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3D Genome Tuner:Compare Multiple Circular Genomes in a 3D Context

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Genomics, Proteomics & Bioinformatics 2009年第3期7卷 143-146页

作者： Qi Wang Qun Liang xiuqing zhang Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China Beijing Genomics Institute at Shenzhen Shenzhen 518083 China

Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not offer feature-based comparison. For remedying these shortcomings, we developed 3D Genome Tuner,a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D space offers great benefits to the study of comparative genomics. The program is freely available （under an LGPL licence） at http：//***/projects/dgenometuner.

关键词： three dimensional circular map genome browser comparative genomics

GNL-Scorer: a generalized model for predicting CRISPR on-target activity by machine learning and featurization

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Journal of Molecular Cell Biology 2020年第11期12卷 909-911页

作者： Jun Wang Xi Xiang Lars Bolund xiuqing zhang Lixin Cheng Yonglun Luo BGI Education Center University of Chinese Academy of SciencesShenzhenChina Department of Critical Care Medicine Shenzhen People’s HospitalThe Second Clinical Medicine College of jinan UniversityShenzhenChina BGI-Shenzhen ShenzhenChina Lars Bolund Institute of Regenerative Medicine BGI-QingdaoBGI-ShenzhenQingdaoChina Department of Biomedicine Aarhus UniversityDenmark

CRISPR/Cas9 is an adaptive immunity system in bacteria and most archaea(Koonin and Makarova,2009;Horvath and Barrangou,2010).The CRISPR/Cas9 gene editing system is comprised of two key components,a small guide RNA(gRN... 详细信息

关键词： Cas9 CRISPR

High-performance single-chip exon capture allows accurate whole exome sequencing using the Illumina Genome Analyzer

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Science China(Life Sciences) 2011年第10期54卷 945-952页

作者： JIANG Tao YANG Lei JIANG Hui TIAN Geng zhang xiuqing Beijing Genomics Institute Shenzhen 518000 China Beijing Institute of Genomics Chinese Academy of Sciences Beijing 101300 China Graduate University of Chinese Academy of Sciences Beijing 100062 China

Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) *** protocol involves two-stage library *** specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of *** of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative *** protocol is also well suited for use with whole genome amplified *** results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.

关键词： whole exome sequencing exon capture SNP detection indel detection high-throughput resequencing

A legacy of the “1% program”-The “Chinese Chapter” of the human genome reference sequence

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Journal of Genetics and Genomics 2018年第11期45卷 565-568页

作者： Wei Dong Xiaoling Wang Zhi Xia xiuqing zhang Huanming Yang BGI-Shenzhen

The year of 2018 marks the 65th anniversary of the discovery of DNA double helix and the 15th anniversary of the successful completion of the international Human Genome Project (HGP),the two revolutions in life sciences (Sharp, 2014). The year also sees the effective implementation of the "1%Program", the Chinese contribution to the reference sequence of the human genome,which coincides with the 40th anniversary of the founding of the Genetics Society of China, one of the most influential national academic organizations in China.

关键词： of the human genome reference sequence A legacy of the Chinese Chapter The program HGP

Retention Mechanism of Phenolic Compounds in Subcritical Water Chromatography

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Chemical Research in Chinese Universities 2015年第1期31卷 103-106页

作者： WUYichao DENG xiuqing MAO Yinchun zhang Yan LIU Jiaqin RONG Li XU Zhihong School of Physics and Chemistry Xihua University Chengdu 610039 P. R. China

The transfer enthalpies and entropies of hydroxyl and nitryl in different mobile phase systems were compared by van＇t Hoff curve. Results suggest that the presence of acetonitrile and methanol in the mobile phase may decrease the interaction of solute and stationary phase with respect to subcritical water, thereby reducing the contribution of enthalpy to the retention. Retention mechanisms of phenolic compound appear to be more similar in subcritical water and water/methanol systems on the PRP-1 column. Hydrogen bond in subcritical water system plays a very important role in the retention of the phenols.

