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Complete genome analysis of Ketogulonigenium sp. WB0104

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chinese Science Bulletin 2006年第8期51卷 941-945页

作者： YANG Fan JIA Qian XIONG Zhaohui ZHANG Xiaobing WU Hongtao ZHAO Ying YANG Jian ZHU Junping DONG Jie XUE Ying SUN Lilian SHEN Yan JIN Qi State Key Laboratory for Molecular Virology and Genetic Engineering Beijing 100176 China North China Pharmaceutical Group Corporation Shijiazhuang 050015 China chinese national human genome center Beijing 100176 China

Ketogulonigenium sp. may convert L-sorbose into 2-keto-L-gulonic acid, the vitamin C precursor. The genome of Ketogulonigenium sp. WB0104 consists of a circular 2765030 bp chromo- some with 61.69% G+C content and two circular plasmids of 267968 and 242707 bp. The genome contains 2727 open reading frames (ORFs). The systems of replication, transcription, translation, carbohydrate and energy metabolism are intact, but the repair system is incomplete. About 640 predicted ORFs have been found to encode transporter pro- teins, which account for about one fourth of total predicted ORFs, noticeably higher than other docu- mented bacteria. This may be due to the fact that WB0104 adapts to soil circumstance.

关键词：基因分析山梨糖维生素C 染色体

The genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 578-583页

作者： Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang Anke Wang Lili Dong Zhewen Zhang Caixia Yu Yanling Sun Lianjiang Chi Huanxin Chen Shuang Zhai Yubin Sun Li Lan Xin Zhang Jingfa Xiao Yiming Bao Yanqing Wang Zhang Zhang Wenming Zhao China national center for Bioinformation Beijing 100101China national Genomics Data center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of chinese Academy of Sciences Beijing 100049China

The genome Sequence Archive(GSA)is a data repository for archiving raw sequence data,which provides data storage and sharing services for worldwide scientific *** explosive data growth with diverse data types,here we present the GSA family by expanding into a set of resources for raw data archive with different purposes,namely,GSA(https://***/gsa/),GSA for human(GSA-human,https://***/gsa-human/),and Open Archive for Miscellaneous Data(OMIX,https://***/omix/).Compared with the 2017 version,GSA has been significantly updated in data model,online functionalities,and web ***-human,as a new partner of GSA,is a data repository specialized in human genetics-related data with controlled access and ***,as a critical complement to the two resources mentioned above,is an open archive for miscellaneous ***,all these resources form a family of resources dedicated to archiving explosive data with diverse types,accepting data submissions from all over the world,and providing free open access to all publicly available data in support of worldwide research activities.

关键词： genome Sequence Archive GSA GSA-human OMIX

Understanding the battery safety improvement enabled by a quasi-solid-state battery design

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chinese Physics B 2022年第11期31卷 36-41页

作者： Luyu Gan Rusong Chen Xiqian Yu Hong Li beijing Advanced Innovation center for Materials genome Engineering Institute of PhysicsChinese Academy of SciencesBeijing 100190China center of Materials Science and Optoelectronics Engineering University of Chinese Academy of SciencesBeijing 100049China beijing Frontier Research center on Clean Energy Huairou DivisionInstitute of PhysicsChinese Academy of SciencesBeijing 101400China

The rapid development of lithium-ion batteries(LIBs)is faced with challenge of its safety bottleneck,calling for design and chemistry *** the proposed strategies,the development of solid-state batteries(SSBs)seems the most promising solution,but to date no practical SSB has been in large-scale *** safety performance of SSBs is also *** this article,a brief review on LIB safety issue is made and the safety short boards of LIBs are emphasized.A systematic safety design in quasi-SSB chemistry is proposed to conquer the intrinsic safety weak points of LIBs and the effects are accessed based on existing *** is believed that a systematic and targeted solution in SSB chemistry design can effectively improve the battery safety,promoting larger-scale application of LIBs.

关键词： battery safety thermodynamics kinetics solid-state batteries

Recent progress in 8igenomic research of liver cancer

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Science China(Life Sciences) 2009年第1期52卷 24-30页

作者： HAN ZeGuang Shanghai-MOST Key Laboratory for Disease and Health Genomics,chinese national human genome center at Shanghai,Shanghai 201203,China 1. Shanghai-MOST Key Laboratory for Disease and Health Genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

Along the course of occurrence and development of liver cancer,the corresponding somatic cells accumulate some important genetic *** variations may be divided into two *** the genetic changes closely related to etiology of liver cancer,the well-known cases include insertion and integration of the hepatitis B virus(HBV) DNA after infection,and mutations at site 249 of the tumor suppressor gene p53 induced by exposure to aflatoxin *** secondary genetic changes include amplification and deletion of certain chromosome regions,mutations in p53 at the sites other than 249,as well as the mutational activation of the Wnt/β-catenin signal *** tumor cells with these genetic variations may gradually become the dominant clones under evolutionary ***,identification of genetic susceptible against risk of liver malignancy is also an important aspect of research in this field.

