Sponge cell reaggregation: Mechanisms and dynamics of the process

Sponges (Porifera) are lower metazoans whose organization is characterized by a high plasticity of anatomical and cellular structures. One of the manifestations of this plasticity is the ability of sponge cells to reaggregate after dissociation of tissues. This review brings together the available data on the reaggregation of sponge cells that have been obtained to date since the beginning of the 20th century. It considers the behavior of dissociated cells in suspension, the mechanisms and factors involved in reaggregation, and the rate and stages of this process in different representatives of this phylum. In addition, this review provides information about the histological structure of multicellular aggregates formed during reaggregation of cells and the regenerative morphogenetic processes leading to the formation of normal sponges from these multicellular aggregates.     

Natural-constructive approach to modeling the cognitive process

We present a “natural-constructive approach” to modeling the cognitive process, which is based on the dynamic theory of information, the technique of nonlinear differential equations, and the concept of a “dynamic formal neuron.” The version of cognitive architecture that was designed within the natural-constructive approach is presented. One important constructive feature of this architecture consists in splitting up the entire system into two similar hemi-systems (by analogy with the right and left cerebral hemispheres). One of these is responsible for the generation of information and learning, with other one being responsible for the reception and processing of well-known information. This functional specialization is provided by the presence of noise (a random factor) in the generation hemi-system; in the reception hemi-system, all the processes should proceed successively rather than stochastically. The interpretation of the concepts of intuition, logic, consciousness, and sub-consciousness is discussed. The architecture that is designed within the natural-constructive approach is compared with other theoretical approaches (graph theory and the “cognitom” concept), and with anatomical data. The concept of an experiment is proposed that could verify or disprove the main inferences of the natural-constructive approach.     

Mathematical modeling of affinity ultrafiltration process

An affinity ultrafiltration process has been developed by exploiting affinity binding in conjunction with cross-flow filtration. The process was proven to possess high resolution, high recovery yield, and ease of scale-up. The process could purify trypsin from a trypsin-chymotrypsin mixture batchwise or continuously. Essential for applying this concept was the synthesis of a water-soluble high-molecular-weight polymer bearing m-aminobenzamidine, a strong and specific trypsin in hibitor. A mathematical model was also developed to describe the dynamic behavior of the newly developed purification process. The model was able to predict the profiles of enzyme concentrations in the process with high accuracy.     

Mechanisms of neovasculogenesis and its regulation in the adult organism

Under regeneration of organs, wound healing, tumour growth, inflammatory processes, under many compensatory and adaptive reactions in the organism of mature persons and animals, an inevitable formation of new blood vessels (neovasculogenesis) takes place. Modern notions on mechanisms of neovasculogenesis are based on the fact that new formation of vessels in a mature organism includes processes of migration and replication of endothelial cells according to the principle: "endothelium from endothelium". The literature data on neovasculogenesis in the mature organism are summarized and compared with the authors' investigations. Characterization of new blood vessels growth is presented; ultrastructural organization of endotheliocytes in growing capillaries, formation of barrier-transport properties in the newly formed vessels, role of inductors and inhibitors of neovasculogenesis in creation of new vascular formations are considered.     

Mathematical modeling and analysis of the flocculation process in chambers in series

In this study, the flocculation process in continuous systems with chambers in series was analyzed using the classical kinetic model of aggregation and break-up proposed by Argaman and Kaufman, which incorporates two main parameters: K _a and K _b. Typical values for these parameters were used, i. e., K _a = 3.68 × 10^?5–1.83 × 10^?4 and K _b = 1.83 × 10^?7–2.30 × 10^?7 s^?1. The analysis consisted of performing simulations of system behavior under different operating conditions, including variations in the number of chambers used and the utilization of fixed or scaled velocity gradients in the units. The response variable analyzed in all simulations was the total retention time necessary to achieve a given flocculation efficiency, which was determined by means of conventional solution methods of nonlinear algebraic equations, corresponding to the material balances on the system. Values for the number of chambers ranging from 1 to 5, velocity gradients of 20–60 s^?1 and flocculation efficiencies of 50–90 % were adopted.     

