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Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species

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Plant Diversity 2017年第5期39卷 294-299页

作者： Hantao Qin guoqian yang Jim Provan Jie Liu Lianming Gao Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201 China University of Chinese Academy of Sciences Beijing100049China Germplasm Bank of Wild Species in Southwest China Kunming Institute of BotanyChinese Academy of SciencesKunming650201China Institute of Biological Environmental and Rural Sciences (IBERS)Aberystwyth UniversityPengiaisAberystwythSY23 3DAUK

Microsatellites are highly polymorphic markers which have been used in a wide range of genetic *** recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively *** this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851(~1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526(~18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten(mean=4.875), and within-population expected heterozygosity from zero to 0.789(mean = 0.530),indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.

关键词： MiddRAD-seq Endangered species Microsatellite Next-generation sequencing Taxus florinii

A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing

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Plant Diversity 2018年第3期40卷 106-116页

作者： Ying Guo guoqian yang Yunmei Chen Dezhu Li Zhenhua Guo Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China University of Chinese Academy of Sciences Beijing 100049 China

Obtaining high-quality plant materials for experiments is challenging for many research ***, it is of special importance to determine the best method for preserving biological macromolecules like DNA, which degrade over time. Although some research has demonstrated that DNA degradation has little effect on traditional molecular markers, the effects of DNA degradation on dd RADseq, a popular reduced-representation sequencing technology, have not been adequately investigated. In this study, we first chose six woody bamboo species(Bambusoideae, Poaceae) to explore appropriate methods for preserving molecular materials with two DNA extraction approaches. Then we sequenced twenty-one bamboos and examined the effects of DNA quality on data generation using the dd RAD-seq technique(Midd RAD-seq). Finally, we reconstructed phylogenies of twenty woody bamboo species. We found that the integrity of dry-powdered DNA was preserved longer than that of TE-dissolved DNA,regardless of whether the DNA was extracted by a modified CTAB protocol or DNAsecure plant kit. The dd RAD-seq data were robust, except when DNA was severely degraded. In addition, we resolved the phylogenetic positions of the sampled Phyllostachys spp. Our results suggest that dry-powdered DNA is the most appropriate preservation method for plant molecular materials. Furthermore, a moderate level of DNA degradation has little effect on reduced representation sequencing techniques represented by dd RAD-seq.

关键词： Molecular materials DNA extraction and preservation DNA quality ddRAD-seq Bamboo Phylogeny

Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L.

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Horticulture Research 2023年第5期10卷 220-235页

作者： Songtao Jiu Baozheng Chen Xiao Dong Zhengxin Lv Yuxuan Wang Chunjin Yin Yan Xu Sen Zhang Jijun Zhu Jiyuan Wang Xunju Liu Wanxia Sun guoqian yang Meng Li Shufeng Li Zhuo Zhang Ruie Liu Lei Wang Muhammad Aamir Manzoor Quero-García José Shiping Wang Yahui Lei Ling yang Elisabeth Dirlewanger yang Dong Caixi Zhang Department of Plant Science School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai200240P.R.China College of Food Science and Technology Yunnan Agricultural UniversityKunmingYunnan Province650201P.R.China Dali Bai Autonomous Prefecture Academy of Agricultural Sciences and Extension DaliYunnan Province671600P.R.China Shanghai Botanical Garden Shanghai200231P.R.China College of Biology and the Environment Nanjing Forestry UniversityNanjingJiangsu Province200037P.R.China INRAe UMR 1332 de Biologie du Fruit et Pathologie33140 Villenave d’OrnonFrance

Prunus pusilliflora is a wild cherry germplasm resource distributed mainly in Southwest *** its ornamental and economic value,a high-quality assembled *** genome is unavailable,hindering our understanding of its genetic background,population diversity,and evolutionary ***,we de novo assembled a chromosome-scale *** genome using Oxford Nanopore,Illumina,and chromosome conformation capture *** assembled genome size was 309.62 Mb,with 76 scaffolds anchored to eight *** predicted 33035 protein-coding genes,functionally annotated 98.27%of them,and identified repetitive sequences covering 49.08%of the *** found that *** is closely related to Prunus serrulata and Prunus yedoensis,having diverged from them∼41.8 million years ago.A comparative genomic analysis revealed that *** has 643 expanded and 1128 contracted gene ***,we found that *** is more resistant to Colletotrichum viniferum,Phytophthora capsici,and Pseudomonas syringae ***(Pst)DC3000 infections than cultivated Prunus *** also has considerably more nucleotide-binding site-type resistance gene analogs than ***,which explains its stronger disease *** cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in ***,81 MADS-box genes were identified in ***,accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 *** assembly of a high-quality *** genome will be valuable for further research on cherries and molecular breeding.

