Class Of Biological Systems Research Articles

MATHEMATICAL MODELING OF RESULTS OF BORROWING FOREIGN WORDS OF THE RUSSIAN LANGUAGE A REFLECTION OF THE PROCESS OF HISTORICAL INTERACTION BETWEEN RUSSIANS AND FOREIGNERS

As was mentioned by known sociologist Kenneth Ewart Boulding, the human community, divided into various social organizations, is the most complex class of biological systems. This article is dedicated for mathematical modeling of the process of historical interaction between Russians and foreigners, which are reflected in the formation of a living Russian language. The difficulty lies not only in the large number of relationships, but also in the complexity experienced by the researcher who is inside the system under study. The natural desire to abstract in this study from the system itself can be realized using a strictly scientific approach and computational programming. Namely, by using formal objects and the same formal methods of comparing them, as is customary in mathematics, physics, and other sciences that study the laws of nature in areas that are not directly related to human being and society. To form an objective knowledge base about the interaction of social groups of people, you can use the analysis of traces of this interaction, one of which is their language. It is in the language of a people that the main factors of influence of other peoples - native speakers of another language-remain. These traces, in particular, are borrowed words and expressions. To work with such words and expressions, you must first discard those matches that can be attributed to random. Only in this case can the nature of our research be objective. This article uses statistical analysis methods to identify the fact of accidental coincidence of phonetic and semantic images of words from different languages. The basic tool we have chosen is the birthday paradox theorem. As a result, a method for identifying borrowed words that appeared in the language as a result of the interaction of native speakers of different languages, excluding the random nature of their coincidence, is obtained. The application of software definition of matching words in digitized dictionaries is justified. The method is applied to the Russian language. Conclusions are made about the history of the development of the Russian people and its language. These conclusions are that the main significant influence on the Russian population and its language was exerted by Europeans, primarily the French. At the same time, no traces of the influence of Mongolian or other Eastern languages were found. The influence of the Turkic language group and the Greek language occupy a middle position. At the same time, if the semantic load of Turkic and Greek borrowings is of a general scientific or economic nature, then European borrowings are primarily associated with trade, administration, war, and luxuries. The authors concludes that the family character of interaction between native English speakers and language groups close to the English geographically with the Russian population, since the names of the main family members are borrowed mainly from the English language, while the corresponding names was already exist in the old Slavonic language.

Parallelisation strategies for agent based simulation of immune systems

BackgroundIn recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological domain due to high demand for a large scale analysis tools for the collection and interpretation of information to solve biological problems. Simulating massive multi-agent systems (i.e. simulations containing a large number of agents/entities) requires major computational effort which is only achievable through the use of parallel computing approaches.ResultsThis paper explores different approaches to parallelising the key component of biological and immune system models within an ABM model: pairwise interactions. The focus of this paper is on the performance and algorithmic design choices of cell interactions in continuous and discrete space where agents/entities are competing to interact with one another within a parallel environment.ConclusionsOur performance results demonstrate the applicability of these methods to a broader class of biological systems exhibiting typical cell to cell interactions. The advantage and disadvantage of each implementation is discussed showing each can be used as the basis for developing complete immune system models on parallel hardware.

The lipid peroxidation intensity of fungi strains from the orders Agaricales and Polyporales

This article is devoted to investigation of the dynamics of growth and level of spontaneous and induced lipid peroxidation intensity of Basidiomycetes strains grown by surface cultivation on a glucose-peptone medium. The materials of the research are mycelium and culture filtrates (CF) of 57 strains (5 belong to 5 species from the order Polyporales s.l., and 52 belong to 7 species of the order Agaricales s.l.). To study the dynamics of growth we used a weighing method for determining the accumulation of absolutely dry biomass. Intensity of lipid peroxidation was determined by a modified spectrophotometric method for content of active to thiobarbituric acid products. It was found that the most productive in absolutely dry biomass accumulation were the strains Flammulina velutipes (Curt.: Fr.) Sing. F-610 and Pleurotus eryngii (DC.: Fr.) Quél. P-er. The level of spontaneous and induced LPO intensity in mycelia of all strains was higher than this figure in the culture filtrate and increased with the duration of cultivation. Dependencies between the content of lipid peroxidation products in the mycelia and CF were not established. The lowest values were recorded for biomass accumulation by the strains Pleurotus ostreatus (Jacq.: Fr.) P. Kumm. P-14, P-192 and P. citrinopileatus Singer. Р-сіtr. Groups of basidiomycete cultures with different levels of TBA-AP were identified. Spontaneous and induced intensivity of lipid peroxidation in all studied strains of mycelia was higher than the figure in the culture filtrate. The intensity of lipid peroxidation in both mycelia and culture filtrate constantly increased, which can be explained by the growing shortage of certain nutrients (primarily carbon) and increased concentration of metabolic products in the medium. The ratio of spontaneous and induced lipid peroxidation intensity is specific to each strain and is independent of its systematic position. Shifting of prooxidant-antioxidant balance to a relatively stationary level is a mark of stress reaction. LPO-products can be both inductors and primary mediators of stress as a special class of biological systems. Selected strains with high rates of growth and LPO ntensity are promising for applications in biotechnology and ecology.