Dynamical modeling of microRNA action on the protein translation process

Background  

Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple mechanisms. It remains unclear what mechanisms of microRNA action are the most dominant: moreover, many experimental reports deliver controversial messages on what is the concrete mechanism actually observed in the experiment. Nissan and Parker have recently demonstrated that it might be impossible to distinguish alternative biological hypotheses using the steady state data on the rate of protein synthesis. For their analysis they used two simple kinetic models of protein translation.     

Parameter and process significance in mechanistic modeling of cellulose hydrolysis

A process-based model relevant to landfill and anaerobic digesters was developed, which included a novel approach to biomass transfer between a cellulose-bound biofilm and biomass in the bulk liquid. Model results highlighted the significance of the bacterial colonization of cellulose particles by attachment through contact in solution. Simulations revealed that both enhanced colonization and cellulose degradation are associated with reduced cellulose particle size, increased biomass populations in solution and increased cellulose-binding ability of the biomass. This suggests that transportation of biomass into the system from elsewhere and/or bacterial inoculation of such systems could enhance degradation significantly. A sensitivity analysis of the system parameters revealed the biological rate and yield properties of the hydrolyzing bacteria are most significant with regard to cellulose degradation in the system.     

Reduced modeling and state observation of an activated sludge process

This article first proposes a reduction strategy of the activated sludge process model with alternated aeration. Initiated with the standard activated sludge model (ASM1), the reduction is based on some biochemical considerations followed by linear approximations of nonlinear terms. Two submodels are then obtained, one for the aerobic phase and one for the anoxic phase, using four state variables related to the organic substrate concentration, the ammonium and nitrate‐nitrite nitrogen, and the oxygen concentration. Then, a two‐step robust estimation strategy is used to estimate both the unmeasured state variables and the unknown inflow ammonium nitrogen concentration. Parameter uncertainty is considered in the dynamics and input matrices of the system. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Cybernetic modeling of the cephalosporin C fermentation process by Cephalosporium acremonium

A cybernetic mathematical model has been developed to describe the production of cephalosporin C. In developing the model, diauxic behavior of substrate consumption, morphological differentiation of cells, and catabolite repression of cephalosporin C production by the preferred substrate, glucose, were considered. The proposed model was tested on the experimental data from the literature and could adequately describe the morphological differentiation of cells, the sequential utilization of carbon sources and the production of cephalosporin C. It could be a useful tool to optimize the production of cephalosporin C by Cephalosporium acremonium in batch, fed-batch or continuous operations.     

The genetic analysis of age-dependent traits: modeling the character process

The extension of classical quantitative genetics to deal with function-valued characters (also called infinite-dimensional characters) such as growth curves, mortality curves, and reaction norms, was begun by Kirkpatrick and co-workers. In this theory, the analogs of variance components for single traits are covariance functions for function-valued traits. In the approach presented here, we employ a variety of parametric models for covariance functions that have a number of desirable properties: the functions (1) are positive definite, (2) can be estimated using procedures like those currently used for single traits, (3) have a small number of parameters, and (4) allow simple hypotheses to be easily tested. The methods are illustrated using data from a large experiment that examined the effects of spontaneous mutations on age-specific mortality rates in Drosophila melanogaster. Our methods are shown to work better than a standard multivariate analysis, which assumes the character value at each age is a distinct character. Advantages over existing methods that model covariance functions as a series of orthogonal polynomials are discussed.     

Computational modeling of synchronization process of the circadian timing system of mammals

This paper presents a model for the circadian temporization system of mammals which associates the synchronization dynamics of coupling oscillators to a set of equations able to reproduce the synaptic characteristics of somatodendritic membrane of neurons. The circadian timing system is organized in a way to receive information from the external and internal environments, and its function is the timing organization of physiological and behavioral processes in a circadian pattern. Circadian timing system in mammals is constituted by a group of structures which includes the suprachiasmatic nucleus, the intergeniculate leaflet and the pineal gland. In suprachiasmatic nucleus are found neuron groups working as a biological pacemaker—the so-called biological master clock. By means of numerical simulations using the Kuramoto model, we simulated the dynamics behavior of the biological pacemaker. For this we used a set of 1,000 coupled oscillators with long-range coupling, which were distributed on a 10 × 10 × 10 spherical lattice, and a new method to estimate the order parameter, which characterizes the degree of synchronization of oscillator system. Our model has been able to produce frequency responses in accordance with physiological patterns, and to reproduce two fundamental characteristics of biological rhythms: the endogenous generation and synchronization to the light–dark cycle.