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Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans

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Acta Pharmaceutica Sinica B 2020年第2期10卷 374-382页

作者： yisong liu Qi Tang Pi Cheng Mingfei Zhu Hui Zhang Jiazhe liu Mengting Zuo Chongyin Huang Changqiao Wu Zhiliang Sun Zhaoying liu Hunan Engineering Technology Research Center of Veterinary Drugs Hunan Agricultural UniversityChangsha 410128China Hunan Key Laboratory of Traditional Chinese Veterinary Medicine Hunan Agricultural UniversityChangsha 410128China College of Veterinary Medicine Hunan Agricultural UniversityChangsha 410128China Nextomics Biosciences Institute Wuhan 430000China

Gelsemium elegans(***)(2 n=2 x=16)is genus of flowering plants belonging to the Gelsemicaeae ***,a high-quality genome assembly using the Oxford Nanopore Technologies(ONT)platform and high-throughput chromosome conformation capture techniques(Hi-C)were used.A total of 56.11 Gb of raw GridION X5 platform ONT reads(6.23 Gb per cell)were *** filtering,53.45 Gb of clean reads were obtained,giving 160 x coverage *** de novo genome assemblies 335.13 Mb,close to the 338 Mb estimated by k-mer analysis,was generated with contig N50 of 10.23 *** vast majority(99.2%)of the *** assembled sequence was anchored onto 8 *** genome completeness was then evaluated and 1338 of the 1440 conserved genes(92.9%)could be found in the *** annotation revealed that 43.16%of the *** genome is composed of repetitive elements and 23.9%is composed of long terminal repeat *** predicted 26,768 protein-coding genes,of which 84.56%were functionally *** genomic sequences of *** could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.

关键词： Gelsemium elegans Nanopore sequencing Genome assembly Hi-C Genome annotation Monoterpene indole alkaloid

Calcium-dependent protein kinases CPK21 and CPK23 phosphorylate and activate the iron-regulated transporter IRT1 to regulate iron deficiency in Arabidopsis

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Science China(Life Sciences) 2023年第11期66卷 2646-2662页

作者： Zhangqing Wang Yanting Zhang yisong liu Dali Fu Zhang You Panpan Huang Huiling Gao Zhenqian Zhang Cun Wang State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences Northwest A&F UniversityYangling 712100China Institute of Future Agriculture Northwest Agriculture&Forestry UniversityYangling 712100China

Iron(Fe)is an essential micronutrient for all *** availability in the soil is usually much lower than that required for plant growth,and Fe deficiencies seriously restrict crop growth and ***(Ca2+)is a second messenger in all eukaryotes;however,it remains largely unknown how Ca2+regulates Fe *** this study,mutations in CPK21 and CPK23,which are two highly homologous calcium-dependent protein kinases,conferredimpaired growth and rootdevelopment under Fe-deficient conditions,whereas constitutively active CPK21 and CPK23 enhanced plant tolerance to Fe-deficient ***,we found that CPK21 and CPK23 interacted with and phosphorylated the Fe transporter IRONREGULATED TRANSPORTER1(IRT1)at the Ser149 *** analyses and complementation of Fe transport in yeast and plants indicated that IRT1 Ser149 is critical for IRT1 transport *** together,these findings suggest that the CPK21/23-IRT1 signaling pathway is critical for Fe homeostasis in plants and provides targets for improving Fe-deficient environments and breeding crops resistant to Fe-deficient conditions.

关键词： Arabidopsis calcium-dependent protein kinases IRT1 iron

A Method for Software Vulnerability Detection Based on Improved Control Flow Graph

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Wuhan University Journal of Natural Sciences 2019年第2期24卷 149-160页

作者： ZHOU Minmin CHEN Jinfu liu yisong ACKAH-ARTHUR Hilary CHEN Shujie ZHANG Qingchen ZENG Zhifeng School of Computer Science and Communication Engineering Jiangsu University

