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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

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Lung microbiome:new insights into the pathogenesis of respiratory diseases

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Signal Transduction and Targeted Therapy 2024年第2期9卷 652-678页

作者： Ruomeng Li Jing Li Xikun Zhou Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu 610041China State Key laboratory of Oral Diseases National Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduSichuan 610041China

The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial *** microbiome of healthy lungs is mainly derived from the upper respiratory tract(URT)microbiome but also has its own characteristic *** selection mechanisms in the lung,including clearance by coughing,pulmonary macrophages,the oscillation of respiratory cilia,and bacterial inhibition by alveolar surfactant,keep the microbiome transient and mobile,which is different from the microbiome in other *** pulmonary bacteriome has been intensively studied recently,but relatively little research has focused on the mycobiome and *** up-to-date review retrospectively summarizes the lung microbiome’s history,composition,and *** focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune *** importantly,we focus on multiple respiratory diseases,including asthma,chronic obstructive pulmonary disease(COPD),fibrosis,bronchiectasis,and *** impact of the lung microbiome on coronavirus disease 2019(COVID-19)and lung cancer has also been comprehensively ***,by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field,we propose an outlook of the direction of lung microbiome research.

关键词： respiratory diseases Lung

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Host plant traits play a crucial role in shaping the composition of epiphytic microbiota in the arid desert,Northwest China

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Journal of Arid Land 2024年第5期16卷 699-724页

作者： ZHANG Jun ZHANG Yuanming ZHANG Qi State Key laboratory of Desert and Oasis Ecology Key Laboratory of Ecological Safety and Sustainable Development in Arid LandsXinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China Xinjiang Key laboratory of Biodiversity Conservation and Application in Arid Lands Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China Xinjiang Field Scientific Observation Research Station of Tianshan Wild Fruit Forest Ecosystem Yili Botanical GardenXinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China College of Life Sciences Shihezi UniversityShihezi 832003China

Phyllosphere microorganisms are a crucial component of environmental microorganisms,highly influenced by host characteristics,and play a significant role in plant health and ***,the impact of host characteristics on shaping phyllosphere microbial communities of plants with different life forms remains *** high-throughput sequencing technology,this study analyzed the diversity and community composition of phyllosphere epiphytic microorganisms(e.g.,bacteria and fungi)of various plant life forms in the hinterland of the Gurbantunggut Desert,Northwest *** annotation of prokaryotic taxa(FAPROTAX)and fungi function guild(FUNGuild)were employed to assess the ecological functions of microorganisms and to investigate the role of stochastic and deterministic processes in shaping phyllosphere microbial *** showed a diverse array of phyllosphere epiphytic microorganisms in the desert plants,with Proteobacteria,Cyanobacteria,and Actinobacteriota dominating bacterial community,while Ascomycota and Basidiomycota were prevalent in fungal *** across different plant life forms highlighted distinct microbial communities,indicating strong filtering effects by plant *** prediction identified intracellular parasites(accounting for 27.44%of bacterial community abundance),chemoheterotrophy(10.12%),and phototrophy(17.41%)as the main functions of epiphytic bacteria on leaves of different life form *** prediction indicated that phyllosphere epiphytic fungi primarily served as Saprotrophs(81.77%),Pathotrophs(17.41%),and Symbiotrophs(0.82%).Co-occurrence network analysis demonstrated a predominance of positive correlations among different microbial ***-Crick dissimilarity index analysis revealed that deterministic processes predominantly influenced phyllosphere bacterial and fungal community *** partitioning analysis and random forest modeling suggested that pla

关键词： phyllosphere epiphytic bacteria phyllosphere epiphytic fungi community structure community diversity functional diversity plant life form plant functional traits

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Inactivated H9N2 vaccines developed with early strains do not protect against recent H9N2 viruses:Call for a change in H9N2 control policy

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Journal of Integrative Agriculture 2024年第6期23卷 2144-2148页

作者： Yanjing Liu Qingqing Yu Xiangyu Zhou Wenxin Li Xinwen He Yan Wang Guohua Deng Jianzhong Shi Guobin Tian Xianying Zeng Hualan Chen College of Veterinary Medicine Gansu Agricultural UniversityLanzhou 730070China State Key laboratory for Animal Disease Control and Prevention Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry DiseasesMinistry of Agriculture and Rural Affairs/Harbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbin 150009China National Poultry laboratory Animal Resource Center Harbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbin 150009China Harbin Weike Biotechnology Co. Ltd.Harbin 150009China

H9N2 virus has been widely distributed in wild birds and poultry around the world since its first emergence in the United States of America in 1966(Gu et al.2017;Carnaccini and Perez 2020).The virus appeared in chickens in China in the early 1990s,and over the last two decades has gradually become the dominant epidemic subtype(Sun and Liu 2015;Bi et al.2020).Although H9N2 virus infection alone cannot cause severe disease or death in poultry,H9N2 virus-infected birds experience a degree of egg production drop and can be easily infected by other pathogens,thus causing economic losses for poultry industry.

