School of BioSciences - Research Publications
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ItemAbsolute Quantitation of In Vitro Expressed Plant Membrane Proteins by Targeted Proteomics (MRM) for the Determination of Kinetic Parameters.(Humana Press, 2018)The purification of a functional soluble protein from biological or in vitro expression systems can be problematic and the enrichment of a functional membrane protein for biochemical analyses can be a serious technical challenge. Recently we have been characterizing plant endomembrane nucleotide sugar transporters using a yeast expression system. However, rather than enriching these in vitro expressed proteins to homogeneity, we have been conducting biochemical characterization of these transport proteins in yeast microsomal fractions. While this approach has enabled us to estimate a variety of kinetic parameters, the accurate determination of the turnover number of an enzyme-substrate complex (k cat) requires that the catalytic site concentration (amount of protein) in the total reaction volume is known. As a result, we have been employing targeted proteomics (multiple reaction monitoring) with peptide standards and a triple quadrupole mass spectrometer to estimate the absolute amount of protein in a mixed protein microsomal fraction. The following method details the steps required to define the absolute quantitation of an in vitro expressed membrane protein to define complete kinetic parameters.
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ItemEnrichment of Golgi Membranes from Triticum aestivum (Wheat) Seedlings(Humana Press, 2017)The Golgi apparatus is an essential component in the plant secretory pathway. The enrichment of Golgi membranes from plant tissue is fundamental to the study of this structurally complex organelle. The utilization of density centrifugation for the enrichment of Golgi membranes is still the most widely employed isolation technique. Generally, the procedure requires optimization depending on the plant tissue being employed. Here we provide a detailed enrichment procedure that has previously been used to characterize cell wall biosynthetic complexes from wheat seedlings. We also outline several downstream analyses procedures, including nucleoside diphosphatase assays, immunoblotting, and finally localization of putative Golgi proteins by fluorescent tags.
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ItemEnrichment of the Plant Cytosolic Fraction(Humana Press, 2017)The cytosol is at the core of cellular metabolism and contains many important metabolic pathways, including glycolysis, gluconeogenesis, and the pentose phosphate pathway. Despite the importance of this matrix, few attempts have sought to specifically enrich this compartment from plants. Although a variety of biochemical pathways and signaling cascades pass through the cytosol, much of the focus has usually been targeted at the reactions that occur within membrane-bound organelles of the plant cell. In this chapter, we outline a method for the enrichment of the cytosol from rice suspension cell cultures which includes sample preparation and enrichment as well as validation using immunoblotting and fluorescence-tagged proteins.
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ItemProteomic characterization of Golgi membranes enriched from Arabidopsis suspension cell cultures(Springer, 2016)The plant Golgi apparatus has a central role in the secretory pathway and is the principal site within the cell for the assembly and processing of macromolecules. The stacked membrane structure of the Golgi apparatus along with its interactions with the cytoskeleton and endoplasmic reticulum has historically made the isolation and purification of this organelle difficult. Density centrifugation has typically been used to enrich Golgi membranes from plant microsomal preparations, and aside from minor adaptations, the approach is still widely employed. Here we outline the enrichment of Golgi membranes from an Arabidopsis cell suspension culture that can be used to investigate the proteome of this organelle. We also provide a useful workflow for the examination of proteomic data as the result of multiple analyses. Finally, we highlight a simple technique to validate the subcellular localization of proteins by fluorescent tags after their identification by tandem mass spectrometry.
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ItemDynamic Programming(Springer Berlin Heidelberg, 2015)
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ItemEstimating detection rates and probabilities(CABI, 2015-03-13)Quantitative Approaches Frith Jarrad, Samantha Low-Choy, Kerrie Mengersen ... CAB International 2015. Biosecurity Surveillance: Quantitative Approaches (eds 1 Introduction to Biosecurity Surveillance: Quantitative Approaches.
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ItemP opulation V iability A nalysis(Wiley, 2012-08-31)Abstract Population viability analysis (PVA) assesses risks of population decline of species, and how those risks can be managed. Typically, stochastic population models are used to characterize the deterministic and stochastic components that govern changes in population size. Sources of stochasticity include demographic stochasticity due to the chance birth and death of individuals, stochasticity in the environment that is common to all individuals, chance variation in genetic composition, and spatial structure. These factors can interact to create extinction vortices that drive population decline. Predicted risks of population decline from PVA models are usually uncertain due to imprecise parameter estimates, imperfect knowledge about factors that influence dynamics, and uncertainty about future conditions. Despite these sources of uncertainty, changes in risks due to management can be predicted more reliably. Using these changes in risk, PVA can help determine efficient management strategies for reducing high contemporary rates of extinction.
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ItemImplications of Future Climate for Seagrass and Soft Sediments.(Glenelg Hopkins Catchment Management Authority, 2013)