BackgroundPseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cultivars of Actinidia chinensis var. chinensis. To gain information about the expression of genes involved in pathogenicity we have carried out transcriptome analysis of Psa during the early stages of kiwifruit infection.ResultsGene expression in Psa was investigated during the first five days after infection of kiwifruit plantlets, using RNA-seq. Principal component and heatmap analyses showed distinct phases of gene expression during the time course of infection. The first phase was an immediate transient peak of induction around three hours post inoculation (HPI) that included genes that code for a Type VI Secretion System and nutrient acquisition (particularly phosphate). This was followed by a significant commitment, between 3 and 24 HPI, to the induction of genes encoding the Type III Secretion System (T3SS) and Type III Secreted Effectors (T3SE). Expression of these genes collectively accounted for 6.3% of the bacterial transcriptome at this stage. There was considerable variation in the expression levels of individual T3SEs but all followed the same temporal expression pattern, with the exception of hopAS1, which peaked later in expression at 48 HPI. As infection progressed over the time course of five days, there was an increase in the expression of genes with roles in sugar, amino acid and sulfur transport and the production of alginate and colanic acid. These are both polymers that are major constituents of extracellular polysaccharide substances (EPS) and are involved in biofilm production. Reverse transcription-quantitative PCR (RT-qPCR) on an independent infection time course experiment showed that the expression profile of selected bacterial genes at each infection phase correlated well with the RNA-seq data.ConclusionsThe results from this study indicate that there is a complex remodeling of the transcriptome during the early stages of infection, with at least three distinct phases of coordinated gene expression. These include genes induced during the immediate contact with the host, those involved in the initiation of infection, and finally those responsible for nutrient acquisition.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5197-5) contains supplementary material, which is available to authorized users.
Pseudomonas syringae pv. actinidiae (Psa), which causes bacterial canker, is the most serious global pathogen of kiwifruit. Like most bacterial pathogens, control options are limited, but elicitors can reduce disease significantly, particularly those that induce the salicylic acid (SA) pathway. Acibenzolar-S-methyl (ASM), a SA analogue, is one of the most effective elicitors for Psa control. In this study, real-time PCR (qPCR) was used to measure the expression of 18 putative defence genes in Actinidia chinensis var. chinensis 'Hort16A' in response to Psa and ASM. Application of ASM led to up-regulation of RPM1 interacting protein 4 (RIN4), phenylalanine ammonia lyase (PAL), a hypersensitivity-induced response protein (HIRP), and β-1,3-glucosidase. Expression of PAL and HIRP was further enhanced when elicitor application and Psa-inoculation were combined. Elevated gene expression was correlated with decreased disease expression, and supports the hypothesis that elicitor-treated plants are primed to react more rapidly and/or strongly to pathogens.
Quantitative methods to describe the participation to debate of Members of Parliament and the parties they belong to are lacking. Here we propose a new approach that combines topic modeling with complex networks techniques, and use it to characterize the political discourse at the New Zealand Parliament. We implement a Latent Dirichlet Allocation model to discover the thematic structure of the government’s digital database of parliamentary speeches, and construct from it two-mode networks linking Members of the Parliament to the topics they discuss. Our results show how topic popularity changes over time and allow us to relate the trends followed by political parties in their discourses with specific social, economic and legislative events. Moreover, the community analysis of the two-mode network projections reveals which parties dominate the political debate as well as how much they tend to specialize in a small or large number of topics. Our work demonstrates the benefits of performing quantitative analysis in a domain normally reserved for qualitative approaches, providing an efficient way to measure political activity.
BackgroundPseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cultivars of Actinidia chinensis var. chinensis. To gain information about the expression of genes involved in pathogenicity we have carried out transcriptome analysis of Psa during the early stages of kiwifruit infection.ResultsGene expression in Psa was investigated during the first five days after infection of kiwifruit plantlets, using RNA-seq. Principal component and heatmap analyses showed distinct phases of gene expression during the time course of infection. The first phase was an immediate transient peak of induction around three hours post inoculation (HPI) that included genes that code for a Type VI Secretion System and nutrient acquisition (particularly phosphate). This was followed by a significant commitment, between 3 and 24 HPI, to the induction of genes encoding the Type III Secretion System (T3SS) and Type III Secreted Effectors (T3SE). Expression of these genes collectively accounted for 6.3% of the bacterial transcriptome at this stage. There was considerable variation in the expression levels of individual T3SEs but all followed the same temporal expression pattern, with the exception of HopAS1, which peaked later in expression at 48 HPI. As infection progressed over the time course of five days, there was an increase in the expression of genes with roles in sugar, amino acid and sulfur transport and the production of alginate and colanic acid. These are both polymers that are major constituents of extracellular polysaccharide substances (EPS) and are involved in biofilm production. Reverse transcription-quantitative PCR (RT-qPCR) on an independent infection time course experiment showed that the expression profile of selected bacterial genes at each infection phase correlated well with the RNA-seq data.ConclusionsThe results from this study indicate that there is a complex remodeling of the transcriptome during the early stages of infection, with at least three distinct phases of coordinated gene expression. These include genes induced during the immediate contact with the host, those involved in the initiation of infection, and finally those responsible for nutrient acquisition.
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