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Development of a rapid and efficient system for CR genes identification based on hairy root transformation in Brassicaceae

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Horticultural Plant Journal 2024年第4期10卷 1049-1060页

作者： Wenlin Yu Lu Yang Yuanyuan Xiang Rongde Li xueqing zhou Longcai Gan Xianyu Xiang Yunyun Zhang Lei Yuan Yanqing Luo Genze Li Youning Wang Yinhua Chen Peng Chen Chunyu Zhang National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology Huazhong Agricultural University National Agro-Tech Extension and Service Center Industrial Crops Research Institute Yunnan Academy of Agricultural Sciences College of Agronomy Northwest A&F University National Key Laboratory for Tropical Crop Breeding Sanya Nanfan Research InstituteHainan University

Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by Plasmodiophora brassicae infection.Breeding of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this disease.The traditional way of R gene functional validation requires stable transformation that is both time-and labor-consuming.In this study,a rapid and efficient hairy-root transgenic protocol mediated by Agrobacterium rhizogenes was developed.The transformation positive rate was over 80% in Brassica napus showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable transformation.The system was applicable to different B.napus varieties and other cruciferous crops including Brassica rapa and Brassica oleracea.In particular,two known CR genes,CRA3.7.1 and CRA8.2.4 were used respectively,as example to show that the system works well for CR gene study combined with subsequent P.brassicae infection in B.napus.Most importantly,it works both in over-expression that led to disease resistance,as well as in RNAi which led to disease susceptible phenotype.Therefore,this system can be used in batch-wise identification of CR genes,and also offered the possibility of manipulating key genes within the P.brassicae genome that could improve our knowledge on host-pathogen interaction.

关键词： Brassicaceae Agrobacterium rhizogenes Hairy root transformation Clubroot Gene function

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Saturation evaluation for fine-grained sediments

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Geoscience Frontiers 2023年第4期14卷 57-71页

作者： Linqi Zhu Shiguo Wu xueqing zhou Jianchao Cai Key Laboratory of Marine Geophysics and Georesource Institute of Deep-sea Science and EngineeringChinese Academy of SciencesSanya 572000China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai 519000China University of Chinese Academy of Sciences Beijing 100049China Sanya Institute of Deep-sea Science and Engineering Chinese Academy of SciencesSanya 572000China State Key Laboratory of Petroleum Resources and Prospecting China University of PetroleumBeijing 102249China

Accurate quantification of the gas hydrate content in the deep sea is useful for assessing the resource potential and understanding the role of gas hydrates in the global carbon cycle.Resistivity logging data combined with Archie’s equation are often used to calculate gas hydrate saturation,but the reliability is dependent on the rationality of the empirical parameter cementation factor and saturation index.At present,an increasing number of fine-grained hydrate-rich sediment regions have been discovered worldwide through drilling efforts,and the reservoir types and hydrate distribution are diverse,which differs greatly from that of coarse-grained reservoirs of hydrate-bearing sediment.This results in vertical variations in m and n through stratigraphy.At present,the saturation evaluation effect of these reservoirs cannot be improved.In this work,a theory for the determination of the cementation factor and saturation index was first proposed to obtain reliable and variable values of the empirical parameters.Then,a hydrate saturation evaluation technique with variables m and n was formed based on the well logging data.This technique was used to evaluate complex fine-grained hydrate-bearing reservoirs in several regions worldwide.It was found that the highest n could be 16,and the log calculation results were more consistent with the core hydrate saturation.Additionally,the cause of the excessively high n values was explained from physical principles,and the result was verified with actually well log data.In future evaluations of the amount of hydrate resources in fine-grained sediment reservoirs worldwide,new saturation estimation methods should be taken into account to advance hydrate research.

关键词： Hydrate Fine-grained Cementation factor Saturation index Archie Petrophysics

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Total organic carbon content logging prediction based on machine learning:A brief review

能源地球科学(英文)

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能源地球科学(英文) 2023年第2期4卷 100-107页

作者： Linqi Zhu xueqing zhou Weinan Liu Zheng Kong Institute of Deep-sea Science and Engineering Chinese Academy of SciencesSanyaHainan572000China Southern Marine Science and Engineering Guangdong Laboratory Zhuhai ZhuhaiGuangdong519000China CNOOC China Limited LtdShenzhen BranchShenzhen518054China Exploration and Development Research Institute Shengli Oilfield CompanySINOPECDongyingShandong257029China

