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Uncovering the dynamic evolution of nucleotidebinding site-leucine-rich repeat(NBS-LRR) genes in Brassicaceae

Journal of Integrative Plant Biology 2016年第2期58卷 165-177页

作者： Yan-Mei Zhang Zhu-Qing Shao Qiang Wang Yue-Yu Hang Jia-Yu Xue Bin Wang Jian-Qun Chen State Key Laboratory of Pharmaceutical Biotechnology Center of Plant Genetics and Molecular EvolutionSchool of Life SciencesNanjing University Institute of Botany Jiangsu Province and Chinese Academy of Sciences

Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat （NBS-LRR） genes; however, the long-term evolutionary history of these resistance genes has not been fully understood, This study focuses on five Brassicaceae genomes and the Carica papaya genome to explore changes in NBS-LRR genes that have taken place in this Rosid II lineage during the past 72 million years. Various numbers of NBS-LRR genes were identified from Arabidopsis lyrata （198）, A. thaliana （165）, Brassica rapa （204）, Capsella rubella （127）, Thellungiella salsuginea （88）, and C. papaya （51）. In each genome, the identified NBS-LRR genes were found to be unevenly distributed among chromosomes and most of them were clustered together. Phylogenetic analysis revealed that, before and after Brassicaceae speciation events, both toll/interleukin-1 receptor-NBS-LRR （TNL） genes and non-toll/interleukin-1 receptor-NBS-LRR （nTNL） genes exhibited a pattern of first expansion and then contraction, suggesting that both subclasses of NBS-LRR genes were responding to pathogen pressures synchronically. Further, by examining the gain/loss of TNL and nTNL genes at different evolutionary nodes, this study revealed that both events often occurred more drastically in TNL genes. Finally, the phylogeny of nTNL genes suggested that this NBS-LRR subclass is composed of two separate ancient gene types： RPW8-NBS-LRR and Coiled-coiI-N BS-LRR.

关键词： Dynamic evolution nucleotide-binding site-leucine-rich repeat gene phylogenetic relationship plant disease resistance

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Tobacco Rattle Virus-induced Phytoene Desaturase (PDS) Silencing in Centaurea cyanus

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Horticultural Plant Journal 2021年第2期7卷 159-166页

作者： Chengyan Deng Fan Zhang Jiaying Wang Yanfei Li He Huang Silan Dai Beijing Key Laboratory of Ornamental Plants Germplasm Innovation&molecular Breeding National Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological Environment and College of Landscape ArchitectureBeijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijing 100083China

Virus-induced gene silencing(VIGS)is a genetic tool used to assess gene function.Tobacco rattle virus(TRV)is a VIGS vector commonly used to induce endogenous gene silencing in plants.However,there is no VIGS system established for Centaurea spp.We evaluated the effectiveness of a TRV-based VIGS system using phytoene desaturase(PDS)as a reporter gene in Centaurea cyanus.Three methods including pressure-,vacuum-and apical meristem-infiltrationwere tested to infect C.cyanus seedlings.Photobleached leaveswere only obtained using apicalmeristem-infiltration after a 14 d treatment.The CcPDS transcripts in photobleached leaves were significantly reduced compared with that in green leaves treated with empty TRV.Four C.cyanus cultivars were tested to detect their VIGS responses,and‘Dwarf Tom Pouce Blue’was the most sensitive.The agro-infiltration condition was optimized by screening for the optimal seedling stage as well as the optimum Agrobacterium density for efficient silencing.Seedlings with four true leaves and infiltration with an Agrobacterium density of OD_(600)0.5 were optimal conditions to obtain more photobleached leaves and more intense photobleached phenotype.The results demonstrated the feasibility of TRV-based VIGS for functional analysis of genes in C.cyanus.