With the rapid development of software technology, software vulnerability has become a major threat to computer security. The timely detection and repair of potential vulnerabilities in software, are of great significance in reducing system crashes and maintaining system security and integrity. This paper focuses on detecting three common types of vulnerabilities: Unused_Variable, Use_of_Uninitialized_Variable, and Use_After_ Free. We propose a method for software vulnerability detection based on an improved control flow graph(ICFG) and several predicates of vulnerability properties for each type of vulnerability. We also define a set of grammar rules for analyzing and deriving the three mentioned types of vulnerabilities, and design three vulnerability detection algorithms to guide the process of vulnerability detection. In addition, we conduct cases studies of the three mentioned types of vulnerabilities with real vulnerability program segments from Common Weakness Enumeration(CWE). The results of the studies show that the proposed method can detect the vulnerability in the tested program segments. Finally, we conduct manual analysis and experiments on detecting the three types of vulnerability program segments(30 examples for each type) from CWE, to compare the vulnerability detection effectiveness of the proposed method with that of the existing detection tool Cpp Check. The results show that the proposed method performs better. In summary, the method proposed in this paper has certain feasibility and effectiveness in detecting the three mentioned types of vulnerabilities, and it will also have guiding significance for the detection of other common vulnerabilities.

关键词： software security software vulnerability improved control flow graph vulnerability detection algorithm

The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism

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Molecular Plant 2017年第7期10卷 975-989页

作者： Xiubin liu yisong liu Peng Huang Yongshuo Ma Zhixing Qing Qi Tang Huifen Cao Pi Cheng Yajie Zheng Zejun Yuan Yuan Zhou Jinfeng liu Zhaoshan Tang Yixiu Zhuo Yancong Zhang Linlan Yu Jialu Huang Peng Yang Qiong Peng dinbo Zhang Wenkai Jiang Zhonghua Zhang Kui Lin Dae-Kyun Ro Xiaoya Chen Xingyao Xiong Yi Shang Sanwen Huang Jianguo Zeng National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients Horticulture and Landscape College Veterinary Medicine College Hunan Agricultural University Changsha 410128 China Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture Sino-Dutch Joint Laboratory of Horticultural Genomics Beijing 100081 China Agricuitural Genome Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518124 China School of Pharmacy Hunan University of Chinese Medicine Changsha 410208 China MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences Beijing Normal University Beijing 100875 China Micolta Bioresource Inc. Changsha 410016 China Herbal Extract Engineering Research Center Changsha 410331 China Biotechnology Research Center Hunan Academy of Agricultural Sciences Changsha 410125 China Novogene Bioinformatics Institute Beijing 100083 China Department of Biological Sciences University of Calgary Calgary T2N1N4 Canada National Key Laboratory of Plant Molecular Genetics National Plant Gene Research Center Institute of Plant Physiology and Ecology Shanghai Institutes forBiological Sciences Chinese Academy of Sciences Shanghai 200032 China Plant Science Research Center Shanghai Chenshan Botanical Garden Shanghai 201602 China

The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids （BIAs） such as sanguinarine （SAN） and chelerythrine （CHE）, but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding ^13C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M. cordata, the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.

关键词： Macleaya cordata genome Benzylisoquinoline alkaloids Secondary metabolism Sanguinarine Chelerythrine Isotopic labeling

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时分多址信道的实时响应测量

通信学报 1989年第6期10卷 37-46页

作者：刘以暠中国科学院遥感卫星地面站

时分多址信道的实时响应测量,即突发型信道分析技术,是监测和均衡该数字信道的必要手段和数字卫星通信领域的重要课题。本文简单介绍了当前在INTELSAT时分多址系统中采用的雷达方法的突发型信道分析器(BMLA/R),而重点介绍了作者近几年... 详细信息

时分多址信道的实时响应测量,即突发型信道分析技术,是监测和均衡该数字信道的必要手段和数字卫星通信领域的重要课题。本文简单介绍了当前在INTELSAT时分多址系统中采用的雷达方法的突发型信道分析器(BMLA/R),而重点介绍了作者近几年探索的另一种完全不同的新方法:最小二乘法突发型信道分析器(BMLA/LS)。文中对BMLA/LS的基本概念、方法论、性能研究和系统实现作了概括性叙述,并阐明了它对BMLA/R的明显优越性,指出这是一种值得进一步深入探索直至其实际应用的很有前途的新技术。

关键词：时分多址信道数传传输实时响应

VRML虚拟空间协同生成原型系统的研究与开发

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计算机应用研究 2000年第1期17卷 26-28页

作者：刘一松江苏理工大学计算机科学系镇江212013

以该文作者自行开发的ＶＲＭＬ虚拟空间协同生成原型系统（ＭＶＲＣ）为基础；提出了借助ＶＲＭＬ的外部程序接口ＥＡＩ，人－机交互地生成ＶＲＭＬ虚拟空间的方法；论述了通过采用集中式系统结构、利用ＴＣＰ／ＩＰ协议下的ＪａｖａＳ... 详细信息

