Image-based time series analysis to establish differential disease progression for two Fusarium head blight pathogens in oat spikelets with variable resistance

Oat-based value-added products have increased their value as healthy foodstuff. Fusarium head blight (FHB) infections and the mycotoxins accumulated to the oat seeds, however, pose a challenge to oat production. The FHB infections are predicted to become more prevalent in the future changing climates and under more limited use of fungicides. Both these factors increase the pressure for breeding new resistant cultivars. Until now, however, genetic links in oats against FHB infection have been difficult to identify. Therefore, there is a great need for more effective breeding efforts, including improved phenotyping methods allowing time series analysis and the identification of molecular markers during disease progression. To these ends, dissected spikelets of several oat genotypes with different resistance profiles were studied by image-based methods during disease progression by Fusarium culmorum or F. langsethiae species. The chlorophyll fluorescence of each pixel in the spikelets was recorded after inoculation by the two Fusarium spp., and the progression of the infections was analyzed by calculating the mean maximum quantum yield of PSII (F-v/F-m) values for each spikelet. The recorded values were (i) the change in the photosynthetically active area of the spikelet as percentage of its initial size, and (ii) the mean of F-v/F-m values of all fluorescent pixels per spikelet post inoculation, both indicative of the progression of the FHB disease. The disease progression was successfully monitored, and different stages of the infection could be defined along the time series. The data also confirmed the differential rate of disease progression by the two FHB causal agents. In addition, oat varieties with variable responses to the infections were indicated.Peer reviewe

Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis Leaves

Image-based symptom scoring of plant diseases is a powerful tool for associating disease resistance with plant genotypes. Advancements in technology have enabled new imaging and image processing strategies for statistical analysis of time-course experiments. There are several tools available for analyzing symptoms on leaves and fruits of crop plants, but only a few are available for the model plant Arabidopsis thaliana (Arabidopsis). Arabidopsis and the model fungus Botrytis cinerea (Botrytis) comprise a potent model pathosystem for the identification of signaling pathways conferring immunity against this broad host-range necrotrophic fungus. Here, we present two strategies to assess severity and symptom progression of Botrytis infection over time in Arabidopsis leaves. Thus, a pixel classification strategy using color hue values from red-green-blue (RGB) images and a random forest algorithm was used to establish necrotic, chlorotic, and healthy leaf areas. Secondly, using chlorophyll fluorescence (ChlFl) imaging, the maximum quantum yield of photosystem II (Fv/Fm) was determined to define diseased areas and their proportion per total leaf area. Both RGB and ChlFl imaging strategies were employed to track disease progression over time. This has provided a robust and sensitive method for detecting sensitive or resistant genetic backgrounds. A full methodological workflow, from plant culture to data analysis, is described

Chlorophyll fluorescence imaging for monitoring effects of Heterobasidion parviporum small secreted protein induced cell death and in planta defense gene expression.

Peer reviewe

Genomic and phenomic screens for flower related RING type ubiquitin E3 ligases in Arabidopsis

Flowering time control integrates endogenous as well as environmental signals to promote flower development. The pathways and molecular networks involved are complex and integrate many modes of signal transduction. In plants ubiquitin mediated protein degradation pathway has been proposed to be as important mode of signaling as phosphorylation and transcription. To systematically study the role of ubiquitin signaling in the molecular regulation of flowering we have taken a genomic approach to identify flower related Ubiquitin Proteasome System components. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosen as targets of the genomic screen. To this end the complete list of Arabidopsis RING E3 ligases were retrieved and verified in the Arabidopsis genome v11. Their differential expression was used for their categorization into flower organs or developmental stages. Known regulators of flowering time or floral organ development were identified in these categories through literature search and representative mutants for each category were purchased for functional characterization by growth and morphological phenotyping. To this end, a workflow was developed for high throughput phenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsis plants in one experimental round.Peer reviewe

Phenotyping Fusarium resistance in oats with National Plant Phenotyping Infrastructure - FUSNAPPI

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Using iterative random forest to find geospatial environmental and Sociodemographic predictors of suicide attempts

