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Single-cell analysis reveals the lncRNA-MEG3/miRNA-133a-3p/PRRT2 axis regulates skeletal muscle regeneration and myogenesis

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Genes & Diseases 2023年第2期10卷 359-362页

作者： Yilong Yao Zishuai Wang Yun Chen Lei Liu Liyuan Wang Guoqiang Yi Yalan Yang Dazhi Wang Kui Li Zhonglin Tang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518000China Kunpeng Institute of Modern Agriculture at Foshan FoshanGuangdong 528226China center for Regenerative medicine University of South Florida Health Heart Institute Morsani College of MedicineUniversity of South FloridaFL 33602USA Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518000China GuangXi engineering Centre for resource Development of Bama Xiang Pig BamaGuangxi 547500China State Key Laboratory of Animal Nutrition Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China

Skeletal muscle is the largest motor and metabolic organ of the body, which has a robust capacity for regeneration following injury or disease. Delayed regeneration after skeletal muscle injury reduces muscle contractility and leads to dysfunction of innervation. Therefore, identifying the regulation components in skeletal muscle regeneration and determining their molecular mechanisms are important to discover novel therapeutic markers for muscular diseases. Long non-coding RNA (LncRNA) has been implicated in skeletal muscle regeneration. Recent developed single-cell RNA sequencing (scRNA-seq) provides a higher resolution of cellular differences than bulk RNA-seq. Here, we re-analyzed single-cell transcriptomes data of skeletal muscle regeneration and identified lncRNA maternally expressed gene 3 (lncRNA-MEG3) was highly expressed in muscle satellite cells (MuSCs). Further study showed that lncRNA-MEG3 regulates skeletal muscle regeneration via sponging miR-133a-3p to regulate proline-rich transmembrane protein 2 (PRRT2) expression level. These results suggested that lncRNA-MEG3 might be a potential target for skeletal muscle diseases.

关键词： MEG3 skeletal muscular

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Analysis on the Construction Path of Database of Zhuang and Yao medicine Information resources

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Medicinal Plant 2022年第6期13卷 31-34,43页

作者： Liang LI Cuiliu PAN Chenyan LIANG Shina QIN Yunli TANG Jianfang FENG College of Pharmacy Guangxi University of Chinese MedicineNanning 530200China Guangxi Dominant Proprietary chinese medicine and Ethnic medicine Development engineering and Technology research center Nanning 530200China Key Laboratory of chinese medicine Pharmacology Nanning 530200China Fangchenggang Hospital of chinese medicine Fangchenggang 538021China

In order to realize the sharing,exchange,protection and rational utilization of Zhuang and Yao medicine resources,the problems encountered in the development of Zhuang and Yao medicine industry can be solved by using modern information technology in accordance with the present situation of Zhuang and Yao medicine resources in Guangxi Zhuang Autonomous Region and the actual needs of the development of ethnic *** paper expounds the significance of constructing the database of Zhuang and Yao medicine information resources from three aspects:the inheritance and development of Zhuang and Yao medicine,the sustainable development of Zhuang and Yao medicine industry and the information service *** this basis,the principle and framework of constructing Zhuang and Yao medicine information resource database are put forward.

关键词： Zhuang and Yao medicine Information resources Database

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Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012–2014

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Virologica Sinica 2022年第6期37卷 883-893页

作者： Jun Wang Jian Xiao Zheng Zhu Siyuan Wang Lei Zhang Zhaojun Fan Yali Deng Zhihong Hu Fang Peng Shu Shen Fei Deng State Key Laboratory of Virology and National Virus resource center Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China Xinjiang Key Laboratory of Biological resources and Genetic engineering College of Life Science and TechnologyXinjiang UniversityUrumqi830046China China center for Type Culture Collection(CCTCC) College of Life SciencesWuhan UniversityWuhan430072China Natisonal Emerging Infectious Diseases Laboratories Boston UniversityBostonMA 02118United States Department of Biochemistry Boston University School of MedicineBostonMA 02118United States

Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses,which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012–2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity,they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein(rep)-encoding single-stranded(CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity,complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils,Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.

