A plant disease extension of the Infectious Disease Ontology

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism

Flavour Enhanced Food Recommendation

We propose a mechanism to use the features of flavour to enhance the quality of food recommendations. An empirical method to determine the flavour of food is incorporated into a recommendation engine based on major gustatory nerves. Such a system has advantages of suggesting food items that the user is more likely to enjoy based upon matching with their flavour profile through use of the taste biological domain knowledge. This preliminary intends to spark more robust mechanisms by which flavour of food is taken into consideration as a major feature set into food recommendation systems. Our long term vision is to integrate this with health factors to recommend healthy and tasty food to users to enhance quality of life.Comment: In Proceedings of 5th International Workshop on Multimedia Assisted Dietary Management, Nice, France, October 21, 2019, MADiMa 2019, 6 page

What Do Complex Adaptive Systems Look Like and What Are the Implications for Innovation Policy?

This paper explores the use of complex adaptive systems theory in development policy analysis using a case study drawn from recent events in Uganda. It documents the changes that took place in the farming system in Soroti district during an outbreak of African cassava mosaic virus disease (ACMVD) and the subsequent decline in cassava production - the main staple food in the area. Resultant adaptation impacts are analysed across cropping, biological, economic and social systems each of which operate as an interlinked sub-system. The policy implications of this story suggest a policy agenda that recognises adaptation capacity as the life blood of complex adaptive systems. Since these types of systems are found in all realms of human activity, it follows that strengthening this capacity is a key developmental priority that requires linking together new configurations of actors and resources to tackle an ever-changing set of contexts.Complex Adaptive Systems, Innovation Policy, Uganda, Cassava, Adaptation Capacity, Smallholder Production, Policy

Perceiving and Knowing as Activities

According to the tradition of most empiricists, perception is the basis for all our knowledge (at least of the world). The tradition also assumes that perception by humans is a passive activity resulting in some static states pertaining perception and belief, which are then, in some versions, modified by the mind before being passed onto memory and knowledge. Following the work of J. J. Gibson, we argue that perceiving involves many activities and actions. This is true of both visual as well as olfactory-taste perception. The main moral of this paper is that perceiving and knowing are best thought of not as involving static states, but rather as ongoing temporal activities involving change. This presumably means giving up a frozen ontology of states and moving towards something like a dynamic ontology as a basis

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

[EN] Background Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. Results Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. Conclusions This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.Herraiz García, FJ.; Blanca Postigo, JM.; Ziarsolo Areitioaurtena, P.; Gramazio, P.; Plazas Ávila, MDLO.; Anderson, GJ.; Prohens Tomás, J.... (2016). 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Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato

Because weevils are the most damaging pests of sweetpotato, the development of cultivars resistant to weevil species is considered the most important aspect in sweetpotato breeding. However, the genes and the underlying molecular mechanisms related to weevil resistance are yet to be elucidated. In this study, we performed an RNA sequencing-based transcriptome analysis using the resistant Kyushu No. 166 (K166) and susceptible Tamayutaka cultivars. The weevil resistance test showed a significant difference between the two cultivars at 30 days after the inoculation, specifically in the weevil growth stage and the suppressed weevil pupation that was only observed in K166. Differential expression and gene ontology analyses revealed that the genes upregulated after inoculation in K166 were related to phosphorylation, metabolic, and cellular processes. Because the weevil resistance was considered to be related to the suppression of larval pupation, we investigated the juvenile hormone (JH)-related genes involved in the inhibition of insect metamorphosis. We found that the expression of some terpenoid-related genes, which are classified as plant-derived JHs, was significantly increased in K166. This is the first study involving a comprehensive gene expression analysis that provides new insights about the genes and mechanisms associated with weevil resistance in sweetpotato

Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward <i>Phytophthora infestans</i>

Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato