Experimental treatments of feeding assay with <i>Osmia bicornis</i> larvae.

<p>Larval pollen provisions were collected and processed by nesting bees. Provisions containing non-transgenic pollen from the isoline were manually ‘spiked’ with insecticidal protein dissolved in water to achieve the test concentrations indicated (w∶w). aPercentage OC-1 of total soluble protein in pollen extract, determined by dot-blot immunoassay. Abbreviations: OC-1, oryzacystatin-1; rOC-1, recombinant OC-1; GNA, <i>Galanthus nivalis</i> agglutinin.</p

Stability of insecticidal proteins over time when added to pollen provisions.

<p>Amount of insecticidal protein determined by ELISA after 14 and 28 days of incubation presented as percentage of the amount detected immediately after protein application. Minimum and maximum values of independent determinations and the sample means (in brackets) are given (n = 3–9). Abbreviations: rOC-1, recombinant oryzacystatin-1; GNA, <i>Galanthus nivalis</i> agglutinin.</p

Bee mortality.

<p>Mortality of <i>Osmia bicornis</i> (in %) observed during development (i.e. from hatching to mature larva), in the cocoon (i.e. from start of cocoon spinning to emergence from cocoon) and over the whole observation time (n = 25–44). The 95% confidence interval is given in brackets. Abbreviations: OC-1, oryzacystatin-1; rOC-1, recombinant OC-1; GNA, <i>Galanthus nivalis</i> agglutinin.</p

Modelling Pathways to Rubisco Degradation: A Structural Equation Network Modelling Approach

<div><p>‘Omics analysis (transcriptomics, proteomics) quantifies changes in gene/protein expression, providing a snapshot of changes in biochemical pathways over time. Although tools such as modelling that are needed to investigate the relationships between genes/proteins already exist, they are rarely utilised. We consider the potential for using Structural Equation Modelling to investigate protein-protein interactions in a proposed Rubisco protein degradation pathway using previously published data from 2D electrophoresis and mass spectrometry proteome analysis. These informed the development of a prior model that hypothesised a pathway of Rubisco Large Subunit and Small Subunit degradation, producing both primary and secondary degradation products. While some of the putative pathways were confirmed by the modelling approach, the model also demonstrated features that had not been originally hypothesised. We used Bayesian analysis based on Markov Chain Monte Carlo simulation to generate output statistics suggesting that the model had replicated the variation in the observed data due to protein-protein interactions. This study represents an early step in the development of approaches that seek to enable the full utilisation of information regarding the dynamics of biochemical pathways contained within proteomics data. As these approaches gain attention, they will guide the design and conduct of experiments that enable ‘Omics modelling to become a common place practice within molecular biology.</p></div

Model of Rubisco degradation following Bayesian estimation of SEM to test the hypothetical model.

<p>The coloured text boxes indicate identical protein sequences in the intact proteins and the degradation products (dp#). Please see Tétard-Jones et al. 2013 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087597#pone.0087597-TtardJones2" target="_blank">[27]</a> for detailed information of the protein sequences. Decimal figures indicate the standardised coefficients for the relationship indicated by the arrows.</p

Hypothetical model of Rubisco Large Subunit (RLS2) and Small Subunit (RSS#) degradation generated by using prior information.

<p>The coloured text boxes indicate identical protein sequences in the intact proteins and the degradation products (dp#). Please see Tétard-Jones et al. 2013 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087597#pone.0087597-TtardJones2" target="_blank">[27]</a> for detailed information of the protein sequences. Arrows connect proteins together that are assumed to have a direct relationship (e.g. dp44 is a degradation product of RSS174 and/or RSS175).</p