Systems biology model

There is quite a large body of literature on films of biological substances and related model compounds, much of it made possible by the sophisticated microscopic techniques discussed in Section IV-3E. There is considerable interest in biomembranes and how they can be modeled by lipid monolayers [35]. In this section we briefly discuss lipid monolayers, lipolytic enzyme reactions, and model systems for studies of biological recognition. The related subjects of membranes and vesicles are covered in the following section. 

As a point of interest, it is possible to form very thin films or membranes in water, that is, to have the water-film-water system. Thus a solution of lipid can be stretched on an underwater wire frame and, on thinning, the film goes through a succession of interference colors and may end up as a black film of 60-90 A thickness [109]. The situation is reminiscent of soap films in air (see Section XIV-9) it also represents a potentially important modeling of biological membranes. A theoretical model has been discussed by Good [110]. 

Biological Antioxidant Models. Tea extracts, tea polyphenol fractions, and purified catechins have all been shown to be effective antioxidants in biologically-based model systems. A balance between oxidants and antioxidants is critical for maintenance of homeostasis. Imbalances between free radicals and antioxidants may be caused by an increased production of free radicals or decreased effectiveness of the antioxidants within the reaction system. These imbalances can be caused by the radicals overwhelming the antioxidants within the system, or by an excess of antioxidants leading to a prooxidant functionaHty (105—118). When antioxidant defense systems are consistently overwhelmed by oxidative reactions, significant damage can... 

Hydrated bilayers containing one or more lipid components are commonly employed as models for biological membranes. These model systems exhibit a multiplicity of structural phases that are not observed in biological membranes. In the state that is analogous to fluid biological membranes, the liquid crystal or La bilayer phase present above the main bilayer phase transition temperature, Ta, the lipid hydrocarbon chains are conforma-tionally disordered and fluid ( melted ), and the lipids diffuse in the plane of the bilayer. At temperatures well below Ta, hydrated bilayers exist in the gel, or Lp, state in which the mostly all-trans chains are collectively tilted and pack in a regular two-dimensional... 

Ochrymowycz and his coworkers have also prepared a number of polysulfur macrocycles for use in biological or biological model systems . The synthetic methodology is essentially similar to that described above except that certain of the sulfur containing fragments were prepared by addition reactions to ethylene. Two examples of this approach, taken from ref. 59, are shown in Eq. (6.9). 

In the biological field, much attention has been directed toward the transport phenomena through membrane. Although the function of some natural ionophores has been known, the investigation of active and selective transport of ions using the artificial ionophores in the simple model systems may be important to simulate the biological systems and clarify the transport behaviour of natural membranes. 

With the adequacy of lipid bilayer membranes as models for the basic structural motif and hence for the ion transport barrier of biological membranes, studies of channel and carrier ion transport mechanisms across such membranes become of central relevance to transport across cell membranes. The fundamental principles derived from these studies, however, have generality beyond the specific model systems. As noted above and as will be treated below, it is found that selective transport... 

Lanthanide ions as structural probes in biological and model systems. E. Nieboer, Struct. Bonding... 

Inorganic oxygen carriers as models for biological systems. G. McLendon and A. E. Martell, Coord. Chem. Rev., 1976,19, 1-39 (235). 

Rojo J, Morales JC, Penades S (2002) Carbohydrate-Carbohydrate Interactions in Biological and Model Systems. 218 45-92 Romerosa A, see Ehses M (2002) 220 107-140 Rouden J, see Lasne M-C (2002) 222 201258... 

Nieboer E (1975) The Lanthanide Ions as Structural Probes in Biological and Model Systems. 

A final example of the simulation of a complex system is a series of MD simulations of bilayer membranes. Membranes are crucial constituents of living organisms they are the scene for many important biological processes. Experimental data are known for model systems for example for the system sodium decanoate, decanol and water that forms smectic liquid crystalline structures at room temperature, with the lipids organized in bilayers. 

The main part of the report describes the results of systematic investigations into the hydrodynamic stress on particles in stirred tanks, reactors with dominating boundary-layer flow, shake flasks, viscosimeters, bubble columns and gas-operated loop reactors. These results for model and biological particle systems permit fundamental conclusions on particle stress and the dimensions and selection of suitable bioreactors according to the criterion of particle stress. 

Fig. 2. Properties of model and biological particle systems Micro scale related particle diameter dp/riL versus maximum energy dissipation e , in stirred reactors explanations see Table 3 and Table 4...

Many results with model systems and also biological particle systems indicate that the stress in technical bioreactors, in which turbulent flow conditions exist, could not be simulated by model studies in small bioreactors, where no fully turbulent flow exists, and especially with laminar flow devices such as viscosimeters, tubes or channels. 

Company Network Tools Disease Models Ontologies Systems Biology Collaborations... 

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. The systems biology markup language (SBML) a medium for representation and exchange of biochemical network models. Bioinformatics 2003 19 524-31. 

Xirasagar S, Gustafson S, Merrick BA, Tomer KB, Stasiewicz S, Chan DD, et al. CEBS object model for systems biology data, SysBio-OM. Bioinformatics 2004 20 2004-15. 

Bugrim A, Nikolskaya T, Nikolsky Y. Early prediction of drug metabolism and toxicity systems biology approach and modeling. Drug Discov Today 2004 9 127-35. 

---