关键词： Centaurea cyanus VIGS tobacco rattle virus PDS seedling photobleached

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Gene expression by simian virus 40 large Tantigen-induced medulloblastomas in mice

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Neural Regeneration Research 2012年第12期7卷 932-937页

作者： Xiaoluan Wei Jie Feng Yinghe Hu Shanghai Engineering Research center of molecular Therapeutics and New Drug Development Key Laboratory of Brain Functional Genomics MOE ＆ STCSM East China Normal University Shanghai 200062 China Shanghai Laboratory Animal Research center Shanghai 200032 China

Signaling pathways known to have components with mutations in human medulloblastoma include sonic hedgehog, Wnt/beta-catenin and insulin-like growth factor. Microarray analysis was applied to examine the gene expression changes in medulloblastomas of pTet-on/pTRE-SV40Tag transgenic mice. Altogether, 14 112 genes were detectable, including 152 genes with significantly different expression levels. These genes were associated with immunity, the cell cycle, signal transduction, cytoskeleton and metabolism. To further confirm the microarray data, real-time polymerase chain reactions were used to examine the expression changes of genes related to sonic hedgehog, Wnt/beta-catenin and insulin-like growth factor signal pathways. Immunohistochemistry detected insulin receptor substrate-1 in the nuclei of brain tumor tissue cells from pTet-on/pTRE-SV40Tag transgenic mice, suggesting that SV40 large T antigen may activate the insulin-like growth factor signal pathway to promote tumorigenesis.

关键词： SV40 large T antigen medulloblastoma cDNA microarray real-time polymerase chain reaction insulin-like growth factor

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无标记光学传感器用于病原体即时检测

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Science Bulletin 2023年第8期68卷 791-794页

作者：张泽英连泽伟苏萌宋延林 Key Laboratory of Green Printing CAS Research/Education Center for Excellence in Molecular SciencesInstitute of ChemistryChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China

Infectious pathogens such as viruses,bacteria present an unprecedented threat to human lives,economics,and social stability.From smallpox to influenza,severe acute respiratory syndrome,Ebola and coronavirus infections,the requirements for the detection and monitoring of pathogens are increasing.The World Health Organization has called for developing fast.

关键词：光学传感器即时检测无标记

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Distinct transcriptomic landscapes of cutaneous basal cell carcinomas and squamous cell carcinomas

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Genes & Diseases 2021年第2期8卷 181-192页

作者： Jun Wan Hongji Dai Xiaoli Zhang Sheng Liu Yuan Lin Ally-Khan Somani Jingwu Xie Jiali Han Department of Medical and molecular Genetics Indiana University School of MedicineIndianapolisIN46202USA center for Computational Biology and Bioinformatics Indiana University School of MedicineIndianapolisIN46202USA School of Informatics and Computing Indiana University e Purdue University at IndianapolisIndianapolisIN46202USA Department of Epidemiology and Biostatistics Key Laboratory of Cancer Prevention and TherapyNational Clinical Research Center of CancerTianjin Medical University Cancer Institute and HospitalTianjin300000PR China Wells center for Pediatric Research Department of PediatricsIndiana University School of MedicineIndianapolisIN46202USA Melvin and Bren Simon Cancer center Indiana University School of MedicineIndianapolisIN46202USA Department of Epidemiology Richard M.Fairbanks School of Public HealthIndiana UniversityIndianapolisIN46202USA Dermatologic Surgery&Cutaneous Oncology Division Department of DermatologyIndiana University School of MedicineIndianapolisIN46202USA

