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PlaD： A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 283-293页

作者： Huan Qi Zhenhong Jiang Kang zhang Shiping Yang Fei He ziding zhang State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural UniversityBeijing 100193China Jiangxi Key Laboratory of Molecular Medicine The Second Affiliated Hospital of Nanchang UniversityNanchang 330006China Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology China Agricultural UniversityBeijing 100193China Biology Department Brookhaven National LabUptonNY 11967USA

High-throughput transcriptomics technologies have been widely used to study plant transcriptional reprogramming during the process of plant defense responses, and a large quantity of gene expression data have been accumulated in public repositories. However, utilization of these data is often hampered by the lack of standard metadata annotation. In this study, we curated2444 public pathogenesis-related gene expression samples from the model plant Arabidopsis and three major crops （maize, rice, and wheat）. We organized the data into a user-friendly database termed as PlaD. Currently, PlaD contains three key features. First, it provides large-scale curated data related to plant defense responses, including gene expression and gene functional annotation ***, it provides the visualization of condition-specific expression profiles. Third, it allows users to search co-regulated genes under the infections of various pathogens. Using PlaD, we conducted a large-scale transcriptome analysis to explore the global landscape of gene expression in the curated data. We found that only a small fraction of genes were differentially expressed under multiple conditions, which might be explained by their tendency of having more network connections and shorter network distances in gene networks. Collectively, we hope that PlaD can serve as an important and comprehensive knowledgebase to the community of plant sciences, providing insightful clues to better understand the molecular mechanisms underlying plant immune responses. PlaD is freely available at http：//***/plad/*** or http：//***/plad/***.

关键词： PlaD Plant Defense response Transcriptomics databaseGene expression analysis

Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome

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mLife 2024年第2期3卷 277-290页

作者： Pan zhang Biliang zhang Yuan-Yuan Ji Jian Jiao ziding zhang Chang-Fu Tian State Key Laboratory of Plant Environmental Resilience and College of Biological SciencesChina Agricultural UniversityBeijingChina MOA Key Laboratory of Soil Microbiology and Rhizobium Research CenterChina Agricultural UniversityBeijingChina Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina State Key Laboratory of Livestock and Poultry Biotechnology Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina

Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function,while accessory genes are dispensable,particularly in nutrient-rich ***,this assumption is seldom tested genetically within the pangenome *** this study,we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open *** evaluate the robustness of fitness category assignment,Tn-seq data for three independent mutant libraries per strain were analyzed by three methods,which indicates that the Hidden Markov Model(HMM)-based method is most robust to variations between mutant libraries and not sensitive to data size,outperforming the Bayesian and Monte Carlo simulation-based ***,the HMM method was used to classify the fitness *** genes,categorized as essential(ES),advantage(GA),and disadvantage(GD)genes for growth,are enriched in core genes,while nonessential genes(NE)are over-represented in accessory *** ES/GA genes showed a lower fitness effect than core ES/GA *** degrees in the cofitness network decrease in the order of ES,GD,and GA/*** addition to accessory genes,1599 out of 3284 core genes display differential essentiality across test *** the pangenome core,both shared quasi-essential(ES and GA)and strain-dependent fitness genes are enriched in similar functional *** analysis demonstrates a considerable fuzzy essential zone determined by cofitness connectivity degrees in Sinorhizobium pangenome and highlights the power of the cofitness network in understanding the genetic basis of ever-increasing prokaryotic pangenome data.

关键词： cofitnessnetwork pangenome Tn-seq

Prediction and analysis of human-herpes simplex virus type 1 protein-protein interactions by integrating multiple methods

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Quantitative Biology 2020年第4期8卷 312-324页

作者： Xianyi Lian Xiaodi Yang Jiqi Shao Fujun Hou Shiping Yang Dongli Pan ziding zhang State Key Laboratory of Agrobiotechnology College of Biological SciencesChina Agricultural UniversityBeijing 100193China National Demonstration Center for Experimental Biological Sciences Education College of Biological SciencesChina Agricultural UniversityBeijing 100193China Department of Medical Microbiology and Parasitology and Department of Infectious Diseases of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou 310058China State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China

Background:Herpes simplex virus type 1(HSV-1)is a ubiquitous infectious pathogen that widely affects human *** decipher the complicated human-HSV-1 interactions,a comprehensive protein-protein interaction(PPI)network between human and HSV-1 is highly ***:To complement the experimental identification of human-HSV-1 PPIs,an integrative strategy to predict proteome-wide PPIs between human and HSV-1 was *** each human-HSV-1 protein pair,four popular PPI inference methods,including interolog mapping,the domain-domain interaction-based method,the domain-motif interaction-based method,and the machine learning-based method,were optimally implemented to generate four interaction probability scores,which were further integrated into a final probability ***:As a result,a comprehensive high-confidence PPI network between human and HSV-1 was established,covering 10,432 interactions between 4,546 human proteins and 72 HSV-1 *** and network analyses of the HSV-1 targeting proteins in the context of human interactome can recapitulate the known knowledge regarding the HSV-1 replication cycle,supporting the overall reliability of the predicted PPI *** that HSV-1 infections are implicated in encephalitis and neurodegenerative diseases,we focused on exploring the biological significance of the brain-specific human-HSV-1 *** particular,the predicted interactions between HSV-1 proteins and Alzheimer's-disease-related proteins were intensively ***:The current work can provide testable hypotheses to assist in the mechanistic understanding of the human-HSV-1 relationship and the anti-HSV-1 pharmaceutical target *** make the predicted PPI network and the datasets freely accessible to the scientific community,a user-friendly database browser was released at http://***/HintHSV/***.

