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m^(6)A modification of plant virus enables host recognition by NMD factors in plants

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Science China(Life Sciences) 2024年第1期67卷 161-174页

作者： Hao He Linhao Ge Yalin Chen Siwen Zhao Zhaolei Li Xueping Zhou Fangfang Li State Key laboratory for biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China State Key laboratory of Rice biology Institute of BiotechnologyZhejiang UniversityHangzhou 310029China

N^(6)-methyladenosine(m^(6)A)is the most abundant eukaryotic mRNA modification and is involved in various biological *** evidence has implicated that m^(6)Amodification is an important anti-viral defense mechanism in mammals and plants,but it is largely unknown how m^(6)Aregulates viral infection in *** we report the dynamic changes and functional anatomy of m^(6)Ain Nicotiana benthamiana and Solanum lycopersicum during Pepino mosaic virus(PepMV)infection.m^(6)Amodification in the PepMV RNA genome is conserved in these two *** of the m^(6)Awriters,mRNA adenosine methylase A(MTA),and HAKAI inhibit the PepMV RNA accumulation accompanied by increased viral m^(6)Amodifications,whereas deficiency of these writers decreases the viral RNA m^(6)Alevels but enhances virus *** study reveals that the cytoplasmic YTH-domain family protein NbECT2A/2B/2C as m^(6)Areaders are involved in anti-viral ***-protein interactions indicate that NbECT2A/2B/2C interact with nonsense-mediated mRNA decay(NMD)-related proteins,including NbUPF3 and NbSMG7,but not with NbUPF1.m^(6)Amodification-mediated restriction to PepMV infection is dependent on NMD-related *** findings provide new insights into the functionality of m^(6)Aanti-viral activity and reveal a distinct immune response that NMD factors recognize the m^(6)Areaders-viral m^(6)ARNA complex for viral RNA degradation to limit virus infection in plants.

关键词： m^(6)A Pepino mosaic virus plant defense m^(6)A readers NMD factors

Development of a cell-permeable adenine-derived probe for capture of nucleotide-binding proteins in living cells

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Chinese Chemical Letters 2024年第3期35卷 243-246页

作者： Lihong Liu Rui Chen Gang Xue Chenzhou Hao Weizhi Weng Zhengying Pan State Key laboratory of Chemical Oncogenomics School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhen 518055China

Adenine is an essential building block of genetic material and a range of *** probes containing an adenine moiety have been used in kinase profiling studies in cell *** we report that adenine-derived small-molecule probes with an activated ester reactive group can covalently modify a conserved lysine residue of protein kinases and capture a number of nucleotide-binding proteins within living cells.

关键词： Adenine-derived probe Cell-permeable Lysine residue Protein kinases Nucleotide-binding proteins

From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

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marine Life Science & Technology 2024年第1期6卷 31-49页

作者： Liping Lyu Xue Zhang Yunyi Gao Tengteng Zhang Jinyu Fu Naomi A.Stover Feng Gao Key laboratory of Evolution&marine Biodiversity(Ministry of Education) and Institute of Evolution&Marine BiodiversityOcean University of ChinaQingdao 266003China Department of biology Bradley UniversityPeoriaIL 61625USA Laoshan laboratory Qingdao 266237China

Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic ***,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of *** expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline *** in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic *** report the partial germline genomes of two spirotrich ciliate species,namely Strombidium *** and Halteria grandinella,along with the most compact and highly fragmented somatic genome for *** provide the first insights into the genome rearrangements of these two species and compare these features with those of other *** analyses reveal:(1)DNA sequence loss through evolution and during PGR in *** has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

关键词： Alternative processing Ciliates Gene scrambling Genome rearrangement Germline genome Somatic genome

A comparative study for petroleum removal capacities of the bacterial consortia entrapped in sodium alginate,sodium alginate/poly(vinyl alcohol),and bushnell haas agar

