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Protein & Cell 2024年第1期15卷 1-5页

作者： Huan Liu Kunlan Zuo Zongzhen Wu Hao Cheng University of Science and Technology of China state key laboratory of virology Institute of microbiology Chinese Academy of Sciences

There is a renowned virologist who dedicated his life to virology and medicine research. He has made important contributions to the study of Chinese polio and hepatitis A vaccines, interferons, and the theory of viral...

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Endogenous retrovirus activation: potential for immunology and clinical applications

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National Science Review 2024年第4期11卷 21-23页

作者： Jundan Yu Peishan Qiu Jingwen Ai Bo Liu Guan-Zhu Han Fan Zhu Wenhong Zhang Jie Cui department of Infectious Diseases Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response National Medical Center for Infectious Diseases Huashan Hospital Shanghai Medical College Fudan University CAS key laboratory of Molecular virology &Immunology Shanghai Institute of Immunity and Infection Chinese Academy of Sciences University of Chinese Academy of Sciences Shanghai Huashen Institute of Microbes and Infections College of Life Sciences Nanjing Normal University state key laboratory of virology and department of medical microbiology School of Basic Medical SciencesWuhan University The Institute of Infection and Health Research Fudan University key laboratory of medical Molecular virology(MOE/MOH) Shanghai Medical CollegeFudan University laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Endogenous retroviruses (ERVs), the remnants of ancient retrovirus infections, constitute approximately 8% of the human genome and play important roles in human evolution, development,and diseases. Multiple drugs, such as DNA methyltransferase inhibitors and lysine-specific histone demethylase 1inhibitors, reactivate ERVs, induce viral mimicry and trigger innate immune responses to enhance tumor immunogenicity.

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Dynamic changes in butyrate levels regulate satellite cell homeostasis by preventing spontaneous activation during aging

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Science China(Life Sciences) 2024年第4期67卷 745-764页

作者： Shujie Chen Liujing Huang Bingdong Liu Huimin Duan Ze Li Yifan Liu Hu Li Xiang Fu Jingchao Lin Yinlan Xu Li Liu Dan Wan Yulong Yin Liwei Xie department of Endocrinology and Metabolism Zhujiang HospitalSouthern Medical UniversityGuangzhou 510280China state key laboratory of Applied microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyInstitute of MicrobiologyGuangdong Academy of SciencesGuangzhou 510070China School of Public Health Xinxiang Medical UniversityXinxiang 453003China department of Infectious Diseases Nanfang HospitalSouthern Medical UniversityGuangzhou 510515China Metabo-Profile Biotechnology(Shanghai)Co.Ltd. Shanghai 201315China Institute of Aging Research Guangdong Provincial Key Laboratory of Medical Molecular DiagnosticsSchool of Medical TechnologyGuangdong Medical UniversityDongguan 524023China department of Rehabilitation Medicine Nanfang HospitalSouthern Medical UniversityGuangzhou 510000China laboratory of Animal Nutritional Physiology and Metabolic Process Key Laboratory of Agro-ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangsha 410125China Bioland laboratory Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhou 510005China

The gut microbiota plays a pivotal role in systemic metabolic processes and in particular functions,such as developing and preserving the skeletal muscle ***,the interplay between gut microbiota/metabolites and the regulation of satellite cell(SC)homeostasis,particularly during aging,remains *** propose that gut microbiota and its metabolites modulate SC physiology and homeostasis throughout skeletal muscle development,regeneration,and aging *** investigation reveals that microbial dysbiosis manipulated by either antibiotic treatment or fecal microbiota transplantation from aged to adult mice,leads to the activation of SCs or a significant reduction in the total ***,employing multi-omics(e.g.,RNA-seq,16S r RNA gene sequencing,and metabolomics)and bioinformatic analysis,we demonstrate that the reduced butyrate levels,alongside the gut microbial dysbiosis,could be the primary factor contributing to the reduction in the number of SCs and subsequent impairments during skeletal muscle ***,butyrate supplementation can mitigate the antibiotics-induced SC activation irrespective of gut microbiota,potentially by inhibiting the proliferation and differentiation of SCs/*** butyrate effect is likely facilitated through the monocarboxylate transporter 1(Mct1),a lactate transporter enriched on membranes of SCs and *** a result,butyrate could serve as an alternative strategy to enhance SC homeostasis and function during skeletal muscle *** findings shed light on the potential application of microbial metabolites in maintaining SC homeostasis and preventing skeletal muscle aging.