关键词： human-virus interaction protein-protein interaction prediction herpes simplex virus type 1 Alzheimer's disease

Interrogating WD40 Proteins within Protein-Protein Interaction Network

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Interrogating WD40 Proteins within Protein-Protein Interacti...

CKSAAPUbSite:a Web Server to Predict Ubiquitination Sites in the Proteome of ***

第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Xiaobao Dong ziding zhang State Key Laboratory of Agrobiotechnology China Agricultural University

WD40 proteins are characterized by a class of repeat units known as WD40-repeats. Evidence indicates WD40 proteins take part in a wide range of eukaryotic biological processes from mRNA processing to apoptosis by playing a key role in macromolecular interactions. Biological molecular network has been proved to be a useful tool to bridge genotype and ***,to our knowledge,the properties of WD40 proteins in proteinprotein interaction network have never been systematically *** the development of various high-throughput experimental methods,protein-protein interaction data have been extensively accumulated in yeast,which enables us to comprehensively investigate these important proteins at the interactome *** this work,we found 92 WD40 proteins in the protein-protein interaction network of Saccharomyces *** found that WD40 proteins have more interacting partners than non-WD40 proteins,which is independent of the disorder content and domain ***,only a few WD40 proteins were observed to be highly positively correlated with their partners in mRNA expression level, suggesting WD40 proteins tend to interact with partners at different *** also demonstrate WD40 proteins include more essential proteins for normal yeast growth in comparison to other randomly selected *** studies highlight as key role in biological pathways of eukaryotes,WD40 proteins perform various functions through interacting with number of partners under mediating by WD40 domain in a highly dynamic *** studies are needed to elucidate the common features of interactions of WD40 proteins in multicellular organisms,and more importantly,to associate these features with WD40-related diseases.

关键词： WD40 protein protein-protein interaction network evolutionary rate expression profile disorder content

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CKSAAPUbSite:a Web Server to Predict Ubiquitination Sites in...

Characterization of calcium-dependent protein kinases 2A,a protein expressed during early development of Cryptosporidium parvum

第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Zhen Chen ziding zhang State Key Laboratory of Agrobiotechnology College of Biological SciencesChina Agricultural University

Background:As one of the most important reversible protein post-translation modifications,ubiquitination has been reported to be involved in lots of biological processes. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Methods:Based on our published ubiqutination site prediction method,a user-friendly web server called CKSAAPUbSite was ***,CKSAAPUbSite is an SVMbased predictor and the employed feature vector is the composition of k-spaced amino acid *** protein sequence input to our server should be in RAW or FASTA *** the 20 conventional amino acid symbols are *** prediction output consists of three items:position,score and ubiquitination site annotations(YES for ubiquitination sites,NO for non-ubiquitination sites).Additionally,graph output is also given in the result page to show all the positions of lysines of a query protein and the corresponding prediction scores. Results:A web server of CKSAAPUbSite was constructed,which is freely available at http://***/cksaapbsite/.When intensively tested on a set of experimentally verified ubiquitination sites,the class-balanced accuracy and MCC of CKSAAPUbSite reached 73.40%and 0.4694,respectively. Conclusions:CKSAAPUbSite can be used for proteome-wide ubiquitination site *** the training dataset was selected from the proteome of ***,the application of CKSAAPUbSite should be favorable in the proteome of ***.

关键词： CKSAAPUbSite Proteome Ubiquitination site prediction Web server

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Characterization of calcium-dependent protein kinases 2A,a p...

金属泡沫型微粒捕集器中颗粒物沉积特性试验研究

2021中国畜牧兽医学会兽医寄生虫学分会第16次学术研讨会

作者： Fanfan Shu Na Li Yaqiong Guo Fuxian Yang Yu Li ziding zhang Yaoyu Feng Lihua Xiao

Calcium-dependent protein kinases(CDPKs) are important kinases in response to calcium,functioning as a trigger for several biological functions in Cryptosporidium *** they are not present in mammals,CDPKs are considered promising drug *** studies have characterized CpCDPK1 and CpCDPK3,but the role of CpCPK2 A is still not fully *** this work,we have expressed and purified recombinant CpCDPK2 A in Escherichia *** biologic functions of CpCDPK2 A were characterized using qRT-PCR,immunofluorescence microscopy,immuno-electron microscopy,and in vitro *** results revealed that CpCDPK2 A protein was highly expressed in sporozoites and merozoites and was located in the apical region of the two invasion *** antibodies of CpCDPK2 A failed to block the invasion of host *** of 44 candidate inhibitors screened through molecular docking of CpCDPK2 A,one inhibitor-K292-0423 was identified as having a potential effect on both *** development and CpCDPK2 A enzyme *** data suggests that CpCDPK2 A may play an essential role in the invasion of C parvum.