Multistability and Its Robustness of a Class of Biological Systems

Multistability of biological systems with complex nonlinear regulatory schemes is an important research topic in system biology. In many models of biological systems, the regulatory functions are of saturation type. The linear sectors, in which the saturation type functions reside, have been extensively adopted to deal with these saturation type functions. The stability analysis resulting from linear sectors is however often conservative as a wide linear section is required to include a large portion of a saturation type function. In this paper, we utilize piecewise linear sectors, recently adopted in nonlinear control theory, to investigate multistability of a class of biological systems with sum regulatory schemes. We will estimate the domain of attraction of each stable equilibrium and examine the robust stability of each equilibrium in the face of disturbances that are bounded in magnitude or energy. A genetic toggle switch in Escherichia coli is employed as an example to illustrate the applicability and effectiveness of our analysis method.

Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy

In living organisms, biological molecules often organize into multicomponent complexes. Such assemblies consist of various proteins and carry out essential functions, ranging from cell division, transport, and energy transduction to catalysis, signaling, and viral infectivity. To understand the biological functions of these assemblies, in both healthy and disease states, researchers need to study their three-dimensional architecture and molecular dynamics. To date, the large size, the lack of inherent long-range order, and insolubility have made atomic resolution studies of many protein assemblies challenging or impractical using traditional structural biology methods such as X-ray diffraction and solution NMR spectroscopy. In the past 10 years, we have focused our work on the development and application of magic angle spinning solid-state NMR (MAS NMR) methods to characterize large protein assemblies at atomic-level resolution. In this Account, we discuss the rapid progress in the field of MAS NMR spectroscopy, citing work from our laboratory and others on methodological developments that have facilitated the in-depth analysis of biologically important protein assemblies. We emphasize techniques that yield enhanced sensitivity and resolution, such as fast MAS (spinning frequencies of 40 kHz and above) and nonuniform sampling protocols for data acquisition and processing. We also discuss the experiments for gaining distance restraints and for recoupling anisotropic tensorial interactions under fast MAS conditions. We give an overview of sample preparation approaches when working with protein assemblies. Following the overview of contemporary MAS NMR methods, we present case studies into the structure and dynamics of two classes of biological systems under investigation in our laboratory. We will first turn our attention to cytoskeletal microtubule motor proteins including mammalian dynactin and dynein light chain 8. We will then discuss protein assemblies from the HIV-1 retrovirus.

Self-Extending Symbiosis: A Mechanism for Increasing Robustness Through Evolution

Robustness is a fundamental property of biological systems, observed ubiquitously across species and at different levels of organization from gene regulation to ecosystem. The theory of biological robustness argues that robustness fosters evolv-ability and that together they entail various tradeoffs as well as characteristic architectures and mechanisms. We argue that classes of biological systems have evolved to enhance their robustness by extending their system boundary through a series of symbioses with foreign biological entities (“self-extending symbiosis”). A series of major biological innovations has been achieved by events consistent with this framework: horizontal gene transfer, serial endosymbiosis, oocytes-mediated vertical infection, and host-symbiont mutualism for bacterial flora. Self-extending symbiosis contributes to robustness because symbiotic foreign biological entities can enhance the adaptative capacity of the system against environmental perturbations as well as contribute novel functions. In addition, evolutionary history indicates that the degree of symbiosis achieved has substantially changed from tight integration into the genome (which is less adaptive) to loose integration as bacterial flora (which can be highly adaptive). The most dramatic example can be seen in the symbiosis of host immune system and bacterial flora in which substantial function of host defense depends on the proper maintenance of bacterial flora and its adaptive capability. Biological systems following this type of evolutionary path might have attained high levels of functionality, robustness, and evolvability. Thus, robustness, evolution, and self-extending symbiosis may form essential system principles for biology.

