Small RNA-mediated switch-like regulation in bacterial quorum sensing
In this study, the authors present a computational model for the switch-like regulation of signal transduction by small regulatory RNA-mediated QS based on intertwined network involving AIs, LuxO, LuxU, Qrr sRNAs and LuxR. In agreement with experimental observations, the model suggests that different feedbacks play critical roles in the switch-like regulation. The authors results reveal that V. harveyi uses multiple feedbacks to precisely control signal transduction. (Source: IET Systems Biology)
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Construction and analysis of single nucleotide polymorphism??single nucleotide polymorphism interaction networks
In this study, the authors are interested in single nucleotide polymorphism (SNP) level and construct SNP??SNP interaction network to understand genetic characters and pathogenetic mechanisms of complex diseases. The authors employ existing methods to mine, model and evaluate a SNP sub-network from SNP??SNP interactions. In the study, the authors employ the two SNP datasets: Parkinson disease and coronary artery disease to demonstrate the procedure of construction and analysis of SNP??SNP interaction networks. Experimental results are reported to demonstrate the procedure of construction and analysis of such SNP??SNP inter...
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Latent factor analysis facilitates modelling of oncogenic genes for colon adenocarcinoma
In this study, a wellestablished latent factor model, Bayesian factor and regression model, are applied to predict unknown colon cancer related genes from colon adenocarcinoma genomic data. Four important latent factors were addressed by the latent factor model, focusing on characterisation of heterogeneity of expression patterns of specific oncogenic genes by using microarray data of 174 colon cancer patients. Based on the fact that variables included in the same latent factor have some common characteristics and known cancer related genes in Online Mendelian Inheritance in Man, the authors found that the four latent fact...
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Wright??Fisher dynamics on adaptive landscape
Adaptive landscape, proposed by Sewall Wright, has provided a conceptual framework to describe dynamical behaviours. However, it is still a challenge to explicitly construct such a landscape, and apply it to quantify interesting evolutionary processes. This is particularly true for neutral evolution. In this work, the authors study one-dimensional Wright Fisher process, and analytically obtain an adaptive landscape as a potential function. They provide the complete characterisation for dynamical behaviours of all possible mutation rates under the influence of mutation and random drift. This same analysis has been applied t...
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data
In this study, the authors propose a Gaussian graphical model to evaluate the documented regulatory networks by the consistency between network architectures and time course gene expression profiles. They derive a dynamic Bayesian network model to evaluate gene regulatory networks in both simulated and true time course microarray data. The regulatory networks are evaluated by matching network structure with gene expression to achieve consistency measurement. To demonstrate the effectiveness of the authors method, they identify significant regulatory networks in response to the time course of circadian rhythm. The knowledge...
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Gene expression rate comparison for multiple high-throughput datasets
Microarray provides genome-wide transcript profiles, whereas RNA-seq is an alternative approach applied for transcript discovery and genome annotation. Both high-throughput techniques show quantitative measurement of gene expression. To explore differential gene expression rates and understand biological functions, the authors designed a system which utilises annotations from Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways and Gene Ontology (GO) associations for integrating multiple RNA-seq or microarray datasets. The developed system is initiated by either estimating gene expression levels from mapping ...
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Functional tunability of biological circuits from additional toggle switches
In many complex regulatory networks with interlinked feedback loops, the simple core circuits are sufficient to achieve the specific biological functions of the whole networks, naturally raising a question: what is the role of the additional feedback loops. By investigating the effect of an additional toggle switch on the auto-activation circuit responsible for competent switch in Bacillus subtilits and on the activator??repressor circuit responsible for cell cycle in Xenopus embryonic, the authors show that the additional toggle switch can elaborate the dynamical behaviour of both circuits. Specifically, the additional to...