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西安交通大学学报 2020年第7期54卷 75-83页

作者：张子鼎梁兴雨王亚军王月森李振国张志军天津大学内燃机燃烧学国家重点实验室天津300072 中国汽车技术研究中心有限公司天津300300 中国北方发动机研究所天津300400

为了探究金属泡沫中颗粒物的沉积过程及沉积特性,自行设计开发了颗粒物快速加载系统,结合体式显微镜图像表征方法,在颗粒物加载量为1.5g/h条件下研究了平均孔径为350μm的径向型金属泡沫微粒捕集器中颗粒物沉积特性随时间及沉积深度的... 详细信息

为了探究金属泡沫中颗粒物的沉积过程及沉积特性,自行设计开发了颗粒物快速加载系统,结合体式显微镜图像表征方法,在颗粒物加载量为1.5g/h条件下研究了平均孔径为350μm的径向型金属泡沫微粒捕集器中颗粒物沉积特性随时间及沉积深度的变化关系。结果表明:燃烧器生成的颗粒物与实际发动机的颗粒物粒径相近,金属泡沫捕集器沉积过程中始终存在深床沉积;颗粒物质量沉积速率先增加后稳定,压降增加先快后慢,碳烟质量浓度捕集效率可达82%;大部分颗粒物沉积在第1层滤芯中,末端第1层滤芯上堵塞最严重,颗粒物覆盖面积逐层减小,沉积均匀度沿径向递减;圆筒上颗粒物覆盖面积占比沿进气方向逐渐增大,第1层最末端近100%,由内至外逐层减小,孔隙则逐层增大。研究结果揭示了金属泡沫型微粒捕集器中颗粒物动态沉积过程及沉积特性变化规律,可为金属泡沫型微粒捕集器后续研究提供理论基础。

关键词：金属泡沫微粒捕集器颗粒物沉积特性

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小鼠蛋白质泛素化位点的预测及分析

中国科技论文 2017年第6期12卷 601-606页

作者：赵佳楠陈嘉婧杨世平张子丁中国农业大学生物学院北京100193

采用机器学习中的支持向量机方法开发了小鼠泛素化位点预测新工具UbiqSite。采用6种编码方式表征泛素化位点周围序列模式,5折交叉检验和独立测试方法用于评价预测模型的表现。通过比较,支持向量机对CKSAAP编码的特征构建出的模型具有较... 详细信息

采用机器学习中的支持向量机方法开发了小鼠泛素化位点预测新工具UbiqSite。采用6种编码方式表征泛素化位点周围序列模式,5折交叉检验和独立测试方法用于评价预测模型的表现。通过比较,支持向量机对CKSAAP编码的特征构建出的模型具有较好性能。独立测试结果显示,UbiqSite的Sn、Sp、Ac、MCC、AUC和AUC01值分别为0.682、0.795、0.739、0.480、0.758和0.019。此结果明显优于其他现有的预测模型。鉴于小鼠泛素化位点的预测精度较高,已具有实用价值,进一步构建了1个可供用户免费使用的网络服务器,网址为:http://***/ubiqsite/***。

关键词：生物信息学机器学习蛋白质翻译后修饰泛素化位点预测

非编码RNA在流感病毒与宿主互作过程中的作用

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病毒学报 2017年第1期33卷 108-115页

作者：於子鼎蔡彬祥张兰兰陈吉龙福建农林大学动物科学学院福建福州350002 中国科学院微生物研究所中国科学院病原微生物与免疫学重点实验室北京100101

非编码RNA(non-coding RNA,ncRNA)是一类不具备蛋白质编码能力的RNA。随着转录组研究和新一代测序技术的发展,ncRNAs被证明能够调控包含病毒与宿主相互作用在内的诸多生命活动过程。流感病毒是严重威胁人类健康和畜牧业生产的重要病毒,... 详细信息

非编码RNA(non-coding RNA,ncRNA)是一类不具备蛋白质编码能力的RNA。随着转录组研究和新一代测序技术的发展,ncRNAs被证明能够调控包含病毒与宿主相互作用在内的诸多生命活动过程。流感病毒是严重威胁人类健康和畜牧业生产的重要病毒,其与宿主互作机制及互作过程中产生的病毒变异情况十分复杂。近年来研究表明,许多ncRNAs在流感病毒与宿主的相互作用过程中发挥重要作用。揭示这些ncRNAs在流感病毒感染、复制等过程中的功能,对于阐明流感病毒的致病机理具有重要意义,也为防控流感提供参考。因此,本文对在流感病毒感染中发挥重要调控作用的ncRNAs进行综述。

关键词：非编码RNA 微小RNA 长链非编码RNA 流感病毒天然免疫