clinical research, creation of new methods for diagnosis, prognosis and treatment, provides an opportunity now to implement a new strategy, called PPPM, and gets promising results, which should lead to further development of an existing medicine.

关键词： Predictive Preventive and Personalized Medicine Biomarkers Subclinical Metabolomics Genomics Proteomics bioinformatics Public Health Predisposition

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bioinformatics Analysis and Experimental Verification of Prognostic and Biological Significance of Autophagy-Related Long Non-Coding RNAs in Gastric Carcinoma

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Proceedings of Anticancer research 2023年第1期7卷 15-29页

作者： Jiebang Jiang Center for Clinical research and Translational Medicine Yangpu HospitalTongji University School of MedicineShanghai 200090China Institute of Gastrointestinal Surgery and Translational Medicine Tongji University School of MedicineShanghai 200090China Department of General Surgery Yangpu Hospital Affiliated to Tongji UniversityTongji University School of MedicineShanghai 200090China

Background:Long non-coding RNAs(lncRNAs)play a vital role in autophagy modulation and tumor ***,the key lncRNAs and their functions in gastric cancer(GC)remain largely ***:A bioinformatic analysis of GC patients’gene expression profiling data from the Cancer Genome Atlas database was performed to identify autophagy-related lncRNAs that are associated with predictive *** Cox regression and Lasso regression analyses,the autophagy-related lncRNAs that are associated with prognosis were identified,and a novel prognostic model for GC was *** model was then used to evaluate the clinical features and predictive risk of individuals with *** using two datasets,GSE 62254(n=300)and GSE 15459(n=192),from Gene Expression Omnibus,its effectiveness was *** set enrichment analysis according to hallmark and Kyoto Encyclopedia of Genes and Genomes were used to determine the possible biological roles of these ***,the HOXD antisense growth-associated long non-coding RNA(HAGLR)mechanism in GC was discovered through in vitro and in vivo ***:Six lncRNAs associated with autophagy in GC were identified,and a new prognostic risk model based on these lncRNAs was *** six-lncRNA signature was significantly associated with adverse clinicopathological features and found to be an independent GC prognostic *** model was proven to be effective and robust by GSE62254 and *** to gene set enrichment analysis,the six lncRNAs appeared to be tightly linked to autophagy-related and cancer-related *** was also found to promote tumor growth by enhancing autophagy signaling in ***:A novel prognostic model integrating HAGLR that can effectively evaluate and predict the prognostic risk of GC patients was *** results indicated that HAGLR promotes gastric cancer progression by enhancing autophagy and is anticipated to be a potential new target for the tr

关键词： Gastric cancer Autophagy Long non-coding RNA Prognostic risk HAGLR

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Csi-let-7a-5p delivered by extracellular vesicles from a liver fluke activates M1 macrophages and exacerbates biliary injuries

Csi-let-7a-5p delivered by extracellular vesicles from a liv...

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2021中国畜牧兽医学会兽医寄生虫学分会第二届青年科学家学术论坛

作者：颜超 Qian-Yang Zhou Jing Wu Na Xu Ying Du Jing Li Ji-Xin Liu Stephane Koda Bei-Bei Zhang Qian Yu Hui-Min Yang Yin-Hai Xu Jia-Xu Chen Zhongdao Wu Xing-Quan Zhu Ren-Xian Tang Kui-Yang Zheng Jiangsu Key Laboratory of Immunity and Metabolism Department of Pathogenic Biology and ImmunologyXuzhou Key Laboratory of Infection and ImmunityXuzhou Medical University National Demonstration Center for Experimental Basic Medical Science Education Xuzhou Medical University Department of Dermatology the Second Affiliated Hospital of Nanjing Medical University Huai'an Center for Disease Control and Prevention Department of Laboratory Medicine The Affiliated Hospital of Xuzhou Medical University National Institute of Parasitic Diseases Chinese Center for Disease Control and PreventionKey Laboratory of Parasite and Vector BiologyMinistry of HealthWHO Collaborating Center of MalariaSchistosomiasis and Filariasis Department of Parasitology Zhongshan School of MedicineKey Laboratory of Tropical Disease Control (SYSU)Ministry of EducationProvincial Engineering Technology Research Center for Biological Vector ControlSun Yat-sen University College of Veterinary Medicine Shanxi Agricultural University

