检索结果-南通市图书馆

Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes

在线全文

学校读者我要写书评

暂无评论

Horticulture Research 2023年第4期10卷 238-248页

作者： Hongtao Song Qi Wang Zhonghua Zhang Kui Lin Erli Pang MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development College of Life SciencesBeijing Normal UniversityBeijing 100875China College of Horticulture Qingdao Agricultural UniversityQingdao 266109China

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://***/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.

关键词： elements conserved sequences

Comparative mitogenomic analyses unveil conserved and variable mitogenomic features and phylogeny of Chedrinae fish

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Zoological Research 2022年第1期43卷 30-32页

作者： Peng Yu Li Zhou Xiao-Li Yang Liang-Liang Li Hui Jin Zhi Li Zhong-Wei Wang Xi-Yin Li Xiao-Juan Zhang Yang Wang Jian-Fang Gui State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyInnovation Academy of Seed DesignChinese Academy of SciencesWuhanHubei 430072China Hubei Hongshan Laboratory WuhanHubei 430070China University of Chinese Academy of Sciences Beijing 10049China

Chedrinae fish,which belong to Danionidae,have important ornamental,economic,and scientific value.At present,however,their mitogenomic features are unclear and their phylogenetic relationships remain controversial.In this study,we presented five new Chedrinae mitochondrial genomes(mitogenomes)and analyzed the conserved and variable mitogenomic characteristics of 17 Chedrinae fish.The gene composition and arrangement and secondary structure of transfer RNAs(tRNAs)were highly conserved among the Chedrinae mitogenomes.However,the length of the control region and base composition were variable.Interestingly,the mitogenome of Barilius barila was unusual,with lower A+T content in the first codon of protein-coding genes(PCGs)(47.32%versus average of 54.47%)and distinct pattern of codons per thousand codons(CDspT).Three Chedrinae fish had a long tandem repeat(>291 bp)in the 5'-end of the control region,which may increase their adaptability.In addition,tRNALys had notably larger DHU and TΨC loops than other tRNAs.The phylogenetic trees of the Chedrinae fish suggested that the Barilius genus was not a monophyletic group but could be divided into two main groups based on significant differences in A+T content.This study provides insights into the mitogenomic features and phylogenetic implications of Chedrinae fish,which should benefit their systematics and conservation.

关键词： conserved fish features

conserved termini and adjacent variable region of Twortlikevirus Staphylococcus phages

在线全文

学校读者我要写书评

暂无评论

Virologica Sinica 2015年第6期30卷 433-440页

作者： Xianglilan Zhang Huaixing Kang Yuyuan Li Xiaodong Liu Yu Yang Shasha Li Guangqian Pei Qiang Sun Peng Shu Zhiqiang Mi Yong Huang Zhiyi Zhang Yannan Liu Xiaoping An Xiaolu Xu Yigang Tong State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology The State Key Laboratory of Medical Genetics and School of Life Sciences Central South University The 307th Hospital of Chinese People's Liberation Army Beijing Aviation Meterological and Chemical Defense Research Institute

Methicillin-resistant Staphylococcus aureus(MRSA) is an increasing cause of serious infection,both in the community and hospital settings. Despite sophisticated strategies and efforts, the antibiotic options for treating MRSA infection are narrowing because of the limited number of newly developed antimicrobials. Here, four newly-isolated MRSA-virulent phages, IME-SA1, IMESA2, IME-SA118 and IME-SA119, were sequenced and analyzed. Their genome termini were identified using our previously proposed "termini analysis theory". We provide evidence that remarkable conserved terminus sequences are found in IME-SA1/2/118/119, and, moreover, are widespread throughout Twortlikevirus Staphylococcus phage G1 and K species. Results also suggested that each phage of the two species has conserved 5′ terminus while the 3′ terminus is variable. More importantly, a variable region with a specific pattern was found to be present near the conserved terminus of Twortlikevirus S. phage G1 species. The clone with the longest variable region had variable terminus lengths in successive generations, while the clones with the shortest variable region and with the average length variable region maintained the same terminal length as themselves during successive generations. IME-SA1 bacterial infection experiments showed that the variation is not derived from adaptation of the phage to different host strains. This is the first study of the conserved terminus and variable region of Twortlikevirus S. phages.

