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Knock-in of exogenous sequences based on CRISPR/Cas9 targeting autosomal genes and sex chromosomes in the diamondback moth,Plutella xylostella

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Journal of Integrative Agriculture 2024年第9期23卷 3089-3103页

作者： Shanyu Li Guifang Lin Haoqi Wen Haiyan Lu Anyuan Yin Chanqin Zheng Feifei Li Qingxuan Qiao Lu Jiao Ling Lin Yi Yan xiujuan xiang Huang Liao Huiting Feng Yussuf Mohamed Salum Minsheng You Wei Chen Weiyi He State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops/Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops/International Joint Research Laboratory of Ecological Pest Control Ministry of EducationInstitute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou 350002China Ganzhou Key Laboratory of Greenhouse Vegetable Gannan Normal UniversityGanzhou 341000China

Genetic pest control strategies based on precise sex separation and only releasing sterile males can be accomplished by site-specific genome *** the current study,we showed that the mutation of single-allele Pxfl(2)d can significantly impair the normal mating behavior and testis development in male adults of the notorious cruciferous insect pest Plutella xylostella,in addition to its known functions in the ovarian development in female adults and egg *** CRISPR/Cas9-based knock-in experiments revealed that site-specific integration of an exogenous green fluorescent protein(GFP)gene into autosomal Pxfl(2)d for labelling mutants could be ***,this gene is not a suitable target for GFP insertion to establish a genetically stable knock-in strain because of the severe decline in reproductive *** further screened for the W-chromosome-linked and Z-chromosome-linked regions to test the knock-in efficiency mediated by CRISPR/*** results verified that both types of chromosomes can be targeted for the site-specific insertion of exogenous *** ultimately obtained a homozygous knock-in strain with the integration of both Cas9 and cyan fluorescent protein(CFP)expression cassettes on a Z-linked region in ***,which can also be used for early sex *** injecting the sgRNA targeting Pxfl(2)d alone into the eggs laid by female adults of the Z-Cas9-CFP strain,the gene editing efficiency reached 29.73%,confirming the success of expressing a functional Cas9 *** together,we demonstrated the feasibility of the knock-in of an exogenous gene to different genomic regions in ***,while the establishment of a heritable strain required the positioning of appropriate *** study provides an important working basis and technical support for further developing genetic strategies for insect pest control.

关键词： cruciferous specialist fl(2)d CRISPR/Cas9 knock-in sex chromosome

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Detecting protein complexes from DPINs by density based clustering with Pigeon-Inspired Optimization Algorithm

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Science China(Information Sciences) 2016年第7期59卷 30-43页

作者： xiujuan LEI Yulian DING Fang-xiang WU School of Computer Science Shaanxi Normal University School of Mathematical Sciences Nankai University Division of Biomedical Engineering University of Saskatchewan

Detecting protein complexes is crucial to understand principles of cellular organization. Plenty evidences have indicated that sub-graphs with high density in protein-protein interaction(PPI) network, especially dynamic PPI network(DPIN), usually correspond to protein complexes. As a well-known density-based clustering algorithm, Density-Based Spatial Clustering of Applications with Noise(DBSCAN) has been used in many areas due to its simplicity and the ability to detect clusters of different sizes and shapes. However, one of its limitations is that the performance of DBSCAN depends on two specified parameters ε and Min Pts, where εrepresents the maximum radius of a neighborhood from an observing point while Min Pts means the minimum number of data points contained in such a neighborhood. In this article, we develop a new method named as P-DBSCAN to detect protein complexes in DPIN by using Pigeon-Inspired Optimization(PIO) Algorithm to optimize the parameters ε and Min Pts in DBSCAN. The experiments on DIP and MIPS datasets show that P-DBSCAN outperforms the state-of-the-art methods for protein complex detection in terms of several criteria such as precision, recall and f-measure.

