Revealing determinants of two-phase dynamics of P53 network under gamma irradiation based on a reduced 2D relaxation oscillator model
This study proposes a two-dimensional (2D) oscillator model of p53 network, which is derived via reducing the multidimensional two-phase dynamics model into a model of ataxia telangiectasia mutated (ATM) and Wip1 variables, and studies the impact of p53-regulators on cell fate decision. First, the authors identify a 6D core oscillator module, then reduce this module into a 2D oscillator model while preserving the qualitative behaviours. The introduced 2D model is shown to be an excitable relaxation oscillator. This oscillator provides a mechanism that leads diverse modes underpinning cell fate, each corresponding to a cell...
Source: IET Systems Biology - January 19, 2018 Category: Biology Source Type: research
Estimation of parameters for plasma glucose regulation in type-2 diabetics in presence of meal
In this study, the authors propose a methodology for the estimation of glucose masses in stomach (both in solid and liquid forms), intestine, plasma and tissue; insulin masses in portal vein, liver, plasma and interstitial fluid using only plasma glucose measurement. The proposed methodology fuses glucose–insulin homoeostasis model (in the presence of meal intake) and plasma glucose measurement with a Bayesian non-linear filter. Uncertainty of the model over individual variations has been incorporated by adding process noise to the homoeostasis model. The estimation is carried out over 24 h for the healthy pe...
Source: IET Systems Biology - January 19, 2018 Category: Biology Source Type: research
Comparison of clustering approaches with application to dual colour protein data
In this study, the authors compare different methods such as hierarchical clustering, extensible Markov models and the gammics method for analysing such a spatial distribution. The methods are examined in a simulation study to determine their optimal use. Afterwards, they analyse experimental imaging data and extend these methods to simulate dual colour data. (Source: IET Systems Biology)
Source: IET Systems Biology - January 19, 2018 Category: Biology Source Type: research
Method for identification of sensitive nodes in Boolean models of biological networks
Biological systems are often represented as Boolean networks and analysed to identify sensitive nodes which on perturbation disproportionately change a predefined output. There exist different kinds of perturbation methods: perturbation of function, perturbation of state and perturbation in update scheme. Nodes may have defects in interpretation of the inputs from other nodes and calculation of the node output. To simulate these defects and systematically assess their effect on the system output, two new function perturbations, referred to as ‘not of function’ and ‘function of not’, are introduc...
Source: IET Systems Biology - January 19, 2018 Category: Biology Source Type: research
Design of dynamic genetic memory
This study proposes a possible genetic DRAM based on the modified electronic configuration, which uses the biological reaction to fulfil an equivalent RC circuit constituting a memory cell. The authors implement fundamental functions of the genetic DRAM by incorporating a genetic toggle switch for data hold. The results of simulation verify that the basic function can be used on a bio-storage module for the future bio-computer. (Source: IET Systems Biology)
Source: IET Systems Biology - November 14, 2017 Category: Biology Source Type: research
Improving GRN re-construction by mining hidden regulatory signals
Inferring gene regulatory networks (GRNs) from gene expression data is an important but challenging issue in systems biology. Here, the authors propose a dictionary learning-based approach that aims to infer GRNs by globally mining regulatory signals, known or latent. Gene expression is often regulated by various regulatory factors, some of which are observed and some of which are latent. The authors assume that all regulators are unknown for a target gene and the expression of the target gene can be mapped into a regulatory space spanned by all the regulators. Specifically, the authors modify the dictionary learning model...
Source: IET Systems Biology - November 14, 2017 Category: Biology Source Type: research
Bogdanov–Takens bifurcation in a neutral BAM neural networks model with delays
In this study, the authors first discuss the existence of Bogdanov–Takens and triple zero singularity of a five neurons neutral bidirectional associative memory neural networks model with two delays. Then, by utilising the centre manifold reduction and choosing suitable bifurcation parameters, the second-order and the third-order normal forms of the Bogdanov–Takens bifurcation for the system are obtained. Finally, the obtained normal form and numerical simulations show some interesting phenomena such as the existence of a stable fixed point, a pair of stable non-trivial equilibria, a stable limit cycles, hete...
Source: IET Systems Biology - November 14, 2017 Category: Biology Source Type: research
Predictable capability control scheme for oxygen-exchange blood flow regulation in an extracorporeal membrane oxygenation system
Extracorporeal membrane oxygenation system is used for rescue treatment strategies for temporary cardiopulmonary function support to facilitate adequately oxygenated blood to return into the systemic and pulmonary circulation systems. Therefore, a servo flow regulator is used to adjust the roller motor speed, while support blood flow can match the sweep gas flow (GF) in a membrane oxygenator. A generalised regression neural network is designed as an estimator to automatically estimate the desired roller pump speed and control parameters. Then, the proportional–integral–derivative controller with tuning contro...