关键词： Prunus resistance release

Machine Learning for Lung Cancer Diagnosis,Treatment,and Prognosis

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 850-866页

作者： Yawei Li Xin Wu Ping yang guoqian Jiang Yuan Luo Department of Preventive Medicine Feinberg School of MedicineNorthwestern UniversityChicagoIL 60611USA Department of Medicine University of Illinois at ChicagoChicagoIL 60612USA Department of Quantitative Health Sciences Mayo ClinicRochesterMN 55905/ScottsdaleAZ 85259USA Department of Artificial Intelligence and Informatics Mayo ClinicRochesterMN 55905USA

The recent development of imaging and sequencing technologies enables systematic advances in the clinical study of lung ***,the human mind is limited in effectively handling and fully utilizing the accumulation of such enormous amounts of *** learningbased approaches play a critical role in integrating and analyzing these large and complex datasets,which have extensively characterized lung cancer through the use of different perspectives from these accrued *** this review,we provide an overview of machine learning-based approaches that strengthen the varying aspects of lung cancer diagnosis and therapy,including early detection,auxiliary diagnosis,prognosis prediction,and immunotherapy ***,we highlight the challenges and opportunities for future applications of machine learning in lung cancer.

关键词： Omics dataset Imaging dataset Feature extraction Prediction Immunotherapy

Environmental dispersivity in free-water-surface-effect dominated wetland:multi-scale analysis

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Frontiers of Environmental Science & Engineering 2011年第4期5卷 597-603页

作者： Zi WU Zhi LI Li ZENG Ling SHAO Hansong TANG Qing yang guoqian CHEN State Key Laboratory of Turbulence and Complex Systems College of EngineeringPeking UniversityBeijing 100871China Department of Civil Engineering City University of New York City CollegeNew YorkNY 10031USA

Distinct from the case with width-dominated shallow wetland flows,the longitudinal evolution of contaminant concentration in the most-typical pattern of wetland as dominated by free-water-surface-effect is characterized by a multi-scale analysis in the present *** environmental dispersion model for the evolution of the mean concentration is deduced as an extension of Taylor's classical formulation by Mei’s multi-scale *** environmental dispersivity is found identical to that determined by the method of concentration moments.

关键词： free-surface wetland environmental dispersion multi-scale analysis

有机覆盖措施对葡萄生长特性和果实品质影响研究进展

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核农学报 2025年第1期39卷 201-211页

作者：王江林徐国前杨帆孙淼裴泓凯程春颖张立霞薛婷婷宁夏大学葡萄酒与园艺学院宁夏银川750021 宁夏葡萄与葡萄酒教育部工程研究中心/宁夏葡萄与葡萄酒工程技术研究中心宁夏银川750021 宁夏博纳佰馥酒庄有限公司宁夏银川750021 宁夏嘉地酒园酒庄有限公司宁夏银川750021

生草、枝条和秸秆等有机覆盖措施作为土壤管理的一种方法,广泛应用于葡萄栽培管理实践。有机覆盖措施不仅可以提高土壤稳定性和土壤养分含量,调节葡萄植株生长以及改善葡萄浆果品质,而且能使有机废弃物得到充分利用,促进资源的可持续循... 详细信息

生草、枝条和秸秆等有机覆盖措施作为土壤管理的一种方法,广泛应用于葡萄栽培管理实践。有机覆盖措施不仅可以提高土壤稳定性和土壤养分含量,调节葡萄植株生长以及改善葡萄浆果品质,而且能使有机废弃物得到充分利用,促进资源的可持续循环。基于此,本文围绕葡萄园有机覆盖措施的最新研究成果,系统回顾了有机覆盖措施的研究进展与发展趋势;综述了有机覆盖措施对葡萄叶片光合作用、植株生长和物候期等葡萄树体生长特性,以及葡萄浆果品质和产量的影响和作用机制;并对该领域的前沿研究方向和应用前景进行了展望。该文可为葡萄园有机覆盖措施的应用提供理论依据。

关键词：生草覆盖枝条覆盖秸秆覆盖葡萄生长特性果实品质

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Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera

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The Innovation 2022年第3期3卷 98-104页

作者： Zefu Wang Yuanzhong Jiang Xiaoyue yang Hao Bi Jialiang Li Xingxing Mao Yazhen Ma Dafu Ru Cheng Zhang guoqian Hao Jing Wang Richard J.Abbott Jianquan Liu State Key Laboratory of Grassland Agro-Ecosystem College of EcologyLanzhou UniversityLanzhou 730000China Key Laboratory for Bio-resource and Eco-environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China Chengdu Institute of Biology Chinese Academy of SciencesChengdu 610041China Sichuan Tea College Yibin UniversityYibin 644000China School of Biology University of St AndrewsSt Andrews KY169THUK

Parallel evolution of reproductive isolation(PERI)provides strong evidence for natural selection playing a fundamental role in the origin of ***,PERI has been rarely demonstrated for well established species drawn from different *** particular,parallel molecular signatures for the same genes in response to similar habitat divergence in such different lineages is ***,based on whole-genome sequencing data.

