BackgroundThe important cereal crop Sorghum bicolor (L.) Moench biosynthesize and accumulate the defensive compound dhurrin during development. Previous work has suggested multiple roles for the compound including a function as nitrogen storage/buffer. Crucial for this function is the endogenous turnover of dhurrin for which putative pathways have been suggested but not confirmed.ResultsIn this study, the biosynthesis and endogenous turnover of dhurrin in the developing sorghum grain was studied by metabolite profiling and time-resolved transcriptome analyses. Dhurrin was found to accumulate in the early phase of grain development reaching maximum amounts 25 days after pollination. During the subsequent maturation period, the dhurrin content was turned over, resulting in only negligible residual dhurrin amounts in the mature grain. Dhurrin accumulation correlated with the transcript abundance of the three genes involved in biosynthesis. Despite the accumulation of dhurrin, the grains were acyanogenic as demonstrated by the lack of hydrogen cyanide release from macerated grain tissue and by the absence of transcripts encoding dhurrinases. With the missing activity of dhurrinases, the decrease in dhurrin content in the course of grain maturation represents the operation of hitherto uncharacterized endogenous dhurrin turnover pathways. Evidence for the operation of two such pathways was obtained by metabolite profiling and time-resolved transcriptome analysis. By combining cluster- and phylogenetic analyses with the metabolite profiling, potential gene candidates of glutathione S-transferases, nitrilases and glycosyl transferases involved in these pathways were identified. The absence of dhurrin in the mature grain was replaced by a high content of proanthocyanidins. Cluster- and phylogenetic analyses coupled with metabolite profiling, identified gene candidates involved in proanthocyanidin biosynthesis in sorghum.ConclusionsThe results presented in this article reveal the existence of two endogenous dhurrin turnover pathways in sorghum, identify genes putatively involved in these transformations and show that dhurrin in addition to its insect deterrent properties may serve as a storage form of reduced nitrogen. In the course of sorghum grain maturation, proanthocyanidins replace dhurrin as a defense compound. The lack of cyanogenesis in the developing sorghum grain renders this a unique experimental system to study CNglc synthesis as well as endogenous turnover.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3360-4) contains supplementary material, which is available to authorized users.

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This paper introduces a new theory of multiparty session types based on symmetric sum types, by which we can type non-deterministic orchestration choice behaviours. While the original branching type in session types can represent a choice made by a single participant and accepted by others determining how the session proceeds, the symmetric sum type represents a choice made by agreement among all the participants of a session. Such behaviour can be found in many practical systems, including collaborative workflow in healthcare systems for clinical practice guidelines (CPGs). Processes using the symmetric sums can be embedded into the original branching types using conductor processes. We show that this type-driven embedding preserves typability, satisfies semantic soundness and completeness, and meets the encodability criteria [18,9] adapted to the typed setting. The theory leads to an efficient implementation of a prototypical tool for CPGs which automatically translates the original CPG specifications from a representation called the Process Matrix to symmetric sum types, type checks programs and executes them.

This paper proposes a new theory of multiparty session types with assertions based on symmetric sum types and demonstrates its applicability to collaborative workflows in healthcare systems for clinical practice guidelines (CPGs). The theory leads to a model-driven implementation of a prototype tool for CPGs which automatically generates deadlock-free distributed programs from user-friendly declarative workflows specified as a Process Matrix spreadsheet. In addition to safety properties, the generated code can ensure the logical properties declared in a Process Matrix. They are subsequently interpreted to provide a trustworthy pervasive workflow execution on Android tablet PCs. We also report on a demonstration of the prototype to a physician, who after having seen an example healthcare workflow being executed, was able to specify her own healthcare workflow declaratively as a Process Matrix spreadsheet and immediately test it on the Android tablet PCs.

Abstract. Regular expression parsing is the problem of producing a parse tree of a string for a given regular expression. We show that a compact bit representation of a parse tree can be produced efficiently, in time linear in the product of input string size and regular expression size, by simplifying the DFA-based parsing algorithm due to Dubé and Feeley to emit the bits of the bit representation without explicitly materializing the parse tree itself. We furthermore show that Frisch and Cardelli's greedy regular expression parsing algorithm can be straightforwardly modified to produce bit codings directly. We implement both solutions as well as a backtracking parser and perform benchmark experiments to gauge their practical performance. We observe that our DFA-based solution can be significantly more time and space efficient than the Frisch-Cardelli algorithm due to its sharing of DFAnodes, but that the latter may still perform better on regular expressions that are "more deterministic" from the right than the left. (Backtracking is, unsurprisingly, quite hopeless.)