Chronic infection with liver flukes(such as Clonorchis sinensis) can induce severe biliary injuries,which can cause cholangitis,biliary fibrosis,and even cholangiocarcinoma(CCA).The release of extracellular vesicles by ***(CsEVs) is of importance in the long-distance communication between the hosts and ***,the biological effects of EVs from liver fluke on biliary injuries and the underlying molecular mechanisms remain poorly *** this study,Differential centrifugation was used to isolate CsEVs from excretory/secretory products of *** were identified by nanoparticle tracking analysis and transmission electron ***-seq,bioinformatics analysis,and dual-luciferase activity assay were used to identify targets of Csi-let-7 a-5 ***,ELISA,and qPCR were employed to investigate the function of Csi-let-7 a-5 p packaged in CsEVs in vivo and in *** found that CsEVs induced M1-like *** addition,the mice that were administrated with CsEVs showed severe biliary injuries associated with remarkable activation of M1-like *** further characterized the signatures of miRNAs packaged in CsEVs and identified a miRNA Csi-let-7 a-5 p was highly *** study showed that Csi-let-7 a-5 p facilitated the activation of Ml-like macrophage by targeting at Socsl and Clec7 a,however,CsEVs with silencing Csi-let-7 a-5 p showed a decrease in pro-inflammatory responses and biliary injuries,which involved in Socsl and Clec7 aregulated NF-κB signaling *** conclusion,our study demonstrates that Csi-let-7 a-5 p delivered by CsEVs plays a critical role in the activation of Ml-like macrophages and contributes to the biliary injuries by targeting at Socsl and Clec7 a-mediated NF-κB signaling pathway,which indicates a novel mechanism contributed to biliary injuries caused by fluke ***,other molecules other than Csi-let-7 a-5 p from CsEVs that may also promote M1 polarization and exacerbate biliary in

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利用生物信息学方法和多抗原表位DNA免疫方法研制有效的抗蛇毒血清

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蛇志 2007年第3期19卷 169-174页

作者：余方芳范泉水蓝海 Simon C. Wagstaff Gavin D. Laing R.David G.Theakston Christina Papaspyridis Robert A. Harrison 云南农业大学动物科技学院云南昆明650201 成都军区疾病预防控制中心军事医学研究所云南昆明650032 中国蛇协急危重症医学研究所广西南宁530021 Alistair Reid Venom research Unit Liverpool School of Tropical MedicinePembroke PlaceLiverpoolUnited Kingdom

传统的抗蛇毒血清是从全毒免疫的马或绵羊的血清中提取,但目前的免疫方法包括对马或绵羊进行的超免也不能达到对大多数临床上重要的毒素都产生免疫应答的目标。目前利物浦大学的Simon. C. Wagstaff等研究人员开发了一种最新的研制抗蛇... 详细信息

传统的抗蛇毒血清是从全毒免疫的马或绵羊的血清中提取,但目前的免疫方法包括对马或绵羊进行的超免也不能达到对大多数临床上重要的毒素都产生免疫应答的目标。目前利物浦大学的Simon. C. Wagstaff等研究人员开发了一种最新的研制抗蛇毒血清的方法—通过鉴定蛇毒金属蛋白酶(SVMPs,SVMPs主要是产生持续性致死性出血,SVMPs很复杂,它具有多种功能型,能作用于多种底物)中有重要临床意义的7个部分,并将它们改造成单链DNA作为免疫原免疫小鼠产生特异抗体。为研发更合理的抗蛇毒血清制备方法提供了依据。

关键词：抗蛇毒血清蛇毒金属蛋白酶多抗原表位

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Impact of apolipoprotein A1 on tumor immune microenvironment, clinical prognosis and genomic landscape in hepatocellular carcinoma

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Precision Clinical Medicine 2023年第3期6卷 158-171页

作者： Ying Wang Shipeng Chen Xiao Xiao Fan Yang Jinhan Wange Hui Zong Yuzhen Gao Chenjun Huang Xuewen Xu Meng Fang Xiaoyan Zhang Chunfang Gao Clinical Laboratory Medicine Center Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghai200437China Department of Laboratory Medicine Shanghai Eastern Hepatobiliary Surgery HospitalShanghai 200438China research Center for Translational Medicine Shanghai East HospitalSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China Department of Medical Microbiology and Infection Prevention Tumor Virology and Cancer ImmunotherapyUniversity Medical Center GroningenUniversity of GroningenGroningen 9712 CPThe Netherlands State Key Laboratory for Diagnosis and Treatment of Infectious Diseases The First Affliated HospitalSchool of MedicineZhejiang UniversityHangzhou 310058China Department of Hepatobiliary and Pancreatic Surgery Shanghai East HospitalTongji University School of MedicineShanghai 200120China Institutes for Systems Genetics Frontiers Science Center for Disease-Related Molecular NetworkWest China HospitalSichuan UniversityChengdu 610041China Department of Clinical Laboratory Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou 310058China