关键词： H9N2 poultry policy

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Constructing efficient bacterial cell factories to enable one-carbon utilization based on quantitative biology:A review

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Quantitative Biology 2024年第1期12卷 1-14页

作者： Yazhen Song Chenxi Feng Difei Zhou Zengxin Ma Lian He Cong Zhang Guihong Yu Yan Zhao Song Yang Xinhui Xing School of Life Sciences Shandong Province Key Laboratory of Applied Mycologyand Qingdao International Center on Microbes Utilizing BiogasQingdao AgriculturalUniversityQingdaoChina Department of Chemical Engineering University of WashingtonSeattleWashingtonUSA Key laboratory of Systems Bioengineering Ministry of EducationTianjin UniversityTianjinChina Key laboratory of Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijingChina Center for Synthetic and Systems Biology Tsinghua UniversityBeijingChina Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate Schooland Insttute of Biomedical Health Technology and EngineeringShenzhen Bay LaboratoryShenzhenChina

Developing methylotrophic cell factories that can efficiently catalyze organic one-carbon(C1)feedstocks derived from electrocatalytic reduction of carbon dioxide into bio-based chemicals and biofuels is of strategic significance for building a carbon-neutral,sustainable economic and industrial *** the rapid advancement of RNA sequencing technology and mass spectrometer analysis,researchers have used these quantitative microbiology methods extensively,especially isotope-based metabolic flux analysis,to study the metabolic processes initiating from C1 feedstocks in natural C1-utilizing bacteria and synthetic C1 *** paper reviews the use of advanced quantitative analysis in recent years to understand the metabolic network and basic principles in the metabolism of natural C1-utilizing bacteria grown on methane,methanol,or *** acquired knowledge serves as a guide to rewire the central methylotrophic metabolism of natural C1-utilizing bacteria to improve the carbon conversion efficiency,and to engineer non-C1-utilizing bacteria into synthetic strains that can use C1 feedstocks as the sole carbon and energy *** progresses ultimately enhance the design and construction of highly efficient C1-based cell factories to synthesize diverse high value-added *** integration of quantitative biology and synthetic biology will advance the iterative cycle of understand–design–build–testing–learning to enhance C1-based biomanufacturing in the future.

关键词： ^(13)C-metabolic flux analysis methylotrophic cell factories one-carbon feedstock quantitative biology

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The multi-kingdom microbiome catalog of the chicken gastrointestinal tract

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Biosafety and Health 2024年第2期6卷 101-115页

作者： Yanan Wang Mengqi Qu Yuhai Bi William J.Liu Sufang Ma Bo Wan Yongfei Hu Baoli Zhu Gaiping Zhang George F.Gao International Joint Research Center of National Animal Immunology College of Veterinary MedicineHenan Agricultural UniversityZhengzhou 450046China CAS Key laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences(CAS)Beijing 100101China Longhu laboratory Zhengzhou 450046China University of Chinese Academy of Sciences Beijing 100049China NHC Key laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China State Key laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Chicken is an important food animal worldwide and plays an important role in human life by providing meat and *** recent significant advances in gut microbiome studies,a comprehensive study of chicken gut bacterial,archaeal,and viral genomes remains *** this study,we constructed a chicken multi-kingdom microbiome catalog(CMKMC),including 18,201 bacterial,225 archaeal,and 33,411 viral genomes,and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes(MAGs)from ten *** found that 812 and 240 MAGs in our dataset were putative novel species and genera,respectively,far beyond what was previously *** newly unclassified MAGs were predominant in Phyla Firmicutes_A(n=263),followed by Firmicutes(n=126),Bacteroidota(n=121),and Proteobacteria(n=87).Most of the classified species-level viral oper-ational taxonomic units belong to ***,63.24%of chicken gut viromes are predicted to infect two or more hosts,including complete circular ***,we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by ***,our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date,functional insights into the chicken gastrointestinal tract microbiota,and paves the way for microbial interventions for better chicken health and productivity.