IntroductionDespite a recent global decrease in suicide rates, death by suicide has increased in the United States. It is therefore imperative to identify the risk factors associated with suicide attempts to combat this growing epidemic. In this study, we aim to identify potential risk factors of suicide attempt using geospatial features in an Artificial intelligence framework.MethodsWe use iterative Random Forest, an explainable artificial intelligence method, to predict suicide attempts using data from the Million Veteran Program. This cohort incorporated 405,540 patients with 391,409 controls and 14,131 attempts. Our predictive model incorporates multiple climatic features at ZIP-code-level geospatial resolution. We additionally consider demographic features from the American Community Survey as well as the number of firearms and alcohol vendors per 10,000 people to assess the contributions of proximal environment, access to means, and restraint decrease to suicide attempts. In total 1,784 features were included in the predictive model.ResultsOur results show that geographic areas with higher concentrations of married males living with spouses are predictive of lower rates of suicide attempts, whereas geographic areas where males are more likely to live alone and to rent housing are predictive of higher rates of suicide attempts. We also identified climatic features that were associated with suicide attempt risk by age group. Additionally, we observed that firearms and alcohol vendors were associated with increased risk for suicide attempts irrespective of the age group examined, but that their effects were small in comparison to the top features.DiscussionTaken together, our findings highlight the importance of social determinants and environmental factors in understanding suicide risk among veterans

Multifaceted roles of RING-type ubiquitin E3 ligases : reverse phenomic approaches

Ubiquitin proteasome system (UPS) is an ATP dependent pathway for targeted protein degradation. The role of UPS is to maintain a healthy protein balance in the cell and to mediate activation and repression of plant developmental processes, hormones and other signalling cascades as well as responses to environmental perturbations. The UPS is composed of several actors, the most important of them being the ubiquitin E3 ligases, which are responsible for providing the specificity for substrate recognition. About 5% of Arabidopsis thaliana genome encodes for ubiquitin E3 ligase genes (~1.400), classified in seven different subgroups, among which the second most abundant group is the RING-type ubiquitin E3 ligase family with nearly 500 members. More than half of the RING-type ubiquitin E3 ligase genes are uncharacterised. Those that are characterized demonstrate their multi-target ability which implies additional roles and cross-reactivity with other pathways. With the emergence of high throughput sequencing, improved Arabidopsis genome assemblies are available and there is a constantly growing amount of transcriptomics data available for the RING-type ubiquitin E3 ligase genes that link them to different developmental stages and perturbations. However, only few of these genes have been associated phenotypically with these processes. Our first aim was to use reverse genetics approach to rescreen Arabidopsis genome in order to update the number of annotated RING-type ubiquitin E3 ligase genes. We further aimed to develop a set of image-based phenotyping methods to systematically assign them in their signalling cascades and developmental pathways, and to functionally characterize the identified molecular networks of the RING-type ubiquitin E3 ligases and their substrates. This study revealed 50 new RING-type ubiquitin E3 ligases genes, while 31 earlier annotated genes were excluded, giving a total new count of 509 RING-type ubiquitin E3 ligases genes. RING-type ubiquitin E3 ligases were then assigned to different developmental, hormonal and/or perturbation related pathways, based on their gene expression profiles. To allow systematic and efficient functional confirmation of these associations in plants, protocols for image-based high throughput phenotypic assays were established. In these assays, the associated knockout lines were studied for rosette shape and growth, cotyledon emergence as a proxy for germination analysis, and Botrytis cinerea symptom progression. These phenotypic screens confirmed 36 flower enriched RING-type ubiquitin E3 ligases, 11 of which were associated to flowering, three rosette and one sepal development. Four of them responded negatively and one positively to ABA treatment at germination. Furthermore, ten RING-type ubiquitin E3 ligases were associated with Botrytis responses, with one characterised at molecular level. Collectively, the results of this study demonstrated the versatility and pleiotropy of RING-type ubiquitin E3 ligases and set the foundation for a systematic screening of phenotypes regulated by UPS components.RING-tyyppisen ubikitiin E3 -liigaasien monipuoliset roolit: käänteiset fenomiset lähestymistava

Fine tuning phenotypic responses to perturbations

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