The majority of non-melanoma skin cancer(NMSC)is cutaneous basal cell carcinoma(BCC)or squamous cell carcinoma(SCC),which are also called keratinocyte carcinomas,as both of them originate from keratinocytes.The incidence of keratinocyte carcinomas is over 5 million per year in the US,three-fold higher than the total incidence of all other types of cancer combined.While there are several reports on gene expression profiling of BCC and SCC,there are significant variations in the reported gene expression changes in different studies.One reason is that tumor-adjacent normal skin specimens were not included in many studies as matched controls.Furthermore,while numerous studies of skin stem cells in mouse models have been reported,their relevance to human skin cancer remains unknown.In this report,we analyzed gene expression profiles of paired specimens of keratinocyte carcinomas with their matched normal skin tissues as the control.Among several novel findings,we discovered a significant number of zinc finger encoding genes up-regulated in human BCC.In BCC,a novel link was found between hedgehog signaling,Wnt signaling,and the cilium.While the SCC cancerstem-cell gene signature is shared between human and mouse SCCs,the hair follicle stem-cell signature of mice was not highly represented in human SCC.Differential gene expression(DEG)in human BCC shares gene signature with both bulge and epidermal stem cells.We have also determined that human BCCs and SCCs have distinct gene expression patterns,and some of them are not fully reflected in current mouse models.

关键词： Basal cell carcinoma Gli1 Hedgehog signaling PTCH1 Squamous cell carcinoma

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Study on the reaction of 3-methyl-2-butenal and 3-methylbutanal with Cl atoms: kinetics and reaction mechanism

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Journal of Environmental Sciences 2022年第6期34卷 25-33页

作者： Bo Shi Weigang Wang Cici Fan Yuchan Zhang Zheng Sun Yanli Zeng Maofa Ge College of Chemistry and Material Sciences Hebei Normal UniversityShijiazhuang 050024China State Key Laboratory for Structural Chemistry of Unstable and Stable Species Beijing National Laboratory for Molecular Sciences(BNLMS)Institute of ChemistryChinese Academy of SciencesBeijing 100190China Lanfang Normal University Langfang 065000China National Demonstration center for Experiment Chemistry Hebei Normal UniversityShijiazhuang 050024China Key Laboratory of Inorganic Nano-material of Hebei Province Shijiazhuang 050024China

The reaction of Cl atoms with two C5aldehydes(3-methyl-2-butenal and 3-methylbutanal)were investigated by proton-transfer-reaction mass spectrum(PTR-MS)using smog chamber at 298±1 K and 760 Torr.A relative rate method was used to determine the rate constants of the title reactions with m-xylene and trans-2-butene as reference compounds:(3.04±0.18)×10^(-10)and(2.07±0.14)×10^(-10)cm^(3)/(molecule·sec)for 3-methyl-2-butenal and 3-methylbutanal,respectively.Additionally,the gas-phase products were also identified by PTR-MS,and the possible reaction mechanisms were proposed basing on the identified products.The detected gas-phase products are similar for two C5aldehydes reactions,mainly including small molecules of aldehydes,ketones and chlorinated aldehyde compounds.The atmospheric lifetimes(τ)calculated for 3-methyl-2-butenal(τ=7.0 hr,marine boundary layer(MBL))and 3-methylbutanal(τ=10.3 hr,MBL)according to the obtained rate constants.The results indicate that Cl atoms at MBL are competitive with OH radicals for the degradation contribution of C5aldehyde compounds.

关键词： Smog chamber Kinetic Reaction mechanism Cl atoms

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A bifunctional vinyl-sulfonium tethered peptide induced by thio-Michael-type addition reaction

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Chinese Chemical Letters 2022年第4期33卷 2001-2004页

作者： Hongkun Xu Xuan Qin Yaping Zhang Chuan Wan Rui Wang Zhanfeng Hou Xiaofeng Ding Hailing Chen Ziyuan Zhou Yang Li Chenshan Lian Feng Yin Zigang Li State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhen 518055China Pingshan translational medicine center Shenzhen Bay LaboratoryShenzhen 518055China Anhui Medical University Hefei 230032China Cancer Hospital Chinese Academy of Medical Sciences Shenzhen CenterShenzhen 518000China

The modification and functionalization of peptides is of great significance in modern biotechnology and drug development. Here we report a highly reactive Michael-type warhead for the covalently modification of cysteine on peptide and protein. By installing a vinyl group onto a methionine residue of peptide,the produced vinyl sulfonium can be efficiently nucleophilic added by appropriate cysteine residue of this peptide, and thus yield a cyclized peptide. This peptide cyclization strategy was proven to exhibit improved cell penetration and good stability. Moreover, a peptide ligand bearing vinyl sulfonium could covalently bind to the cysteine in the target protein, indicating the potential of vinyl sulfonium as a novel warhead for developing covalent peptide inhibitor.