关键词： gut microbiota aging satellite cells butyrate Slc16a1(Mct1)

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Licorice-saponin A3 is a broad-spectrum inhibitor for COVID-19 by targeting viral spike and anti-inflammation

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Journal of Pharmaceutical Analysis 2024年第1期14卷 115-127页

作者： Yang Yi Wenzhe Li Kefang Liu Heng Xue Rong Yu Meng Zhang Yang-Oujie Bao Xinyuan Lai Jingjing Fan Yuxi Huang Jing Wang Xiaomeng Shi Junhua Li Hongping Wei Kuanhui Xiang Linjie Li Rong Zhang Xin Zhao Xue Qiao Hang Yang Min Ye state key laboratory of Natural and Biomimetic Drugs School of Pharmaceutical SciencesPeking UniversityBeijing100191China Yunnan Baiyao International medical Research Center Peking UniversityBeijing100191China CAS key laboratory of Pathogen microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing100101China CAS key laboratory of Special Pathogens and Biosafety Center for Biosafety Mega-ScienceWuhan Institute of VirologyChinese Academy of SciencesWuhan430071China University of Chinese Academy of Sciences Beijing100049China department of microbiology and Infectious Disease Center School of Basic Medical SciencesPeking University Health Science CenterPeking UniversityBeijing100191China Hubei Jiangxia laboratory Wuhan430000China Shenzhen Children's Hospital ShenzhenGuangdong518036China

Currently,human health due to corona virus disease 2019(COVID-19)pandemic has been seriously *** coronavirus severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)spike(S)protein plays a crucial role in virus transmission and several S-based therapeutic approaches have been approved for the treatment of ***,the efficacy is compromised by the SARS-CoV-2 evolvement and *** we report the SARS-CoV-2 S protein receptor-binding domain(RBD)inhibitor licorice-saponin A3(A3)could widely inhibit RBD of SARS-CoV-2 variants,including Beta,Delta,and Omicron BA.1,XBB and ***,A3 could potently inhibit SARS-CoV-2 Omicron virus in Vero E6 cells,with EC50 of 1.016μ*** mechanism was related to binding with Y453 of RBD determined by hydrogen-deuterium exchange mass spectrometry(HDX-MS)analysis combined with quantum mechanics/molecular mechanics(QM/MM)***,phosphoproteomics analysis and multi fluorescent immunohistochemistry(mIHC)respectively indicated that A3 also inhibits host inflammation by directly modulating the JNK and p38 mitogen-activated protein kinase(MAPK)pathways and rebalancing the corresponding immune *** work supports A3 as a promising broad-spectrum small molecule drug candidate for COVID-19.

关键词： COVID-19 Inflammation Licorice-saponin A3 Receptor-binding domain(RBD) SARS-CoV-2

shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

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Journal of Genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie Xuan-An Zhu Zijing Xie Jianfeng Lin Lin Li Wenli Tang Rui Wang Lin Deng Yufan Liao Bingdong Liu Yantong Cai Qianwen Wang Shuangbin Xu Guangchuang Yu department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China state key laboratory of Applied microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary *** a relaxed molecular clock model better aligns with the complexities of *** root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic *** its utility,there remains a lack of corresponding software implementations for broader *** address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

关键词： Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal

Phomaketals A and B,pentacyclic meroterpenoids from a eupC overexpressed mutant strain of Phoma sp.

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Chinese Chemical Letters 2024年第7期35卷 350-354页

作者： Chuan Li Yangyang Han Yanan Zhai Ke Li Xingzhong Liu Zhuan Zhang Cai Jia Yongsheng Che NHC key laboratory of Biotechnology of Antibiotics Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China state key laboratory of Toxicology&medical Countermeasures Beijing Institute of Pharmacology&ToxicologyBeijing 100850China department of microbiology College of Life SciencesNankai UniversityTianjin 300071China

Phomaketals A(1)and B(2),two tropolonic meroterpenoids with the unprecedented pentacyclic skeletons,were isolated from the solid-substrate fermentation cultures of a eupC overexpressed mutant strain of the fungus Phoma sp.,together with a biogenetically related secondary metabolite pughiinin B(3),and the known one noreupenifeldin B(4).The structures of 1–3 were elucidated primarily by nuclear magnetic resonance(NMR)*** absolute configurations of 1 and 2 were assigned by electronic circular dichroism calculations and the calculated NMR with DP4+analysis,while that of 3 was established by single-crystal X-ray diffraction analysis using Cu Kα***,phomaketals A(1)and B(2)could be derived from the hypothetical tropolonic sesquiterpene intermediates neosetophomone B(6)and 9-R-neosetophomone B(6),respectively,via different reactions *** 1 showed antiproliferative effect only against the SUPB15 cells,with an 50%inhibitory concentration(IC50)value of 4.85μmol/L,while the co-isolated known meroterpenoid 4 displayed potent effects against three tumor cell lines,SUPB15,EL4,and H9,showing IC50values of 0.36–27.08μmol/L.