关键词： dynamic protein-protein interaction network(DPIN) pigeon-inspired optimization(PIO) protein complex density based clustering gene expression

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CircR2Disease v2.0:An Updated Web Server for Experimentally Validated circRNA–disease Associations and Its Application

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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 435-445页

作者： Chunyan Fan xiujuan Lei Jiaojiao Tie Yuchen Zhang Fang-xiang Wu Yi Pan School of Computer Science Shaanxi Normal UniversityXi’an 710119China Division of Biomedical Engineering University of SaskatchewanSaskatoonSK S7N 5A9Canada Department of Computer Science Georgia State UniversityAtlantaGA 30302USA

With accumulating dysregulated circular RNAs(circRNAs)in pathological processes,the regulatory functions of circRNAs,especially circRNAs as microRNA(miRNA)sponges and their interactions with RNA-binding proteins(RBPs),have been widely ***,the collected information on experimentally validated circRNA-disease associations is only ***,an updated CircR2Disease database providing a comprehensive resource and web tool to clarify the relationships between circRNAs and diseases in diverse species is ***,we present an updated CircR2Disease v2.0 with the increased number of circRNA-disease associations and novel ***2Disease v2.0 provides more than 5-fold experimentally validated circRNA-disease associations compared to its previous *** version includes 4201 entries between 3077 circRNAs and 312 disease ***,the information of circRNA-miRNA,circRNA-miRNA-target,and circRNA-RBP interactions has been manually collected for various ***,the gene symbols of circRNAs and disease name IDs can be linked with various nomenclature *** descriptions such as samples and journals have also been integrated into the updated ***,CircR2Disease v2.0 can serve as a platform for users to systematically investigate the roles of dysregulated circRNAs in various diseases and further explore the posttranscriptional regulatory function in ***,we propose a computational method named circDis based on the graph convolutional network(GCN)and gradient boosting decision tree(GBDT)to illustrate the applications of the CircR2Disease v2.0 ***2Disease v2.0 is available at http://***/CircR2Disease_v2.0 and https://***/bioinforlab/CircR2Disease-v2.0.

关键词： circRNA circRNA-disease association Graph convolutional network Gradient boosting decision tree Machine learning

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Genome editing of PAR2 through targeted delivery of CRISPR-Cas9 system for alleviating acute lung inflammation via ERK/NLRP3/IL-1β and NO/iNOS signalling

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Acta Pharmaceutica Sinica B 2024年第3期14卷 1441-1456页

作者： Xin Zhuo Yue Wu xiujuan Fu Jianbin Li Yuxin xiang Xiaoyu Liang Canquan Mao Yuhong Jiang Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs School of Life Science and EngineeringSouthwest Jiaotong UniversityChengdu 610031China

Excessive and uncontrollable inflammatory responses in alveoli can dramatically exacerbate pulmonary disease progressions through vigorous cytokine releases,immune cell infiltration and protease-driven tissue *** is an urgent need to explore potential drug strategies for mitigating lung ***-activated receptor 2(PAR2)as a vital molecular target principally participates in various inflammatory diseases via intracellular signal ***,it has been rarely reported about the role of PAR2 in lung *** study applied CRISPR-Cas9 system encoding Cas9 and sg RNA(p Cas9-PAR2)for PAR2 knockout and fabricated an anionic human serum albuminbased nanoparticles to deliver p Cas9-PAR2 with superior inflammation-targeting efficiency and stability(TAP/p Cas9-PAR2).TAP/p Cas9-PAR2 robustly facilitated p Cas9-PAR2 to enter and transfect inflammatory cells,eliciting precise gene editing of PAR2 in vitro and in ***,PAR2 deficiency by TAP/p Cas9-PAR2 effectively and safely promoted macrophage polarization,suppressed proinflammatory cytokine releases and alleviated acute lung inflammation,uncovering a novel value of *** also revealed that PAR2-mediated pulmonary inflammation prevented by TAP/p Cas9-PAR2was mainly dependent on ERK-mediated NLRP3/IL-1β and NO/i NOS ***,this work indicated PAR2 as a novel target for lung inflammation and provided a potential nanodrug strategy for PAR2 deficiency in treating inflammatory diseases.

