Systems Biology: To Meet Challenges for Biology in the Twenty-first Century

Genomics, structural biology, and bioinformatics deal with identification, cataloguing and characterization of the components that make up a cell. The focus on individual genes and proteins, which has proven so powerful for the molecular genetics in the past century, is in itself inadequate to describe the dynamic processes involving interactions among tens, hundreds and even thousands of components. Cell function, including growth, differentiation, division, and apoptosis, are temporal processes and we will only be able to  understand them if we treat them as dynamic systems. There is a general agreement that systems approach is necessary to understand the causal and functional relationships that generate the dynamics of biological networks and pathways

Non-Linear Effort dynamics for Harvesting in a Predator- Prey System

In this paper, a non-linear harvesting of prey is considered in a prey-predator system. The predator is considered to be of modified Leslie- Gower type. The effort is taken as dynamic variable. The steady states of the system are determined and the dynamical behavior of the system for its all steady states is discussed under certain conditions. Necessary condition for global stability of the system is analyzed at the positive interior equilibrium point. Numerical simulations are carried out to explore the dynamics of the system for the suitable choice of parameters. Keywords: Modified Leslie-Gower predation, Nonlinear Harvesting, stability, Numerical Simulations

Computational prediction and analysis of impact of the cross‐talks between JNK and P38 kinase cascades

Signal transduction is a complex protein signaling process with a rich network of multifunctional interactions that occur in a non‐linear fashion. Mitogen‐activated protein kinase (MAPK) signal transduction pathways regulate diverse cellular processes ranging from proliferation and differentiation to apoptosis. In mammals, out of five, there are three well characterized subfamilies of MAPKs ‐ ERKs (Extracellular signal‐regulated kinases), JNKs (c‐Jun N‐terminal kinases), and P38 kinases, and their activators, are implicated in human diseases and are targets for drug development. Kinase cascades in MAPK pathways mediate the sensing and processing of stimuli. To understand how cells makes decisions, the dynamic interactions of components of signaling cascades are important rather than just creating static maps. Based on enzyme kinetic reactions, we have developed a mathematical model to analyze the impact of the cross‐talks between JNK and P38 kinase cascades. Cross‐talks between JNK and P38 kinase cascades influence the activities of P38 kinases. Responses of the signals should be studied for network of kinase cascades by considering cross‐talks

Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each other: A systems approach

The classical concept of linear pathways is being increasingly challenged by network representations, which emphasize the importance of interactions between components of a biological system, and motivates for adopting a system‐level approach in biology. We have developed a dynamical system that integrates quantitative, dynamic and topological representation of network of ERK5 (Extracellular signal‐regulated kinases 5), JNK(c‐Jun N‐terminal kinases) and P38 kinase cascades. We have observered that, the transient activation of ERK5, JNK1 and P38β kinase, and the persistent activation of JNK2, JNK3 and P38 δ kinase does not get affected due to the cross‐talks between ERK5, JNK and P38 kinase cascades. But it is due to the cross ‐ talks, the transiently activated P38α kinase become inactivated, and the transiently activated P38γ kinase become persistently activated. The impacts of one‐way cross‐talks between the cascades are insignificant and differ from the impact of two‐way cross‐talks. We generate a hypothesis that, signaling pathways should be studied as a system by considering the cross‐talks between the two adjacent cascades

Control of chaos due to additional predator in the Hastings–Powell food chain model

AbstractA three species Hastings and Powell (HP) food chain model involving another predator of top prey is proposed and studied. The modified food web model is analyzed to obtain the different conditions for which system exhibits stability around the biological feasible equilibrium points. The permanence is established and global stability of boundary equilibrium point Ex is discussed. It is observed through numerical simulations, that four-dimensional model may show stable dynamics in contrast to chaotic dynamics that occurred in three species food chain. Varieties of dynamical behaviors in the food web are possible depending upon the sharing of food between the two predators of the top prey. The results demonstrate that the additional predator play the crucial role in reducing the complexity in the dynamical behavior of the system

HORI: a web server to compute Higher Order Residue Interactions in protein structures

Background: Folding of a protein into its three dimensional structure is influenced by both local and global interactions within a protein. Higher order residue interactions, like pairwise, triplet and quadruplet ones, play a vital role in attaining the stable conformation of the protein structure. It is generally agreed that higher order interactions make significant contribution to the potential energy landscape of folded proteins and therefore it is important to identify them to estimate their contributions to overall stability of a protein structure. Results: We developed HORI [Higher order residue interactions in proteins], a web server for the calculation of global and local higher order interactions in protein structures. The basic algorithm of HORI is designed based on the classical concept of four-body nearest-neighbour propensities of amino-acid residues. It has been proved that higher order residue interactions up to the level of quadruple interactions plays a major role in the three-dimensional structure of proteins and is an important feature that can be used in protein structure analysis. Conclusion: HORI server will be a useful resource for the structural bioinformatics community to perform analysis on protein structures based on higher order residue interactions. HORI server is a highly interactive web server designed in three modules that enables the user to analyse higher order residue interactions in protein structures. HORI server is available from the URL: http://caps. ncbs.res.in/hori