关键词： Phoma sp. Tropolonic sesquiterpenes Biosynthetic pathways Hetero-Diels–Alder Cytotoxicity

Phomaketals A and B, pentacyclic meroterpenoids from a eupC overexpressed mutant strain of Phoma sp.

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Chinese Chemical Letters 2024年第7期 376-380页

作者： Chuan Li Yangyang Han Yanan Zhai Ke Li Xingzhong Liu Zhuan Zhang Cai Jia Yongsheng Che NHC key laboratory of Biotechnology of Antibiotics Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences & Peking Union Medical College state key laboratory of Toxicology & medical Countermeasures Beijing Institute of Pharmacology & Toxicology department of microbiology College of Life SciencesNankai University

Phomaketals A(1) and B(2), two tropolonic meroterpenoids with the unprecedented pentacyclic skeletons, were isolated from the solid-substrate fermentation cultures of a eupC overexpressed mutant strain of the fungus Phoma sp., together with a biogenetically related secondary metabolite pughiinin B(3),and the known one noreupenifeldin B(4). The structures of 1–3 were elucidated primarily by nuclear magnetic resonance(NMR) experiments. The absolute configurations of 1 and 2 were assigned by electronic circular dichroism calculations and the calculated NMR with DP4+ analysis, while that of 3 was established by single-crystal X-ray diffraction analysis using Cu Kα radiation. Biogenetically, phomaketals A(1) and B(2) could be derived from the hypothetical tropolonic sesquiterpene intermediates neosetophomone B(6) and 9-R-neosetophomone B(6), respectively, via different reactions cascades. Compound 1 showed antiproliferative effect only against the SUPB15 cells, with an 50% inhibitory concentration(IC50) value of 4.85 μmol/L, while the co-isolated known meroterpenoid 4 displayed potent effects against three tumor cell lines, SUPB15, EL4, and H9, showing IC50values of 0.36–27.08 μmol/L.

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LonP1 Links Mitochondria–ER Interaction to Regulate Heart Function

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Research 2024年第1期2023卷 595-609页

作者： Yujie Li Dawei Huang Lianqun Jia Fugen Shangguan Shiwei Gong Linhua Lan Zhiyin Song Juan Xu Chaojun Yan Tongke Chen Yin Tan Yongzhang Liu Xingxu Huang Carolyn K.Suzuki Zhongzhou Yang Guanlin Yang Bin Lu The Affiliated Nanhua Hospital and School of Basic medical Sciences Hengyang Medical SchoolUniversity of South ChinaHengyangHunan 421001China School of laboratory Medicine and Life Sciences Wenzhou Medical UniversityWenzhouZhejiang 325035China National Health Commission key laboratory of Birth Defect Research and Prevention Hunan Provincial Maternal and Child Health Care HospitalChangshaHunan 410008China key laboratory of Ministry of Education for TCM Viscera-state Theory and Applications Ministry of Education of ChinaLiaoning University of Traditional Chinese MedicineShenyangLiaoning 110847China key laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province The First Affiliated Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina Hubei key laboratory of Cell Homeostasis College of Life SciencesWuhan UniversityWuhanHubei 430072China Nanjing Maternity and Child Health Care Hospital Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical UniversityNanjing 210004China Animal Center Wenzhou Medical UniversityWenzhouZhejiang 325035China department of Cardiology The First Affiliated Hospital of University of South ChinaHengyangHunanChina School of Life Science and Technology Shanghai Tech UniversityShanghai 201210China department of microbiology Biochemistry and Molecular GeneticsNew Jersey Medical School-RutgersThe State University of New JerseyNewarkNJUSA state key laboratory of Pharmaceutical Biotechnology Department of CardiologyNanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease StudyModel Animal Research CenterNanjing UniversityNanjing 210061China

