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CircAST:full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs

Genomics, Proteomics & Bioinformatics 2019年第5期17卷 522-534页

作者： Jing Wu Yan Li Cheng Wang Yiqiang Cui Tianyi Xu Chang Wang Xiao Wang Jiahao Sha Bin Jiang Kai Wang Zhibin Hu Xuejiang Guo Xiaofeng Song Department of Biomedical Engineering Nanjing University of Aeronautics and AstronauticsNanjing 211106China School of Biomedical Engineering and Informatics Nanjing Medical UniversityNanjing 211166China State Key Laboratory of Reproductive Medicine Nanjing Medical UniversityNanjing 211166China Center of Pathology and Clinical Laboratory Sir Run Run HospitalNanjing Medical UniversityNanjing 211166China Center for Cellular and Molecular Therapeutic Children’s Hospital of PhiladelphiaPhiladelphiaPA 19104USA

Circular RNAs(circ RNAs),covalently closed continuous RNA loops,are generated from cognate linear RNAs through back splicing events,and alternative splicing events may generate different circ RNA isoforms at the same locus.However,the challenges of reconstruction and quantification of alternatively spliced full-length circ RNAs remain unresolved.On the basis of the internal structural characteristics of circ RNAs,we developed Circ AST,a tool to assemble alternatively spliced circ RNA transcripts and estimate their expression by using multiple splice graphs.Simulation studies showed that Circ AST correctly assembled the full sequences of circ RNAs with a sensitivity of 85.63%–94.32%and a precision of 81.96%–87.55%.By assigning reads to specific isoforms,Circ AST quantified the expression of circ RNA isoforms with correlation coefficients of 0.85–0.99 between theoretical and estimated values.We evaluated Circ AST on an in-house mouse testis RNA-seq dataset with RNase R treatment for enriching circ RNAs and identified 380 circ RNAs with full-length sequences different from those of their corresponding cognate linear RNAs.RT-PCR and Sanger sequencing analyses validated 32 out of 37 randomly selected isoforms,thus further indicating the good performance of Circ AST,especially for isoforms with low abundance.We also applied Circ AST to published experimental data and observed substantial diversity in circular transcripts across samples,thus suggesting that circ RNA expression is highly regulated.Circ AST can be accessed freely at https://***/xiaofengsong/CircAST.

关键词： Circular RNA full-length reconstruction Isoform quantification Multiple splice graph model Transcriptome

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Effects of dendritic cells transfected with full length wild-type p53 and modified by bile duct cancer lysates on immune response

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Hepatobiliary & Pancreatic Diseases International 2005年第1期4卷 121-125页

作者： HuaWen Sun QiBing Tang Chong Tang ShengQuan Zou Department of General Surgery Renmin Hospital Wuhan University Wuhan 430060 China. sxshwyq@***

BACKGROUND:Dendritic cells (DCs) are the most potent antigen-presenting cells and are actively used in cancer immunotherapy. Wild-type p53 can be recognized as an antigen and can induce specific cytotoxic T lymphocytes (CTLs) in the host body. The aim of this study was to investigate the effects of DCs transfected with full length wild-type p53 and modified by bile duct lysates on immune response.;METHODS:The wild-type p53 was transducted to DCs with adenovirus, which were modified by bile duct lysates (Lywtp53DC). The concentration of the surface molecules (B7-1, B7-2, MHC-I, MHC-II) of all DCs was detected with fluorescence activated cell sorter (FACS), and the ability of the DCs to induce efficient and specific immunological response in anti-(51)Cr-labeled target cells was studied. BALB/c mice infected with the DCs and QBC939 were used. CTL response in mice immunized with Lywtp53DC and treatment of tumor-bearing mice with Lywtp53DC and CTL response in these mice were studied.;RESULTS:The surface molecules of Lywtp53DC had a high expression B7-1 (86.70%+/-0.07%), B7-2 (18.77%+/-0.08%), MHC-I(87.20%+/-0.05%), MHC-II(56.70%+/-0.07%) with FACS. The T lymphocytes had a specific CTL lysing ability induced by Lywtp53DC, with a CTL lysis rate of 81%. The immune protection of Lywtp53DC group was obvious, and the tumor diameter of the Lywtp53DC group was 3.10+/-0.31 mm, 2.73+/-0.23 mm, 3.70+/-0.07 mm on days 13, 16 and 19, smaller than those of any control groups (P<0.05), DC, wtp53DC and LyDC. On the other hand, the growth rate of tumor of the Lywtp53DC group was slower than that of any other groups (P<0.05).;CONCLUSIONS:Dendritic cells transfected with wild-type p53 and modified by bile duct lysates have specific CTL killing capability.

关键词： lysate bile duct cancer dendritic cells full-length wild-type p53 lymphocytes

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斯黛西·阿莱莫:《暴露:后人类时代的环境政治与欢愉》,双子城:明尼苏达大学出版社,2016年版,252页（英文）

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国际比较文学（中英文） 2018年第2期1卷 328-330页

作者：罗艾琳 Tamkang University

In Stacy Alaimo's latest full-length study,Exposed:Environmental Politics and Pleasures in Posthuman Times,Alaimo continues her interests in ecofeminism and material ecocriticism and expands that to include posthumanism.The author of an early important ecofeminist study entitled Undomesticated Grounds(2000)(in which she reappraised the ideological ties between women and the so-called natural world that were being denigrated by other poststructuralist thinkers),Alaimo catapulted to become a major force in ecocriticism and the environmental humanities at large with her term transcorporeality.Now a keyword in ecocriticism,trans-corporeality fi rst gained widespread attention in Alaimo and Susan Hekman's edited anthology,Material Feminisms(2008)and Alaimo's monograph Bodily Natures(2010).

关键词： Stacy Alaimo's latest full-length study

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construction and Analysis of Silkworm Pupa (Bombyx mori) cDNA Library

construction and Analysis of Silkworm Pupa (Bombyx mori) cDN...

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浙江省生物化学与分子生物学学术交流会

作者： Yaozhou Zhang, Jian Chen, Zhengbing Lv, Zuoming Nie, Caiying Jiang, Lili Liu, Dan Wang, Yulan Lou, Fukun Zhao, Xiangfu Wu and Genjun Xu Institute of Biochemisty, Zhejiang Sci-Tech University, Hangzhou 310018,China

A cDNA library was constructed from whole silkworm pupae (Bombyx mori) and 1500 clones were randomly selected for sequencing to reveal the gene expression profile of the pupae phase. The general cDNA

关键词： Bombyx mori cDNA construction ORF full-length

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