关键词： Chicken Microbiome Metagenome assembled genomes Archaeome Virome Antibiotic resistance gene

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SARS-CoV-2 breakthrough infections following inactivated vaccine vaccination induce few neutralizing antibodies against the currently emerging Omicron XBB variants

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Virologica Sinica 2024年第1期39卷 173-176页

作者： Fan Shen Chun Liang Cui-Xian Yang Ying Lu An-Qi Li Ying Duan Mi Zhang c Ren-Rong Tian a Xing-Qi Dong Yong-Tang Zheng Wei Pang Key laboratory of Bioactive Peptides of Yunnan Province/Key laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common DiseasesKunming Institute of ZoologyChinese Academy of SciencesKunming650223China University of Chinese Academy of Sciences Beijing100049China Yunnan Provincial Infectious Disease Hospital Kunming650399China Department of Pathogen Biology and Immunology Faculty of Basic Medical ScienceKunming Medical UniversityKunming650500China

Dear Editor,COVID-19 inactivated vaccines have been extensively administered ***,the majority of the Chinese population has experiencedbreakthrough infections from SARS-CoV-2 ancestral,Delta or Omicronvariants over the past three years,particularly during the wave of Omicron BA.5 and BA.7 variants at the end of 2022(Zhu et al.,2023).Subsequently,new Omicron variants,such as BQ.1,BQ.1.1,XBB,XBB.1/XBB.1.9,and XBB.1.5/XBB.1.9.1,are emerging in China(Yueetal.,2023;Zhu et al.,2023).Therefore,it is an urgentneed and a publichealth imperative to assess the extent of the immunoprotection established in this population.

关键词： breakthrough neutral Omi

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Targeting proprotein convertase subtilisin/kexin type 9(PCSK9):from bench to bedside

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Signal Transduction and Targeted Therapy 2024年第2期9卷 509-557页

作者： Xuhui Bao Yongjun Liang Hanman Chang Tianji Cai Baijie Feng Konstantin Gordon Yuekun Zhu Hailian Shi Yundong He Liyi Xie Institute of Therapeutic Cancer vaccines Fudan University Pudong Medical CenterShanghaiChina Shanghai Key laboratory of Regulatory Biology School of Life SciencesEast China Normal UniversityShanghaiChina Department of Oncology Fudan University Pudong Medical CenterShanghaiChina Center for Clinical Research Fudan University Pudong Medical CenterShanghaiChina Clinical Research Center for Cell-based Immunotherapy Fudan UniversityShanghaiChina Department of Pathology Duke University Medical CenterDurhamNCUSA Center for Medical Research and Innovation Fudan University Pudong Medical CenterShanghaiChina Institute for Food Safety and Health Illinois Institute of TechnologyChicagoILUSA Department of Sociology University of MacaoTaipaMacaoChina Medical Institute Peoples’Friendship University of RussiaMoscowRussia A.Tsyb Medical Radiological Research Center ObninskRussia Department of Colorectal Surgery The First Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina Shanghai Key laboratory of Compound Chinese Medicines Institute of Chinese Materia MedicaShanghai University of Traditional Chinese MedicineZhangjiang Hi-tech ParkShanghaiChina Department of Radiation Oncology Fudan University Shanghai Cancer CenterShanghaiChina Department of Oncology Shanghai Medical CollegeFudan UniversityShanghaiChina