Interorganelle contacts and communications are increasingly recognized to play a vital role in cellular function and *** particular,the mitochondria–endoplasmic reticulum(ER)membrane contact site(MAM)is known to regulate ion and lipid transfer,as well as signaling and organelle ***,the regulatory mechanisms of MAM formation and their function are still ***,we identify mitochondrial Lon protease(LonP1),a highly conserved mitochondrial matrix protease,as a new MAM tethering *** removal of LonP1 substantially reduces MAM formation and causes mitochondrial ***,deletion of LonP1 in the cardiomyocytes of mouse heart impairs MAM integrity and mitochondrial fusion and activates the unfolded protein response within the ER(UPR^(ER)).Consequently,cardiac-specific LonP1 deficiency causes aberrant metabolic reprogramming and pathological heart *** findings demonstrate that LonP1 is a novel MAM-localized protein orchestrating MAM integrity,mitochondrial dynamics,and UPR^(ER),offering exciting new insights into the potential therapeutic strategy for heart failure.

关键词： offering programming insight

Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

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Avian Research 2024年第1期15卷 1-11页

作者： Qi Lu Pengcheng Wang Jiang Chang De Chen Shenghan Gao Jacob Hoglund Zhengwang Zhang Ministry of Education key laboratory for Biodiversity Science and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing100875China Jiangsu key laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing210023China state key laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing100012China state key laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing100101China department of Ecology and Genetics Animal EcologyUppsala UniversityUppsalaSweden

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened ***’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat *** is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened ***,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic ***,we identified candidate genes linked with adaptation across the current distribution of Reeves’s *** present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 *** also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those *** comparing with other threatened species,we found that Reeves’s Pheasants have low genetic *** of homozygosity suggest that the Shennongjia population has experienced serious *** demographic history results indicated that three populations experienced several declines during the glacial *** adaptative analysis among the populations identified 241 candidate genes under directional *** are involved in a large variety of processes,including the immune response and *** results suggest that the three populations should be considered as three different conservation *** current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

关键词： Conservation genetics Local adaptation Pheasant Whole-genome sequencing

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Reduced clinical severity during 2022 Shanghai Spring epidemic of SARS-CoV-2 omicron BA.2 variant infection——an integrated account of virus pathogenicity and vaccination effectiveness

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National Science Review 2024年第4期11卷 24-27页

作者： Xingyue Wu Yao Chen Kangli Cao Yao Shen Xueling Wu Yilin Yang Zhongshu Kuang Qingrun Li Zhenzhen Lu Yichen Jia Mian Shao Guorong Gu Xiangwei Wang Ye Yao Ying Wang Shaodie Chen Zhigao Yu Wei Wei Longfei Ding Lulu Lan Tianwen Gu Xiangyu Long Jian Sun Lingyu Xing Jiayuan Shen Yi Han Yue Luo Sucheng Mu Mengna Lin Xiaoyan Zhang Rong Zeng Jianqing Xu Guoping Zhao Lihong Huang Zhenju Song department of Emergency Medicine Clinical Center for Bio-Therapy Department of Biostatistics and Department of UrologyShanghai Key Laboratory of Lung Inflammation and Injury Zhongshan Hospital Fudan University department of Respiratory and Critical Care Medicine Shanghai Pudong Hospital Fudan University department of Pulmonology Renji Hospital Shanghai Jiao Tong University School of Medicine key laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai Public Health Clinical Center Fudan University department of Biostatistics School of Public Health Key Laboratory of Public Health Safety of Ministry of Education and Shanghai Institute of Infectious Disease and Biosecurity School of Public Health Fudan University Shanghai Institute of Immunology Department of Immunology and Microbiology Shanghai Institute of Virology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationSchool of Medicine Shanghai Jiao Tong University state key laboratory of Genetic Engineering Fudan Microbiome CenterSchool of Life Sciences Fudan University Bio-Med Big Data Center Shanghai Institute of Nutrition and Health Chinese Academy of Sciences

The emergence of SARS-Co V-2 variant of concern omicron BA.2 led to high infection incidence rates as well as reduced severity of COVID-19 during the Shanghai Spring epidemic of 2022 [1]. We assessed the role of viral pathogenicity and the effectiveness of inactivated vaccines in a retrospective observational study including 10 258 confirmed COVID-19cases identified between April and June of 2022, from four COVID-19 designated hospitals located in two areas of Shanghai, namely the West Bund and the East Bund, where the populations’ demographic characteristics varied significantly (Table S1, Fig. S1).

关键词： REPLICATION