以该文作者自行开发的ＶＲＭＬ虚拟空间协同生成原型系统（ＭＶＲＣ）为基础；提出了借助ＶＲＭＬ的外部程序接口ＥＡＩ，人－机交互地生成ＶＲＭＬ虚拟空间的方法；论述了通过采用集中式系统结构、利用ＴＣＰ／ＩＰ协议下的ＪａｖａＳｏｃｋｅｔ网络通信机制以及构造相应的网络通信数据包等方法，实现异地多个用户协同工作的过程。ＭＶＲＣ可以成为实现诸如虚拟教室、多用户虚拟展览馆应用系统以及虚拟社区的基础。

关键词： VRML 虚拟空间生成虚拟现实 MVRC 多媒体

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一种基于有色网的行动推理表示模型

江苏大学学报（自然科学版） 2010年第3期31卷 334-338,372页

作者：刘一松钟珊詹永照江苏大学计算机科学与通信工程学院江苏镇江212013

针对行动推理中的异步并发、真并发和冲突难以被表示的问题,利用有色网具有严格的数学模型、易于形式化地描述系统异步、并发等特征的优点,提出一种基于有色网表示行动推理的形式化模型—CPNRAA网.运用其对状态、动作以及复合动作进行... 详细信息

针对行动推理中的异步并发、真并发和冲突难以被表示的问题,利用有色网具有严格的数学模型、易于形式化地描述系统异步、并发等特征的优点,提出一种基于有色网表示行动推理的形式化模型—CPNRAA网.运用其对状态、动作以及复合动作进行了形式化的描述,通过构造动作及复合动作的CPNRAA网并加入一个用于保存动作序列的库所,得出一个可以生成动作序列的CPNRAA网系统,并提出了该网系统动作序列的生成方法.对办公室环境下送咖啡实例的CPNRAA网系统进行了建模和仿真,自动生成的动作序列验证了CPNRAA网表示行动推理的可行性和有效性.

关键词： Petri网人工智能行动推理规划并发

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基于聚类与二分图匹配的语义Web服务发现

计算机工程 2016年第2期42卷 157-163页

作者：刘一松朱丹江苏大学计算机科学与通信工程学院

为高效准确地查找语义Web服务,引入聚类与二分图匹配技术,提出一种新的语义Web服务发现方法。根据服务描述信息将相似服务聚集到一起,采用空间向量模型表示服务,针对标准K-Means算法的缺陷设计基于k值优化和粒子群优化的K-Means聚类算... 详细信息

为高效准确地查找语义Web服务,引入聚类与二分图匹配技术,提出一种新的语义Web服务发现方法。根据服务描述信息将相似服务聚集到一起,采用空间向量模型表示服务,针对标准K-Means算法的缺陷设计基于k值优化和粒子群优化的K-Means聚类算法对服务进行聚类。借鉴带权二分图最优匹配思想对服务的功能属性进行匹配,设计基于Word Net的概念间语义相似度计算方法用于计算二分图的权值,并针对如何构建满足最优匹配条件的带权二分图问题给出解决方案。实验结果表明,该方法在查全率和匹配效率上均优于OWLS-MX方法。

关键词：服务发现 k值优化粒子群优化算法 K-Means算法概念相似度二分图匹配

和谐·交融——当涂县太白生态乐园总体规划解读

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中外建筑 2008年第6期 105-107页

作者：刘屹松安徽省芜湖市规划设计研究院

生态乐园是一种以生态性为主要特征的游乐园。生态乐园是人们对大自然的美好向往。一个完美、和谐、生态稳定的生态乐园,其外部形式应符合美学规律,内部结构与整体功能应符合生态学原理。当涂县太白生态乐园以和谐、生态、人居环境和景... 详细信息

生态乐园是一种以生态性为主要特征的游乐园。生态乐园是人们对大自然的美好向往。一个完美、和谐、生态稳定的生态乐园,其外部形式应符合美学规律,内部结构与整体功能应符合生态学原理。当涂县太白生态乐园以和谐、生态、人居环境和景观美学等理念进行合理规划设计,为游人提供了一个与大自然和谐交融的场所。

关键词：生态乐园规划理念和谐当涂县