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Petroleum Science 2024年第1期21卷 705-715页

作者： Sezen Bilen Ozyurek Department of biology(biotechnology) Faculty of ScienceHacettepe UniversityAnkaraBeytepe06800Turkey

The purpose of this study was to identify and compare the degradation efficiencies of free and entrapped bacterial consortia(Staphylococcus capitis CP053957.1 and Achromobacter marplatensis MT078618.1)to different polymers such as Sodium Alginate(SA),Sodium Alginate/Poly(Vinyl Alcohol)(SA/PVA),and Bushnell Haas Agar(BHA).In addition to SA and SA/PVA,which are cost-effective,non-toxic and have different functional groups,BHA,which is frequently encountered in laboratory-scale studies but has not been used as an entrapment material until *** on these,the polymers with different surface morphologies and chemical compositions were analyzed by SEM and *** the petroleum removal efficiency was higher with the entrapped bacterial consortia than with the free one,BHA-entrapped bacterial consortium enhanced the petroleum removal more than SA and SA/***,the degradation rate of bacterial consortia entrapped with BHA was 2.039 day^(-1),SA/PVA was 1.560,SA was 0.993,the half-life period of BHA-entrapped bacterial consortia is quite low(t_(1/2)=0.339)compared with SA(t_(1/2)=0.444)and SA/PVA(t_(1/2)=0.697).The effects of the four main factors such as:amount of BHA(0.5,1,1.5,2,2.5,3 g),disc size(4,5,6,7,8 mm),inoculum concentration(1,2.5,5,7.5,10 mL),and incubation period on petroleum removal were also *** maximum petroleum removal(94.5%)was obtained at≥2.5 mL of bacterial consortium entrapped in 2 g BHA with a 7 mm disc size at 168 h and the results were also confirmed by statistical *** a decrease was observed during the reuse of bacterial consortium entrapped in BHA,the petroleum removal was still above 50%at 10th *** on GC-MS analysis,the removal capacity of BHA-entrapped consortium was over 90%for short-chain n-alkanes and 80%for medium-chain ***,the obtained data are expected to provide a potential guideline in cleaning up the large-scale oil pollution in the *** there has been no similar stud

关键词： Entrapment of bacterial consortia Petroleum RemovalBushnell Haas agar Sodium alginate Sodium alginate/poly(vinyl alcohol)

Understanding the cooperative effects in the catalysis of homodimeric fluoroacetate dehalogenase

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Science China Chemistry 2024年第7期67卷 2382-2391页

作者： Ke-Wei Chen Jia-Nan Chen Jun Zhang Chao Wang Tian-Yu Sun Yun-Dong Wu Key laboratory of Computational Chemistry and Drug Design State Key Laboratory of Chemical OncogenomicSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhen 518055China Institute of Chemical biology Shenzhen Bay LaboratoryShenzhen 518132China College of Chemistry and Molecular Engineering Peking UniversityBeijing 100871China Changping laboratory Beijing 102200China

Fluoroacetate dehalogenases(FAcD),a homodimeric enzyme,catalyzes the conversion of fluoroacetic acid to glycolic acid(GoA).It has been proved that the enzyme has a half-of-the-site ***,its catalytic(C)subunit converts the first substrate to a covalent intermediate;then,the non-catalytic(NC)subunit binds a second substrate and promotes the conversion of the intermediate in the C subunit into the final *** the release of the product,the C subunit becomes the NC subunit,and the previous NC subunit becomes the C *** elucidate the detailed mechanism behind this cooperative catalysis,we have conducted microsecond-scale MD simulations along the reaction *** simulations indicate that the substrate in the NC subunit induces W185 and Y141 adopting an open conformation in the C *** opening of W185(C)facilitates the entry of catalytic water,enhancing the catalytic activity for product formation,while the opening of Y141(C)creates an unfavorable environment for product binding,promoting its *** interaction network analysis reveals that the substrate in the NC subunit can induce conformational changes through a conserved water chain at the interface.

