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Differential selection in HIV-1 gp120 between subtype B and East Asian variant B'

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Virologica Sinica 2014年第1期29卷 40-47页

作者： Stefan Dang Yan Wang Bettina Budeus Jens Verheyen Rongge Yang Daniel Hoffmann research Group Bioinformatics Center of Medical Biotechnology and Faculty of BiologyUniversity of Duisburg-Essen AIDS and HIV research Group State Key Laboratory of VirologyWuhan Institute of VirologyChineseAcademy of Sciences Institute of virology University of Duisburg-Essen

HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the *** instance,distinct genomic backgrounds can be observed between the pandemic subtype B,prevalent in Europe and North-America,and its offspring clade B＇ in East *** we ask whether this differentiation affects the selection pressure experienced by the *** answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio ka/ks of amino acid changes to synonymous *** validate the approach we compare results to those from a state-of-the-art mixed-effect *** agreement is acceptable,but the analysis also demonstrates some limitations of the simpler ***,we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B＇ with more directional selection pressure in variable loops and more stabilizing selection in the constant *** on codons with increased ka/ks values in B＇,we show that these codons are scattered over the whole of gp120,with remarkable clusters of higher density in regions flanking the variable *** identify a significant statistical association of glycosylation sites and codons with increased ka/ks values.

关键词： human immunodeficiency virus 1 selection pressure genomic background

Immune modulatory function of abundant immune-related microRNAs in microvesicles from bovine colostrum

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Protein & Cell 2013年第3期4卷 197-210页

作者： Qi Sun Xi Chen Jianxiong Yu Ke Zen Chen-Yu Zhang Liang Li Jiangsu Engineering research center for microRNA Biology and biotechnology State Key Laboratory of Pharmaceutical BiotechnologyNanjing University School of Life SciencesNanjing 210093China Department of virology University of California School of Public HealthBerkeleyCA 94720USA

Colostrum provides essential nutrients and immunologically active factors that are beneficial to *** previous work demonstrated that milk contains large amounts of miRNA that is largely stored in milk-derived microvesicles(MVs).In the present study,we found that the MVs from colostrum contain signifi cantly higher levels of several immune-related *** hypothesized that the colostrum MVs may transfer the immune-related miR-NAs into cells,which contribute to its immune modulatory *** isolated colostrum MVs by ultracentrifugation and demonstrated several immune modulation features associated with *** also provide evidence that the physical structure of milk-derived MVs is essential for transfer miRNAs and following immune modulation ***,we found that colostrum powder-derived MVs also contains higher levels of immune-related miRNAs that display similar immune modulation *** together,these results show that MV-containing immunerelated miRNAs may be a novel mechanism by which co-lostrum modulates body immune response.

关键词： colostrum miRNAs microvesicles immune modulation

Antigenic analysis of grass carp reovirus using single-chain variable fragment antibody against IgM from Ctenopharyngodon idella

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Science China(Life Sciences) 2013年第1期56卷 59-65页

作者： CHEN CongLin SUN XiaoYun LIAO LanJie LUO ShaoXiang LI ZhouQuan ZHANG XiaoHua WANG YaPing GUO QionLin FANG Qin DAI HePing state Key Laboratory of Freshwater Ecology and biotechnology Institute of HydrobiologyChinese Academy of Sciences state Key Laboratory of virology Wuhan Institute of VirologyChinese Academy of Sciences

Grass carp （Ctenopharyngodon idella） is an important species of freshwater aquaculture fish in China. However, grass carp reovirus （GCRV） can cause fatal hemorrhagic disease in yearling populations. Until now, a strategy to define the antigenic ca- pacity of the virus＇s structural proteins for preparing an effective vaccine has not been available. In this study, some sin- gle-chain variable fragment antibodies （scFv）, which could specifically recognize grass carp IgM, were selected from a con- structed mouse naive antibody phage display cDNA library. The identified scFv C1B3 clone was shown to possess relatively higher specific binding activity to grass carp IgM. Furthermore, ELISA analysis indicated that the IgM level in serum from vi- rus-infected grass carp was more than two times higher than that of the control group at 5-7 days post infection. Moreover, Western blot analysis demonstrated that the outer capsid protein VP7 has a specific immuno-binding-reaction with the serum IgM from virus-infected grass carp. Our results suggest that VP7 can induce a stronger immune response in grass carp than the other GCRV structural proteins, which implies that VP7 protein could be used as a preferred immunogen for vaccine design.