关键词： Protease-activated receptor 2(PAR2) CRISPR-Cas9 Gene editing Inflammation Acute lung inflammation NLRP3 Nanoparticles Drug delivery

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A Bran Specks Detection Method Based on PCNN

A Bran Specks Detection Method Based on PCNN

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2015年中国智能自动化学术会议

作者： Tianfei Chen xiang Wu xiujuan Li School of Electrical Engineering Henan University of Technology

In order to achieve vision detection for tiny bran specks in flour, this paper proposes a new detection method based on pulse coupled neural network(PCNN). First, the flour image is mapped into gray entropy image using local gray entropy transformation, so the location of bran specks in flour can be enhanced in image. Then, the PCNN is utilized for the gray entropy image, and final target segmentation can be completed after iterative processing, while the optimal iteration number is determined according to the minimum cross entropy. The compared experimental results not only demonstrate the effectiveness but also show that the proposed method has a higher detection sensitivity.

关键词： Vision detection Bran specks Gray entropy transformation PCNN

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四川盆地震旦-寒武系油气成藏的Re-Os年代学约束

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地球科学 2019年第3期44卷 713-726页

作者：沈传波葛翔白秀娟中国地质大学构造与油气资源教育部重点实验室湖北武汉430074 中国地质大学资源学院湖北武汉430074 英国杜伦大学地球科学系

四川盆地震旦-寒武系储层具有万亿立方米以上的油气地质储量,具有广阔的勘探前景.复杂的地质条件及多期次构造作用限制了对其油气成藏演化过程的精细刻画.近年来,流体包裹体^(40)Ar/^(39)Ar和烃类Re-Os同位素定年等新技术在油气成藏研... 详细信息

四川盆地震旦-寒武系储层具有万亿立方米以上的油气地质储量,具有广阔的勘探前景.复杂的地质条件及多期次构造作用限制了对其油气成藏演化过程的精细刻画.近年来,流体包裹体^(40)Ar/^(39)Ar和烃类Re-Os同位素定年等新技术在油气成藏研究中表现出良好的潜力和广泛的应用前景.针对四川盆地深部油气成藏演化的定量解析这一问题,在总结前人对震旦-寒武系油气成藏演化地质分析的基础上,结合近期对川中威远气田、川西龙门山矿山梁古油藏和川北米仓山古油藏中沥青Re-Os同位素的定年结果,认为四川盆地震旦-寒武系油气存在～450Ma、205～162Ma两期成藏作用,其中天然气藏形成的关键时期为205～162Ma.还指出了Re-Os同位素分析在定量解析油气演化研究中需要解决的关键问题,并认为烃类的Re-Os同位素定年将会推动我国成藏年代学的发展,促进诸如四川盆地等复杂地质条件深层油气成藏过程和成藏机理的研究.

关键词：成藏作用古油藏沥青成藏年代 Re-Os定年石油地质

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Quantifying climate conditions for the formation of coals and evaporites

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National Science Review 2023年第6期10卷 143-150页

作者： xiujuan Bao Yongyun Hu Christopher R.Scotese xiang Li Jiaqi Guo Jiawenjing Lan Qifan Lin Shuai Yuan Mengyu Wei Zhibo Li Kai Man Zihan Yin Jing Han Jian Zhang Qiang Wei Yonggang Liu Jun Yang Ji Nie Laboratory for Climate and Ocean-Atmosphere Studies Department of Atmospheric and Oceanic Sciences School of Physics Peking University Department of Earth and Planetary Sciences Northwestern University

Coals and evaporites are commonly used as qualitative indicators of wet and dry environments in deep-time climate studies,***,we combine geological records with climate simulations to establish quantitative relationships of coals and evaporites with temperature and precipitation over the *** show that coal records were associated with a median temperature of 25℃ and precipitation of1300 mm yr-1before 250 ***,coal records appeared with temperatures between 0℃ and 21℃and precipitation of 900 mm *** records were associated with a median temperature of 27℃and precipitation of 800 mm *** most remarkable result is that net precipitation associated with coal and evaporite records remained constant across *** results here have important implications for quantifying climate conditions for other lithologic indicators of climate and for predicting exogenetic ore deposits.

