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An automated approach for global identification of srna-encoding regions in rna-Seq data from Mycobacterium tuberculosis

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生物化学与生物物理学报（英文版） 2016年第6期48卷 544-553页

作者： Ming Wang Joy Fleming Zihui Li Chuanyou Li Hongtai Zhang Yunxin Xue Maoshan Chen Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China Beijing Chest Hospital Capital Medical University Beijing 101149 China BGI-Shenzhen Shenzhen 518083China

Deep-sequencing of bacterial transcriptomes using rna-Seq technology has made it possible to identify small non-coding rnas,rna molecules which regulate gene expression in response to changing environments, on a genome-wide scale in an ever-increasingrange of prokaryotes. However, a simple and reliable automated method for identifying srna candidates in these large datasetsis lacking. Here, after generating a transcriptome from an exponential phase culture of Mycobacterium tuberculosis H37Rv, we developed and validated an automated method for the genome-wide identification of srna candidate-containing regionswithin rna-Seq datasets based on the analysis of the characteristics of reads coverage maps. We identified 192 novel candidatesrna-encoding regions in intergenic regions?and 664 rna transcripts transcribed from regions antisense (as) to open readingframes (ORF), which bear the characteristics of asrnas, and validated 28 of these novel srna-encoding regions by northernblotting. Our work has not only provided a simple automated method for genome-wide identification of candidate srna-encodingregions in rna-Seq data, but has also uncovered many novel candidate srna-encoding regions in M. tuberculosis, reinforcing the view that the control of gene expression in bacteria is more complex than previously anticipated.

关键词： rna-Seq transcriptome non-coding rna Mycobacterium tuberculosis

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Author Correction: Tuning microtubule dynamics to enhance cancer therapy by modulating FER-mediated CRMP2 phosphorylation

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Nature communications 2022年第1期13卷 3352页

作者： Yiyan Zheng Ritika Sethi Lingegowda S Mangala Charlotte Taylor Juliet Goldsmith Ming Wang Kenta Masuda Eli M Carrami David Mannion Fabrizio Miranda Sandra Herrero-Gonzalez Karin Hellner Fiona Chen Abdulkhaliq Alsaadi Ashwag Albukhari Donatien Chedom Fotso Christopher Yau Dahai Jiang Sunila Pradeep Cristian Rodriguez-Aguayo Gabriel Lopez-Berestein Stefan Knapp Nathanael S Gray Leticia Campo Kevin A Myers Sunanda Dhar David Ferguson Robert C Bast Anil K Sood Frank von Delft Ahmed Ashour Ahmed Ovarian Cancer Cell Laboratory Weatherall Institute of Molecular Medicine University of Oxford Headington Oxford OX3 9DS UK. Nuffield Department of Obstetrics & Gynaecology University of Oxford Women's Centre John Radcliffe Hospital Oxford OX3 9DU UK. Structural Genomics Consortium Nuffield Department of Medicine University of Oxford Old Road Campus Research Building Oxford OX3 7DQ UK. Department of Gynecologic Oncology The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd Houston TX 77030 USA. Center for RNAi and Non-Coding RNA The University of Texas MD Anderson Cancer Center 1515 Holcombe Blvd Houston TX 77030 USA. Biochemistry Department Faculty of Science King Abdulaziz University Jeddah 21551 Saudi Arabia. Wellcome Trust Centre for Human Genetics and NIHR Biomedical Research Centre Roosevelt Drive Oxford OX3 7BN UK. Department of Statistics 1 South Parks Road Oxford OX1 3TG UK. Department of Experimental Therapeutics University of Texas MD Anderson Cancer Center Houston TX USA. Goethe-University Frankfurt Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences Riedberg Campus Frankfurt am Main 60438 Germany. Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA 02115 USA. Department of Cancer Biology Dana-Farber Cancer Institute Boston MA 02215 USA. Department of Oncology University of Oxford Old Road Campus Research Building Roosevelt Drive Oxford OX3 7DQ UK. Department of Histopathology Oxford University Hospitals Oxford OX3 9DU UK. Nuffield Division of Clinical Laboratory Sciences Radcliffe Department of Medicine University of Oxford Oxford University Hospitals Oxford UK. Diamond Light Source Ltd Harwell Science and Innovation Campus Didcot OX11 0QX UK. Department of Biochemistry University of Johannesburg Auckland Park 2006 South Africa. Ovarian Cancer Cell Laboratory Weatherall Institute of Molecular Medicine University of Oxford Headingt

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Dissemination of mupirocin resistance among Staphylococcus aureus clinical isolates

Dissemination of mupirocin resistance among Staphylococcus a...