Single-Molecule FRET

Single molecule studies have revolutionized our understanding of how biomolecules work. The ability to watch one molecule at a time reveals not only the average properties detected in ensemble measurements, but can yield the entire distribution of relevant properties, including subpopulations and rare events. Single molecule studies also reveal the time evolution of biochemical reactions,which, if asynchronous, are not observable via ensemble measurements. In the 1970s, for example, the development of the patch-clamp technique enabled the electrical current through a single ion channel to be measured, revealing many properties, including that ion channels are on/off devices. More recently, single molecule techniques applicable beyond ion channels have been developed. Methods such as optical (or magnetic) tweezers and scanning force microscopy are making it possible to follow, in real-time, the movements, forces and strains that develop during the course of a reaction (reviewed in [1]). These methods can be used to measure directly the forces that hold together molecular structures. New developments in single molecule fluorescence methodology are also broadening the scope of single molecule studies. Single biomolecules are labeled with an extrinsic fluorophore, and the fluorescent properties of the fluorophore can report on conformational changes occurring in the biomolecules. For example, intensity fluctuations of a single or small number of molecules can also measure reaction rates as well as the number of molecules present. Single enzyme reaction kinetics, for example, were measured in this way and found to have both static and dynamic disorder, as well as a rate which depended on the enzyme's history, properties which were undetectable via ensemble methods [2]. In addition, single molecule fluorescence polarization can be used to infer local rotation or changes in flexibility of biomolecules (reviewed in [3, 4]). Perhaps the most general approach is the use of two fluorophores rather than one, in the form of fluorescence resonance energy transfer (FRET). In FRET, a “donor” dye transfers energy to an “acceptor” dye, and the donor intensity decreases and the acceptor intensity increases as the two dyes approach each other (reviewed in [5]). Importantly, it is sensitive to sub-nanometer distance changes in the range of 20-80 A, a sensitivity and range well suited for studying biomolecules. Excitation energy of the donor is transferred to the acceptor via an induced-dipole, induced-dipole interaction. The efficiency of energy transfer, E, is given by: where R is the distance between the donor and acceptor and R0 is the distance at which 50% of the energy is transferred and is a function of the properties of the dyes. Because of this strong distance dependence, structural changes of biomolecules or relative motion and interaction between two different molecules can be detected via FRET. These conformational changes are often difficult to synchronize or too rare to detect using ensemble FRET studies. Single-molecule FRET (smFRET) overcomes these difficulties, creating new opportunities to probe structural changes of biological molecules during biological events in real time. SmFRET is also relatively insensitive to incomplete labeling of host molecule with donor and acceptor because donor-only species simply show up as an FRET = 0 peak while acceptor-only species are excited only very weakly by the excitation light if the probes are selected with a large spectral separation. Unlike other single-molecule methodologies measuring forces (optical or magnetic tweezers and atomic force microscopy) [1], single-molecule FRET is sensitive to the internal motion or arrangement of host biological molecules in its center of mass frame; therefore it does not suffer from Brownian motion of the whole molecule. In addition, it can be applied to a much broader class of biological systems, because it does not require force-generating molecules. It is especially powerful in capturing rare, transient events and in dissecting complex multi-step processes. Since our first demonstration of single molecule FRET, there have been a number of biological applications (and see review in [4, 6]). Ever expanding list of biological systems that have been studied by single molecule FRET includes DNA rulers [7-9], Staphylococcal nuclease [10], biotin-Streptavidin [11], GCN4 peptides [12], a-tropomyosin [13], S15 binding RNA junction [14], Tetrahymena ribozyme [15], calmodulin [16], and Rep helicase (Ha et al, unpublished data). There are already excellent reviews on the existing single molecule FRET works [4, 6] and a review focused on practical issues regarding smFRET implementation is available [17].

Hierarchical functional organization of formal biological systems: a dynamical approach. I. The increase of complexity by self-association increases the domain of stability of a biological system

In this series of papers, a theory of functional organization is proposed for biological systems (formal biological system, FBS), which is based on the concept of 'functional interaction', and on a 'functional self-association hypothesis'. From the specific properties of functional interactions, i.e. non-symmetry, non-locality, and non-instantaneity, it is shown that a biological system can be considered as constituted by two hierarchical systems: (i) the (O-FBS) that describes the topology of the FBS, i.e. the functional organization, with a hierarchical directed graph; (ii) the (D-FBS) that describes the continuous non-linear dynamics of the FBS with a field. In the framework of this theory, the problem of the relation between structure and function is considered to be due to the distinction between structural organization and functional organization. Some advantages of this approach are: (i) the description of the time evolution, during development, of the organization of an FBS with an optimum principle, which leads to a clear comparison with a physical system (paper II); (ii) the description of the space-time dynamics as the variation in space and time of field variables in a hierarchical 'space of structural units'; and, consequently, the relation between topology and geometry, and the existence of non-locality in these hierarchical spaces (paper III). In this paper, the basic concepts of functional interaction, hierarchical functional organization, and physiological function are discussed from a mathematical viewpoint, and arguments for the validity of the self-association hypothesis are given. Specifically, it is shown that, for a particular class of biological systems that are taken as an example, the domain of stability of the (D-FBS) is increased after functional association. This property, which is specifically due to the nature of the biological system, corresponds to an increase in complexity. It will be shown in the second paper that such a self-organization corresponds also to an optimal principle for the (O-FBS). The case of real biological systems (RBSS) is considered in relation with the present theory, which leads to a new hierarchical representation in terms of fields. Such representation could be a base for integrative physiology. As an example, some physiological functions, respiratory and cardio-vascular, are considered and it is shown that the heart shock emerges from the formulation as a cyclic sub-graph.