关键词： grass carp grass carp reovirus (GCRV) IgM single-chain variable fragment (scFv) antigenicity

Dengue outbreaks in northern Nigeria: Evaluating the recommended Takeda vaccine and future prevention strategies

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World Journal of virology 2024年第3期13卷 41-48页

作者： Ismail Rabiu Hafsat Abubakar Musa Zephaniah Isaiah Mujahid Hussaini Muhammad Muhsin Umar Suleiman Mustapha Jaafaru Isah Abdullahi Aminu Shehu Mariya Abdullahi Sani College of Life Science Department of Biomedical Science and Environmental BiologyKaohsiung Medical UniversityKaohsiung 80708Taiwan Department of Microbiology Faculty of Life ScienceBayero University KanoKano 700006Kano StateNigeria Department of Microbiology Umaru Musa Yar’adua UniversityKatsina 820102Katsina StateNigeria Department of Microbiology Faculty of ScienceKaduna State UniversityTafawa Balewa Way 800283Kaduna StateNigeria National Reference Laboratory Nigeria Center for Disease ControlGaduwa 900231AbujaNigeria Department of Microbiology and biotechnology Federal UniversityDutse 720223Jigawa StateNigeria Monitoring and Evaluation Unit(Jigawa state Office) World Health OrganizationDutse 720223Jigawa StateNigeria

Dengue fever,caused by the dengue virus(DENV),poses a significant public health challenge globally,with Nigeria experiencing sporadic outbreaks.A clear understanding of the dengue burden has not been achieved in Nigeria,just as in other African *** the epidemiology and burden of dengue fever is essential for effective prevention and control *** paper examines the recent dengue outbreaks in northern Nigeria,particularly in Sokoto state,and evaluates the recommended Takeda dengue vaccine(TDV)along with future prevention *** limited surveillance and underreporting,dengue fever is endemic in Nigeria(with over 5 million cases and 5000 dengue-related deaths in 2023),with recent outbreaks indicating a growing *** TDV,a live attenuated tetravalent vaccine,has shown promise in preventing dengue fever,but challenges such as vaccine acceptance and access-ibility need to be *** urbanization contributes to the disease's spread,which is influenced by factors such as population density,cultural beliefs,water storage practices,hygiene,and water supply *** prevention strategies must focus on government intervention,community practices,and innovative vector control measures to mitigate the spread of DENV in *** study will serve as a valuable reference for policy-makers,researchers,and clinicians in the management and control of DENV in Nigeria and Africa as a whole.

关键词： Dengue outbreaks Northern Nigeria Takeda dengue vaccine Vaccine acceptance Epidemiology

Glycosylation and an amino acid insertion in the head of hemagglutinin independently affect the antigenic properties of H5N1 avian influenza viruses

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Science China(Life Sciences) 2019年第1期62卷 76-83页

作者： Chunyang Gu Xianying Zeng Yangming Song Yanbing Li Liling Liu Yoshihiro Kawaoka Dongming Zhao Hualan Chen state Key Laboratory of Veterinary biotechnology Harbin Veterinary Research Institute Chinese Academy of Agricultural Sciences Division of virology Department of Microbiology and Immunology Institute of Medical Science University of Tokyo

Antigenic drift forces us to frequently update influenza vaccines; however, the genetic basis for antigenic variation remains largely unknown. In this study, we used clade 7.2 H5 viruses as models to explore the molecular determinants of influenza virus antigenic variation. We generated eight monoclonal antibodies(MAbs) targeted to the hemagglutinin(HA) protein of the index virus A/chicken/Shanxi/2/2006 and found that two representative antigenically drifted clade 7.2 viruses did not react with six of the eight MAbs. The E131 N mutation and insertion of leucine at position 134 in the HA protein of the antigenically drifted strains eliminated the reactivity of the virus with the MAbs. We also found that the amino acid N131 in the H5 HA protein is glycosylated. Our results provide experimental evidence that glycosylation and an amino acid insertion or deletion in HA influence antigenic variation.