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Guest editorial: computational systems biology
Systems biology and bioinformatics have become intensive research topics in the recent decade because of the emergence of high-throughput biological technologies. The generated large biological data have provided an alternative and a comprehensive way to decipher the biological systems at molecular and network levels. These research topics have attracted many leading scientists in Biology, Physics, Mathematics, Systems Science, Computer Science, Control Science and Statistics. Many computational and mathematical systems biology methods have been widely developed to meet the request for big data. (Source: IET Systems Biology)
Source: IET Systems Biology - October 1, 2013 Category: Biology Source Type: research
Quantitative analysis of the effects of iododeoxyuridine and ionising radiation treatment on the cell cycle dynamics of DNA mismatch repair deficient human colorectal cancer cells
In this study, the authors have developed asynchronous probabilistic cell cycle models to assess the isolated effects of IUdR and IR and the combined effects of IUdR + IR treatments on MMR damage processing. The authors used both synchronous and asynchronous MMRproficient/ MMR-deficient cell populations and followed treated cells for up to two cell cycle times. They have observed and quantified differential cell cycle responses to MMR damage processing following IR and IUdR + IR treatments, principally in the duration of both G1 and G2/M cell cycle phases. The models presented in this work form the foundation for the devel...
Source: IET Systems Biology - August 1, 2013 Category: Biology Source Type: research
Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets
In this study, the authors address this problem using coloured stochastic Petri nets SPNc as high-level description to generate continuous-time Markov chains. The authors develop several models with increasing complexity. They first apply SPNc to model single clusters of coupled Ca2+ channels arranged in a regular or irregular lattice, where they describe how to represent the geometrical arrangement of Ca2+ channels relative to each other using colours. They then apply this modelling idea to construct more complex models by modelling spatially arranged clusters of channels. The authors?? models can be easily reproduced and...
Source: IET Systems Biology - August 1, 2013 Category: Biology Source Type: research
Design of synthetic biological logic circuits based on evolutionary algorithm
In this study, a real-structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis-regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting opti...
Source: IET Systems Biology - August 1, 2013 Category: Biology Source Type: research
Constant drug dose in human immuno-deficiency virus-infected patients to induce long-term non-progressor status: bifurcation and controllability approach
The authors propose a therapy consisting of a constant dosage of reverse transcription inhibitor and protease inhibitor to achieve long-term non-progressor (LTNP) status in human immuno-deficiency virus (HIV) patients. Based on the authors analyses of cytotoxic T lymphocyte precursor (CTLp) concentration at several equilibrium points and the bifurcation of these equilibrium points, they find that administration of drugs with an efficacy lower than a certain level induces a higher CTLp concentration. As a result, drug doses of moderate efficacy result in more patients with LTNP status than doses with high efficacy. In analy...
Source: IET Systems Biology - June 1, 2013 Category: Biology Source Type: research
Theoretical analysis on the relationship between left ventricular energetic efficiency and acute infarct size
In this study, the relationship is analysed by means of simulation using a theoretical model of the guinea pig left ventricle. In simulation with varied ratios of infarct area, pressure??volume area (PVA), which is an index of total mechanical energy by ventricular contraction, and myocardial oxygen consumption (MVO2) are calculated for each infarct ratio. Then, change of PVA when MVO2 alters (PVA/MVO2) as a well-known index of energy conversion efficiency is evaluated. In addition, PVA/VO2 (Source: IET Systems Biology)
Source: IET Systems Biology - June 1, 2013 Category: Biology Source Type: research
Colorectal cancer through simulation and experiment
Colorectal cancer (CRC) has formed a canonical example of tumourigenesis ever since its use in Fearon and Vogelstein??s linear model of genetic mutation, and continues to generate a huge amount of research interest. Over time, the field has witnessed a transition from solely experimental work to the inclusion of mathematical and computational modelling. The fusion of these disciplines has the potential to provide valuable insights into oncologic processes, but also presents the challenge of uniting many diverse perspectives. Furthermore, the cancer cell phenotype defined by the `Hallmarks of Cancer?? has been extended in r...
Source: IET Systems Biology - June 1, 2013 Category: Biology Source Type: research
In vivo measurement of blood flow in a micro-scale stenosis model generated by laser photothermal blood coagulation
Blood flow in a stenosed vessel is one of the most important issues, because it is closely related to the outbreak of circulatory diseases. To overcome the technological limitations encountered in the haemodynamic studies using in vitro stenosis models, the authors induced a stenosed flow model in the extraembryonic vessels of a chicken embryo. Blood was coagulated by laser irradiation to artificially form a stenosis on the designated spot in a straight blood vessel. Owing to photothermal coagulation of red blood cells (RBCs), the blood is denatured and a stable blood coagulum is induced in the vessel. The blood coagulum a...
Source: IET Systems Biology - April 1, 2013 Category: Biology Source Type: research