关键词： enzyme catalysis molecular dynamics cooperative effect pre-reaction state

Production and characterization of monoclonal antibodies against grass carp CD4-1 and CD4-2

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Aquaculture and Fisheries 2024年第2期9卷 154-163页

作者： Bangjie Wang Yuting Qin Zhaosheng Sun Xiaozhen Zhu Zhao Jia Kangyong Chen Danjie Liu Junya Wang Jun Zou Key laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of EducationShanghai Ocean UniversityShanghai201306China International Research Center for marine Biosciences at Shanghai Ocean University Ministry of Science and TechnologyShanghai201306China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai201306China laboratory for marine biology and biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao266071China

CD4 T helper cells are an important group of cells in the immune system of vertebrates and express CD4 receptor on the cell *** mammals,the CD4 receptor is encoded by a single copy gene,whilst in fish,two copies of cd4 genes,namely cd4-1 and cd4-2,are *** this study,the ectodomains of grass carp(Ctenopharyngodon idella,Ci)CD4-1 and CD4-2 were expressed in the *** cells and used to generate monoclonal antibodies in *** blotting,confocal microscopy and flow cytometry were performed to characterize the monoclonal *** has been shown that the CiCD4-1 and CiCD4-2 monoclonal antibodies had good specificity to react with the recombinant ectodomains of CiCD4-1 and CiCD4-2 expressed in the CHO-S cells and the native CD4 molecules of grass *** CiCD4-1 monoclonal antibody did not recognize CiCD4-2 and verse *** addition,the CD4-1 and CD4-2 monoclonal antibodies specifically recognized the CD4-1 and CD4-2 receptors expressed in the HEK293 cells and native molecules of fish ***,the percentages of lymphocytes in immune tissues of healthy fish were analyzed by flow *** was found that 17.6%of lymphocytes were CD4-1^(+)cells and 22.5%were CD4-2^(+)in the head *** the spleen,13.1%of lymphocytes were CD4-1^(+)and 18.6%were CD4-2^(+)while 7.3%of blood lymphocytes were CD4-1^(+)cells and 8.8%were CD4-2^(+)*** availability of the CD4-1 and CD4-2 monoclonal antibodies provides antibody-based tools for further elucidation of the functions of CD4 T cells in grass carp.

关键词： Grass carp CD4 Monoclonal antibodies Flow cytometry Confocal microscopy

Characterisation of IL-21 and IL-21Rαin grass carp:IL-21-producing cells are upregulated during Flavobacterium columnare infection

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Aquaculture and Fisheries 2024年第2期9卷 126-135页

作者： Jiawen Xu Junya Wang Qingyu Min Wei Wang Yuting Qin Lina Lei Qian Gao Jun Zou Key laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of EducationShanghai Ocean UniversityShanghai201306China International Research Center for marine Biosciences at Shanghai Ocean University Ministry of Science and TechnologyShanghai201306China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai201306China laboratory for marine biology and biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao266200China

Interleukin-21(IL-21)is produced mainly by activated CD4^(+)T cells and promotes the proliferation,survival and differentiation of immune *** study characterised a high affinity binding receptor of IL-21(IL-21 Rα)from grass carp(Ctenopharyngodon idella,Ci)and analyzed the expression of CiIL-21 and CiIL-21 Rα.It has been shown that they were modulated by PAMPs and during infection with bacterial and viral *** CiIL-21 protein produced in bacteria was active in inducing the expression of genes involved in Th responses.A monoclonal CiIL-21 antibody was generated against the rCiIL-21 and showed good reactive specificity with the rCiIL-21 proteins expressed in *** cells,and HEK293 T cells and the native protein from PHA-stimulated kidney *** addition,the IL-21-producing cells detected by the CiIL-21 monoclonal antibody were found to be increased to in the kidney,spleen and hindgut after infection with Flavobacterium *** data indicate that IL-21 is involved in the regulation of immune response to bacterial and viral infection.