关键词： Subcritical water chromatography Phenols Retention mechanism Hydrogen bond

In situ synthesized homochiral dysprosium-oxo clusters with threonine Schiff bases

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Chinese Chemical Letters 2023年第8期34卷 458-461页

作者： Song Peng Xiaoming Ouyang Yihan Wang Qinghu Teng Yan Li xiuqing zhang Zhaobo Hu Kai Wang Fupei Liang Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials College of Chemistry and BioengineeringGuilin University of TechnologyGuilin 541004China Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry Jiangxi University of Science and TechnologyGanzhou 341000China

Chiral high-nuclearity lanthanide(4f)clusters have shown fantastic properties in various ***,their synthesis is still of great ***,we report two pairs of enantiomers of highnuclearity Dy-oxo clusters synthesized through in situ *** are[Dy18(^(R/S)Hftp)4(^(R/S)H_(2)btp)4(μ2-OH)_(8)(μ3-OH)20(μ6-O)(NO_(3))_(4)(μ-H_(2)O)_(8)]·[solvents](1R and 1S)and[Dy9(^(R/S)Hftp)2(^(R/S)H_(2)btp)_(2)(OAc)_(6)(μ3-OH)_(10)(H_(2)O)_(6)](OAc)·[solvents](2R and 2S),where^(R/S)Hftp2−and^(R/S)H_(2)btp^(3−)represent in situ formed 2-formyl-6-[N-(threonine)iminomethyl]-4-methylphenol and 2,6-bis[N-(threonine)iminomethyl]-4-methylphenol anions,*** in situ formed clusters were endowed with not only homochirality via introducing^(R/S)Hftp2−and^(R/S)H_(2)btp^(3−)ligands,but also rich oxo-bridges by controlling the hydrolysis of Dy^(III)*** anions from DyIII salts further induced structural variation between two sets of clusters.1R and 1S feature an unprecedent four-blade propeller shaped{Dy18}core,whose centered octahedral{Dy6}unit are surrounded by four triangular{Dy3}***,they represent the second largest chiral 4f cluster species so far.2R and 2S display a sandglass-like{Dy9}skeleton that consist of two square pyramid{Dy5}units sharing a Dy^(III)*** investigation revealed possible antiferromagnetic interactions between the Dy^(III)centers in these clusters.

关键词： Chirality Lanthanide-oxo cluster In situ synthesis Threonine Schiff bases Hydrolysis Magnetic properties

An α-expansin, VfEXPA1, is involved in regulation of stomatal movement in Vicia faba L.

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Chinese Science Bulletin 2011年第33期56卷 3531-3537页

作者： WEI PengCheng CHEN Su zhang xiuqing ZHAO Ping XIONG YanMei WANG WenLong CHEN Jia WANG XueChen State Key Laboratory of Plant Physiology and Biochemistry College of Biological Sciences China Agricultural University Beijing 100094 China Institute of Rice Research Anhui Academy of Agricultural Sciences Hefei 230031 China Changde Normal School Changde 415000 China

The wall loosening of guard cells differs from other types of plant cells. However, the regulation of wall loosening during stomatal movement is poorly understood. VfEXPA1 is an α-expansin gene cloned from Vicia faba epidermal strips. Expression of VfEXPA1 is regulated by darkness and submergence, and is not affected by light and abscisic acid (ABA). In situ hybridization showed that VfEXPA1 is expressed primarily in the guard cells. Overexpression of VfEXPA1 in transgenic tobacco accelerated light-induced stomatal opening, and increased both transpiration and photosynthetic rates under favorable growth conditions. Our results indicate the guard cell-expressed expansin VfEXPA1 plays an important role in regulation of stomatal opening.

