Browsing by Author "Hilgart, Amelia"

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    Open Access
    Determination of a robust metabolic barcoding model for chemotaxonomy in Aizoaceae species : expanding morphological and genetic understanding
    (2016) Hilgart, Amelia; Gammon, David W; Farrant, Jill M
    The use of metabolic fingerprints as taxonomic markers is becoming more common. Many studies have found that by comparing the vast metabolic fingerprints of closely related species to each other, secondary metabolites tend to be unique to the samples of individual species and are identified in clustering algorithms as the variables responsible for species-specific clustering. A holistic approach to metabolic fingerprinting was thus employed to assess the stability of various metabolomic markers and finally to distinguish taxonomically difficult Aizoaceae species. Many secondary metabolites are not constitutively produced. Because at least some Aizoaceae species facultatively use crassulacean acid metabolism (CAM), there was a potentially interesting molecular switch that could be monitored for transitions in metabolic fingerprints. In order to contextualise the changes in carbon uptake, 20 different climate, nutrient, physiological, and other variables were monitored over the course of 12 months to build up a store of species-specific information to use in model optimisation across 5 Aizoaceae species (Galenia africana, Aridaria noctiora, Carpobrotus edulis, Ruschia robusta, and Tetragonia fruticosa) using two Crassulaceae species as CAM controls (Cotyledon orbiculata and Tylecodon wallichii ). Metabolic fingerprints of the leaves of various Aizoaceae species were generated using LC/TOFMS, following which Principal Components Analysis (PCA) was used to identify the LC-MS ions which distinguished the species from each other, or in statistical terms, were informative. Once isolated, this subset of informative data was established as metabolic barcodes for the identification of the study species. A machine learning algorithm, Random Forest, was used to build a classification model based on the metabolic barcodes which was then trained on various trends from the factors monitored over the year. The use of these trends in the development of a classification model based on metabolic barcodes resulted in a highly robust classification model for species identification. Clustering analysis of a subset of ions which corresponded to compounds previously isolated from Aizoaceae species did not show species-specific clustering and was inevitably biased by compounds from species with a greater number of studies focusing on compound isolation. Ideally, this model should be expanded to include other species from the Aizoaceae family to further check robustness of the model. Application of this model to these and other species could facilitate not only species identification and distribution, but also the identification of novel chemical constructs associated with particular species.
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    Open Access
    A molecular physiological review of vegetative desiccation tolerance in the resurrection plant Xerophyta viscosa (Baker)
    (Springer, 2015-08) Farrant, Jill M; Cooper, Keren; Hilgart, Amelia; Abdalla, Kamal O; Bentley, Joanne; Thomson, Jennifer Ann; Dace, Halford; Mundree, Sagadevan G; Rafudeen, Mohamed S
    Xerophyta viscosa (Baker) is a monocotyledonous resurrection plant from the family Vellociacea that occurs in summer-rainfall areas of South Africa, Lesotho and Swaziland. It inhabits rocky terrain in exposed grasslands and frequently experiences periods of water deficit. Being a resurrection plant it tolerates the loss of 95 % of total cellular water, regaining full metabolic competency within 3 days of rehydration. In this paper, we review some of the molecular and physiological adaptations that occur during various stages of dehydration of X. viscosa, these being functionally grouped into early and late responses, which might be relevant to the attainment of desiccation tolerance. During early drying (to 55 % RWC) photosynthesis is shut down, there is increased presence and activity of housekeeping antioxidants and a redirection of metabolism to the increased formation of sucrose and raffinose family oligosaccharides. Other metabolic shifts suggest water replacement in vacuoles proposed to facilitate mechanical stabilization. Some regulatory processes observed include increased presence of a linker histone H1 variant, a Type 2C protein phosphatase, a calmodulin- and an ERD15-like protein. During the late stages of drying (to 10 % RWC) there was increased expression of several proteins involved in signal transduction, and retroelements speculated to be instrumental in gene silencing. There was induction of antioxidants not typically found in desiccation-sensitive systems, classical stress-associated proteins (HSP and LEAs), proteins involved in structural stabilization and those associated with changes in various metabolite pools during drying. Metabolites accumulated in this stage are proposed, inter alia, to facilitate subcellular stabilization by vitrification process which can include glass- and ionic liquid formation.