Mathematical model for the ecosystem response of Lake Ladoga to phosphorus loading

The ecosystem response model described in this paper combines an ecosystem model and a three-dimensional circulation model of Lake Ladoga developed earlier by the authors. The ecosystem model describes the process of Lake Ladoga eutrophication, and its biological submodel describes changes in the phyto- and zooplankton. In the earlier model version, lake circulation was determined using a two-dimensional hydrodynamical model which was not completely adequate. The present model allows calculation of the distributions of phyto- and zooplankton and mineral phosphorus and nitrogen. One of its main advantages is that reliable computations of the ecosystem dynamics over an extended period of time are possible. The response of the ecosystem to different levels of phosphorus pollution loading and to weather conditions is studied.     

The history of development of evolutionary methods in St. Petersburg school of computer simulation in biology

The history of rise and development of evolutionary methods in Saint Petersburg school of biological modelling is traced and analyzed. Some pioneering works in simulation of ecological and evolutionary processes, performed in St.-Petersburg school became an exemplary ones for many followers in Russia and abroad. The individual-based approach became the crucial point in the history of the school as an adequate instrument for construction of models of biological evolution. This approach is natural for simulation of the evolution of life-history parameters and adaptive processes in populations and communities. In some cases simulated evolutionary process was used for solving a reverse problem, i. e., for estimation of uncertain life-history parameters of population. Evolutionary computations is one more aspect of this approach application in great many fields. The problems and vistas of ecological and evolutionary modelling in general are discussed.     

History of development of evolutionary methods in St. Petersburg school of computer simulation in biology

The work presents a short history of development of evolutionary methods in the St. Petersburg school of computer simulation of biological processes. Several moments confirm priority of this school in modeling of micro- and macroevolutionary processes. A peculiarity of the school is a combination of the applied and theoretical study, penetration into the biological essence of phenomenon, consideration of real interrelationships of ecological and physiological parameters. The natural tendency for transition to modeling at the level of single individuals and then-to imitation of evolutionary processes on computer is traced. Paradoxically, such detalization sometimes does not worsen, but improves prognostic properties of models of populations, communities, and ecosystems, and besides, makes unnecessary monitoring of some variable characteristics, because the individual-based approach allows to direct account for adaptive processes and hidden evolutionary relationships between the life history parameters. Problems and perspectives of development of evolutionary methods of modeling are analyzed.     

Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling

Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.     

Attempt at computer modeling of evolution of the human society

A model of evolution of human society and biosphere, which is based on concepts of V.I. Vernadskii and of L.N. Gumilev about ethnogenesis has been developed and studied. The mathematical apparatus of the model is composition of finite stochastic automats. By using this model, a possibility of the global ecological crisis is demonstrated in the case of preservation of the current tendencies of interaction of the biosphere and the human civilization.     

Mapping the amino acid properties of constituent nucleoporins onto the yeast nuclear pore complex

Visualization of molecular structures aids in the understanding of structural and functional roles of biological macromolecules. Macromolecular transport between the cell nucleus and cytoplasm is facilitated by the nuclear pore complex (NPC). The ring structure of the NPC is large and contains several distinct proteins (nucleoporins) which function as a selective gate for the passage of certain molecules into and out of the nucleus. In this note we demonstrate the utility of a python code that allows direct mapping of the physiochemical properties of the constituent nucleoporins on the scaffold of the yeast NPC׳s cytoplasmic view. We expect this tool to be useful for researchers to visualize the NPC based on their physiochemical properties and how it alters when specific mutations are introduced in one or more of the nucleoporins. The code developed using Python is available freely from the authors.     

Imitational modeling of process of evolution: From organic macromolecules to protocell and animal cell

A dynamic imitational model of initial stages of cell evolution has been developed based on role of environmental calcium concentration. The model is designed from our hypothesis about the medium of the appearance of protocells, which could be potassium water reservoirs rather than sea salt water with its predominance of sodium salts. The necessary elements of the appearance of the protocells served organic molecules, code of their synthesis, and formation of macromolecules under favorable ion concentration in environment: a high K⁺ and Mg²⁺ and a low Na⁺ concentration. The model is based on an assumption that one of the first stages in evolution of life was the appearance in the potassium-magnesium water reservoirs of organic molecules capable for self-replication on the basis of genetic code and formation of protocell with the potassium cytoplasm. The model has demonstrated necessity of formation of cell envelope for development of the protocell. Replacement of the dominant cation in water reservoirs—potassium by sodium—required the appearance of ion-transporting devices in plasma membrane and their participation in adaptation of cells to environment. This stage of evolution was accompanied by the most important morphofunctional event—formation of the plasma membrane instead of cell envelope. The membrane provided the ion asymmetry in the cell (preservation of K⁺ in it) relatively to the sodium external medium for maintaining optimal intracellular medium. In the model system, predecessors of animal cells elaborated mechanism of maintenance of the potassium cytoplasm with the sodium counterion dominating in the environment.     

Imitational modeling of evolution: from organic macromolecules to protocell and animal cell

A dynamic imitational model is developed of initial stages of cell evolution based on role of environmental cation concentration. The model is developed on our hypothesis, concerning the medium of the appearance of protocells. Could be potassium water reservoirs rather than sea salt water with its predominance of sodium salts. The necessary elements of appearance the protocells served organic molecules, code of their synthesis, and formation of macromolecules under favorable ion concentration in environment High K+ and Mg2+ concentration and bow Na+. The model is based on an assumption that one of the first stages in evolution of life was the appearance in potassium-magnesium water reservoirs of organic molecules capable for selfreplication on the basis of genetic code and formation of protocells with potassium cytoplasm. The model has demonstrated necessity of formation of cell envelope for development of the protocell. Replacement of the dominant cation in water reservoirs-potassium by sodium-required the appearance of ion-transporting devices in plasma membrane and their participation in adaptation of cells to environment. This stage of evolution was accompanied by the most important morpho-functional event--formation of the plasma membrane instead of cell envelope. The membrane provided the ion asymmetry in the cell (preservation of K+ in it) relatively to the sodium external medium for maintaining optimal intracellular medium. In the model system, predecessors of animal cells elaborated mechanism of maintenance of the potassium cytoplasm with the sodium counter-ion dominating in the environment.