关键词： Twortlikevirus Staphylococcus phage conserved termini variable region

Biogenesis of flavor-related linalool is diverged and genetically conserved in tree peony (Paeonia × suffruticosa)

在线全文

学校读者我要写书评

暂无评论

Horticulture Research 2023年第2期10卷 15-27页

作者： Shanshan Li Ling Zhang Miao Sun Mengwen Lv Yong Yang Wenzhong Xu Liangsheng Wang Key Laboratory of Plant Resources Institute of BotanyChinese Academy of SciencesBeijing 100093China China National Botanical Garden Beijing 100093China University of Chinese Academy of Sciences Beijing 100049China School of Landscape Architecture Beijing Forestry UniversityBeijing 100083China

Floral scent is an important and genetically complex trait in horticultural plants.Tree peony(Paeonia×suffruticosa)originates in the Pan-Himalaya and has nine wild species divided into two subsections,Delavayanae and Vaginatae.Their f lowers are beloved worldwide for their sweet f loral fragrance,yet the f lavor-related volatiles and underlying biosynthetic pathways remain unknown.Here,we characterized the volatile blends of all wild tree peony species and found that the flavor-related volatiles were highly divergent,but linalool was a unique monoterpene in subsect.Delavayanae.Further detection of volatiles in 97 cultivars with various genetic backgrounds showed that linalool was also the characteristic aroma component in Paeonia delavayi hybrid progenies,suggesting that linalool was conserved and dominant within subsect.Delavayanae and its hybrids,instead of species and cultivars from subsect.Vaginatae.Global transcriptome analysis of all wild tree peony species and 60 cultivars revealed five candidate genes that may be involved in key steps of linalool biosynthesis;especially the expressions of three TPS genes,PdTPS1,PdTPS2,and PdTPS4,were significantly positively correlated with linalool emissions across tree peony cultivars.Further biochemical evidence demonstrated that PdTPS1 and PdTPS4were the pivotal genes determining the species-specific and cultivar-specific emission of linalool.This study revealed a new insight into floral scent divergence in tree peony and would greatly facilitate our understanding of the phylogeny and evolution of Paeonia.

关键词： conserved tree steps

Putting the brakes on pollen wall development:A conserved negative feedback loop regulates pollen exine formation in flowering plants

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Molecular Plant 2023年第9期16卷 1376-1378页

作者： Yuan Zhou Anna A.Dobritsa Department of Molecular Genetics Ohio State UniversityColumbusOH 43210USA

Pollen grains are covered by a complex multi-layered structure,the pollen wall.Exine,the outermost layer of this wall,is made from the biopolymer sporopollenin that exhibits remarkable physical and chemical stability.In different plants,exine,which shields pollen from harsh environmental stresses,has very diverse morphologies and forms different patterns(Wang and Dobritsa,2018).It also contributes to pollination,pollen–stigma interaction,pollen hydration,and eventual release of the pollen tube.Formation of exine begins after male meiosis when four microspores are arranged in a tetrad configuration and enclosed by the callose wall(Ariizumi and Toriyama,2011).At this stage,microspores secrete primexine,the precursor of exine that accumulates between the microspore plasma membrane and the callose wall,providing a scaffold for exine patterning(Wang et al.,2021).As the callose wall gradually gets degraded,sporopollenin is secreted by the nearby tapetal cells and deposited onto the primexine template to form mature exine.This process requires coordination of activities between microspores and the surrounding tapetum.

关键词： template conserved pollen

Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Bulletin of the Chinese Academy of Sciences 2020年第2期34卷 116-117页

作者： CHEN Lingling Center for Excellenee in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology CAS

Long noncoding RNAs(lncRNAs),which are longer than 200 nucleotides in length and lack protein coding potential,are pervasively transcribed in eukaryotic genomes.It is well established that lncRNAs play important roles... 详细信息

关键词： lncRNA conserved diverse

Dissecting conserved cis-regulatory modules of Glu-1 promoters which confer the highly active endosperm-specific expression via stable wheat transformation

在线全文

学校读者我要写书评

暂无评论

The Crop Journal 2019年第1期7卷 8-18页

作者： Jihu Li Ke Wang Genying Li Yulian Li Yong Zhang Zhiyong Liu Xingguo Ye Xianchun Xia Zhonghu He Shuanghe Cao National Wheat Improvement Center Institute of Crop Sciences Chinese Academy of Agricultural Sciences College of Agronomy and Biotechnology China Agricultural University Crop Research Institute Shandong Academy of Agricultural Sciences International Maize and Wheat Improvement Center (CIMMYT) China Office c/o CAAS

Wheat high-molecular-weight glutenin subunits(HMW-GS) determine dough elasticity and play an essential role in processing quality. HMW-GS are encoded by Glu-1 genes and controlled primarily at transcriptional level, implemented through the interactions between cis-acting elements and trans-acting factors. However, transcriptional mechanism of Glu-1 genes remains elusive. Here we made a comprehensive analysis of cis-regulatory elements within 1-kb upstream of the Glu-1 start codon(-1000 to-1) and identified 30 conserved motifs. Based on motif distribution pattern, three conserved cis-regulatory modules(CCRMs), CCRM1(-300 to-101), CCRM2(-650 to-400), and CCRM3(-950 to-750), were defined, and their functions were characterized in wheat stable transgenic lines transformed with progressive 5′ deletion promoter::GUS fusion constructs. GUS staining, qP CR and enzyme activity assays indicated that CCRM2 and CCRM3 could enhance the expression level of Glu-1, whereas the 300-bp promoter(-300 to-1), spanning CCRM1 and core region(-100 to-1), was enough to ensure accurate Glu-1 initiation at 7 days after flowering(DAF) and shape its spatiotemporal expression pattern during seed development. Further transgenic assays demonstrated that CCRM1-2(-300 to-209) containing Complete HMW Enhancer(-246 to-209) was important for expression level but had no effect on expression specificity in the endosperm. In contrast, CCRM1-1(-208 to-101) was critical for both expression specificity and level of Glu-1. Our findings not only provide new insights to uncover Glu-1 transcription regulatory machinery but also lay foundations for modifying Glu-1 expression.

