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| 1 | The lifestyle transition of Arthrobotrys oligospora is mediated by microRNA-like RNAs显示文摘The lifestyle transition of fungi,defined as switching from taking organic material as nutrients to pathogens,is a fundamental phenomenon in nature.However,the mechanisms of such transition remain largely unknown.Here we show microRNA-like RNAs(milRNAs)play a key role in fungal lifestyle transition for the first time.We identified milRNAs by small RNA sequencing in Arthrobotrys oligospora,a known nematode-trapping fungus.Among them,7 highly expressed milRNAs were confirmed by northern-blot analysis.Knocking out two milRNAs significantly decreased A.oligospora’s ability to switch lifestyles.We further identified that two of these milRNAs were associated with argonaute protein QDE-2 by RNA-immunoprecipitation(RIP)analysis.Three of the predicted target genes of milRNAs were found in immunoprecipitation(IP)products of QDE-2.Disruption of argonaute gene qde-2 also led to serious defects in lifestyle transition.Interestingly,knocking out individual milRNAs or qde-2 lead to diverse responses under different conditions,and qde-2 itself may be targeted by the milRNAs.Collectively,it indicates the lifestyle transition of fungi is mediated by milRNAs through RNA interference(RNAi)machinery,revealing the wide existence of miRNAs in fungi kingdom and providing new insights into understanding the adaptation of fungi from scavengers to predators and the mechanisms underlying fungal infections. | Xinglai Ji Heng Li Weihua Zhang Jiai Wang Lianming Liang Chenggang Zou Zefen Yu Shuqun Liu Ke-Qin Zhang | 2020 | Science China(Life Sciences)2020，63，4： | 4 |
| 2 | Bioinformatical study on the proteomics and evolution of SARS-CoV显示文摘A novel coronavirus has been identified as the causative agent of the severe acute respiratory syndrome(SARS). For all the SARS-CoV associated proteins derivatedfrom the SARS-CoV genome, the physiochemical propertiessuch as the molecular weight, isoelectric point and extinction coefficient of each protein were calculated. Thetransmembrane segments and subcellular localization(SubLocation) prediction and conserved protein motifssearch against database were employed to analyze thefunction of SARS-CoV proteins. Also, the homology protein sequence alignment and evolutionary distance matrixcalculation between SARS-CoV associated proteins and the corresponding proteins of other coronaviruses wereemployed to identify the classification and phylogeneticrelationship between SARS-CoV and other coronaviruses.The results showed that SARS-CoV is a novel coronavirus which is different from any of the three previously knowngroups of coronviruses, but it is closer to BoCoV and MHV than to other coronaviruses. This study is in aid ofexperimental determination of SARS-CoV proteomics andthe development of antiviral vaccine. | LIU Shuqun*, GUO Tao*, JI Xinglai & SUN Zhirong Institute of Bioinformatics, Department of Biological Sciences andBiotechnology, Tsinghua University, Beijing 100084, China * The two authors contributed equally to this work. Correspondence should be addressed to Sun Zhirong (e-mail: sunzhr @mail.tsinghua.edu.cn) | 2003 | Chinese Science Bulletin2003，48，13： | 1 |
| 3 | Mining gene expression data using a novel approach based on hidden Markov models显示文摘 | Ji Xinglai Li Ling Sun Zhirong | 2008 | Evolutionary Computation Journal2008，56，1： | 1 |
| 4 | A new method of research on molecular evolution of proteinase superfamily显示文摘The molecular evolutionary tree, also known as a phylogenetic tree, of the serine proteinase superfamily was constructed by means of structural alignment. Three-dimensional structures of proteins were aligned by the SSAP program of Orengo and Taylor to obtain evolutionary distances. The resulting evolutionary tree provides a topology graph that can reflect the evolution of structure and function of homology proteinase. Moreover, study on evolution of the serine proteinase superfamily can lead to better understanding of the relationship and evolutionary difference among proteins of the superfamily, and is of significance to protein engineering, molecular design and protein structure prediction. Structure alignment is one of the useful methods of research on molecular evolution of protein. | SUN Zhirong JI Xinglai HU Shengmin WANG Yu HE Fuchu | 2001 | Chinese Science Bulletin2001，46，7： | 1 |
| 5 | Digital gene expression profiling analysis of DNA repair pathways in colon cancer stem population of HT29 cells显示文摘癌症干细胞(CSC ) 贡献新瘤损害的恶化和发展。当很可得到的临床的途径例如化学药品和放射治疗,将杀死癌症房间的多数时,他们都不杀死他们。一些抵抗房间象 CSC 一样,能由于他们的优秀自我维持的能力幸存,甚至在挑战性的环境。在现在的学习,我们响应单个海滨的损坏和双海滨从 HT29 房间线调查了冒号 CSC 的 DNA 修理基因的 mRNA 水平裂缝,以及在基础切除的关键基因的明显的 upregulation 修理,失配修理,非相应加入结束,并且在这些房间的相应再结合小径。数字基因表示分析在可以在 DNA 修理起重要作用的 CD44 + HT29 房间识别了 upregulated 基因。我们的结果表明冒号 CSC 忍受有效 DNA 修理能力,它可能在重复化学药品和放射治疗以后解释冒号 CSC 的幸存。 | Wenxue Wang Guoxiu Zhang Jing Yang Huan Gu Lei Ding Haijing Yu Min Yu Qinghua Cui Xinglai Ji Meizhang Li | 2017 | Acta Biochimica et Biophysica Sinica2017，49，1： | 1 |
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