IET Systems Biology
Volume 12, Issue 3, June 2018
Volumes & issues:
Volume 12, Issue 3
June 2018
-
- Author(s): Snehal B. Shinde and Manish P. Kurhekar
- Source: IET Systems Biology, Volume 12, Issue 3, p. 83 –92
- DOI: 10.1049/iet-syb.2017.0073
- Type: Article
- + Show details - Hide details
-
p.
83
–92
(10)
The immune system is an inherent protection system in vertebrate animals including human beings that exhibit properties such as self-organisation, self-adaptation, learning, and recognition. It interacts with the other allied systems such as the gut and lymph nodes. There is a need for immune system modelling to know about its complex internal mechanism, to understand how it maintains the homoeostasis, and how it interacts with the other systems. There are two types of modelling techniques used for the simulation of features of the immune system: equation-based modelling (EBM) and agent-based modelling. Owing to certain shortcomings of the EBM, agent-based modelling techniques are being widely used. This technique provides various predictions for disease causes and treatments; it also helps in hypothesis verification. This study presents a review of agent-based modelling of the immune system and its interactions with the gut and lymph nodes. The authors also review the modelling of immune system interactions during tuberculosis and cancer. In addition, they also outline the future research directions for the immune system simulation through agent-based techniques such as the effects of stress on the immune system, evolution of the immune system, and identification of the parameters for a healthy immune system.
Review of the systems biology of the immune system using agent-based models
-
- Author(s): Abhishek Dey and Shaunak Sen
- Source: IET Systems Biology, Volume 12, Issue 3, p. 93 –100
- DOI: 10.1049/iet-syb.2017.0026
- Type: Article
- + Show details - Hide details
-
p.
93
–100
(8)
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of analytical and computational approaches, the authors adapt and develop the method of describing functions to represent the input–output responses of biomolecular signalling systems. They approximate representative systems exhibiting various saturating and hysteretic dynamics in a way that is better than the standard linearisation. Furthermore, they develop analytical upper bounds for the computational error estimates. Finally, they use these error estimates to augment the limit cycle analysis with a simple and quick way to bound the predicted oscillation amplitude. These results provide system approximations that can add more insight into the local behaviour of these systems than standard linearisation, compute responses to other periodic inputs and to analyse limit cycles.
- Author(s): Muhammad Rizwan Azam ; Sahar Fazal ; Mukhtar Ullah ; Aamer I. Bhatti
- Source: IET Systems Biology, Volume 12, Issue 3, p. 101 –107
- DOI: 10.1049/iet-syb.2017.0025
- Type: Article
- + Show details - Hide details
-
p.
101
–107
(7)
The authors have proposed a systems theory-based novel drug design approach for the p53 pathway. The pathway is taken as a dynamic system represented by ordinary differential equations-based mathematical model. Using control engineering practices, the system analysis and subsequent controller design is performed for the re-activation of wild-type p53. p53 revival is discussed for both modes of operation, i.e. the sustained and oscillatory. To define the problem in control system paradigm, modification in the existing mathematical model is performed to incorporate the effect of Nutlin. Attractor point analysis is carried out to select the suitable domain of attraction. A two-loop negative feedback control strategy is devised to drag the system trajectories to the attractor point and to regulate cellular concentration of Nutlin, respectively. An integrated framework is constituted to incorporate the pharmacokinetic effects of Nutlin in the cancerous cells. Bifurcation analysis is also performed on the p53 model to see the conditions for p53 oscillation.
- Author(s): Adam Kozak ; Dorota Formanowicz ; Piotr Formanowicz
- Source: IET Systems Biology, Volume 12, Issue 3, p. 108 –117
- DOI: 10.1049/iet-syb.2017.0015
- Type: Article
- + Show details - Hide details
-
p.
108
–117
(10)
Atherosclerosis is a complex process of gathering sub-endothelial plaques decreasing lumen of the blood vessels. This disorder affects people of all ages, but its progression is asymptomatic for many years. It is regulated by many typical and atypical factors including the immune system response, a chronic kidney disease, a diet rich in lipids, a local inflammatory process and a local oxidative stress that is here one of the key factors. In this study, a Petri net model of atherosclerosis regulation is presented. This model includes also some information about stoichiometric relationships between its components and covers all mentioned factors. For the model, a structural analysis based on invariants was made and biological conclusions are presented. Since the model contains inhibitor arcs, a heuristic method for analysis of such cases is presented. This method can be used to extend the concept of feasible t-invariants.
- Author(s): Yingjun Sheng ; Jilei Tang ; Kewei Ren ; Lydia C. Manor ; Hongbao Cao
- Source: IET Systems Biology, Volume 12, Issue 3, p. 118 –122
- DOI: 10.1049/iet-syb.2017.0043
- Type: Article
- + Show details - Hide details
-
p.
118
–122
(5)
In recent years, numerous studies reported over a hundred of genes playing roles in the etiologyof postmenopausal osteoporosis (PO). However, many of these candidate genes were lack of replicationand results were not always consistent. Here, the authors proposed a computational workflow tocurate and evaluate PO related genes. They integrate large-scale literature knowledge data and geneexpression data (PO case/control: 10/10) for the marker evaluation. Pathway enrichment, sub-networkenrichment, and gene–gene interaction analysis were conducted to study the pathogenic profile of thecandidate genes, with four metrics proposed and validated for each gene. By using the authors'approach, a scalable PO genetic database was developed; including PO related genes, diseases,pathways, and the supporting references. The PO case/control classification supported theeffectiveness of the four proposed metrics, which successfully identified eight well-studied top POgenes (e.g. TGFB1, IL6, IL1B, TNF, ESR2, IGF1, HIF1A, and COL1A1) and highlighted one recentlyreported PO genes (e.g. IFNG). The computational biology approach and the PO database developed inthis study provide a valuable resource which may facilitate understanding the genetic profile ofPO.
Describing function-based approximations of biomolecular systems
System-based strategies for p53 recovery
Structural analysis of a Petri net model of oxidative stress in atherosclerosis
Integrative computational approach to evaluate risk genes for postmenopausalosteoporosis
Most viewed content
Most cited content for this Journal
-
Protein sequestration versus Hill-type repression in circadian clock models
- Author(s): Jae Kyoung Kim
- Type: Article
-
Blood glucose regulation in type 1 diabetic patients: an adaptive parametric compensation control-based approach
- Author(s): Anirudh Nath ; Dipankar Deb ; Rajeeb Dey ; Sipon Das
- Type: Article
-
Lung cancer prediction from microarray data by gene expression programming
- Author(s): Hasseeb Azzawi ; Jingyu Hou ; Yong Xiang ; Russul Alanni
- Type: Article
-
Modular bond-graph modelling and analysis of biomolecular systems
- Author(s): Peter J. Gawthrop and Edmund J. Crampin
- Type: Article
-
Remote health monitoring system for detecting cardiac disorders
- Author(s): Ayush Bansal ; Sunil Kumar ; Anurag Bajpai ; Vijay N. Tiwari ; Mithun Nayak ; Shankar Venkatesan ; Rangavittal Narayanan
- Type: Article