关键词： conserved cis-regulatory modules Glu-1 Transcriptional regulation Transgenic wheat Triticum aestivum

Detection of hyper-conserved regions in hepatitis B virus X gene potentially useful for gene therapy

在线全文

学校读者我要写书评

暂无评论

World Journal of Gastroenterology 2018年第19期24卷 2095-2107页

作者： Carolina González David Tabernero Maria Francesca Cortese Josep Gregori Rosario Casillas Mar Riveiro-Barciela Cristina Godoy Sara Sopena Ariadna Rando Marcal Yll Rosa Lopez-Martinez Josep Quer Rafael Esteban Maria Buti Francisco Rodríguez-Frías Liver Pathology Unit Departments of Biochemistry and MicrobiologyHospital Universitari Vall d’HebronUniversitat Autònoma de BarcelonaBarcelona 08035Spain Liver Unit Liver Disease Laboratory-Viral HepatitisVall d’Hebron Institut Recerca-Hospital Universitari Vall d’HebronUniversitat Autònoma de BarcelonaBarcelona 08035Spain Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas(CIBERehd) Instituto de Salud Carlos IIIMadrid 28029Spain Roche Diagnostics SL Sant Cugat del Vallès 08174Spain Liver Unit Department of Internal MedicineHospital Universitari Vall d'HebronUniversitat Autònoma de BarcelonaBarcelona 08035Spain

AIM To detect hyper-conserved regions in the hepatitis B virus(HBV) X gene(HBX) 5' region that could be candidates for gene therapy.METHODS The study included 27 chronic hepatitis B treatmentnaive patients in various clinical stages(from chronic infection to cirrhosis and hepatocellular carcinoma, both HBeA g-negative and HBeA g-positive), and infected with HBV genotypes A-F and H. In a serum sample from each patient with viremia > 3.5 log IU/m L, the HBX 5' end region [nucleotide(nt) 1255-1611] was PCRamplified and submitted to next-generation sequencing(NGS). We assessed genotype variants by phylogenetic analysis, and evaluated conservation of this region by calculating the information content of each nucleotide position in a multiple alignment of all unique sequences(haplotypes) obtained by NGS. Conservation at the HBx protein amino acid(aa) level was also analyzed.RESULTS NGS yielded 1333069 sequences from the 27 samples, with a median of 4578 sequences/sample(2487-9279, IQR 2817). In 14/27 patients(51.8%), phylogenetic analysis of viral nucleotide haplotypes showed a complex mixture of genotypic variants. Analysis of the information content in the haplotype multiple alignments detected 2 hyper-conserved nucleotide regions, one in the HBX upstream non-coding region(nt 1255-1286) and the other in the 5' end coding region(nt 1519-1603). This last region coded for a conserved amino acid region(aa 63-76) that partially overlaps a Kunitz-like domain.CONCLUSION Two hyper-conserved regions detected in the HBX 5' end may be of value for targeted gene therapy, regardless of the patients' clinical stage or HBV genotype.

关键词： Hepatitis B virus Hepatitis B X gene Hepatitis B X protein Gene therapy Next-generation sequencing HBV conserved regions Small interference RNA

PARAREAL ALGORITHMS APPLIED TO STOCHASTIC DIFFERENTIAL EQUATIONS WITH conserved QUANTITIES

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of Computational Mathematics 2019年第1期37卷 48-60页

作者： Liying Zhang Weien Zhou Lihai Ji School of Mathematical Science China University of Mining and TechnologyBeijing 100083China National Innovation Institute of Defense Technology Beijing 100000China College of Science National University of Defense TechnologyChangsha 410072China Institute of Applied Physics and Computational Mathematics Beijing 100088China

In this paper,we couple the parareal algorithm with projection methods of the trajectory on a specifc manifold,defined by the preservation of some conserved quantities of stochastic differential equations.First,projection methods are introduced as the coarse and fine propagators.Second,we apply the projection methods for systems with conserved quantities in the correction step of original parareal algorithm.Finally,three mumerical experiments are performed by different kinds of algorithms to show the property of convergence in iteration,and preservation in conserved quantities of model systems.

关键词： Stochastic differential equation Parareal algorithm conserved quantity Structurepreserving method