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第十一届西南三省一市生物化学与分子生物学学术研讨会

作者： Xingmei Liu Jinwei Huang Yaling Huang Yu Zhang Qin Yan Yanhong Wang Baodong Ling Xu Jia Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province Chengdu Medical College Cheng Institute of Antibiotics the Fifth Affiliated Hospital Wenzhou Medical University Lishui 323000 Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province Chengdu Medical College Cheng Small Molecule Drugs Key Laboratory of Sichuan Province Institute of Materia Medica Chengdu Medica

Objective: The reports of mupirocin resistance among *** in China are ***, this study aims to study the relationship between the resistance to mupiroc in and genetic relatedness of *** strains isolated from a China Te... 详细信息

关键词： Staphylococcus aureus Mupirocin Resistance Resistance determinants Molecular characteristic

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Bayesian localization microscopy based on intensity distribution of fluorophores

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Protein & Cell 2015年第3期6卷 211-220页

作者： Fan Xu Mingshu Zhang Zhiyong Liu Pingyong Xu Fa Zhang Key Lab of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China University of Chinese Academy of Sciences Beijing 100049 China Laboratory of Non Coding RNA Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

Super-resolution microscopy techniques have overcome the limit of optical diffraction. Recently, the Bayesian analysis of Bleaching and Blinking data （3B） method has emerged as an important tool to obtain super-resolution fluorescence images. 3B uses the change in information caused by adding or removing fiuorophores in the cell to fit the date. When adding a new fluorophore, 3B selects a random initial position, optimizes this position and then determines its reliability. However, the fluorophores are not evenly distributed in the entire image region, and the fluorescence intensilty at a given position positively correlates with the probability of observing a fluorophore at this position. In this paper, we present a Bayesian analysis of Bleaching and Blinking microscopy method based on fluorescence intensity distribution （FID3B）. We utilize the intensity distribution to select more reliable positions as the initial positions of fluorophores. This approach can improve the reconstruction results and significantly reduce the computational time. We validate the perfor. mance of our method using both simulated date and experimental date from cellular structures. The results confirm the effectiveness of our method.

关键词： super-resolution fluorescence image 3B,intensity distribution

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OUGENE： a disease associated over-expressed and under-expressed gene database

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Science Bulletin 2016年第10期61卷 752-754页

作者： Xiaoyong Pan Hong-Bin Shen Section for Animal Genetics Bioinformatics and Breeding Center for Non-Coding RNA in Technology and Health University of Copenhagen 1870 Frederiksberg Denmark Department of Disease Systems Biology Novo NordiskFoundation Center for Protein Research University ofCopenhagen 1870 Frederiksberg Denmark Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai 200240 China

Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available to provide the association information between gene over- or under-expression and various diseases. In this study, we presented a comprehensive disease-associated over- and under-expressed gene database （OUGene） based on our proposed text mining pipeline and several open curated databases. It contains total 41,269 unique associa- tions between 7,238 over- or under-expressed genes and 1,480 diseases, which are supported by 81,974 evidence sentences from 56,442 articles. The OUGene is compre- hensive and covers most important therapeutic areas. Meanwhile a new scoring system is designed to rank the associations based on benchmarking against hand-curated data. OUGene provides an easy-of-use web interface for researchers to analyze these data and visualize the associ- ated networks, which can give insights to the complex relationships between over- and under-expressed genes and diseases at a system level. It is available at ***. ***/bioinf/OUGene/.

关键词： Text mining Gene over- and under-expression Disease Database

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Publisher Correction: Regulation of cellular sterol homeostasis by the oxygen responsive noncoding rna lincNORS

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Nature communications 2020年第1期11卷 5737页

作者： Xue Wu Cristina M Niculite Mihai Bogdan Preda Annalisa Rossi Toma Tebaldi Elena Butoi Mattie K White Oana M Tudoran Daniela N Petrusca Amber S Jannasch William P Bone Xingyue Zong Fang Fang Alexandrina Burlacu Michelle T Paulsen Brad A Hancock George E Sandusky Sumegha Mitra Melissa L Fishel Aaron Buechlein Cristina Ivan Spyros Oikonomopoulos Myriam Gorospe Amber Mosley Milan Radovich Utpal P Davé Jiannis Ragoussis Kenneth P Nephew Bernard Mari Alan McIntyre Heiko Konig Mats Ljungman Diana L Cousminer Paolo Macchi Mircea Ivan Department of Microbiology and Immunology Indiana University School of Medicine Indianapolis IN 46202 USA. Department of Medicine Indiana University School of Medicine Indianapolis IN 46202 USA. "Victor Babes" National Institute of Pathology Bucharest Romania. Institute of Cellular Biology and Pathology "Nicolae Simionescu" Bucharest Romania. Laboratory of Molecular and Cellular Neurobiology Department of Cellular Computational and Integrative Biology-CIBIO University of Trento Trento Italy. Laboratory of Translational Genomics Department of Cellular Computational and Integrative Biology-CIBIO University of Trento Trento Italy. Yale Cancer Center Yale University School of Medicine New Haven CT 06520 USA. The Oncology Institute "Prof Dr. Ion Chiricuta" Cluj-Napoca Romania. Metabolite Profiling Facility Bindley Bioscience Center Purdue University West Lafayette IN 47907 USA. Department of Genetics Department of Systems Pharmacology and Translational Therapeutics Institute of Translational Medicine and Therapeutics Perelman School of Medicine University of Pennsylvania Philadelphia PA 19104 USA. Department of Cellular and Integrative Physiology Indiana University School of Medicine Indianapolis IN USA. Departments of Radiation Oncology and Environmental Health Sciences Center for RNA Biomedicine University of Michigan Ann Arbor MI 48109 USA. Department of Surgery Indiana University School of Medicine Indianapolis IN 46202 USA. Department of Pathology and Laboratory Medicine Indiana University School of Medicine Indianapolis IN 46202 USA. Melvin and Bren Simon Cancer Center Indiana University Indianapolis IN USA. Department of Obstetrics and Gynecology Indiana University School of Medicine Indianapolis IN 46202 USA. Department of Pharmacology and Toxicology Department of Pediatrics Wells Center for Pediatric Research Indiana University School of Medicine Indianapolis IN 46202 USA. Indiana University Center for Genomics and Bioinformatics