Background:Current knowledge on apolipoprotein A1(APOA1)in hepatocellular carcinoma(HCC)is fragmented and even ***-dimensional analyses are required to comprehensively elucidate its value and underlying ***:We collected 49 RNA-seq datasets,40 cell line types data and 70 scRNA pan-cancer datasets public available,including 17 HCC datasets(1754 tumor samples),and enrolled 73 pairs of HCC tissue and 516 blood samples independently from our ***1 impacting on the HCC tumor microenvironment(TME)was analyzed using intensive data *** sequencing,flow cy-tometry,quantitative PCR,western blot,immunohistochemistry and clinical chemistry assays were conducted for wet experimental ***:The APOA1 ontology fingerprint indicated that it played various crucial biological roles in HCC,primarily involved in choles-terol *** findings at histology,serology,and clinical follow-up revealed that high APOA1 was a good prognosis indicator of *** in the APOA1 promoter region was found in clinical samples which is in accordance with the reduction of APOA1 in *** cell cycle,DNA replication,mismatch repair pathways,and tumor cell proliferation were less observed in the HCC APOAihigh *** favorable immunoregulatory abilities of APOA1 showed interesting findings:a positive correlation between APOA1 and anti-tumor immune cells(NK,CD8+T cells)and a negative association with immune cells exerting immunosuppressive effects,including M2 ***:This is an integrative multidimensional exploration of APOA1 using bioinformatics and *** the prognostic value and anti-tumor effects based on APOA1 panoramic exploration in the HCC TME demonstrate a new potential clinicai target for HCC assessment and intervention in the future.

关键词： APOA1 HCC prognosis tumor microenvironment immune cells NK cell

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Current status and trends in forest genomics

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Forestry research 2022年第1期2卷 99-120页

作者： Dulal Borthakur Victor Busov Xuan Hieu Cao Qingzhang Du Oliver Gailing Fikret Isik Jae-Heung Ko Chenghao Li Quanzi Li Shihui Niu Guanzheng Qu Thi Ha Giang Vu Xiao-Ru Wang Zhigang Wei Lin Zhang Hairong Wei Department of Molecular Biosciences and Bioengineering University of Hawaii at Manoa1955 East-West RoadHonoluluHI 96822USA College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931USA Forest Genetics and Forest Tree Breeding Faculty for Forest Sciences and Forest EcologyUniversity of GöttingenBüsgenweg 237077 GöttingenGermany National Engineering research Center of Tree Breeding and Ecological Restoration College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083P.R.China Cooperative Tree Improvement Program North Carolina State UniversityRaleighNC 27695USA Department of Plant&Environmental New Resources Kyung Hee University1732 Deogyeong-daeroYongin 17104Republic of Korea State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040P.R.China State Key Laboratory of Tree Genetics and Breeding Chinese Academy of ForestryBeijing 100093P.R.China Department of Ecology and Environmental Science UmeåPlant Science CentreUmeåUniversityUmeå90187Sweden College of Life Sciences Heilongjiang UniversityHarbin 150080P.R.China Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees Ministry of EducationCentral South University of Forestry and TechnologyChangsha 410004Hunan ProvinceP.R.China

Forests are not only the most predominant of the Earth's terrestrial ecosystems,but are also the core supply for essential products for human ***,global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest *** genomics has great potential of increasing forest productivity and adaptation to the changing *** the last two decades,the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies,single cell RNA-seq,clustered regularly interspaced short palindromic repeats(CRISPR)-mediated genome editing,and spatial transcriptomes,as well as bioinformatics analysis technologies,which have led to the generation of multidimensional,multilayered,and spatiotemporal gene expression *** technologies,together with basic technologies routinely used in plant biotechnology,enable us to tackle many important or unique issues in forest biology,and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and *** this review,we recapitulated the advancement and current status of 12 research branches of forest genomics,and then provided future research directions and focuses for each ***,a shift from simple biotechnology-based research to advanced and integrative genomics research,and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.

