School of BioSciences - Research Publications

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    Using Computer-Assisted Argument Mapping to Teach Reasoning to Students
    Davies, W ; van Gelder, T ; Barnett, A ; Blair, A (Windsor Studies in Argumentation, 2021-03-01)
    Critical thinking deserves both imaginative teaching and serious theoretical attention. Studies in Critical Thinking assembles an all-star cast to serve both.
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    Gene Regulatory Network Inference
    Babtie, AC ; Stumpf, MPH ; Thorne, T (Elsevier, 2021)
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    Scicurious as method: Learning from GLAM Young People Living in a Pandemic about Cultivating Digital Co-Research-Creation Spaces that Ignite Curiosity and Creativity
    Coleman, K ; Healy, S ; Wouters, N ; Martin, J ; Campbell, L ; Peck, S ; Belton, A ; Hiscock, R ; Kara, H ; Khoo, S-M (Policy Press, 2020)
    Could COVID-​19, this unexpected crisis, act as a comma 6 in a co-​research-​creation project to become a breathing space and not a full stop? Maybe this pause is a colon: the two different periods of the project (and life in general) on either side of the pandemic, equally important and dependent on each other for full meaning. In this chapter, we tell the story of how a co-​research-​creation event (the Sci Curious Project) unfolded before and during the COVID-​19 pandemic 7 ; the lead-​up to its irruption (St. Pierre, 1997) and then what came after. ‘Scicurious as method’ emerged out of the unexpected pause and recalibration of the project; a method that emphasizes the creation of research spaces that activate scicuriosity in situated practice. We understand scicuriosity as emerging from collaborative research-​creation events that ignite curiosity and creativity. Scicurious as method is presented through an encounter with speculative fiction and scicurious zine travels. Scicurious as method has significant ethical implications, these reify the potential of co-​designed speculative inquiries with creativity and curiosity at their heart. This is, in part, due to its contingency on cultivating digital co-​research-​creation spaces that enfold rather than eschew the analogue and highlight the joyous potential of a deeply situated, co-​designed speculative inquiry; an inquiry with galleries, libraries, archives and museums (GLAM) young people living in a pandemic.
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    Model structures and structural identifiability:What? Why? How?
    Whyte, J ; Wood, D ; de Gier, J ; Praeger, C ; Tao, T (Springer Verlag, 2021-02-11)
    We may attempt to encapsulate what we know about a physical system by a model structure, S. This collection of related models is defined by parametric relationships between system features; say observables (outputs), unobservable variables (states), and applied inputs. Each parameter vector in some parameter space is associated with a completely specified model in S. Before choosing a model in S to predict system behaviour, we must estimate its parameters from system observations. Inconveniently, multiple models (associated with distinct parameter estimates) may approximate data equally well. Yet, if these equally valid alternatives produce dissimilar predictions of unobserved quantities, then we cannot confidently make predictions. Thus, our study may not yield any useful result. We may anticipate the non-uniqueness of parameter estimates ahead of data collection by testing S for structural global identifiability (SGI). Here we will provide an overview of the importance of SGI, some essential theory and distinctions, and demonstrate these in testing some examples.
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    Scanning horizons in research, policy and practice
    Wintle, B ; Kennicutt II, MC ; Sutherland, WJ ; Sutherland, WJ ; Brotherton, P ; Davies, Z ; Pettorelli, N ; Vira, B ; Vickery, J (Cambridge University Press, 2020-04-01)
    New and emerging environmental issues make policy and practice difficult. A pressing need to respond when knowledge of the problem is limited is added to an already challenging conservation agenda. Horizon-scanning is an evolving approach that draws on diverse information sources to identify early indications of poorly recognised threats and opportunities. There are many ways to conduct horizon scans, ranging from automated techniques that scan online content and mine text to manual methods that systematically consult large groups of people (often experts). These different approaches aim to sort through vast volumes of information to look for signals of change, for example the rise in microplastics or the use of mobile phones to gather data in remote forests. Identifying these new threats and opportunities is the first important step towards further researching and managing them. This chapter reviews different approaches to horizon-scanning, together with ways of encouraging uptake of scanning outputs. It concludes by introducing emerging technologies that will add value to horizon-scanning in the future.
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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)