关键词： Vinyl sulfonium Michael-type addition Peptide cyclization Covalent peptide inhibitor Proximity-induced ligation

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General synthesis of 2D rare-earth oxide single crystals with tailorable facets

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National Science Review 2022年第5期9卷 22-29页

作者： Linyang Li Fangyun Lu Wenqi Xiong Yu Ding Yangyi Lu Yao Xiao Xin Tong Yao Wang Shuangfeng Jia Jianbo Wang Rafael G.Mendes Mark H.Rümmeli Shengjun Yuan Mengqi Zeng Lei Fu College of Chemistry and molecular Sciences Wuhan University Key Laboratory of Artificial Micro-and Nano-Structures of Ministry of Education and School of Physics and Technology Wuhan University The Institute for Advanced Studies Wuhan University College of Physics Optoelectronics and Energy and Collaborative Innovation Center of Suzhou Nano Science and TechnologySoochow University Institute for Complex Materials IFW Dresden Centre of Polymer and Carbon Materials Polish Academy of Sciences Institute of Environmental Technology VSB-Technical University of Ostrava

Two-dimensional(2D) rare-earth oxides(REOs) are a large family of materials with various intriguing applications and precise facet control is essential for investigating new properties in the 2D limit.However,a bottleneck remains with regard to obtaining their 2D single crystals with specific facets because of the intrinsic non-layered structure and disparate thermodynamic stability of different facets.Herein,for the first time,we achieve the synthesis of a wide variety of high-quality 2D REO single crystals with tailorable facets via designing a hard-soft-acid-base couple for controlling the 2D nucleation of the predetermined facets and adjusting the growth mode and direction of crystals.Also,the facet-related magnetic properties of 2D REO single crystals were revealed.Our approach provides a foundation for further exploring other facet-dependent properties and various applications of 2D REO,as well as inspiration for the precise growth of other non-layered 2D materials.

关键词： 2D materials cerium crystal engineering rare earth CVD

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Malaria vaccines:looking back and lessons learnt

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Asian Pacific Journal of Tropical Biomedicine 2011年第1期1卷 74-78页

作者： Veronique Lorenz Panagiotis Karanis Panagiotis Karanis Medical and Molecular Parasitology LaboratoryUniversity of CologneMedical SchoolCenter of AnatomyInstitute Ⅱ

The current status of malaria vaccine approaches has the background of a long and arduous path of malaria disease control and vaccine development.Here,we critically review with regard to unilateral interventional approaches and highlight the impact of socioeconomic elements of malaria endemicity. The necessity of re-energizing basic research of malaria life-cycle and Plasmodium developmental biology to provide the basis for promising and cost-effective vaccine approaches and to reach eradication goals is more urgent than previously believed.We closely analyse the flaws of various vaccine approaches,outline future directions and challenges that still face us and conclude that the focus of the field must be shifted to the basic research efforts including findings on the skin stage of infection.We also reflect on economic factors of vaccine development and the impact of public perception when it comes to vaccine uptake.

关键词： Malaria Vaccine Current state

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A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

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The Crop Journal 2024年第2期12卷 354-363页

作者： Linhua Wu Min Hu Shuwei Lyu Wenfeng Chen Hang Yu Qing Liu Wei He Chen Li Zuofeng Zhu Rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina National center for Evaluation of Agricultural Wild Plants(Rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China State Key Laboratory for Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina Guangdong Key Laboratory of New Technology in Rice Breeding Guangzhou 510640GuangdongChina Guangdong Rice Engineering Laboratory Guangzhou 510640GuangdongChina

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement.To investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle phenotype.This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch.Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway.We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

关键词： Upstream region Panicle architecture Gene expression BR Rice

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