关键词：气孔运动膨大调控蚕豆转基因烟草保卫细胞气孔开放植物细胞

Correlation between genotypes of Orientia tsutsugamushi and clinical characteristics of patients with scrub typhus in Guangzhou,China

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Asian Pacific Journal of Tropical Medicine 2024年第7期17卷 299-309,I0008,I0009页

作者： Jiali Long Ziyi Zeng Haiyan Chen Xia Tao Xinwei Wu Shouyi Chen Liqun Fang xiuqing zhang Jianxiong Xu Lin zhang Yuehong Wei Guangzhou Center for Disease Control and Prevention GuangzhouChina Institute of Public Health Guangzhou Medical UniversityGuangzhouChina Outpatient department of Baogang the First Affiliated Hospital of Guangdong Pharmaceutical UniversityGuangzhouChina State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and EpidemiologyBeijingChina Guangzhou Institute of Biomedicine and Health Chinese Academy of SciencesGuangzhouChina

Objective:To explore the correlation between genotypes of Orientia(O.)tsutsugamushi and clinical characteristics of scrub typhus ***:Clinical data of patients with scrub typhus admitted to different types of medical institutions in Guangzhou from September 2012 to December 2016 were collected using medical *** data,clinical manifestations,as well as hematological and biochemical indicators of patients infected with different genotypes were analyzed and ***:A total of 192 patients were included in this study,including 121 patients with Karp genotype of *** infection(63.0%),36 patients with Gilliam genotype(19.0%),23 patients with Kato genotype(12.0%),and 12 patients with TA763 genotype(6.0%)*** median value of albumin in patients with Karp genotype infection was significantly lower than that of Gilliam-infected patients(P=0.032).Patients with Karp genotype infection had a significantly longer hospital stay(9 days)than those with Gilliam genotype(7 days)(P=0.009)and Kato genotype infection(6 days)(P=0.005).Karp-infected patients also represented for the largest number of patients with complicated organ involvement(88/133,66.2%).Furthermore,Karp-infected patients had higher risk of developing multiple organ dysfunction syndrome(18.2%)and requiring intensive care unit treatment(15.9%).Besides,patients with Gilliam genotype(8 days)and TA763 genotype infection(7.5 days)had shorter fever duration than those with Karp genotype(9 days)and Kato genotype(9 days)infection,***:Genotypes of Orientia tsutsugamushi were associated with varying clinical manifestations,organ involvement,and treatment outcomes,suggesting that genotypes ranged in virulence.

关键词： Scrub typhus Orientia tsutsugamushi Genotype Clinical characteristics

A single-cell approach to engineer CD8+ T cells targeting cytomegalovirus

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Cellular & Molecular Immunology 2021年第5期18卷 1326-1328页

作者： Fei Wang Qumiao Xu Zhenkun Zhuang Ziyi Li Qianqian Gao Yaling Huang Yonglun Luo xiuqing zhang Linnan Zhu Cheng-chi Chao BGI Education Center University of Chinese Academy of SciencesShenzhen518083China BGI-Shenzhen Shenzhen518083China Department of Biomedicine Aarhus University8000AarhusDenmark China National GeneBank BGI-ShenzhenShenzhen518120China Shenzhen Key Laboratory of Genomics Beishan Industrial ZoneShenzhen518083China School of Biology and Biological Engineering South China University of TechnologyGuangzhou510006China Northwest A&F University Yangling712100ShaanxiChina Guangdong Enterprise Key Laboratory of Human Disease Genomics Beishan Industrial ZoneShenzhen518083China AbVision IncMilpitasCAUSA

T lymphocytes are crucial for antiviral responses and provide a promising repertoire for potential therapies of viral diseases such as cytomegalovirus(CMV)infection1 and the ongoing COVID-19 pandemic caused by SARS-CoV-2.^(2) CMV-related diseases occur once the host immune system is impaired or lacks a protective repertoire of virus-specific T lymphocytes.3 Adoptive transfer of T-cell receptor(TCR)-engineered T cells(TCR-Ts)provides an encouraging alternative treatment option for patients with CMV reactivation.^(4) However,generating TCR-Ts requires the identification of epitope-specific and functional TCR *** single-cell sequencing techniques open up the ability to unravel TCR repertoires,^(5 )which offers a potential opportunity to screen functional TCR pairs for TCR-T ***,we report an efficient approach that combines ex vivo CD8+T-cell stimulation with single-cell RNA and TCR V(D)J sequencing to identify CMV-specific TCRs for generating TCR-Ts.

关键词： impaired protective stimulation