Mathematical modelling and analysis of cellular signalling in macrophages

Cell signalling pathways play a crucial role in proper cell development and behaviour, with implications to survival, chemotaxis, proliferation, and even programmed cell death known as apoptosis. In this article, we outline a mathematical model of the G-protein signalling pathway in a particular cell line of macrophages, focusing on activation of a particular G-protein-coupled receptor, P2Y(6). The model is based on the kinetics of P2Y(6) surface receptors, inositol trisphosphate, cytosolic calcium, and differential dynamics of multiple species of diacylglycerol. Insight into the dynamics of the system is given through recently available experimental results and incorporated into the model. Mathematical analysis of the model, including establishment of global existence, uniqueness, positivity, and boundedness of solutions, and global stability of a unique steady-state solution is discussed.     

Mathematical modelling of metabolism

Mathematical models of the cellular metabolism have a special interest within biotechnology. Many different kinds of commercially important products are derived from the cell factory, and metabolic engineering can be applied to improve existing production processes, as well as to make new processes available. Both stoichiometric and kinetic models have been used to investigate the metabolism, which has resulted in defining the optimal fermentation conditions, as well as in directing the genetic changes to be introduced in order to obtain a good producer strain or cell line. With the increasing availability of genomic information and powerful analytical techniques, mathematical models also serve as a tool for understanding the cellular metabolism and physiology.     

Mathematical modelling in physiology

The article illustrates the method of mathematical modelling in physiology as a unique tool to study physiological processes. A number of demonstrated examples appear as a result of long-term experience in mathematical modelling of electrical and mechanical phenomena in the heart muscle. These examples are presented here to show that the modelling provides insight into mechanisms underlying these phenomena and is capable to predict new ones that were previously unknown. While potentialities of the mathematical modelling are analyzed with regard to the myocardium, they are quite universal to deal with any physiological processes.     

Mathematical modelling of tumour acidity

Acid-mediated tumour invasion is receiving increasing experimental and clinical attention. Previous models proposed to describe this phenomenon failed to capture key properties of the system, such as the existence of the benign steady state, or predicted incorrectly the size of the inter-tissue gap. Here we show that taking proper account of quiescence ameliorates these drawbacks as well as revealing novel behaviour. The simplicity of the model allows us to fully identify the key parameters controlling different aspects of behaviour.     

Mathematical modelling of the mitochondrial apoptosis pathway

Mitochondria are pivotal for cellular bioenergetics, but are also a core component of the cell death machinery. Hypothesis-driven research approaches have greatly advanced our understanding of the role of mitochondria in cell death and cell survival, but traditionally focus on a single gene or specific signalling pathway at a time. Predictions originating from these approaches become limited when signalling pathways show increased complexity and invariably include redundancies, feedback loops, anisotropies or compartmentalisation. By introducing methods from theoretical chemistry, control theory, and biophysics, computational models have provided new quantitative insights into cell decision processes and have led to an increased understanding of the key regulatory principles of apoptosis. In this review, we describe the currently applied modelling approaches, discuss the suitability of different modelling techniques, and evaluate their contribution to the understanding of the mitochondrial apoptosis pathway. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.     

Mathematical modelling of biofilm structures

The morphology of biofilms received much attention in the last years. Several concepts to explain the development of biofilm structures have been proposed. We believe that biofilm structure formation depends on physical as well as general and specific biological factors. The physical factors (e.g. governing substrate transport) as well as general biological factors such as growth yield and substrate conversion rates are the basic factors governing structure formation. Specific strain dependent factors will modify these, giving a further variation between different biofilm systems. Biofilm formation seems to be primarily dependent on the interaction between mass transport and conversion processes. When a biofilm is strongly diffusion limited it will tend to become a heterogeneous and porous structure. When the conversion is the rate-limiting step, the biofilm will tend to become homogenous and compact. On top of these two processes, detachment processes play a significant role. In systems with a high detachment (or shear) force, detachment will be in the form of erosion, giving smoother biofilms. Systems with a low detachment force tend to give a more porous biofilm and detachment occurs mainly by sloughing. Biofilm structure results from the interplay between these interactions (mass transfer, conversion rates, detachment forces) making it difficult to study systems taking only one of these factors into account. This revised version was published online in August 2006 with corrections to the Cover Date.     