Proprotein convertase subtilisin/kexin type 9(PCSK9)has evolved as a pivotal enzyme in lipid metabolism and a revolutionary therapeutic target for hypercholesterolemia and its related cardiovascular diseases(CVD).This comprehensive review delineates the intricate roles and wide-ranging implications of PCSK9,extending beyond CVD to emphasize its significance in diverse physiological and pathological states,including liver diseases,infectious diseases,autoimmune disorders,and notably,*** exploration offers insights into the interaction between PCSK9 and low-density lipoprotein receptors(LDLRs),elucidating its substantial impact on cholesterol homeostasis and cardiovascular *** also details the evolution of PCSK9-targeted therapies,translating foundational bench discoveries into bedside applications for optimized patient *** advent and clinical approval of innovative PCSK9 inhibitory therapies(PCSK9-iTs),including three monoclonal antibodies(Evolocumab,Alirocumab,and Tafolecimab)and one small interfering RNA(siRNA,Inclisiran),have marked a significant breakthrough in cardiovascular *** therapies have demonstrated unparalleled efficacy in mitigating hypercholesterolemia,reducing cardiovascular risks,and have showcased profound value in clinical applications,offering novel therapeutic avenues and a promising future in personalized medicine for cardiovascular ***,emerging research,inclusive of our findings,unveils PCSK9’s potential role as a pivotal indicator for cancer prognosis and its prospective application as a transformative target for cancer *** review also highlights PCSK9’s aberrant expression in various cancer forms,its association with cancer prognosis,and its crucial roles in carcinogenesis and cancer *** conclusion,this synthesized review integrates existing knowledge and novel insights on PCSK9,providing a holistic perspective on its transformative impact in reshaping therapeutic paradigms acr

关键词： PCSK9 metabolism convert

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Expanding the horizons of targeted protein degradation:A non-small molecule perspective

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Acta Pharmaceutica Sinica B 2024年第6期14卷 2402-2427页

作者： Xiaowei Huang Fengbo Wu Jing Ye Lian Wang Xiaoyun Wang Xiang Li Gu He Department of Pharmacy and Department of Dermatology&Venerology West China HospitalSichuan UniversityChengdu 610041China Department of Urology West China HospitalSichuan UniversityChengdu 610041China laboratory of Dermatology Clinical Institute of Inflammation and ImmunologyFrontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu 610041China

Targeted protein degradation(TPD)represented by proteolysis targeting chimeras(PROTACs)marks a significant stride in drug discovery.A plethora of innovative technologies inspired by PROTAC have not only revolutionized the landscape of TPD but have the potential to unlock functionalities beyond ***-small-molecule-based approaches play an irreplaceable role in this field.A wide variety of agents spanning a broad chemical spectrum,including peptides,nucleic acids,antibodies,and even vaccines,which not only prove instrumental in overcoming the constraints of conventional small molecule entities but also provided rapidly renewing *** we summarize the burgeoning non-small molecule technological platforms inspired by PROTACs,including three major trajectories,to provide insights for the design strategies based on novel paradigms.

关键词： Targeted protein degradation Proteolysis targeting chimera Endocytosis Autophagy Proximity-inducing modality Post-translational modification

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Exploring groundwater quality in semi-arid areas of Algeria:Impacts on potable water supply and agricultural sustainability

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Journal of Arid Land 2024年第2期16卷 147-167页

作者： Noua ALLAOUA Hinda HAFID Haroun CHENCHOUNI laboratory of Natural Resources and Management of Sensitive Environments Larbi Ben M'hidi UniversityOum-El-Bouaghi 04000Algeria Department of Nature and Life Sciences Faculty of Exact Sciences and Nature and Life SciencesLarbi Ben M'hidi UniversityOum-El-Bouaghi 04000Algeria laboratory of Algerian Forests and Climate Change Higher National School of ForestsKhenchela 40000Algeria

Groundwater quality assessment is important to assure safe and durable water *** semi-arid areas of Algeria,groundwater represents the main water resource for drinking water supply of the rural population as well as for irrigation of agricultural *** samples from wells and springs were collected from the Gargaat Tarf and Annk Djemel sub-watersheds of the Oum El Bouaghi,Algeria,and were analyzed and compared with the World Health Organization(WHO)*** showed that most of the measured physical and chemical parameters exceeded the quality limits according to the WHO *** had a slightly alkaline water pH(7.00-7.79),electrical conductivity>1500μS/cm,chloride>500 mg/L,calcium>250 mg/L,and magnesium>155 mg/*** quality index(WQI)results showed that 68%of the area had excellent water quality,24%of the samples fell into good category,and only 8%were of poor quality and unsuitable for human *** wells in the area showed bacterial *** coliforms(453.9(±180.3)CFU(colony-forming units)/100 mL),fecal coliforms(243.2(±99.2)CFU/100 mL),and fecal streptococci(77.9(±32.0)CFU/100 mL)loads were above the standard limits set by the *** results confirmed that water resources in the study area were strongly influenced by anthropogenic activities and were not recommended for consumption as drinking water.

关键词： bacteriological indicator groundwater watershed physical-chemical parameter water quality index

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