关键词： Arctic soil Antarctica animal feces Metagenomics Virus diversity

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Highly reliable and efficient encoding systems for hexadecimal polypeptide-based data storage

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Fundamental research 2023年第2期3卷 298-304页

作者： Yubin Ren Yi Zhang Yawei Liu Qinglin Wu Hong-Gang Hu Jingjing Li Chunhai Fan Dong Chen Kai Liu Hongjie Zhang Department of Chemistry Tsinghua UniversityBeijing 100084China State Key Laboratory of Rare Earth resource Utilization Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchun 130022China Institute of Process Equipment College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic SystemsZhejiang UniversityHangzhou 310027China Institute of Translational medicine Shanghai UniversityShanghai 200444China Frontiers Science center for Transformative Molecules School of Chemistry and Chemical Engineeringand Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai 200240China

Polypeptides consisting of amino acid(AA)sequences are suitable for high-density information ***,the lack of suitable encoding systems,which accommodate the characteristics of polypeptide synthesis,storage and sequencing,impedes the application of polypeptides for large-scale digital data *** address this,two reliable and highly efficient encoding systems,***-Arithmetic-Base64-Shuffle-RS(RABSR)and RaptorQArithmetic-Huffman-Rotary-Shuffle-RS(RAHRSR)systems,are developed for polypeptide data *** two encoding systems realized the advantages of compressing data,correcting errors of AA chain loss,correcting errors within AA chains,eliminating homopolymers,and pseudo-randomized *** coding efficiency without arithmetic compression and error correction of audios,pictures and texts by the RABSR system was 3.20,3.12 and 3.53 Bits/AA,*** that using the RAHRSR system reached 4.89,4.80 and 6.84 Bits/AA,*** implemented with redundancy for error correction and arithmetic compression to reduce redundancy,the coding efficiency of audios,pictures and texts by the RABSR system was 4.43,4.36 and 5.22 Bits/AA,*** efficiency further increased to 7.24,7.11 and 9.82 Bits/AA by the RAHRSR system,***,the developed hexadecimal polypeptide-based systems may provide a new scenario for highly reliable and highly efficient data storage.

关键词： Biomaterial Polypeptide Data storage Hexadecimal Encoding system

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Metallophilicity-Induced Clusterization:Single-Component White-Light Clusteroluminescence with Stimulus Response

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CCS Chemistry 2022年第8期4卷 2570-2580页

作者： Xueqian Zhao Parvej Alam Jianyu Zhang Shiyun Lin Qian Peng Jun Zhang Guodong Liang Sijie Chen Jing Zhang Herman HYSung Jacky WYLam Ian DWilliams Xinggui Gu Zheng Zhao Ben Zhong Tang Department of Chemistry and Hong Kong Branch of chinese National engineering research center for Tissue Restoration and Reconstruction The Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong 999077 MOE Key Laboratory of Organic OptoElectronics and Molecular engineering Department of ChemistryTsinghua UniversityBeijing 100084 CAS Key Laboratory of Organic Solids Institute of ChemistryBeijing National Laboratory for Molecular SciencesChinese Academy of SciencesBeijing 100190 School of Materials and Chemical engineering Anhui Jianzhu UniversityHefei 230601 PCFM and GDHPPC Labs School of Materials Science and EngineeringSun Yat-sen UniversityGuangzhou 510275 Ming Wai Lau Centre for Reparative medicine Karolinska InstitutetHong Kong 999077 Beijing Advanced Innovation center for Soft Matter Science and engineering College of Materials Science and EngineeringState Key Laboratory of Chemical Resource EngineeringBeijing University of Chemical TechnologyBeijing 100029 Shenzhen Institute of Molecular Aggregate Science and engineering School of Science and EngineeringThe Chinese University of Hong KongShenzhenGuangdong 518172 center for Aggregation-Induced Emission SCUT-HKUST Joint Research InstituteState Key Laboratory of Luminescent Materials and DevicesSouth China University of TechnologyGuangzhou 510640 AIE Institute Guangzhou Development DistrictHuangpuGuangzhou 510530

Materials showing metallophilic interactions continue to attract considerable theoretical and experimental attention largely because of their unusual and unanticipated photophysical behavior as well as their unique stimuli-responsive behavior in an aggregate or solid *** interactions are mostly found between metals with either identical(d^(10)–d^(10))or different(s^(2)–d^(8),d^(8)–d^(10))*** various metallophilic interactions,aurophilic interactions(Au⋯Au)are well-known and widely *** this study,a new phosphorescent gold(I)complex,[(CF_(3)Ph)_(3)PAuC≡CPh](TPPGPA)was reported.

