School of BioSciences - Research Publications

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    Absolute Quantitation of In Vitro Expressed Plant Membrane Proteins by Targeted Proteomics (MRM) for the Determination of Kinetic Parameters.
    Rautengarten, C ; Ebert, B ; Heazlewood, JL ; Mock, H-P ; Matros, A ; Witzel, K (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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    Enrichment of Golgi Membranes from Triticum aestivum (Wheat) Seedlings
    Zeng, W ; Ebert, B ; Parsons, HT ; Rautengarten, C ; Bacic, A ; Heazlewood, JL ; Taylor, NL ; Millar, AH (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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    Enrichment of the Plant Cytosolic Fraction
    Lao, J ; Smith-Moritz, AM ; Mortimer, JC ; Heazlewood, JL ; Taylor, NL ; Millar, AH (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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    Proteomic characterization of Golgi membranes enriched from Arabidopsis suspension cell cultures
    Hansen, SF ; Ebert, B ; Rautengarten, C ; Heazlewood, JL ; Brown, WJ (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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    The technology revolution: improving species detection and monitoring using new tools and statistical methods
    Lahoz-Monfort, J ; Tingley, R ; Legge, S ; Lindenmayer, D ; Natasha, R ; Scheele, B ; Southwell, D ; Wintle, B (CSIRO Publishing, 2018)
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    Dynamic Programming
    Sniedovich, M (Springer Berlin Heidelberg, 2015)
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    Estimating detection rates and probabilities
    HAUSER, CE ; Garrard, GE ; Moore, JL ; Jarrad, F ; Low Choy, S ; Mengersen, K (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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    What Is Expert Knowledge, How Is Such Knowledge Gathered, and How Do We Use It to Address Questions in Landscape Ecology?
    McBride, MF ; Burgman, MA ; Perera, AH ; Drew, CA ; Johnson, CJ (SPRINGER, 2012-01-01)
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    P opulation V iability A nalysis
    McCarthy, MA ; Possingham, HP ; Levin, S (Wiley, 2012-08-31)
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    Implications of Future Climate for Seagrass and Soft Sediments.
    MORRIS, E ; Klemke, J ; Arundel, H (Glenelg Hopkins Catchment Management Authority, 2013)