关键词： signature divergence Molecular

Laser-driven plasma collider for nuclear studies

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Science Bulletin 2015年第13期60卷 1211-1213页

作者： Changbo Fu Jie Bao Liming Chen Jianjun He Long Hou Liang Li Yanfei Li Yutong Li guoqian Liao Yongjoo Rhee yang Sun Shiwei Xu Dawei Yuan Xiaopeng Zhang Gang Zhao Jiarui Zhao Baojun Zhu Jianqiang Zhu Jie Zhang Department of Physics and Astronomy Shanghai Jiao Tong University Physics Department China Institute of Atomic Energy Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences IFSA Collaborative Innovation Center Shanghai Jiao Tong University Institute of Modern Physics Chinese Academy of Sciences Nuclear Data Center Korea Atomic Energy Research Institute National Astronomical Observatories Chinese Academy of Sciences Shanghai Institute of Optics and Fine Mechanics Chinese Academy of Sciences

A novel method of initiating nuclear fusion reactions in a full plasma environment was suggested, and a proof-of-concept experiment was carried out with the D ＋D → n＋3He reaction. In this new approach, two plasma jets generated by high-intensity lasers collide headon-head. The center-of-mass energy of the nuclei increases accordingly, and therefore, reaction products can be significantly enhanced, especially in the sub-Coulomb barrier ranges. As a result of the fusion reaction, up to - 7.6 ×105 neutrons had been observed. This new type of ＂plasma collider＂ could provide an innovative tool to study nuclear reactions under astrophysical conditions.

关键词： Plasma collider - D-D neutron .Laboratory nuclear astrophysics - High-intensity laser

肝癌组织中EGFL9基因的表达及其对Huh-7肝癌细胞系增殖、侵袭和迁移的影响

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现代肿瘤医学 2022年第7期30卷 1179-1184页

作者：谭国钳王洋吴帆广州市红十字会医院广东广州510220 贵州医科大学贵州贵阳550025

目的:研究表皮生长因子样结构域9(epiderma growth factor-like domain 9,EGFL9)基因在肝癌组织及细胞系中的表达水平及其对Huh-7肝癌细胞系增殖、侵袭和迁移的影响。方法:采用实时荧光定量PCR(quantitative real-time PCR,RT-qPCR)方... 详细信息

目的:研究表皮生长因子样结构域9(epiderma growth factor-like domain 9,EGFL9)基因在肝癌组织及细胞系中的表达水平及其对Huh-7肝癌细胞系增殖、侵袭和迁移的影响。方法:采用实时荧光定量PCR(quantitative real-time PCR,RT-qPCR)方法检测EGFL9基因在20例肝癌及对应的癌旁肝组织标本中的表达水平。下载癌症基因组图谱(The Cancer Genome Atlas,TCGA)数据库内肝癌基因表达数据,对EGFL9在肝癌中的表达进行分析。RT-qPCR检测EGFL9基因在Huh-7、SMMC-7721及HepG2三种常见的肝癌细胞系和HL-7702正常肝脏细胞系中的表达水平。采用慢病毒介导的siRNA及基因转导技术分别构建EGFL9基因敲减及过表达的Huh-7肝癌细胞,以噻唑蓝(methyl thiazolyl tetrazolium,MTT)法、Transwell侵袭实验和迁移实验观察EGFL9基因敲减及过表达对Huh-7肝癌细胞增殖、侵袭和迁移的影响。结果:RT-qPCR结果显示,EGFL9基因在20例肝癌组织中的表达量高于对应的癌旁组织。TCGA数据库分析结果也显示,EGFL9在肝癌组织中的平均表达量明显高于癌旁组织。EGFL9在3株肝癌细胞系中的表达水平均高于正常肝脏细胞系。EGFL9基因敲减的Huh-7肝癌细胞的增殖速度明显慢于对照Huh-7肝癌细胞,其侵袭、迁移能力也明显被抑制;EGFL9基因过表达的Huh-7肝癌细胞实验结果则与之相反。结论:EGFL9在肝癌组织和细胞中的表达水平明显上调,且可促进肝癌细胞的增殖、侵袭及迁移能力,提示EGFL9可能是一个潜在的肝癌治疗靶点。

关键词：肝癌 EGFL9 小干扰RNA 基因转导增殖侵袭迁移