Pressure and life: some biological strategies

All biological processes of life on Earth experience varying degrees of pressure. Aquatic organisms living in the deep-sea, as well as chondrocytic cells of articular cartilage are exposed to hydrostatic pressures that rise up to several hundred times that of atmospheric pressure. In the case of marine larvae that disperse through the oceanic water column, pressure changes might be responsible for stress conditions during development, limiting colonisation capabilities. In a number of biological systems, life strategies may be significantly influenced by pressure. In this review, we will focus on the consequences of pressure changes on various biological processes, and more specifically on animals living in the deep-sea. Revisiting general principles of pressure effects on biological systems, we present recent data illustrating the diversity of effects pressure may have at different levels in biological systems, with particular attention to effects on gene expression. After a review of the main pressure equipments available today for studying species living naturally at high pressure, we summarise what is known concerning pressure impact during animal development.     

Extended Kalman Filter for Estimation of Parameters in Nonlinear State-Space Models of Biochemical Networks

It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimate their parameters are an essential issue for studying dynamic behaviors of biological systems which include metabolic networks, genetic regulatory networks and signal transduction pathways, under perturbation of external stimuli. In general, biological dynamic systems are partially observed. Therefore, a natural way to model dynamic biological systems is to employ nonlinear state-space equations. Although statistical methods for parameter estimation of linear models in biological dynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamic systems remains a challenging task. In this report, we apply extended Kalman Filter (EKF) to the estimation of both states and parameters of nonlinear state-space models. To evaluate the performance of the EKF for parameter estimation, we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signaling transduction pathways datasets. The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks.     

Adaptation as a manifestation of informational connections in living systems

The problem of adaptation of living systems in terms of the concept of informational communications is considered. The informational communication means the qualitative evaluation of information and determines correspondence of living systems to concrete conditions of life during interaction of these living systems to the source of the information. The system of the wholeorganism regulatory chemical communication is the main functional basis for the informational communication. Due to it, the transformation of the information signal in biological systems is performed, which results in their adequate response according to this information. The existence of living systems and their adaptation are determined by peculiarities of functioning of elements of their regulatory systems according to the character of the informational communication.     

Comparative assessment of inductive effects of Azospirillum lectins with different antigenic properties on the signal systems of wheat seedling roots

The lectins of associative nitrogen-fixing bacteria Azospirillum brasilense Sp7 and its mutant A. brasilense Sp7.2.3 were shown to have different effects on the components of the wheat seedling root signal system, namely to regulate the levels of cAMP, nitric oxide, diacylglycerol, and salicylic acid, as well as to induce the activities of superoxide dismutase and lipoxygenase. Our results make it possible to consider azospirilla lectins as inducers of the signal systems in wheat seedling roots, since they cause development of several flows of primary signals. These data are of general biological importance, since lectins are present in all living organisms and most of the functions of lectins remain insufficiently understood.     

On the relationships between the rate of cytoskeletal stable assemblies turnover, stability of the differentiated state, development and aging

There is a general consensus that biological specificity is a structure-derived property. If a living system is going to maintain its structure and function then the newly synthesized molecules should replace the faulty ones at the correct time and in the correct places so that the previously established cellular topology will be preserved. In addition, pre-existing spatial determinants which will direct the asymmetrical assembly of the newly synthesized molecules should be available. Therefore, regulation of turnover of cellular architecture represents an essential feature of living systems. In considering the underlying causes of cellular senescence it seemed reasonable to focus on the relationship between development of a stable phenotype and the turnover of cellular and extracellular stable assemblies, currently thought to be involved in maintaining the stability of the differentiated state. In recent years evidence has accumulated suggesting a reciprocal relationship between cytoarchitecture turnover rate and achievement of a stable structure. The lack of a feedback control on the turnover of cellular stable assemblies and/or a low turnover rate of cytoarchitecture components would mean that they will be subjected to damaging processes such as oxidation, cross-linking, aminoacid racemization or non-enzymatic browning which are known to occur in other long-lived proteins. The consequence would be the generation, with advancing age, of faulty cellular structures which, in turn, would alter the deposition of newly synthesized molecules. This process may lead to a progressive breakdown in cellular and extracellular stable structures. The process of directed assembly seems to be general for biological systems displaying history-dependent development. We believe that it is this strategy which imposes severe limitations on presegregated spatial determinants turnover rates and, therefore plays a major role in initiating the aging process. We also suggest that species-specific life-span might be determined by the species-specific regulatory networks which governs the cell-specific cytoarchitecture damaging rate. Moreover, aging appears to be an intrinsic feature of biological systems displaying history-dependent development and should be absent in systems displaying history-independent life-cycles, such as bacteria, some species of protozoa, and certain transformed cell lines. An important feature of protein turnover is that this process requires metabolic energy. Therefore, we can expect that structure preservation strategy is a part of a more general energy-saving strategy, a view previously expressed by T.B.L. Kirkwood (Nature, Lond., 1977, 270, 301-304).     