Mathematical modelling of corneal swelling

This paper presents a differential model of the corneal transport system capable of modelling thickness changes in response to osmotic perturbations applied to either limiting membrane. The work is directed towards understanding corneal behaviour in vivo. The model considers the coupled viscous flows within the corneal stroma and across the epithelial and endothelial membranes. The flows within the stroma are established based on transport theory in porous media, while the flows across the membranes are described using the phenomenological equations of irreversible thermodynamics. The ability of the numerical model to reproduce corneal thickness changes in response to endothelial perturbations was tested against available experimental data. The sensitivity of the model to changes in stromal and membrane transport coefficients was examined.     

Mathematical modelling of juxtacrine patterning

Spatial pattern formation is one of the key issues in developmental biology. Some patterns arising in early development have a very small spatial scale and a natural explanation is that they arise by direct cell—cell signalling in epithelia. This necessitates the use of a spatially discrete model, in contrast to the continuum-based approach of the widely studied Turing and mechanochemical models. In this work, we consider the pattern-forming potential of a model for juxtacrine communication, in which signalling molecules anchored in the cell membrane bind to and activate receptors on the surface of immediately neighbouring cells. The key assumption is that ligand and receptor production are both up-regulated by binding. By linear analysis, we show that conditions for pattern formation are dependent on the feedback functions of the model. We investigate the form of the pattern: specifically, we look at how the range of unstable wavenumbers varies with the parameter regime and find an estimate for the wavenumber associated with the fastest growing mode. A previous juxtacrine model for Delta-Notch signalling studied by Collier et al. (1996, J. Theor. Biol. 183, 429–446) only gives rise to patterning with a length scale of one or two cells, consistent with the fine-grained patterns seen in a number of developmental processes. However, there is evidence of longer range patterns in early development of the fruit fly Drosophila. The analysis we carry out predicts that patterns longer than one or two cell lengths are possible with our positive feedback mechanism, and numerical simulations confirm this. Our work shows that juxtacrine signalling provides a novel and robust mechanism for the generation of spatial patterns.     

Mathematical modelling of skeletal repair

Tissue engineering offers significant promise as a viable alternative to current clinical strategies for replacement of damaged tissue as a consequence of disease or trauma. Since mathematical modelling is a valuable tool in the analysis of complex systems, appropriate use of mathematical models has tremendous potential for advancing the understanding of the physical processes involved in such tissue reconstruction. In this review, the potential benefits, and limitations, of theoretical modelling in tissue engineering applications are examined with specific emphasis on tissue engineering of bone. A central tissue engineering approach is the in vivo implantation of a biomimetic scaffold seeded with an appropriate population of stem or progenitor cells. This review will therefore consider the theory behind a number of key factors affecting the success of such a strategy including: stem cell or progenitor population expansion and differentiation ex vivo; cell adhesion and migration, and the effective design of scaffolds; and delivery of nutrient to avascular structures. The focus will be on current work in this area, as well as on highlighting limitations and suggesting possible directions for future work to advance health-care for all.     

Mathematical modelling of tissue-engineered angiogenesis

We present a mathematical model for the vascularisation of a porous scaffold following implantation in vivo. The model is given as a set of coupled non-linear ordinary differential equations (ODEs) which describe the evolution in time of the amounts of the different tissue constituents inside the scaffold. Bifurcation analyses reveal how the extent of scaffold vascularisation changes as a function of the parameter values. For example, it is shown how the loss of seeded cells arising from slow infiltration of vascular tissue can be overcome using a prevascularisation strategy consisting of seeding the scaffold with vascular cells. Using certain assumptions it is shown how the system can be simplified to one which is partially tractable and for which some analysis is given. Limited comparison is also given of the model solutions with experimental data from the chick chorioallantoic membrane (CAM) assay.     

Cardiac mechanics at the cellular level.

