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Mass spectrometry profiling analysis enables the identification of new modifications in ribosomal rna

Chinese Chemical Letters 2023年第3期34卷 157-161页

作者： Xiao-Meng Tang Tian-Tian Ye Xue-Jiao You Xiao-Ming Yin Jiang-Hui Ding Wen-Xuan Shao Meng-Yuan Chen Bi-Feng Yuan Yu-Qi Feng Sauvage Center for Molecular Sciences Department of ChemistryWuhan UniversityWuhan 430072China School of Public Health Wuhan UniversityWuhan 430071China

ribosomal rnas(rrnas) provide the structural framework of ribosomes and play critical roles in protein *** ribosome biogenesis,rrnas acquire various modifications that can influence the structure and catalytic activity of ***,rrna modifications in plants have yet to be fully ***,we proposed a method to purify rrnas by a successive isolation with different strategies,including poly A-based m rna depletion and agarose gel electrophoresis-based purification,with which highly pure rrnas could be *** addition,we developed a liquid chromatography-electrospray ionization-tandem mass spectrometry(LC-ESI-MS/MS) method to systematically profile and characterize modifications from the isolated highly pure plant 18S rrna and 25S ***-ESI-MS/MS analysis showed that 10 and 12 kinds of modifications were present in plant 18S rrna and 25S rrna,***,among these identified modifications,2 kinds of modifications of N^(2),N^(2)-dimethylguanosine(m^(2,2)G)and N^(6),N^(6)-dimethyladenosine(m^(6,6)A) in 18S rrna,and 4 kinds of modifications of m^(2,2)G,m^(6,6)A,N7-methylguanosine(m^(7)G) and 3-methyluridin(m^(3)U) in 25S rrna,were first reported to be present in ***,exposure of Arabidopsis thaliana to cadmium(Cd) led to significant changes of modifications in both 18S rrna and 25S rrna of plants,indicating that rrna modifications play important roles in response to environmental *** discovery of new modifications in plant rrnas improves the spectra of plant rrna modifications and may promote the investigation of the functional roles of plant ribosomes in regulating gene expression.

关键词： ribosomal rna rna modification Plant Arabidopsis thaliana Profiling Mass spectrometry

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Monophyly of the ring-forming group in Diplopoda(Myriapoda,Arthropoda) based on SSU and LSU ribosomal rna sequences

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Progress in Natural Science:Materials International 2009年第10期19卷 1297-1303页

作者： Peiyun Conga,b,Xuhua Xiac,Qun Yanga,a State Key Laboratory of Palaeobiology and Strategraphy,Nanjing Institute of Geology and Palaeontology,Chinese Academy of Sciences,Nanjing 210008,China b Yunnan Key Laboratory for Paleobiology,Yunnan University,Kunming 650091,China c Department of Biology,University of Ottawa,Ont.,Canada K1N 6N5 State Key Laboratory of Palaeobiology and Strategraphy Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Nanjing 210008 China Yunnan Key Laboratory for Paleobiology Yunnan University Kunming 650091 China Department of Biology University of Ottawa Ont. Canada K1N 6N5

Two controversies exist in the phylogeny of the derived millipedes(Diplopoda).The first is whether millipedes with a fusion ring,including Polydesmida,Spirobolida,Spirostreptida and Julida,form a monophyletic group(the ring-forming group).The second concerns the phylogenetic relationship within the three orders of Juliformia,***,Spirostreptida and *** resolve these phylogenetic controversies,we sequenced 18S and 28S rDNA from six millipede orders and retrieved several homologous sequences from *** results give robust support to the monophyly of the ring-forming group based on maximum parsimony methods,max-imum likelihood methods and Bayesian *** monophyly of the ring-forming group suggests that the fusion of segment sclerites might have occurred only once during millipede evolutionary *** also established a sister-group relationship between Spirobol-ida and Spirostreptida within Juliformia after eliminating a short-branch attraction phenomenon,which is consistent with that from the mitochondrial genome analysis.

关键词： Diplopoda Ring-forming group ribosomal rna Monophyly Short-branch attraction

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A new contribution to the taxonomy and phylogeny of the ciliate genus Spirostomum(Alveolata,Ciliophora,Heterotrichea),with comprehensive descriptions of two species from wetlands in China

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Water Biology and Security 2022年第2期1卷 23-37页

作者： Yong Chi Zhe Wang Tingting Ye Ya Wang Junli Zhao Weibo Song William A.Bourland Xiangrui Chen Institute of Evolution&Marine Biodiversity and College of FisheriesOcean University of ChinaQingdao266003China School of Marine Sciences Ningbo UniversityNingbo315800China Weishan Fishery Development Service Center Jining277600China Department of Zoology Faculty of ScienceCharles UniversityPrague12843Czech Republic

Species of the ciliate genus Spirostomum Ehrenberg,1834 are distributed worldwide and have a research history spanning more than two ***,species delimitation and phylogenetic relationships within this genus are still uncertain due to the paucity of stable morphologic characters for species separation and the unavailability of accompanying morphological data for most molecular sequences in public *** the present study,*** Shigenaka,1959(three populations)and ***(Müller,1786)Delphy,1939(one population)were investigated using morphological and molecular methods for the first time in *** morphological data for the two species were documented,and improved diagnoses were supplied based on a combination of previous studies and the current *** should be highlighted that there were three different atypical morphotypes identified in a Ningbo population of *** which may represent various stages in conjugative *** phylogenies based on 18S,ITS1-5.8S-ITS2,and 28S rrna gene sequences show that the genus Spirostomum is monophyletic,however,the internal relationships inferred from different genes were poorly resolved but suggest that the species with a moniliform macronucleus comprise an early-diverging clade within this ***,the global distribution of Spirostomum is summarized based on previous and present studies.