关键词： Influenza virus H5N1 antigenic variation genetic basis

Diversity of coronaviruses in wild and domestic birds in Vietnam

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Asian Pacific Journal of Tropical Medicine 2022年第10期15卷 442-450页

作者： Vasily Y.Marchenko Natalia P.Kolosova Alexey V.Danilenko Maria K.Bragina Tran Thi Nhai Alexander B.Ryzhikov Federal Budgetary research Institution state research center of virology and biotechnology“Vector”Rospotrebnadzor 630559Novosibirsk regionKoltsovoRussia Joint Russian-Vietnamese Tropical research and Technology Centre 650000Nguyen Van HuyenNghia DoCau GiayHanoiVietnam

Objective:To investigate the genetic diversity of coronaviruses in wild and domestic birds in the bird park and live poultry markets of Ca Mau province in Vietnam in ***:A total of 228 samples(121 from wild birds and 107 from poultry)were collected in the territory of Ca Mau province of Vietnam in *** avian samples were tested for the presence of the four genera of coronaviruses using reverse transcription and nested *** genetic analysis using targeted NGS sequencing of RdRp gene was performed for 29 representative samples(12 samples from wild birds and 17 from poultry).Phylogenetic analysis was performed using the neighbour joininig method with 1000 bootstrap replications using MEGA X ***:Among wild birds,21.5%samples were positive for the genetic material of coronaviruses and 38.3%samples were positive for coronaviruses among *** analysis of the partial sequence of RdRp gene from representative samples revealed that wild birds were carriers of gammacoronaviruses and *** poultry,three genotypes of infectious bronchitis virus(QX,Mass and Q1)were detected in chickens,with QX genotypes being predominant,and viruses of DCoV group were detected in domestic *** was no detection of alphacoronaviruses or betacoronaviruses in the studied ***:Coronaviruses of genera Gammacoronavirus and Deltacoronavirus were detected in wild birds.A high percentage of infectious bronchitis virus was detected in ***,there is a need for broader surveillance of coronaviruses in birds,which can be used for evaluation of diversity,evolution and distribution of coronaviruses in *** surveillance of coronaviruses circulation in wild and domestic animals is necessary for implementing strategic measures for poultry and domestic animal protection and for evaluation of possible risk of circulating coronaviruses to human health.

关键词： Avian coronavirus Gammacoronavirus Deltacoronavirus Surveillance Wild birds Poultry Vietnam

Designer cell-self-implemented labeling of microvesicles in situ with the intracellular-synthesized quantum dots

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Science China Chemistry 2020年第4期63卷 448-453页

作者： Ling-Hong Xiong Jia-Wei Tu Ya-Nan Zhang Ling-Ling Yang Ran Cui Zhi-Ling Zhang Dai-Wen Pang College of Chemistry and Molecular Sciences State Key Laboratory of VirologyInstitute for Advanced Studiesand Wuhan Institute of BiotechnologyWuhan UniversityWuhan 430072China state Key Laboratory of Medicinal Chemical Biology Tianjin Key Laboratoryof Biosensing and Molecular RecognitionResearch Center for Analytical Sciencesand College of ChemistryNankai UniversityTianjin 300071China