The total organic carbon content usually determines the hydrocarbon generation potential of a formation.A higher total organic carbon content often corresponds to a greater possibility of generating large amounts of oil or gas.Hence,accurately calculating the total organic carbon content in a formation is very important.Present research is focused on precisely calculating the total organic carbon content based on machine learning.At present,many machine learning methods,including backpropagation neural networks,support vector regression,random forests,extreme learning machines,and deep learning,are employed to evaluate the total organic carbon content.However,the principles and perspectives of various machine learning algorithms are quite different.This paper reviews the application of various machine learning algorithms to deal with total organic carbon content evaluation problems.Of various machine learning algorithms used for TOC content predication,two algorithms,the backpropagation neural network and support vector regression are the most commonly used,and the backpropagation neural network is sometimes combined with many other algorithms to achieve better results.Additionally,combining multiple algorithms or using deep learning to increase the number of network layers can further improve the total organic carbon content prediction.The prediction by backpropagation neural network may be better than that by support vector regression;nevertheless,using any type of machine learning algorithm improves the total organic carbon content prediction in a given research block.According to some published literature,the determination coefficient(R^(2))can be increased by up to 0.46 after using machine learning.Deep learning algorithms may be the next breakthrough direction that can significantly improve the prediction of the total organic carbon content.Evaluating the total organic carbon content based on machine learning is of great significance.

关键词： Total organic carbon content Well logging Machine learning Backpropagation neural network Support vector regression

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基于深度学习的多模态新闻数据主题发现研究

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数据分析与知识发现 2024年第3期8卷 85-97页

作者：倪亮吴鹏周雪晴南京理工大学网络空间安全学院南京210094 南京理工大学智能制造学院南京210094 南京理工大学经济管理学院南京210094

【目的】基于多模态学习方法,对新闻中文本和图片相结合内容,构建多模态主题模型,自动挖掘新闻中的潜在主题。【方法】采用结合词嵌入的主题模型,从图片和文本两方面进行主题建模,并且使用多模态联合表征学习和协同表征学习的方法进行... 详细信息

【目的】基于多模态学习方法,对新闻中文本和图片相结合内容,构建多模态主题模型,自动挖掘新闻中的潜在主题。【方法】采用结合词嵌入的主题模型,从图片和文本两方面进行主题建模,并且使用多模态联合表征学习和协同表征学习的方法进行特征融合。最后,对发现的多模态新闻主题进行可视化分析,结合N15News数据集进行实证研究。【结果】实验结果表明,相对于仅使用文本特征的Label-ETM,多模态主题建模方法可以获得更好的主题的可解释性和多样性。这说明多模态主题建模方法具有一定的可行性与合理性。【局限】本文假设新闻中的图片和文字在语义和主题上是相关的,在弱相关和不相关领域多模态融合方法仍需要改善。【结论】多模态主题建模可以发现不同模态数据之间的联系,提高发现主题的多样性。

关键词：主题模型多模态联合表征多模态协同表征新闻主题发现

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Controllable coating NiAl-layered double hydroxides on carbon nanofibers as anticorrosive microwave absorbers

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Journal of Materials Science & Technology 2023年第20期151卷 109-118页

作者： Ying Zhang Liang Li Changlong Du Gengping Wan Qiyi Wei xueqing zhou Yanran Su Yang Xu Guizhen Wang State Key Laboratory of Marine Resource Utilization in South China Sea School of Chemical Engineering and TechnologyHainan UniversityHaikou 570228China Collaborative Innovation Center of Ecological Civilization Hainan UniversityHaikou 570228China

For harsh real-world service settings,it is essential to build corrosion-resistant,diverse,and effective microwave absorbers.Herein,we successfully prepared a 3D NiAl-layered double hydroxide/carbon nanofibers(NiAl-LDH/CNFs)composite material as an anticorrosive microwave absorber assisted by an atomic layer deposition(ALD)method.The size,coating thickness,and content of NiAl-LDH can be readily adjusted by changing the ALD cycling numbers.The optimized NiAl-LDH/CNFs demonstrates prominent microwave absorbing properties including the strongest reflection loss of–55.65 dB and the widest effective absorption bandwidth of 4.80 GHz with only 15 wt%loading.The reasons for performance improvement are the cooperative effect of interfacial polarization loss,conduction loss,and three-dimensional porous structure.Moreover,due to the synergistic effects between the excellent impermeability of CNFs and the trapping ability of NiAl-LDH for chloride ions,NiAl-LDH/CNFs exhibits strong corrosion resistances under acidic,neutral,and alkaline conditions.NiAl-LDH/CNFs should be a potential candidate to simultaneously use for microwave absorption and corrosion resistance,and this work provides a certain guiding significance for designing microwave absorbers that satisfy the corrosion resistance.