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Molecular Characterization of Reduced Susceptibility to Biocides in Acinetobacter baumannii

Molecular Characterization of Reduced Susceptibility to Bioc...

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第十一届西南三省一市生物化学与分子生物学学术研讨会

作者： Fei Lin Ying Xu Yaowen Chang Chao Liu Xu Jia Baodong Ling Small Molecule Drugs Key Laboratory of Sichuan Province Institute of Materia Medica Chengdu Medica Clinical Laboratory the First Affiliated Hospital Chengdu Medical College Chengdu Sichuan China Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province Chengdu Medical College Cheng Small Molecule Drugs Key Laboratory of Sichuan Province Institute of Materia Medica Chengdu Medica

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Crystal structure of E. coli arginyl-trna synthetase and ligand binding studies revealed key residues in arginine recognition

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Protein & Cell 2014年第2期5卷 151-159页

作者： Kelei Bi Yueting Zheng Feng G"ao Jianshu Dong Jiangyun Wang Yi Wang Weimin Gong Laboratory of Non-coding RNA Institute of Biophysics Chinese Academy of Sciences

The arginyl-trna synthetase(ArgRS) catalyzes the esterification reaction between L-arginine and its cognate trnaArg. Previously reported structures of ArgRS shed considerable light on the trna recognition mechanism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli ArgRS(eArgRS) complexed with L-arginine, and a series of mutational studies using isothermal titration calorimetry(ITC). Combined with previously reported work on ArgRS, our results elucidated the structural and functional roles of a series of important residues in the active site, which furthered our understanding of this unique enzyme.

关键词： arginyl-trna synthetase amino acyl-trna synthetase isothermal titration calorimetry site-directed mutation X-ray crystal structure E. coli

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Crystal structure of E. synthetase and ligand revealed key residues coil arglnyl-trna binding studies in arginine recognition

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Protein & Cell 2014年第2期5卷 151-159页

作者： Kelei Bi Yueting Zheng Feng Gao Jianshu Dong Jiangyun Wang Yi Wang Weimin Gong Laboratory of Non-coding RNA Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

The arginyl-trna synthetase （ArgRS） catalyzes the esterification reaction between L-arginine and its cog- nate trnaArg. Previously reported structures of ArgRS shed considerable light on the trna recognition mech- anism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli ArgRS （eArgRS） complexed with L-arginine, and a series of mutational studies using isothermal titration calorimetry （ITC）. Combined with previously reported work on ArgRS, our results eluci- dated the structural and functional roles of a series of important residues in the active site, which furthered our understanding of this unique enzyme.

关键词： arginyl-trna synthetase amino acyl-trnasynthetase isothermal titration calorimetry site-directedmutation X-ray crystal structure E. coil

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Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy

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Protein & Cell 2014年第10期5卷 770-782页

作者： Derong Xu Guifeng Wei Ping Lu Jianjun Luo Xiaomin Chen Geir Skogerbo Runsheng Chen Laboratory of Non-coding RNA Institute of Biophysics University of Chinese Academy of Sciences Beijing 100101 China Graduate University of Chinese Academy of Sciences Beijing 100080 China Key Laboratory of Forest Protection State Forestry Administration/Research Institute of Forest Ecology Environment andProtection Chinese Academy of Forestry Beijing 100091 China

In recent years, large numbers of non-coding rnas （ncR- NAs） have been identified in C. elegans but their functions are still not well studied. In C. elegans, CEP-1 is the sole homolog of the p53 family of genes. In order to obtain transcription profiles of ncrnas regulated by CEP-1 under normal and UV stressed conditions, we applied the ＇not-so- random＇ hexamers priming strategy to rna sequencing in C. elegans, This NSR-seq strategy efficiently depleted rrna transcripts from the samples and showed high technical replicability. We identified more than 1,000 ncR- NAs whose apparent expression was repressed by CEP-1, while around 200 were activated. Around 40% of the CEP-1 activated ncrnas promoters contain a putative CEP-1- binding site. CEP-1 regulated ncrnas were frequently clustered and concentrated on the X chromosome. These results indicate that numerous ncrnas are involved in CEP-1 transcriptional network and that these are espe- cially enriched on the X chromosome in C. elegans.

关键词： p53/CEP-1 C. elegans ncrna removalrrna NSR-seq high technical replicability

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