Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

BACKGROUND: Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have recently proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format and is, thus, usable for analysis via existing simulation techniques. RESULTS: Here we use a high-level narrative language in designing a computational model of the gp130/JAK/STAT signalling pathway and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then "experiment" on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. CONCLUSION: The described narrative model of the gp130/JAK/STAT pathway represents an interesting case study showing how, by using this approach, researchers can model biological systems without explicitly dealing with formal notations and mathematical expressions (typically used for biochemical modelling), nevertheless being able to obtain simulation and analysis results. We present the model and the sensitivity analysis results we have obtained, that allow us to identify the parameters which are most sensitive to perturbations. The results, which are shown to be in agreement with existing mathematical models of the gp130/JAK/STAT pathway, serve us as a form of validation of the model and of the approach itself

Visualising Silicon in Plants: Histochemistry, Silica Sculptures and Elemental Imaging.

Silicon is a non-essential element for plants and is available in biota as silicic acid. Its presence has been associated with a general improvement of plant vigour and response to exogenous stresses. Plants accumulate silicon in their tissues as amorphous silica and cell walls are preferential sites. While several papers have been published on the mitigatory effects that silicon has on plants under stress, there has been less research on imaging silicon in plant tissues. Imaging offers important complementary results to molecular data, since it provides spatial information. Herein, the focus is on histochemistry coupled to optical microscopy, fluorescence and scanning electron microscopy of microwave acid extracted plant silica, techniques based on particle-induced X-ray emission, X-ray fluorescence spectrometry and mass spectrometry imaging (NanoSIMS). Sample preparation procedures will not be discussed in detail, as several reviews have already treated this subject extensively. We focus instead on the information that each technique provides by offering, for each imaging approach, examples from both silicifiers (giant horsetail and rice) and non-accumulators (Cannabis sativa L.)

Change-of-direction deficit vs. deceleration deficit: a comparison of limb dominance and inter-limb asymmetry between forwards and backs in elite male rugby union players

The aims of the present study were to: 1) determine whether limb dominance and inter-limb asymmetry were the same across both change of direction (COD) and deceleration (DEC) deficits and, 2) determine the association between the COD and DEC-deficits and other physical performance tests in elite male rugby union players. Twenty five players performed a series of bilateral jumps, linear and COD speed tests at the end of the pre-season period. COD and DEC-deficits were calculated for both left and right sides, and inter-limb asymmetry thereafter. Kappa coefficients revealed moderate levels of agreement in limb dominance between COD and DEC-deficits (Kappa = 0.41 on left; 0.48 on right). For the direction of asymmetry, perfect levels of agreement (Kappa = 1) were evident between 505 time and COD-deficit, but only moderate levels of agreement (Kappa = 0.41) between other asymmetry measures. Pearson’s r correlations showed moderate to large relationships between jumps and linear (r = -0.42 to -0.68) and COD speed (r = -0.41 to -0.58), but not with the COD-deficit (r = 0.15 to -0.31), DEC-deficit (r = 0.01 to -0.32) or asymmetry (r = 0.16 to -0.29). When analyzing by playing position, backs were significantly faster than forwards over 15-m (ES = -0.86) and across all jump tests (ES = 0.86-0.94), with the exception of the squat jump. This study is the first to provide a direct comparison of the COD and DEC-deficits and highlights that limb dominance and asymmetry cannot be guaranteed between tasks