关键词： single-component white-light emission gold(I)complex aurophilic interactions stimuli-responsive materials metallophilicity-induced clusterization

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Identification of microRNA-like RNAs in Ophiocordyceps sinensis

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Science China(Life Sciences) 2019年第3期62卷 349-356页

作者： Wen Zhang Xiaona Li Lina Ma Uzair Urrehman Xilinqiqige Bao Yujing Zhang Chen-Yu Zhang Dongxia Hou Zhen Zhou State Key Laboratory of Pharmaceutical Biotechnology Jiangsu Engineering Research Center for microRNA Biology and Biotechnology NJU Advanced Institute for Life Sciences (NAILS) School of Life Sciences Nanjing University The Drug Laboratory of Mongolian medicine and Pharmacy Institute Inner Mongolia International Mongolian Hospital

Ophiocordyceps sinensis is well known as a traditional chinese medicine and has widely been used for over 2,000 years to stimulate immune system, decrease blood pressure and to inhibit tumor growth. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less studied until the discovery of microRNA-like RNA(milRNA). High-throughput sequencing and bioinformatics approaches were used to identify conserved and novel milRNAs in O. sinensis. 40 conserved milRNAs were identified, while 23 pre-miRNA candidates encoding 31 novel milRNAs were predicted. Furthermore, the potential target genes of milRNAs in human were predicted and gene ontology analysis was applied to these genes. Enrichment analysis of GO-represented biological process showed that target genes of both conserved and novel milRNAs are involved in development, metabolic and immune processes, indicating the potential roles of milRNAs of O. sinensis in pharmacological effects as health food and traditional chinese medicine. This study is the first report on genome-wide analysis of milRNAs in O. sinensis and it provides a useful resource to further study the potential roles of milRNAs as active components of O. sinensis in health food or traditional chinese medicine.

关键词： Ophiocordyceps sinensis O.sinensis miRNA milRNA high-throughput sequencing

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Chokeberry(Aronia melanocarpa)as a new functional food relationship with health:an overview

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Journal of Future Foods 2021年第2期1卷 168-178页

作者： Yiwen Zhang Yingchun Zhao Xinglong Liu Xueyan Chen Chuanbo Ding Ling Dong Jinping Zhang Shuwen Sun Qiteng Ding Sadia Khatoom Zhiqiang Cheng Wencong Liu Liqian Shen Fengyan Xiao College of chinese Medicinal Matenials Jilin Agnicultural UniversityChangchuom 130118China College of resource cnod Emvironment Jilin Agnicultural TUniversityChangchuom 130118China State Local Joint engineering research center of Ginseng Breeding and Application Changchun 130118China Jilin Jianwei Natural Biotechnology Co LtadChangchum 130118China Jilin Agriculnural Science and Technology Uriversiry Jilin 132001China

As a consumer product,black chokeberry(Aronia melanocarpa)is diffi cult to consume due to its pungent *** is mainly used in various food industries to produce a variety of juices,preserves,extracts,fruit teas and nutritional ***,Potawatomi Native Americans used black chokeberry to treat colds,coughs and *** has been found to contain numerous active ***,there are many health and medical products that contain black *** purpose of this review is to understand the nutritional benefi ts of black chokeberry and to explore its benefi cial effects on biological systems in vitro,thereby emphasizing its therapeutic prospects.

关键词： Aronia melamocarpa Chokebenry Functional food Human health

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Morphine analgesia in male inbred genetic diversity mice recapitulates the among-individual variance in response to morphine in humans

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Animal Models and Experimental medicine 2022年第3期5卷 288-296页

作者： Yin Yang Bowen Guan Qiang Wei Wei Wang Aimin Meng Key Laboratory of Human Disease Comparative medicine Ministry of HealthBeijing Engineering Research Center for Laboratory Animal Models of Human Critical DiseasesInstitute of Laboratory Animal SciencesChinese Academy of Medical Sciences(CAMS)and Peking Union Medical College(PUMC)BeijingChina Department of Physiology and Neurobiology School of Basic Medical SciencesZhengzhou UniversityZhengzhouChina

Morphine is a widely used analgesic, but its use in clinical precision medicine is limited by the variance in response among individuals. Although previous studies have shown that individual differences in morphine can be explained in terms of pharmacodynamics and pharmacokinetics, genetic polymorphisms also play an important role. However, the genetic basis of different sensitivity and tolerance susceptibility to morphine remains ambiguous. Using 15 strains of inbred Genetic Diversity(GD) mice,a new resource with wide genetic and phenotypic variation, we demonstrated great variance in sensitivity to morphine analgesia and susceptibility to morphine tolerance between different GD strains. Among-i ndividual variance in response to morphine analgesia in the population can be modeled in GD mice. Two loci respectively may be associated with the among-i ndividual variance in morphine sensitivity and tolerance,confirming the role of genetic factors in among-i ndividual different responses to morphine. These results indicate that GD mice may be a potential tool for the identification of new biomarkers to improve the clinical administration of morphine.