"Meaning-making" in language and biology

The linguistic metaphor in biology adheres to a representational theory that seeks similarities between pre-given domains. The point of departure of this paper is the generative and nonrepresentational conception of metaphor. This paper argues that by adopting the nonrepresentational conception of metaphor, meaning-making may be the appropriate perspective for understanding biological systems. In both cases (the linguistic and the biological), boundary conditions between different levels of organization use micro-level disorganization to create macro-level organization.     

Nitric Oxide Cycle in Mammals and the Cyclicity Principle

This paper continues a series of reports considering nitric oxide (NO) and its cyclic conversions in mammals. Numerous facts are summarized with the goal of developing a general concept that would allow the statement of the multiple effects of NO on various systems of living organisms in the form of a short and comprehensive law. The current state of biological aspects of NO research is analyzed in term of elucidation of possible role of these studies in the system of biological sciences. The general concept is based on a notion on cyclic conversions of NO and its metabolites. NO cycles in living organisms and nitrogen turnover in the biosphere and also the Bethe nitrogen–carbon cycle in star matter are considered. A hypothesis that the cyclic organization of processes in living organisms and the biosphere reflects the evolution of life is proposed: the development of physiological functions and metabolism are suggested to be closely related to space and evolution of the Earth as a planet of the Solar System.     

Imaging [Ca2+]i dynamics during signal transduction

The elevation of free intracellular Ca2+ activity ([Ca2+]i) is widely recognised as a central event in many signal transduction processes in cellular physiology. Recent advances in optical techniques for measuring [Ca2+]i as well as developments in quantitative low light level fluorescence microscopy have led to the application of these methods to the study of subcellular [Ca2+]i in many biological systems. In the following paper we describe some techniques in our laboratory to provide quantitative high spatio-temporal resolution measurements of [Ca2+]i in individual living cells during the signal transduction of cell surface receptor ligand interactions. In particular, we are studying the changes in [Ca2+]i induced by the micro-aggregation of immunoglobulin E (IgE) receptor complexes on the surface of rat basophilic leukemia (RBL) cells (a tumor mast cell line) by multivalent antigen. We seek to understand the mechanisms which are involved in the detection of these cell surface events which lead to changes in [Ca2+]i as well as the interactions between the various subcellular components which impart the delicate control of [Ca2+]i during cellular stimulation. The limitations and properties of the technology used for these studies will be discussed, and some illustrative examples of the type of [Ca2+]i changes found in this biological system will be given.     

蓝藻对UV-B增强的响应与适应

平流层臭氧破坏导致地球表面紫外辐射(主要是UV-B)增强逐渐受到人们重视。由于蓝藻在生态系统中的重要性和在生物进化过程中的特殊性,用于研究UV-B对生物体的影响具有诸多优势。目前国内关于UV-B与蓝藻的研究报道较少,所以本文介绍了近年来国外该领域的相关研究,主要包括UV-B对蓝藻生物量、光合机构以及固氮等方面的影响,同时着重介绍了蓝藻对UV-B的适应策略。     

Microfluidics-based systems biology

Systems biology seeks to develop a complete understanding of cellular mechanisms by studying the functions of intra- and inter-cellular molecular interactions that trigger and coordinate cellular events. However, the complexity of biological systems causes accurate and precise systems biology experimentation to be a difficult task. Most biological experimentation focuses on highly detailed investigation of a single signaling mechanism, which lacks the throughput necessary to reconstruct the entirety of the biological system, while high-throughput testing often lacks the fidelity and detail necessary to fully comprehend the mechanisms of signal propagation. Systems biology experimentation, however, can benefit greatly from the progress in the development of microfluidic devices. Microfluidics provides the opportunity to study cells effectively on both a single- and multi-cellular level with high-resolution and localized application of experimental conditions with biomimetic physiological conditions. Additionally, the ability to massively array devices on a chip opens the door for high-throughput, high fidelity experimentation to aid in accurate and precise unraveling of the intertwined signaling systems that compose the inner workings of the cell.     

A modified Ising model of Barabási–Albert network with gene-type spins

The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in quasi-steady state type equilibrium in continuous exchange with their environment, computational techniques that have been successfully applied in statistical thermodynamics to describe phase transitions may provide new insights to the emerging behavior of biological systems. Here we systematically evaluate the translation of computational techniques from solid-state physics to network models that closely resemble biological networks and develop specific translational rules to tackle problems unique to living systems. We focus on logic models exhibiting only two states in each network node. Motivated by the apparent asymmetry between biological states where an entity exhibits boolean states i.e. is active or inactive, we present an adaptation of symmetric Ising model towards an asymmetric one fitting to living systems here referred to as the modified Ising model with gene-type spins. We analyze phase transitions by Monte Carlo simulations and propose a mean-field solution of a modified Ising model of a network type that closely resembles a real-world network, the Barabási–Albert model of scale-free networks. We show that asymmetric Ising models show similarities to symmetric Ising models with the external field and undergoes a discontinuous phase transition of the first-order and exhibits hysteresis. The simulation setup presented herein can be directly used for any biological network connectivity dataset and is also applicable for other networks that exhibit similar states of activity. The method proposed here is a general statistical method to deal with non-linear large scale models arising in the context of biological systems and is scalable to any network size.