关键词： deep-time climate evolution coals evaporites temperature precipitation

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Adaptive optical microscopy via virtual‑imaging‑assisted wavefront sensing for high‑resolution tissue imaging

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PhotoniX 2022年第1期3卷 292-311页

作者： Zhou Zhou Jiangfeng Huang xiang Li xiujuan Gao Zhongyun Chen Zhenfei Jiao Zhihong Zhang Qingming Luo Ling Fu Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and TechnologyWuhan 430074China MoE Key Laboratory for Biomedical Photonics Huazhong University of Science and TechnologyWuhan 430074China School of Biomedical Engineering Hainan UniversityHaikou 570228China

Adaptive optics(AO)is a powerful tool for optical microscopy to counteract the effects of optical aberrations and improve the imaging performance in biological *** diversity of sample characteristics entails the use of different AO schemes to measure the underlying ***,we present an indirect wavefront sensing method leveraging a virtual imaging scheme and a structural-similarity-based shift measurement algorithm to enable aberration measurement using intrinsic structures even with temporally varying *** achieved high-resolution two-photon imaging in a variety of biological samples,including fixed biological tissues and living animals,after aberration *** present AO-incorporated subtractive imaging to show that our method can be readily integrated with resolution enhancement techniques to obtain higher resolution in biological *** robustness of our method to signal variation is demonstrated by both simulations and aberration measurement on neurons exhibiting spontaneous activity in a living larval zebrafish.

关键词： Adaptive optics Microscopy Tissue imaging

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基于累积量的DoS攻击检测算法

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北京工业大学学报 2017年第9期43卷 1328-1334页

作者：王秀娟相从斌北京工业大学信息学部北京100124

针对现有DoS攻击检测算法中检测率较低,检测时间较长的问题,提出一种基于高阶统计量的DoS攻击检测算法.算法分割并量化网络流量数据包,提取累积量特征,将累积量应用到DoS攻击检测中.通过分析1998DARPA入侵检测数据集,该算法能够有效检测... 详细信息

针对现有DoS攻击检测算法中检测率较低,检测时间较长的问题,提出一种基于高阶统计量的DoS攻击检测算法.算法分割并量化网络流量数据包,提取累积量特征,将累积量应用到DoS攻击检测中.通过分析1998DARPA入侵检测数据集,该算法能够有效检测DoS攻击.相对于传统基于网络流量熵值的异常检测法,该算法在检测精度上有较大提高,在1 s的时间窗口内,检测率提高了8%.

关键词：网络安全 DoS攻击入侵检测累积量

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以协作项目为驱动的教学实践与应用

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中国电化教育 2011年第5期 92-96页

作者：伍秀娟项荣健广州市广播电视大学实训中心广东广州510091

"以协作项目为驱动的教学"是针对"哥伦布式的学习"现象而提出的,旨在帮助学生减少学习的盲从性,增加学习的内动力。本文首先阐释了该教学方式内涵,阐述了其特点和教学过程的设计思路,接着以"网页设计"课程为例进行了教学实践,并对应用... 详细信息

"以协作项目为驱动的教学"是针对"哥伦布式的学习"现象而提出的,旨在帮助学生减少学习的盲从性,增加学习的内动力。本文首先阐释了该教学方式内涵,阐述了其特点和教学过程的设计思路,接着以"网页设计"课程为例进行了教学实践,并对应用效果进行了分析,验证了教学方式对学习的积极作用。

关键词：项目协作教学设计

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