关键词： forest routine biotechnology

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Computational biology in topical bioactive peptide discovery for cosmeceutical application:a concise review

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Biomedical Engineering Communications 2023年第3期2卷 7-15页

作者： Xu-Hui Li Wen-Rou Su Fei-Fei Wang Ke Li Jing-Yong Zhu Si-Yu Zhu Si-Ning Kang Cong-Fen He Jun-Xiang Li Xiao Lin AGECODE R&D Center Yangtze Delta Region Institute of Tsinghua UniversityJiaxing 314000China Zhejiang Provincial Key Laboratory of Applied Enzymology Yangtze Delta Region Institute of Tsinghua UniversityJiaxing 314000China Yunnan Botanee Bio-technology Group Co. Ltd.Yunnan 650000China Yunnan Yunke Characteristic Plant Extraction Laboratory Co. Ltd.Yunnan 650000China Shenzhen Accompany Technology Co. LtdShenzhen 518000China College of Life Sciences and Medicine Zhejiang Sci-tech UniversityHangzhou 310018China Harvest Biotech(Zhejiang)Co. Ltd.Jiaxing 314000China School of Beijing Key Lab of Plant Resources research and Development Beijing Technology and Business UniversityBeijing 100048China School of Life Sciences Northwestern Polytechnical UniversityXi’an 710072China

Regenerative medicine and anti-aging research have made great strides at the molecular and cellular levels in dermatology and the medical aesthetic field,targeting potential treatments with skin therapeutic and intervention pathways,which make it possible to develop effective skin regeneration and repair *** the rapid development of computational biology,bioinformatics as well as artificial intelligence(A.I.),the development of new ingredients for regenerative medicine has been greatly accelerated,and the success rate has been *** application cases have appeared in topical skin regeneration and repair *** review will briefly introduce the application of bioactive peptides in skin repair and anti-aging as emerging ingredients in cosmeceutics and emphasize how *** computational biology technology may accelerate the development of innovative peptide molecules and ultimately translate them into potential skin regenerative and anti-aging ***,two research routines have been summarized and current limitations as well as directions were discussed for border applications in future research.

关键词： computational biology artificial intelligence cosmeceutical bioactive peptide regenerative medicine

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Single-cell technologies:From research to application

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The Innovation 2022年第6期3卷 92-108页

作者： Lu Wen Guoqiang Li Tao Huang Wei Geng Hao Pei Jialiang Yang Miao Zhu Pengfei Zhang Rui Hou Geng Tian Wentao Su Jian Chen Dake Zhang Pingan Zhu Wei Zhang Xiuxin Zhang Ning Zhang Yunlong Zhao Xin Cao Guangdun Peng Xianwen Ren Nan Jiang Caihuan Tian Zi-Jiang Chen Biomedical Pioneering Innovation Centre(BIOPIC) Peking UniversityBeijing 100871China Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China School of Chemical Engineering and Technology Sun Yat-Sen UniversityZhuhai 519082China Mozhuo Biotech(Zhejiang)Co. Ltd.TongxiangJiaxing 314500China Geneis(Beijing)Co. Ltd.Beijing 100102China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou 510530China Department of Medical Oncology Zhongshan HospitalFudan UniversityShanghai 200032China School of Food Science and Technology Dalian Polytechnic UniversityDalian 116034China State Key Laboratory of Transducer Technology Aerospace Information Research InstituteChinese Academy of SciencesBeijing 100190China Key Laboratory of Biomechanics and Mechanobiology Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing 100083China Department of Mechanical Engineering City University of Hong KongHong Kong 999077China Chongqing Institute of Green and Intelligent Technology Chinese Academy of SciencesChongqing 400714China Center of Peony Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Flower Crops(North China)Key Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsBeijing 100081China Department of Hepatic Surgery Fudan University Shanghai Cancer CenterShanghai 200032China Advanced Technology Institute University of SurreyGuildfordSurreyGU27XHUK National Physical Laboratory TeddingtonMiddlesex TW110LWUK Institute of Clinical Science Zhongshan HospitalFudan UniversityShanghai 200032China West China School of Basic Medical Sciences&Forensic Medicine Sichuan UniversityChengdu 610041China Jinfeng Laboratory Chongqing 401329China Center for Reproduc

In recent years,more and more single-cell technologies have been developed.A vast amount of single-cell omics data has been generated by large projects,such as the Human Cell Atlas,the Mouse Cell Atlas,the Mouse RNA Atlas,the Mouse ATAC Atlas,and the Plant Cell *** on these single-cell big data,thousands of bioinformatics algorithms for quality control,clustering,cell-type annotation,developmental inference,cell-cell transition,cell-cell interaction,and spatial analysis are *** powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence,the molecular landscape at the single-cell level can be revealed.

关键词： Atlas landscape application

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