关键词： hepatocellular carcinoma chromosomal instability gene mutation oncogene tumor suppressor gene

Tangled but ordered human mitochondrial tRNA maturation

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Science China Life Sciences 2025年

作者： Shi-Ying Yao Xiao-Long Zhou Key Laboratory of RNA Innovation Science and Engineering CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory of Systems Health Science of Zhejiang Province School of Life Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences

Mitochondria are cellular organelles that originate from an endosymbiotic bacterial ancestor and are primarily responsible for ATP generation via oxidative phosphorylation (OXPHOS). OXPHOS is conducted by five mitochondrial respiratory complexes in the inner mitochondrial membrane. human mitochondria possess a distinct genome, a small, circular, doublestranded DNA (mtDNA) of 16,569 base pairs.

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Genomic structure of metabotropic glutamate receptor 7 and comparison of genomic structures of extracellular domains of mGluR family

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chinese Science Bulletin 2002年第16期47卷 1330-1336页

作者： Qingfa Wu Wei Dong Xiaohua Qi Weidong Bao Yuxin Niu Yiling Zhang Haiqing Zhang Chong Chen Bin Liu Songnian Hu et al. chinese Acad Sci Inst Genet Beijing Gen Inst Ctr Human Genome Beijing 100101 Peoples R China

Metabotropic glutamate receptor 7, coupled with a chemical neurotransmitter L-glutamate, plays an important role in the development of many psychiatric and neurological disorders. To study the biological and genetic mechanism of the mGluR7-related diseases, a physical map covering the full-length mGluR7 genomic sequence has been constructed through seed clone screening and fingerprinting database searching. These BAC clones in the physical map have been sequenced with shotgun strategy and assembled by Phred-Phrap-Consed software; the error rate of the final genoniic sequence is less than 0.01%. mGluR7 spans 880 kb genoniic region, the GC content and repeat content of mGluR7 genoniic sequence are 38% and 37.5% respectively. mGluR7 has a typical 'house-keeping' promoter and consists of 11 exons, with introns ranging from 6 kb to 285 kb. mGluR7a and mGluR7b are two known alternatively splicing variants. Comparing the genomic structures of extracellular domains of mGluR family, their genomic structures can

关键词： metabotropic glutamate receptor physical map genome exon intron extracellular domain.

Identification and Analysis of Genes Present in Leptospira interrogans serovar lai but Absent in L. biflexa serovar monvalerio

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 832-839页

作者： Ping HE, Xiang-Yan ZHANG, Xiao-Kui GUO*, Bao-Yu HU, Xiao-Tian HUANG, Yang YANG, and Guo-Ping ZHAO1,2* Department of Microbiology and Parasitology, Shanghai Second Medical University, Shanghai 200025, China 1 Research center of Biotechnology, Institutes for Biological Sciences, chinese Academy of Sciences, Shanghai 200031, China 2chinese national human genome center at Shanghai, Zhangjiang High Tech Park, Shanghai 201203, China Department of Microbiology and Parasitology Shanghai Second Medical UniversityShanghai 200025 China Research center of Biotechnology Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200031 China chinese national human genome center at ShanghaiZhangjiang High Tech Park Shanghai 201203 China

Genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogans serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 24 contained the tester strain specific genomic regions, of which, 5 were non-coding fragments while the others contained 23 distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12 genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridiza- tion is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.

关键词： Leptospira interrogans serovar lai suppression subtractive hybridization (SSH) specific genes

An online coronavirus analysis platform from the national Genomics Data center

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Zoological Research 2020年第6期41卷 705-708页

作者： Zheng Gong Jun-Wei Zhu Cui-Ping Li Shuai Jiang Li-Na Ma Bi-Xia Tang Dong Zou Mei-Li Chen Yu-Bin Sun Shu-Hui Song Zhang Zhang Jing-Fa Xiao Yong-Biao Xue Yi-Ming Bao Zheng-Lin Du Wen-Ming Zhao China national center for Bioinformation&national Genomics Data center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of chinese Academy of Sciences Beijing 100049China

DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 countries and regions *** continued research progress and virus detection,SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate.

关键词： acute respiratory continued

Toward A New Paradigm of Genomics Research——Celebration of the 20th Anniversary of beijing Institute of Genomics

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 904-909页

作者： Zhang Zhang Songnian Hu Jun Yu national Genomics Data center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of chinese Academy of Sciences Beijing 100049China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Twenty years after the completion and forty years after the proposal of the human genome Project(HGP),genomics,together with its twin field-bioinformatics,has entered a new paradigm,where its bioscience-related,discipline-centric applications have been creating many new research *** Institute of Genomics(BIG),now also known as China national center for Bioinformation(CNCB),will play key roles in supporting and participating in these frontier research *** the 20th anniversary of the establishment of BIG,we provide a brief retrospective of its historic events and ascertain strategic research directions with a broader vision for future genomics,where digital genome,digital medicine,and digital health are so structured to meet the needs of human life and healthcare,as well as their related metaverses.

关键词： Genomics Bioinformatics BIG CNCB NGDC