关键词： Microwave absorption Anticorrosion Atomic layer deposition(ALD) Double layered hydroxides(LDHs) Carbon nanofibers(CNFs)

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Erratum to: Inhibition of chemotherapy-related breast tumor EMT by application of redox-sensitive siRNA delivery system CSO-ss-SA/siRNA along with doxorubicin treatment

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2022年第2期23卷 171-172页

作者： Xuan LIU xueqing zhou Xuwei SHANG Li WANG Yi LI Hong YUAN Fuqiang HU College of Pharmaceutical Science Zhejiang UniversityHangzhou 310058China

The original version of this article(Liu et al.,2020)unfortunately contained some mistakes.1.Figs.7c and 7d in p.229 were incorrect.The upper left and bottom left pictures in Fig.7c were accidentally duplicated with t... 详细信息

关键词： treatment picture

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基于知识图谱的煤矿建设安全领域知识管理研究

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中国安全科学学报 2024年第5期34卷 28-35页

作者：许娜梁燕翔王亮赵丽丽周雪晴张博中国矿业大学力学与土木工程学院江苏徐州221116 中国矿业大学安全工程学院江苏徐州221116 上海勘测设计研究院有限公司上海200434 中国矿业大学计算机科学与技术学院江苏徐州221116

为解决煤矿建设过程中数据积累存在的知识冗余现象,研究基于知识图谱(KG)的安全领域知识管理。从安全管理系统结构和安全隐患风险管理2个维度,系统化分析领域标准规范文本,界定煤矿建设安全管理领域的12类实体类型和10种关系类型,完善... 详细信息

为解决煤矿建设过程中数据积累存在的知识冗余现象,研究基于知识图谱(KG)的安全领域知识管理。从安全管理系统结构和安全隐患风险管理2个维度,系统化分析领域标准规范文本,界定煤矿建设安全管理领域的12类实体类型和10种关系类型,完善知识结构模式;选取领域43部标准规范为数据源,引入规则、机器学习法、深度学习法识别文本实体和关系;针对不同实体类型,提出领域知识综合方法框架,并对比分析双向长短期记忆(BiLSTM)和条件随机场(CRF)与双向编码器表示(BERT)-BiLSTM-CRF模型。研究结果表明:BERT-BiLSTM-CRF模型在准确率、召回率和F1值方面均比BiLSTM-CRF模型高出7%,验证了所选模型的优越性和准确性;通过知识抽取、知识存储及可视化等过程,挖掘出煤矿建设安全领域不同实体类型所包含的实体和不同实体间的关系。

关键词：知识图谱(KG) 煤矿建设安全领域安全管理知识结构实体类型

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Pterostilbene accelerates wound healing by modulating diabetes-induced estrogen receptorβsuppression in hematopoietic stem cells

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Burns & Trauma 2021年第1期9卷 629-641页

作者： Weiguo Xie xueqing zhou Weigang Hu Zhigang Chu Qiongfang Ruan Haimou Zhang Min Li Hongyu Zhang Xiaodong Huang Paul Yao Institute of Burns Tongren Hospital of Wuhan University(Wuhan Third Hospital)Wuhan 430060China State Key Lab of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan430062China Department of Hematology Peking University Shenzhen HospitalShenzhen518036China

Background:Delayed wound healing is one of the major complications of diabetes mellitus and is characterized by prolonged inflammation,delayed re-epithelialization and consistent oxidative stress,although the detailed mechanism remains unknown.In this study,we aimed to investigate the potential role and effect of pterostilbene(PTE)and hematopoietic stem cells(HSCs)on diabetic wound healing.Methods:Diabetic rats were used to measure the epigenetic changes in both HSCs and peripheral blood mononuclear cells(PBMCs).A cutaneous burn injury was induced in the rats and PTE-treated diabetic HSCs were transplanted for evaluation of wound healing.In addition,several biomedical parameters,including gene expression,oxidative stress,mitochondrial function and inflammation in macrophages,were also measured.Results:Our data showed that PTE had a much stronger effect than resveratrol on accelerating diabetic wound healing,likely because PTE can ameliorate diabetes-induced epigenetic changes to estrogen receptorβpromoter in HSCs,while resveratrol cannot.Further investigation showed that bone marrow transplantation of PTE-treated diabetic HSCs restores diabetes-induced suppression of estrogen receptorβand its target genes,including nuclear respiratory factor-1 and superoxide dismutase 2,and protects against diabetes-induced oxidative stress,mitochondrial dysfunction and elevated pro-inflammatory cytokines in both PBMCs and macrophages,subsequently accelerating cutaneous wound healing.Conclusions:HSC may play an important role in wound healing through transferring epigenetic modifications to subsequent PBMCs and macrophages by differentiation,while PTE accelerates diabetic wound healing by modulating diabetes-induced epigenetic changes in HSCs.Thus,PTE may be a novel therapeutic strategy for diabetic wound healing.

