Cellular networks

Cavalieri D, De Filippo C. Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Discov Today 2005 10 727-34. 

A considerable improvement over purely graph-based approaches is the analysis of metabolic networks in terms of their stoichiometric matrix. Stoichiometric analysis has a long history in chemical and biochemical sciences [59 62], considerably pre-dating the recent interest in the topology of large-scale cellular networks. In particular, the stoichiometry of a metabolic network is often available, even when detailed information about kinetic parameters or rate equations is lacking. Exploiting the flux balance equation, stoichiometric analysis makes explicit use of the specific structural properties of metabolic networks and allows us to put constraints on the functional capabilities of metabolic networks [61,63 69]. 

S. Klamt, J. Saez Rodriguez, and E. D. Gilles, Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1, 2 (2007). 

The National Institutes of Health (NIH) has characterized "[t]he general aim of metabolomics. .. to identify, measure and interpret the complex, time-related concentration, activity and flux of endogenous metabolites in cells, tissues and other biosamples such as blood, urine and saliva."3 Taken together, the three "omics" disciplines represent a systemic and powerful approach to mapping cellular networks, allowing for faster and more predictive biology in terms of risk assessment, potential therapeutic benefit, as well as diagnosis. 

T. Nowotny and M. Requardt, Pregeometric concepts on graphs and cellular networks, invited paper, J. Chaos, Solitons and Fractals 10, 469 (1999) hep-th/9801199. 

Figure 4. A scanning electron micrograph showing the replicas of lacunae and canalicuh in situ in mandibular bone from a young subject aged 22 years. The inset shows enlarged lacunae identified by a rectangle. This micrograph illustrates the interconnectivity of the connected cellular network (CCN). Copied from Atkinson and Hallsworth (1983).

Moss, M.L. (1991a) Bone as a connected cellular network modeling and testing. Topics in Biomedical Engineering. Editor G. Ross 117-119. Pergamon Press, New York... 

Moss, M.L (1991b) Alternate mechanisms of bone remodeling their representation in a connected cellular network model. Annals of Biomedical Engineering 19 636... 

Moss, M.L. (1997b) The functional matrix hypothesis revisited. 2. The role of an osseous connected cellular network. American Journal of Orthodontal and Dentofacial Orthopedics 112 221-6... 

One of the major liver functions is detoxification of substances carried by blood, which are perfused through the cellular network in the organ. These functions can... 

Bj 1 Akims Potrrt-L e Molecules J i Biological. Mhcto-IJe molecule Sell Assembling Organizations Cefis Cellular Networks (Organisms)... 

Ultimate cell surface Information (X, Y, 2, etc.) derived from (A, B, C) determines the nature of the blo-cellular network (organism)... 

Fig. 5. Molecular information transfer from DNA to cellular protein during bio-cellular network development...

Wiechert, W. (2002) An introduction to 13C metabolic flux analysis. Genet. Eng. (NY) 24, 215-238. Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R.Y., Alon, U. andMargalit, H. (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc. Natl Acad. Sci. U.S.A. 101, 5934-5939. 

A particularly well studied example of functional amyloid is provided by Curli assembly (53). Curli amyloids are assembled by bacteria such as Escherichia coli and Salmonella. Once assembled on the extracellular surface, Curli amyloid fibers function as natural ceU adhesion molecules that link together bacterial cells into robust cellular networks of biofilms. Other examples of functional amyloids include the silk fibers observed commonly in spider webs the Chorion proteins of egg shells Factor XII, which is an activator of the hemostatic system and other naturally produced adhesives and materials (54). 

Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004 303 799-805. 98. 

The actin cytoskcleton is one of the most fascinating cellular networks that mediates a variety of essential biological processes critical for the survival of the cell. Its dynamic properties provide the basic force for various processes like cell migration, endocytosis, vesicular trafficking and cytokinesis. In order to efficiently execute all these dynamic processes the differential reguladon and recruitment of a plethora of actin-bindingproteins with distinctive activities is required. One of the major actin binding proteins that has been extensively studied in recent years is coronin. 

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