Biological cell models

In the meantime, the intense study of the simpler vesicle systems has unravelled novel, unsuspected physicochemical aspects - for example growth, fusion and fission, the matrix effect, self-reproduction, the effect of osmotic pressure, competition, encapsulation of enzymes, and complex biochemical reactions, as will be seen in the next chapter. Of course the fact that vesicles are viewed under the perspective of biological cell models renders these findings of great interest. In particular, one tends immediately to ask the question, whether and to what extent they might be relevant for the origin of life and the development of the early cells. In fact, the basic studies outlined in this chapter can be seen as the prelude to the use of vesicles as cell models, an aspect that we will considered in more detail in the next chapter. 

Fermentation systems obey the same fundamental mass and energy balance relationships as do chemical reaction systems, but special difficulties arise in biological reactor modelling, owing to uncertainties in the kinetic rate expression and the reaction stoichiometry. In what follows, material balance equations are derived for the total mass, the mass of substrate and the cell mass for the case of the stirred tank bioreactor system (Dunn et ah, 2003). 

By means of the Coulter channelizer 256 module an optional extra on the model ZM but built-in on the multisizer, enables biological cell-size distributions to be measured. This provides an ability to measure suspension... 

It can be expected that the discussed possibilities may help to synthesize stabilized cell models and to simulate biological processes. 

The vast majority of research focused on selenium in biology (primarily in the fields of molecular biology, cell biology, and biochemistry) over the past 20 years has centered on identification and characterization of specific selenoproteins, or proteins that contain selenium in the form of selenocysteine. In addition, studies to determine the unique machinery necessary for incorporation of a nonstandard amino acid (L-selenocysteine) during translation also have been central to our understanding of how cells can utilize this metalloid. This process has been studied in bacterial models (primarily Escherichia colt) and more recently in mammals in vitro cell culture and animal models). In this work, we will review the biosynthesis of selenoproteins in bacterial systems, and only briefly review what is currently known about parallel pathways in mammals, since a comprehensive review in this area has been recently published. Moreover, we summarize the global picture of the nonspecific and specific use of selenium from a broader perspective, one that includes lesser known pathways for selenium utilization into modified nucleosides in tRNA and a labile selenium cofactor. We also review recent research on newly identified mammalian selenoproteins and discuss their role in mammalian cell biology. 

Another attractive application of polymer brushes is directed toward a biointerface to tune the interaction of solid surfaces with biologically important materials such as proteins and biological cells. For example, it is important to prevent surface adsorption of proteins through nonspecific interactions, because the adsorbed protein often triggers a bio-fouling, e.g., the deposition of biological cells, bacteria and so on. In an effort to understand the process of protein adsorption, the interaction between proteins and brush surfaces has been modeled like the interaction with particles, the interaction with proteins is simplified into three generic modes. One is the primary adsorption. 

It is important to point out the main message of these experiments. This is that, by a very simple set-up, a spontaneous self-reproduction of spherical compartments can be obtained. Since such spherical compartments can be considered as models and/or precursors of biological cells, the hypothesis was put forward, (Bachmann et al, 1992), that this autocatalytic self-reproduction process might have been of relevance for the origin of life. 

Let us now look at some properties of vesicles and liposomes (liposomes can be defined as vesicles made out of lipids, although often the two terms are used synonymously). This will be a preliminary to the next chapter, where the reactivity of vesicles as models for biological cells will be considered in more detail. 

Vesicles are commonly considered models for biological cells. This is due to the bilayer spherical structure which is also present in most biological cells, and to the fact that vesicles can incorporate biopolymers and host biological reactions. Self-reproduction, an autocatalytic reaction already illustrated in the chapters on self-reproduction and autopoiesis, also belongs to the field of reactivity of vesicles. Some additional aspects of this process will be considered here, together with some particular properties of the growth of vesicles - the so-called matrix effect. 

A very brief description of biological membrane models, and model membranes, is given. Studies of lateral diffusion in model membranes (phospholipid bilayers) and biological membranes are described, emphasizing magnetic resonance methods. The relationship of the rates of lateral diffusion to lipid phase equilibria is discussed. Experiments are reported in which a membrane-dependent immunochemical reaction, complement fixation, is shown to depend on the rates of diffusion of membrane-bound molecules. It is pointed out that the lateral mobilities and distributions of membrane-bound molecules may be important for cell surface recognition. 

Figure 13.7 The fluid mosaic model of biological cells, (image courtesy of www.wikipedia.org).

An analytical elastic membrane model was developed by Feng and Yang (1973) to model the compression of an inflated, non-linear elastic, spherical membrane between two parallel surfaces where the internal contents of the cell were taken to be a gas. This model was extended by Lardner and Pujara (1980) to represent the interior of the cell as an incompressible liquid. This latter assumption obviously makes the model more representative of biological cells. Importantly, this model also does not assume that the cell wall tensions are isotropic. The model is based on a choice of cell wall material constitutive relationships (e.g., linear-elastic, Mooney-Rivlin) and governing equations, which link the constitutive equations to the geometry of the cell during compression. 

E-Cell Keio University Object-oriented software suite for modeling, simulation, and analysis of large-scale complex systems such as biological cells (http //www. e -cell, org/models/)... 

Biosimulation has a dominant role to play in systems biology. In this chapter, we briefly outline two approaches to systems biology and the role that mathematical models has to play in them. Our focus is on kinetic models, and silicon cell models in particular. Silicon cell models are kinetic models that are firmly based on experiment. They allow for a test of our knowledge and identify gaps and the discovery of unanticipated behavior of molecular mechanisms. These models are very complicated to analyze because of the high level of molecular-mechanistic detail included in them. To facilitate their analysis and understanding of their behavior, model reduction is an important tool for the analysis of silicon cell models. We present balanced truncation as one method to perform model reduction and apply it to a silicon cell model of glycolysis in Saccharomyces cerevisiae. 

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