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Search Results: 1 - 10 of 277 matches for " Radhika Desikan "
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Nitric oxide in cell damage and protection
Neill Steven,Bright Jo,Desikan Radhika,Harrison Judy
BMC Plant Biology , 2005, DOI: 10.1186/1471-2229-5-s1-s25
Abstract:
Squeeze-and-Breathe Evolutionary Monte Carlo Optimisation with Local Search Acceleration and its application to parameter fitting
Mariano Beguerisse-Diaz,Baojun Wang,Radhika Desikan,Mauricio Barahona
Mathematics , 2011,
Abstract: Motivation: Estimating parameters from data is a key stage of the modelling process, particularly in biological systems where many parameters need to be estimated from sparse and noisy data sets. Over the years, a variety of heuristics have been proposed to solve this complex optimisation problem, with good results in some cases yet with limitations in the biological setting. Results: In this work, we develop an algorithm for model parameter fitting that combines ideas from evolutionary algorithms, sequential Monte Carlo and direct search optimisation. Our method performs well even when the order of magnitude and/or the range of the parameters is unknown. The method refines iteratively a sequence of parameter distributions through local optimisation combined with partial resampling from a historical prior defined over the support of all previous iterations. We exemplify our method with biological models using both simulated and real experimental data and estimate the parameters efficiently even in the absence of a priori knowledge about the parameters.
Linear models of activation cascades: analytical solutions and coarse-graining of delayed signal transduction
Mariano Beguerisse-Diaz,Radhika Desikan,Mauricio Barahona
Mathematics , 2011,
Abstract: Activation cascades are a prevalent feature in cellular mechanisms for signal transduction. Here we study the classic model of linear activation cascades and obtain analytical solutions in terms of lower incomplete gamma functions. We show that in the special but important case of optimal gain cascades (i.e., when all the deactivation rates are identical) the downstream output of an entire cascade can be represented exactly as a single nonlinear module containing an incomplete gamma function with parameters dependent on the input signal as well as the rates and length of the cascade. Our results can be used to represent optimal cascades efficiently by reducing the number of equations and parameters in computational ODE models under a variety of inputs. If the requirement for strict optimality is relaxed (under random deactivation rates), we show that the reduced representation can also reproduce the observed variability of downstream responses. In addition, we show that cascades can be rearranged so that homogeneous blocks can be lumped and represented by incomplete gamma functions. We also illustrate how the reduced representation can be used to fit data; in particular, the length of the cascade appears as a real-valued parameter and can thus be fitted in the same manner as Hill coefficients. Finally, we use our results to show how the output of delay differential equation models can be approximated with the use of simple expressions involving the incomplete gamma function.
Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells
Mariano Beguerisse-D?az, Mercedes C Hernández-Gómez, Alessandro M Lizzul, Mauricio Barahona, Radhika Desikan
BMC Systems Biology , 2012, DOI: 10.1186/1752-0509-6-146
Abstract: Toshed light on this unexplained behaviour, we have collected time course measurements of stomatal aperture and hydrogen peroxide production in Arabidopsis thaliana guard cells treated with abscisic acid, ethylene, and a combination of both. Our experiments show that stomatal closure is linked to sustained high levels of hydrogen peroxide in guard cells. When treated with a combined dose of abscisic acid and ethylene, guard cells exhibit increased antioxidant activity that reduces hydrogen peroxide levels and precludes closure. We construct a simplified model of stomatal closure derived from known biochemical pathways that captures the experimentally observed behaviour.Our experiments and modelling results suggest a distinct role for two antioxidant mechanisms during stomatal closure: a slower, delayed response activated by a single stimulus (abscisic acid ‘or’ ethylene) and another more rapid ‘and’ mechanism that is only activated when both stimuli are present. Our model indicates that the presence of this rapid ‘and’ mechanism in the antioxidant response is key to explain the lack of closure under a combined stimulus.Stomata are tiny pores located mainly in the lower epidermis of plant leaves. Each stoma is formed by two guard cells attached to each other by their extremes. When the guard cells are turgid, due to their vacuoles being full of water, the pore opens (Figure 1A). When the vacuoles are emptied and water exits the cells, the guard cells become flaccid and the pore closes (Figure 1B) [1]. Loss of turgor pressure (and the resulting closure of the stomatal pore) is a consequence of the efflux of ions out of the cell. Ion efflux may be caused by a variety of stimuli including different light conditions and atmospheric carbon dioxide (CO2) levels, or signalling hormones such as abscisic acid (ABA) and ethylene [2,3]. Open pores allow the plant to absorb CO2 from the air to perform photosynthesis and to release oxygen and water into the atmosphere. If the por
Snippets
Desikan P
Indian Journal of Medical Microbiology , 2010,
Abstract:
Research snippets
Desikan P
Indian Journal of Medical Microbiology , 2010,
Abstract:
Research snippets from the medical world
Desikan Prabha
Indian Journal of Medical Microbiology , 2009,
Abstract:
Research snippets from the medical world
Desikan Prabha
Indian Journal of Medical Microbiology , 2010,
Abstract:
Research snippets from the medical world
Desikan P
Indian Journal of Medical Microbiology , 2010,
Abstract:
Research snippets from the world of medicine
Desikan P
Indian Journal of Medical Microbiology , 2008,
Abstract:
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