关键词： Conjugation Morphogenesis Morphology Phylogeny ribosomal rna

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Detection of Prorocentrum donghaiense using sandwich hybridization integrated with nuclease protection assay

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Acta Oceanologica Sinica 2009年第2期28卷 121-126页

作者： CHEN Jie ZHEN Yu MI Tiezhu YU Zhigang College of Marine Life Science Ocean University of China Qingdao 266003 China College of Environmental Science and Engineering Ocean University of China Qingdao 266100 China College of Chemistry and Chemical Engineering Ocean University of China Qingdao 266100 China

Prorocentrum donghaiense is an important harmful algae bloom （HAB） causing creature in China＇s seas, and the conventional visual detection can not cope with long-term monitoring and highthroughput sampling projects. An assay for P. donghaiense with sandwich hybridization integrated with nuclease protection assay （NPA-SH） was established. Tests with mixed samples and spiked field ones confirmed its good specificity and sensitivity. The cell number of P. donghaiense correlated well with the optical density, and the regression equation is y=4× 10^- 6x＋ 0.694 9, in which x is the cell number, and y is the optical density, with r2=0.953 5. These results show that the NPA-SH method has good feasibility in the detection of P. donghaiense. Results of NPA-SH and microscopy are excellent for each sample. The NPA-SH method was a simple way in quantitative detection of P. donghaiense, and the whole process could be finished in about six hours, which provided a new approach in high-throughput sampling and long-term monitoring of P. donghaiense.

关键词： Prorocentrum donghaiense ribosomal rna S1 enzyme sandwich hybridization integrated with nuclease protection assay (NPA-SH)

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FGF13A represses transcription of rrna genes as a nucleolar protein

FGF13A represses transcription of rRNA genes as a nucleolar ...

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中国神经科学学会第四次会员代表大会暨第八届全国学术会议

作者： Liu YANG~1,Lan BAO~2,Xu ZHANG~(1,*) 1 Institute of Neuroscience and State Key Laboratory of Neuroscience 2 Institute of Biochemistry and Cell Biology and Laboratory of Molecular Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,Shanghai,200031,China

Objective Fibroblast growth factors(FGFs) are among the first-indentified families of growth *** are polypeptides with diverse biological activities including cell proliferation,differentiation,migration and so *** their functions are much more evident in the nervous system than in *** FGFs have N-terminal signal peptides and can be secreted ***,FGF11 subfamily(FGFs 11-14) is a special *** FGFs lack signal peptides, remain intracellularly and function within cells in a receptor-independent manner,hereafter referred to as *** growth factor 13(FGF13) is a member of the intracellular FGF homologous factor subfamily(iFGFs) and highly expressed in nervous system,however its functions are still *** The subcellular localization of FGF13A was investigated by *** interaction between FGF13A and UBF1 was investigated by coimmunoprecipitation (co-IP) *** function of FGF13A on the neurite outgrowth of DRG neurons was investigated by electroporation and ***(1) The expression of FGF13A-EGFP in transfected ND7-23 cells or dissociated primary DRG neurons was highly enriched in the nucleolus of the two types of cells and colocalized with the nucleolus marker,fibrillarin and nucleolin.(2) Overexpression of FGF13A repressed rrna transcription through interacting with upstream binding factor 1(UBF1),a rna pol I transcription factor.(3) Overexpression of FGF13A significantly inhibited neurite outgrowm of dissociated DRG *** Nucleolus-localized FGF13A represses rrna transcription and therefore inhibits DRG neurite outgrowth.

关键词： iFGF UBF1 ribosomal rna transcription neurite outgrowth

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Dual-mode Detection of Bacterial Pathogens by ThermallyActivatedDelayed Fluorescence Probe

Dual-mode Detection of Bacterial Pathogens by ThermallyActiv...

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第十一届全国化学生物学学术会议

作者： Shengnan Xu Qingyang Zhang Yali Wang Xiang Wang Jian-Dong Jiang Hai-Yu Hu State Key Laboratory of Bioactive Substances and Function of Natural Medicines Beijing Key Laboratory of Active Substances Discovery and Drugability EvaluationInstitute of Materia MedicaChinese Academy of Medical Sciences ＆ Peking Union Medical College

With the accumulation of bacterial resistance to antibiotics, bacterial infection has become a global crisis. Specific detection of pathogens has long been recognized as a vital strategy in the control of bacterial infections.[1] Herein, a novel hydrophilic aromatic-imide-based[2] thermally activated delayed fluorescence（TADF） probe, AI-Cz-Neo, is rationally designed and efficiently synthesized by conjugating a broad spectrum aminoglycoside antibiotic,[3] neomycin. AI-Cz-Neo shows specific targetability to bacterial ribosomal rna, which provides not only high specificity for bacteria but also a practical strategy for long-lived delayed fluorescence emission in oxygenic environments. Notably, AI-Cz-Neo was successfully utilized for the specific detection of broad-spectrum bacterial pathogens with high reliability and accuracy on the basis of the dual-mode imaging of confocal fluorescence imaging and fluorescence lifetime imaging in cells and tissues. To our best knowledge, AI-Cz-Neo is the first molecule providing the dual-mode fluorescence responses in detection of bacterial pathogens, which will arouse more attention to discover more molecular probes for bacterial imaging and diagnosis. Furthermore, this study greatly expanded the applications of TADF fluorophores in time-resolved biological imaging.

关键词： Dual-mode detection bacterial pathogens ribosomal rna thermally activated delayed fluorescence time-resolved fluorescence imaging

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