关键词： IL-21 IL-21Rα Gene expression IL-21-Producing cell Bacterial and viral infection Fish

Bird specimen number linked with species trait and climate niche breadth

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Avian Research 2024年第1期15卷 108-115页

作者： Xiaoyu Duan Xiongwei Huang Jingya Zhang Shuo Lv Gang Song Yanping Wang Gang Feng Ministry of Education Key laboratory of Ecology and Resource Use of the Mongolian Plateau&Inner Mongolia Key laboratory of Grassland Ecology School of Ecology and EnvironmentInner Mongolia UniversityHohhot010020China Key laboratory of marine biotechnology of Fujian Province Institute of OceanologyCollege of Marine SciencesFujian Agriculture and Forestry UniversityFuzhou350002China Key laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing100101China laboratory of Island Biogeography and Conservation biology College of Life SciencesNanjing Normal UniversityNanjing210023China

Biological specimens are fundamental for taxonomy and flora/fauna *** importantly,they also play crucial roles in recording environmental impacts on morphology and behavior,which is vital for biodiversity research and ***,there are few systematic studies on the patterns and drivers of bird specimen number at regional *** study is the first attempt to examine the relationships between bird specimen number and species traits as well as climate niche breadth in China,aiming to answer two questions:1)how do species’temperature niche breadth and precipitation niche breadth influence specimen number?2)which trait is most associated with bird specimen number?The associations between bird specimen number and explanatory variables were examined using ordinary least squares,generalized linear models,phylogenetic generalized linear mixed models,and multiple *** results showed that Muscicapidae was the family with the highest specimen number,and Passeriformes was the order with the highest specimen *** specimen number significantly increased with larger temperature niche breadth and precipitation niche *** number was also positively associated with geographic range size,habitat specificity,hunting vulnerability and clutch size,but negatively associated with body *** findings suggest that future bird specimen collection should pay more attention to birds with limited ecological niches,large body sizes,and small clutch *** research enhances the use of bird specimen data to study and preserve biodiversity.

关键词： Biodiversity conservation Biological specimens Bird traits Scientific collection Specimen number Temperature and precipitation

RNA-seq analysis of a zebrafish caudal fin cell line in response to infection with spring viraemia of carp virus

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Aquaculture and Fisheries 2024年第2期9卷 181-192页

作者： Wenji Huang Ning Ji Xin Zhao Jiahong Guo Jianhua Feng Kangyong Chen Yaxin Wu Junya Wang Jun Zou Key laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of EducationShanghai Ocean UniversityShanghai201306China International Research Center for marine Biosciences Ministry of Science and TechnologyShanghai Ocean UniversityShanghai201306China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai201306China laboratory for marine biology and biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao266071China

A cell line,termed ZFIN,was established from the caudal fin of zebrafish and was shown to be susceptible to spring viremia of carp virus(SVCV).The ZFIN cells are epithelial like cells and have a moderate plasmid transfection efficiency of 13.9%.Using an RNA-seq approach,differentially expressed genes(DEGs)regulated by SVCV were *** of SVCV gave rise to 3931 DEGs and up-regulated DEGs were mostly enriched into the biological regulation and cellular processes,among which pathways for the type I interferon signaling and the response to exogenous dsRNA were the top two GO *** KEGG signaling pathways including TLR signaling pathway,RLR receptor signaling pathway,cytosolic DNA-sensing pathway,NLR signaling pathway,cytokine-cytokine receptor interaction and ferroptosis were significantly *** genes including ifnφ1,isg15 and mx were significantly *** addition,key DEGs involved in autophagy were *** results indicate that the ZFIN cell line provides a useful in vitro tool for study on the gene functions and cellular responses to viral infection in fish.

关键词： Caudal fin cells SVCV RNA-seq DEGs Innate antiviral response