关键词： inbred genetic diversity mice morphine analgesia morphine tolerance quantitative trait loci mapping

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CHDbase:A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 216-227页

作者： Wei-Zhen Zhou Wenke Li Huayan Shen Ruby W.Wang Wen Chen Yujing Zhang Qingyi Zeng Hao Wang Meng Yuan Ziyi Zeng Jinhui Cui Chuan-Yun Li Fred Y.Ye Zhou Zhou State Key Laboratory of Cardiovascular Disease Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalNational Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100037China International Joint Informatics Laboratory&Jiangsu Key Laboratory of Data engineering and Knowledge Service School of Information ManagementNanjing UniversityNanjing 210023China Institute of Molecular medicine Peking UniversityBeijing 100871China

Congenital heart disease(CHD)is one of the most common causes of major birth defects,with a prevalence of 1%.Although an increasing number of studies have reported the etiology of CHD,the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical *** therefore developed CHDbase,an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications,linking 1124 susceptibility genes and 3591 variations to more than 300 CHD types and related *** such as the information of each publication and the selected population and samples,the strategy of studies,and the major findings of studies were integrated with each item of the research *** also integrated functional annotations through parsing50 databases/tools to facilitate the interpretation of these genes and variations in disease *** further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 *** clear genetic landscape of CHD enables the phenotype classification based on the shared genetic ***,CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities,supporting a wide range of users in the scientific and medical *** is accessible at http://***.

关键词： Congenital heart disease Congenital heart defect Database Genetics Classification

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Factors Predicting Progression to Severe COVID-19: A Competing Risk Survival Analysis of 1753 Patients in Community Isolation in Wuhan, China

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engineering 2022年第6期8卷 99-106页

作者： Simiao Chen Hui Sun Mei Heng Xunliang Tong Pascal Geldsetzer Zhuoran Wang Peixin Wu Juntao Yang Yu Hu Chen Wang Till Bärnighausen chinese Academy of Medical Sciences&Peking Union Medical College Beijing 100730China Heidelberg Institute of Global Health(HIGH) Faculty of Medicine and University HospitalHeidelberg UniversityHeidelberg 69120Germany Institute of Hematology Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430022China Department of Pulmonary and Critical Care medicine Beijing HospitalBeijing 100730China National center of Gerontology Institute of Geriatric MedicineBeijing 100730China Division of Primary Care and Population Health Department of MedicineStanford UniversityStanfordCA 94305USA Peking Union Medical College Hospital Beijing 100730China State Key Laboratory of Medical Molecular Biology Institute of Basic Medical SciencesChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China National Clinical research center for Respiratory Diseases Beijing 100029China Department of Pulmonary and Critical Care medicine Center of Respiratory MedicineChina–Japan Friendship HospitalBeijing 100029China

Most studies of coronavirus disease 2019(COVID-19)progression have focused on the transfer of patients within secondary or tertiary care hospitals from regular wards to intensive care *** is known about the risk factors predicting the progression to severe COVID-19 among patients in community iso-lation,who are either asymptomatic or suffer from only mild to moderate *** a multivari-able competing risk survival analysis,we identify several important predictors of progression to severe COVID-19—rather than to recovery—among patients in the largest community isolation center in Wuhan,China from 6 February 2020(when the center opened)to 9 March 2020(when it closed).All patients in community isolation in Wuhan were either asymptomatic or suffered from mild to moderate COVID-19 *** performed competing risk survival analysis on time-to-event data from a cohort study of all COVID-19 patients(n=1753)in the isolation *** potential predictors we inves-tigated were the routine patient data collected upon admission to the isolation center:age,sex,respira-tory symptoms,gastrointestinal symptoms,general symptoms,and computed tomography(CT)scan *** main outcomes were time to severe COVID-19 or *** factors predicting progression to severe COVID-19 were:male sex(hazard ratio(HR)=1.29,95%confidence interval(CI)1.04–1.58,p=0.018),young and old age,dyspnea(HR=1.58,95%CI 1.24–2.01,presource-poor set-tings(dyspnea,sex,and age)can be used to identify mild COVID-19 patients who are at increased risk of disease *** for CT signs of ground-glass opacity and i

关键词： COVID-19 Asymptomatic and mild Community isolation Fangcang shelter hospital Competing risk survival analysis

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