Cell-derived microvesicles(MVs) are secreted from almost all kinds of mammalian cells into the extracellular space, and play crucial roles in intercellular communication and transporting biomolecules between cells. However, there is a great challenge for visualizing and monitoring of MVs’ bio-behaviors due to the limitations of existing labeling methods. Herein, we report the first paradigm of designer cell-self-implemented labeling of MVs secreted from living mammalian MCF-7 cells in situ using the intracellular-synthesized fluorescent quantum dots(QDs) during the formation of MVs. By elaborately coupling intracellular biochemical reactions and metabolism pathways, the MCF-7 cells can be illuminated brightly by intracellular-biosynthesized fluorescent CdSe QDs. Simultaneously, intracellular-synthesized QDs can be in situ encapsulated by the secreted MVs budding from the plasma membrane of the fluorescing cells to label the MVs with an efficiency of up to 89.9%. The whole labeling process skillfully combines designer precise cell-tuned intricate synthesis of CdSe QDs with mild in-situ labeling via cell-selfimplementation just after feeding the cell with suitable chemicals, which is structure-or function-nondestructive and much more straightforward and milder than those by chemical conjugation or indirect encapsulation with conventional fluorogenic labels.

关键词： in situ labeling live cell synthesis cell-derived microvesicles quantum dot cell-self-implementation

Decreased inhibition of exosomal miRNAs on SARS-CoV-2 replication underlies poor outcomes in elderly people and diabetic patients

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Signal Transduction and Targeted Therapy 2021年第9期6卷 2822-2830页

作者： Yanbo Wang Xiaoju Zhu Xia-Ming Jiang Jingwei Guo Zheng Fu Zhen Zhou Ping Yang Hongyuan Guo Xu Guo Gaoli Liang Ping Zeng Gengfu Xiao Jizheng Ma Xin Yin Lei-Ke Zhang Chao Yan Chen-Yu Zhang Nanjing Drum Tower Hospital center of Molecular Diagnostic and Therapy Chinese Academy of Medical Sciences Research Unit of Extracellular RNAState Key Laboratory of Pharmaceutical BiotechnologyJiangsu Engineering Research Center for MicroRNA Biology and BiotechnologyNJU Advanced Institute of Life Sciences(NAILS)NJU Institute of Al Biomedicine and BiotechnologyChemistry and Biomedicine Innovation Center(ChemBIC)School of Life SciencesNanjing UniversityNanjingChina state Key Laboratory of virology Wuhan Institute of VirologyCenter for Biosafety Mega-ScienceChinese Academy of SciencesWuhanHubeiChina Department of Clinical Laboratory The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina The MOH Key Laboratory of Geriatrics Beijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina The research center of Military Exercise Science The Army Engineering University of PLANanjingJiangsuChina

Elderly people and patients with comorbidities are at higher risk of COVID-19 infection,resulting in severe complications and high ***,the underlying mechanisms are *** this study,we investigate whether miRNAs in serum exosomes can exert antiviral functions and affect the response to COVID-19 in the elderly and people with diabetes.

关键词： patients mortality infection

Fungal Bioactive Compounds with Antiviral Effect

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Journal of Pharmacy and Pharmacology 2015年第8期3卷 357-371页

作者： Tamara Teplyakova Tatiana Kosogova state research center of virology and biotechnology Vector Koltsovo Novosibirsk Region 630559 Russia

Basidial fungi have long been known as sources of antitumor compounds such as polysaccharides. Studies conducted by scientists from different countries demonstrate that polysaccharides and other fungal compounds （proteins, glycoproteins, terpenoids, melanins, nucleosides, etc.） exhibit antiviral activity against many viruses pathogenic for humans. The review presents data on the studied antiviral activities of higher basidial fungi against herpes, West Nile, influenza, human immunodeficiency and hepatitis viruses as well as orthopoxviruses including variola virus. Many species of basidial fungi and various classes of biologically active compounds obtained from them are capable of effectively inhibiting the development of viruses in cells and animals while possessing low toxicity. Biologically active compounds from the same fungal species can exhibit antiviral effects against different pathogens. Effective strains isolated from wild mushrooms in culture represent promising objects for the development of biotechnological drugs, including ones possessing antiviral activity. The data on antitumor and antiviral activities of compounds from the same fungal species indicate the correlation of these properties. In this connection, preparations of basidial fungi may have prophylactic value in preventing cancers of viral etiology.

关键词： Biologically active compounds basidial fungi pathogenic viruses antiviral activity.