Abstract
We propose an approach for estimating the efficiency of biological systems and mechanisms in vivo. We compare two mechanisms for chemical transport: diffusion and endosome transport with a cargo along a system of microtubules. Our efficiency evaluation is based on a comparison of the organism’s energy expenditure for cell house-keeping and the transport system’s operation with the speed of cargo delivery. We study the relation between transport efficiency and adaptability of the transport network. Our approach can be used to study models of live systems and solve problems of artificial life design.
Similar content being viewed by others
References
Gingold, H. and Pilpel, Y., Determinants of Translation Efficiency and Accuracy, Molecul. Syst. Biolog., 2011, vol. 7, no. 1.
Stearns, S.C., The Evolution of Life Histories, Oxford: Oxford Univ. Press, 1992.
Smith, M.J., Optimization Theory in Evolution, Ann. Rev. Ecolog. Syst., 1978, vol. 9, pp. 31–56.
Rosen, R., Optimality Principles in Biology, New York: Butterworths, 1967. Translated under the title Printsip optimal’nosti v biologii, Moscow: Mir, 1969.
Human Physiology, New York: Springer, 1984, vol. 4. Translated under the title Fiziologiya cheloveka, Schmidt, R.F. and Thews, G., Eds., Moscow: Mir, 1985.
Lodish, H., Molecular Cell Biology, New York: W.H. Freeman, 2008.
Alberts, B. et al., Molecular Biology of the Cell, New York: Garland Science, 2002. Translated under the title Molekulyarnaya biologiya kletki, Izhevsk: R&D Dynamics, 2013.
Cytrynbaum, E.N., Rodionov, V., and Mogilner, A., Computational Model of Dynein-Dependent Self- Organization of Microtubule Asters, J. Cell Sci., 2004, vol. 117, pp. 1381–1397.
Cangiani, A. and Natalini, R., A Spatial Model of Cellular Molecular Trafficking Including Active Transport along Microtubules, J. Theoret. Biolog., 2010, vol. 267, no. 4, pp. 614–625.
Liu, J., Munoz-Alicea, R., Huang, T., Tavener, S., and Chen, C., A Mathematical Model for Intracellular HIV-1 Gag Irotein Transport and its Parallel Numerical Simulations, Procedia CS, 2012, vol. 9, pp. 679–688.
Dinh, A.-T., Theofanous, T., and Mitragotri, S., A Model for Intracellular Trafficking of Adenoviral Vectors, Biophys. J., 2005, vol. 89, no. 3, pp. 1574–1588.
Collinet, C., Stoter, M., Bradshaw, C.R., et al., Systems Survey of Endocytosis by Multiparametric Image Analysis, Nature, 2010, vol. 464, no. 7286, pp. 343–350.
Rink, J., Ghigo, E., Kalaidzidis, Y., and Zerial, M., Rab Conversion as a Mechanism of Progression from Early to Late Endosomes, Cell, 2005, vol. 122, pp. 735–749.
Flores-Rodriguez, N., Rogers, S.S., Kenwright, D.A., et al., Roles of Dynein and Dynactin in Early Endosome Dynamics Revealed Using Automated Tracking and Global Analysis, PLoS ONE, 2011, vol. 6, no. 9.
Foret, L., Dawson, J.E., Villaseñor, R., et al., A General Theoretical Framework to Infer Endosomal Network Dynamics from Quantitative Image Analysis, Current Biolog., 2012, vol. 22, no. 15, pp. 1381–1390.
Rogers, S.S., Flores-Rodriguez, N., Allan, V.J., et al., The First Passage Probability of Intracellular Particle Trafficking, Phys. Chem. Chem. Phys., 2010, vol. 12, no. 15, pp. 3753–3761.
Kalwarczyk, T., Ziebacz, N., Bielejewska, A., et al., Comparative Analysis of Viscosity of Complex Liquids and Cytoplasm of Mammalian Cells at the Nanoscale, Nano Lett., 2011, vol. 11, no. 5, pp. 2157–2163.
Segrest, J.P., Jones, M.K., De Loof, H., and Dashti, N., Structure of Apolipoprotein B-100 in Low Density Lipoproteins, J. Lipid Res., 2001, vol. 42, no. 9, pp. 1346–1367.
Novikov, K.A., Romanyukha, A.A., Gratchev, A.N., Kzhyshkowska, J.G., and Melnichenko, O.A., Mathematical Model of Cellular Transport Network Self-Organization and Functioning, Math. Models Comput. Simulations, 2015, vol. 7, no. 5, pp. 475–484.
McMahon, H.T. and Boucrot, E., Molecular Mechanism and Physiological Functions of Clathrin- Mediated Endocytosis, Nat. Rev. Mol. Cell. Biol., 2011, vol. 12, no. 8, pp. 517–533.
West, G.B., Woodruff, W.H., and Brown, J.H., Allometric Scaling of Metabolic Rate from Molecules and Mitochondria to Cells and Mammals, Proc. Natl. Acad. Sci., 2002, vol. 99, no. 1, pp. 2473–2478.
Unger, E., Böhm, K.J., and Vater, W., Structural Diversity and Dynamics of Microtubules and Polymorphic Tubulin Assemblies, Electron Microscop. Rev., 1990, vol. 3, no. 2, pp. 355–395.
Kirschner, M. and Mitchison, T., Beyond Self-Assembly: From Microtubules to Morphogenesis, Cell, 1986, vol. 45, no. 3, pp. 329–342.
van Deurs, B., Petersen, O.W., Olsnes, S., and Sandvig, K., The Ways of Endocytosis, Int. Rev. Cytol., 1989, vol. 117, pp. 131–177.
Walker, R.A., O’Brien, E.T., Pryer, N.K., et al., Dynamic Instability of Individual Microtubules Analyzed by Video Light Microscopy: Rate Constants and Transition Frequencies, J. Cell Biolog., 1988, vol. 107, no. 4, pp. 1437–1448.
Huotari, J. and Helenius, A., Endosome Maturation, EMBO J., 2011, vol. 30, no. 7, pp. 3481–3500.
O’Connell, C.B. and Khodjakov, A.L., Cooperative Mechanisms of Mitotic Spindle Formation, J. Cell Sci., 2007, vol. 120, no. 10, pp. 1717–1722.
Heald, R. and Nogales, E., Microtubule Dynamics, J. Cell Sci., 2002, vol. 115, no. 1, pp. 3–4.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © K.A. Novikov, A.A. Romanyukha, 2016, published in Avtomatika i Telemekhanika, 2016, No. 5, pp. 136–147.
Rights and permissions
About this article
Cite this article
Novikov, K.A., Romanyukha, A.A. Evaluating the efficiency of cell mechanisms and systems. Autom Remote Control 77, 862–871 (2016). https://doi.org/10.1134/S000511791605009X
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S000511791605009X