The active mechanical properties of heart muscle are load, length, and time-dependent. The capability for investigating cardiac mechanisms at the cellular level may help to distinguish between those properties of the myocardium which arise from myocardial cells and those which arise from the tissue architecture and extracellular matrix of connective fibers. We present here, for the first time, a general approach for subjecting single heart cells to isometric, isotonic, afterloaded, or physiological loading sequences, while obtaining on-line measures of cell force and length. This approach has been implemented and tested on freshly dissociated, adult frog ventricular myocytes. Examples are presented for each of the four loading sequences.     

Soy isoflavones and cellular mechanics

Soy isoflavones are diphenolic compounds that are frequently used for alternative treatment of ageing symptoms in both genders. They operate at principally two hierarchical levels of functional organization – cellular and molecular, while these ‘types’ of action appear to have indefinite borders. Soy isoflavone action at the cellular level involves inter alia the effects on cell mechanics. This epigenetic and modular determinant of cell function and fate is defined by: the anchorage to extracellular matrix (ECM) and neighboring cells, cytoskeleton organization, membrane tension and vesicle trafficking. Soy isoflavones have been reported to: (i) generally fashion an inert cell phenotype in some cancers and enhance the cell anchorage in connective tissues, via the effects on ECM proteins, focal adhesion kinases-mediated events and matrix metalloproteinases inhibition; (ii) affect cytoskeleton integrity, the effects being related to Ca²⁺ ions fluxes and involving cell retraction or differentiation/proliferation-related variations in mechanical status; (iii) increase, remain “silent” or decrease membrane tension/fluidity, which depends on polarity and a number and arrangement of functional groups in applied isoflavone; (iv) provoke inhibitory effects on vesicle trafficking and exo-/endocytosis, which are usually followed by changed cell morphology. Here we present and discuss the abundance of effects arising from cells’ “encounter” with soy isoflavones, focusing on different morphofunctional definers of cell mechanics.     

数学模型与自然保护科学

日益加剧的人类干扰和景观破碎化已危及全球的生物多样性。自然保护成为人类所面临的最重要也最富有挑战性的任务。指导这一实践的理论和原则极为需要。本文试图综述与自然保护科学有关的几个学科在理论和实际研究(尤其是模型)方面的近期成果以及发展趋势,从而提出自然保护模型的发展方向。文中涉猎基于不同方法论、不同组织水平的模型,并对数学模型在自然保护科学中的作用和实用性加以讨论。     

Mathematical modelling of the intravenous glucose tolerance test

 Several attempts at building a satisfactory model of the glucose-insulin system are recorded in the literature. The minimal model, which is the model currently mostly used in physiological research on the metabolism of glucose, was proposed in the early eighties for the interpretation of the glucose and insulin plasma concentrations following the intravenous glucose tolerance test. It is composed of two parts: the first consists of two differential equations and describes the glucose plasma concentration time-course treating insulin plasma concentration as a known forcing function; the second consists of a single equation and describes the time course of plasma insulin concentration treating glucose plasma concentration as a known forcing function. The two parts are to be separately estimated on the available data. In order to study glucose-insulin homeostasis as a single dynamical system, a unified model would be desirable. To this end, the simple coupling of the original two parts of the minimal model is not appropriate, since it can be shown that, for commonly observed combinations of parameter values, the coupled model would not admit an equilibrium and the concentration of active insulin in the “distant” compartment would be predicted to increase without bounds. For comparison, a simple delay-differential model is introduced, is demonstrated to be globally asymptotically stable around a unique equilibrium point corresponding to the pre-bolus conditions, and is shown to have positive and bounded solutions for all times. The results of fitting the delay-differential model to experimental data from ten healthy volunteers are also shown. It is concluded that a global unified model is both theoretically desirable and practically usable, and that any such model ought to undergo formal analysis to establish its appropriateness and to exclude conflicts with accepted physiological notions. Received: 22 June 1998 / Revised version: 24 February 1999     

Mathematical modelling of clostridial acetone-butanol-ethanol fermentation

Applied Microbiology and Biotechnology - Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to...