Bioenergetic models

Kraft, C. E. Estimation of Phosphorus Cycling by Fish Using a Bioenergetics Modeling Approach. Ph.D. Thesis. University of Wisconsin—Madison, Madison, WI, 1991. 

Kitchell, J.F., Stewart, D.J. and Weininger, D. (1977). Applications of a bioenergetics model to yellow perch and walleye. Journal of the Fisheries Research Board of Canada 34,1922-1935. 

Simplified fugacity models may not predict the existence of biomagnification, although bioenergetic models allow for biomagnification which may be especially significant for compounds with values of log Pow > 4 (Connolly and Pedersen 1988). Considerable attention has been directed to theoretical considerations, and the data appear to suggest only moderate levels of... 

Because of these reasons, my colleagues and I initiated a few years ago a detailed study of proton transfer in an aqueous system, where the event is synchronized by a laser pulse. This technique, using signal averaging, retains the temporal parameters of the event and allows the evaluation of the probabilities of finding a proton in putative environments assigned for it by the different bioenergetic models. 

Redox reactions at the interface between immiscible liquids fall into two classes. The first class includes spontaneous processes that occur in the absence of external electromagnetic fields [16-77]. This type of redox transformation has been investigated in bioenergetics, model membrane systems and at oil/water interfaces [78-99]. Redox reactions in the second class occur at the interface between immiscible electrolytes when external electrical fields are applied to the interface, and under these conditions interfacial charge-transfer reactions take place at controlled interfacial potentials [100-139]. 

Norstrom, R.J., McKinnon, A.E., and de Freitas, A.S.W. (1976). A bioenergetic based model for pollutant accumulation by fish. Journal of Fisheries Research Board of Canada 33, 248-267. 

Rodgers DW. 1994. You are what you eat and a httle bit more bioenergetics-based models of methyhnercrrry accumulation in fish revisited. In Watras CJ, Huckabee JW, editors. Mercury pollution integration and synthesis. Boca Raton (FL) Lewis Publishers, p. 427-439. 

Nichols JW, Larsen CP, McDonald ME, Niemi GJ, Ankley GT. 1990. Bioenergetics-based model for accumulation of polychlorinated biphenyls by nestling tree swallows, Tachycineta bicolor. Environ Sci Technol 29 604-612. 

Fig. 1.5 Schematic representation of the evolution of life from its precursors, on the basis of the definition of life given by the authors. If bioenergetic mechanisms have developed via autonomous systems, the thermodynamic basis for the beginning of the archiving of information, and thus for a one-polymer world such as the RNA world , has been set up. Several models for this transition have been discussed. This phase of development is possibly the starting point for the process of Darwinian evolution (with reproduction, variation and heredity), but still without any separation between genotype and phenotype. According to the authors definition, life begins in exactly that moment when the genetic code comes into play, i.e., in the transition from a one-polymer world to a two-polymer world . The last phase, open-ended evolution, then follows. After Ruiz-Mirazo et al. (2004)...

Sturtevant, J.M. 1980. Differential scanning calorimetry processes involving proteins. In Bioenergetics and Thermodynamics Model Systems. A. Braibanti, editor. John Wiley Sons, New York, 391-396. 

Thomann et al. (1992) and Morrison et al. (1997) have developed kinetic models employing rate constants to assess the extent of chemical bioaccumulation in zooplankton, as Tables 9.1 and 9.2 summarize. Thomann et al. (1992) list relationships which incorporate organism physiology, bioenergetics, and chemical characteristics to estimate uptake and elimination rate constants which are used to estimate bioaccumulation. Morrison et al. (1997) rely on physiological information to estimate bioaccumulation. Both models provide a potentially more realistic description of bioaccumulation by zooplankton, although, to date, neither model has been tested independently against field data. 

Thomann et al. (1992) developed a steady-state food web bioaccumulation model that combines kinetic and bioenergetic parameters to quantify chemical uptake and elimination by zooplankton, benthic invertebrates and fish. First-order kinetic rate constants quantify uptake of freely-dissolved chemical from interstitial water and overlying water and total chemical elimination from gills and feces. Various physiological and bioenergetic parameters quantify chemical uptake from diet and growth dilution. 

Efforts to model foodweb dynamics are hampered by calibration data, particularly the lower trophic levels, and by the large uncertainties associated with bioenergetic input parameters, such as PCB assimilation efficiencies for different organisms. Another major hindrance in aquatic foodweb models is a lack of understanding of the bioaccumulation of PCBs from water to the first trophic level, phytoplankton.61,62 Research in this laboratory has revealed that... 

This has been one of the most controversial areas of bioenergetics and is concerned with the role of coenzyme Q. The simplest view of the role of this coenzyme is that it acts as a mobile (2H+ + 2e ) carrier, linking complexes I and II with complex III. However, coenzyme Q may be involved in (H+ + e ) transfer within complex III. One model for this is the proton-motive Q cycle (Fig. 14-6), developed by Mitchell in 1975. This model satisfies prediction (2) of Example 14.10, in that coenzyme Q acts as an (H+ +e ) carrier in two loops. In this model, reduced coenzyme Q (QH2) is linked to oxidized coenzyme Q (Q) via the free-radical semiquinone (QH-) This model provides an explanation for the H+/e stoichiometry. 

Norstrom, R. J., McKinnon, A. E. and DeFreitas, A. S. W. A bioenergetics-based model for pollutant accumulation by fish. Simulations of PCB and methylmercury residue levels in Ottawa River yellow perch (Perea flavesceus), Fish. Res. Bd. Can. 

Seki A, Kubo I, Sasabe H and Tomioka H 1994 A new anion-sensitive biosensor using an ion-sensitive field effect transistor and a light-driven chloride pump, halorhodopsin Appl. Biochem. Biotechnol. 48 205-11 Fuller B E, Okajima T L and Hong F T 1995 Analysis of the d.c. photoelectric signal from model bacteriorhodopsin membranes d.c. photoconductivity determination by means of the null current method and the effect of proton ionophores Bioelectrochem. Bioenerget. 37 109-24 Cone R A 1967 Early receptor potential photoreversible charge displacement in rhodopsin Science 155 1128-31... 

We summarise recent work on computer modelling and simulation of proteins involved in bioenergetic processes and in peptide-membrane interactions. Homology modelling, electrostatic calculations and conformational analysis of a photosynthetic reaction centre protein are described. Bacteriorhodopsin, a light-driven proton pump protein is examined from several aspects, including its hydration and conformational thermodynamics. Finally, we present results on lipid perturbation on interaction with a cyclic decapeptide antibiotic, gramicidin S. 

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