关键词： Hematopoietic stem cells Inflammation Oxidative stress Pterostilbene Wound healing

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Hypoxia sensitive chitosan-nitroimidazole micelles for treating metastatic breast cancer

Hypoxia sensitive chitosan-nitroimidazole micelles for treat...

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2018年第十二届中国药物制剂大会

作者：刘璇 xueqing zhou Xuwei Shang Fuqiang Hu Colloege of Pharmaceutical Science Zhejiang University

Hypoxia is a shared niche characteristic in maintaining quiescence in metastatic cancer cell type, which is associated with cell proliferation, invasion and metastasis, apoptosis and resistance to therapies. Nitroreductase（NTR） is an enzyme highly expressed in hypoxic solid tumors. It is reported that, under hypoxic conditions, hydrophobic 2-nitroimidazole（2-NI） is converted to hydrophilic 2-aminoimidazole via selective bioreductions by NTRs. Among all the nitroaromatic derivatives investigated, 2-NI has been most widely used. Thus, we designed a chitosan-nitroimidazole micelles which can selectively release drugs under hypoxic conditions due to the NTR sensitivity. 2-NI was conjugated to the hydrophilic chitonsan（Mw 5 k Da） forming hypoxia sensitive micelles（CS-NI）. The particle size of CS-NI ranged from 117±2.1 nm to 128±3.2 nm, with the zeta potential ranging from 25.29±0.05 mV to 14.22±0.15 mV. Doxorubicin（DOX） or coumarin 6（C6） could be effectively encapsulated into CS-NI as model drugs. Compared to the non-hypoxia sensitive drug delivery system, CS-NI/DOX exhibited increased drug release under hypoxic condition in vitro. Microscopic observation showed that the CS-NI/DOX represent higher drug release rate in 4 T1 cells or 4 T1 3 D cellular spheroids compared to non-hypoxia sensitive drug loading micelles. The obvious separation of red and green spots in microscopy images showed that RITC labelled CS-NI/C6 could release C6 efficiently in hypoxic 4 T1 cells. It was also found that CS-NI/DOX showed higher toxicity to metastatic breast cancer cells hypoxic conditions. Furthermore, modified with tetraiodothy-roacetic acid（TET）, a ligand of integrin αvβ3 receptor, TET-CS-NI showed an increased tumor distribution and represented enhanced drug release in hypoxia tumor in vivo. In conclusion, CS-NI has the potential to be a nanocarrier for drug delivery to hypoxic metastatic cancer cells.

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Correction of a CADASIL point mutation using adenine base editors in hiPsCsandbloodvessel organoids

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Journal of Genetics and Genomics 2024年第2期51卷 197-207页

作者： Jingwen Wang Lei Zhang Guanglan Wu Jinni Wu Xinyao zhou Xiaolin Chen Yongxia Niu Yiren Jiao Qianyi Liu Puping Liang Guang Shi xueqing Wu Junjiu Huang MOE Key Laboratory of Gene Function and Regulation State Key Laboratory of BiocontrolSchool of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China Key Laboratory of Reproductive Medicine of Guangdong Province The First Affiliated Hospital and School of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China Center of Reproductive Medicine Children's Hospital of Shanxi and Women Health Center of ShanxiTaiyuanShanxi 030013China

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a monogenic small vessel disease caused by mutations in the NOTCH3 gene. However, the pathogenesis of CADASIL remains unclear, and patients have limited treatment options. Here, we use human induced pluripotent stem cells (hiPSCs) generated from the peripheral blood mononuclear cells of a patient with CADASIL carrying a heterozygous NOTCH3 mutation (c.1261C>T, p.R421C) to develop a disease model. The correction efficiency of different adenine base editors (ABEs) is tested using the HEK293T-NOTCH3 reporter cell line. ABEmax is selected based on its higher efficiency and minimization of predicted off-target effects. Vascular smooth muscle cells (VSMCs) differentiated from CADASIL hiPSCs show NOTCH3 deposition and abnormal actin cytoskeleton structure, and the abnormalities are recovered in corrected hiPSC-derived VSMCs. Furthermore, CADASIL blood vessel organoids generated for in vivo modeling show altered expression of genes related to disease phenotypes, including the downregulation of cell adhesion, extracellular matrix organization, and vessel development. The dual adeno-associated virus (AAV) split-ABEmax system is applied to the genome editing of vascular organoids with an average editing efficiency of 8.82%. Collectively, we present potential genetic therapeutic strategies for patients with CADASIL using blood vessel organoids and the dual AAV split-ABEmax system.

关键词： CADASIL Induced pluripotent stem cells Adenine base editors AAV Blood vessel Organoid

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