Source: IET Systems Biology - November 14, 2017 Category: Biology Source Type: research
Controllability and observability analysis of basal ganglia model and feedback linearisation control
This study shows that the BG model is controllable and observable. The authors also propose the idea of stimulating the two BG areas simultaneously. A two-part controller is then designed: a feedback linearisation controller for subthalamic nucleus stimulation and a partial state feedback controller for globus pallidus internal stimulation. The controllers are designed to decrease three indicators: the hand tremor, the level of delivered stimulation signal in disease condition, and the ratio of the level of delivered stimulation signal in health condition to disease condition. Considering these three indicators, the simula...
Source: IET Systems Biology - September 15, 2017 Category: Biology Source Type: research
Non-fragile reliable control synthesis of the sugarcane borer
This study considers the problem of non-fragile reliable control synthesis for mathematical model of interaction between the sugarcane borer (Diatraea saccharalis) and its egg parasitoid Trichogramma galloi. In particular, the control could be substituted by periodic releases of a small population of natural enemies and hence it is important to propose the time-varying controller in sugarcane borer. The main aim of this study is to design a state feedback non-fragile (time-varying) reliable controller such that the states of the sugarcane borer system reach the equilibrium point within the desired period. A novel approach ...
Source: IET Systems Biology - September 15, 2017 Category: Biology Source Type: research
Bond graph modelling of chemoelectrical energy transduction
Energy-based bond graph modelling of biomolecular systems is extended to include chemoelectrical transduction thus enabling integrated thermodynamically compliant modelling of chemoelectrical systems in general and excitable membranes in particular. Our general approach is illustrated by recreating a well-known model of an excitable membrane. This model is used to investigate the energy consumed during a membrane action potential thus contributing to the current debate on the trade-off between the speed of an action potential event and energy consumption. The influx of ${\rm N}{\rm a}^ + $Na+ is often taken as a proxy for ...
Source: IET Systems Biology - September 15, 2017 Category: Biology Source Type: research
Blood glucose concentration control for type 1 diabetic patients: a non-linear suboptimal approach
In this study, a closed-loop treatment strategy is proposed for the control of blood glucose levels in type 1 diabetic patients. Toward this end, a non-linear technique for designing suboptimal tracking controllers, called the state-dependent Riccati equation tracker, is used based on a mathematical model of the glucose–insulin regulatory system. Since two state variables of the utilised model are not available to the controller, a non-linear filter is also designed to estimate these variables using the measured blood glucose concentration. Effects of unannounced meals and regular exercise are investigated for a nom...
Source: IET Systems Biology - July 21, 2017 Category: Biology Source Type: research
Isolation, characterisation and enzymatic activity of Streptomyces sp. and its pH control during fermentation process
Streptomyces sp. with grey white mycelium was isolated from Kodiyakkarai marine segment of east coastal of India. The isolate produced spiny spores and did not produce any diffusible pigments. Various biochemical tests were carried out to confirm the isolate classification. The amylolytic enzyme activity was estimated using the isolated strain which was confirmed by golden yellowish zone formation after using the Gram's iodine stain. The amount of amylase produced by the isolate was 6.15 U/ml. Higher living cells always produce better enzymes, so that the process parameters especially pH was maintained in fermentati...
Source: IET Systems Biology - July 21, 2017 Category: Biology Source Type: research
Two faces of competition: target-mediated reverse signalling in microRNA and mitogen-activated protein kinase regulatory networks
Biomolecular regulatory networks are organised around hubs, which can interact with a large number of targets. These targets compete with each other for access to their common hubs, but whether the effect of this competition would be significant in magnitude and in function is not clear. In this review, the authors discuss recent in vivo studies that analysed the system level retroactive effects induced by target competition in microRNA and mitogen-activated protein kinase regulatory networks. The results of these studies suggest that downstream targets can regulate the overall state of their upstream regulators, and thus ...
Source: IET Systems Biology - July 21, 2017 Category: Biology Source Type: research
Analysis of healthy and tumour DNA methylation distributions in kidney-renal-clear-cell-carcinoma using Kullback–Leibler and Jensen–Shannon distance measures
In this study, the authors study the probability density function distribution of DNA methylation in various significant genes and across the genome in healthy and tumour samples. They propose a unique ‘average healthy methylation distribution’ based on the methylation values of several healthy samples. They then obtain the Kullback–Leibler and Jensen–Shannon distances between methylation distributions of the healthy and tumour samples and the average healthy methylation distribution. The distance measures of the healthy and tumour samples from the average healthy methylation distribution are co...
Source: IET Systems Biology - May 26, 2017 Category: Biology Source Type: research