     

Spontaneous switching of frequency-locking by periodic stimulus in oscillators of plasmodium of the true slime mold

Microfabrication technique was used to construct a model system with a living cell of plasmodium of the true slime mold, Physarum polycephalum, a living coupled oscillator system. Its parameters can be systematically controlled as in computer simulations, so that results are directly comparable to those of general mathematical models. As the first step, we investigated responses in oscillatory cells, the oscillators of the plasmodium, to periodic stimuli by temperature changes to elucidate characteristics of the cells as nonlinear systems whose internal dynamics are unknown because of their complexity. We observed that the forced oscillator of the plasmodium show 1:1, 2:1, 3:1 frequency locking inside so-called Arnold tongues regions as well as in other nonlinear systems such as chemical systems and other biological systems. In addition, we found spontaneous switching behavior from certain frequency locking states to other states, even under certain fixed parameters. This technique can be applied to more complex systems with multiple elements, such as coupled oscillator systems, and would be useful to investigate complicated phenomena in biological systems such as information processing.     

Stochastic noise interferes coherently with a model biological clock and produces specific dynamic behaviour.

The influence of noise is unavoidable in all living systems. Its impact on a model of a biological clock, normally running in regular oscillating modes, is examined. It is shown that in a specific system in which endogenous rhythmicity is produced by a beat oscillator acting on a feedback coupled metabolic pool system, noise can act coherently to produce unexpected dynamic behaviour, running from regular over pseudo-regular to irregular time-structures. If the biological system consists of a set of identical weakly coupled cells, stochasticity may lead to phase decoupling producing irregular spatio-temporal patterns. Synchronization via phase resetting can be achieved by external short-time temperature pulses. Explicit results are obtained for the well-studied circadian photosynthesis oscillations in plants performing crassulacean acid metabolism. Because of the generic structure of the underlying nonlinear dynamics they can, however, be regarded as a general property of the influence of noise on nonlinear excitable systems with fixed points occuring close to limit cycles.     

Diversity and dynamics of microbial communities in engineered environments and their implications for process stability

The availability of molecular biological tools for studying microbial communities in bioreactors and other engineered systems has resulted in remarkable insights linking diversity and dynamics to process stability. As engineered systems are often more manageable than large-scale ecosystems, and because parallels between engineered environments and other ecosystems exist, the former can be used to elucidate some unresolved ecological issues. For example, the process stability of methanogenic bioreactors containing well-defined trophic groups appears to depend on the diversity of the functional groups within each trophic level as well as on how these functional groups complement each other. In addition to using engineered systems to study general ecological questions, microbial ecologists and environmental engineers need to investigate conditions, processes, and interactions in engineered environments in order to make the ecological engineering of bioreactor design and operation more practicable.     

蓝藻对UV-B增强的响应及其紫外屏蔽物质的研究

紫外线辐射对生物体危害日趋严重,逐渐引起了人们的重视.由于蓝藻在生物进化中的特殊性和在生态系统中的重要性,用于研究UV-B对生物体的影响具有诸多优势,目前国内关于UV-B对蓝藻的影响相关报道较少.本文介绍了近年来国外该领域的相关研究,主要包括UV-B对蓝藻生物量、生理效应,特别是光合作用等方面的影响,同时着重介绍了蓝藻中的紫外吸收物质的研究现状,并进一步探讨了其应用情况.     

Oscillatory reaction of chondroitin sulfate induced by gradual introduction of calcium ion

Rhythm is an important dynamic behavior in biological systems. We have been studying oscillatory reactions of enzymes induced by gradual entry of substances through semipermeable membrane. Not only enzymes but also a few species of substance of living system have been elucidated to cause oscillatory reaction. Here we present the oscillatory reaction by chondroitin sulfate in a system of gradual entry of calcium ion. Introducing calcium ion through dialysis membrane into chondroitin sulfate solution induces an oscillation of free calcium ion concentration in chondroitin sulfate solution. Simultaneously, it is elucidated that oscillation of conformation occurs with permeation of calcium ion. In both measurements, oscillations with 25h period are obtained. The phases of oscillation, however, differ slightly from each other. From these results, it is suggested that autocatalysis exerts in the contraction of chondroitin sulfate conformation. These phenomena are very intriguing for elucidating oscillation in living system.     

Biological probability: cognitive processes of generating probabilities of events in biological systems.

This paper analyses relationships between probabilities of events happening in biological systems (or probabilistic disposition of systems) and cognitive properties of biological entities comprising such systems. Two kinds of cognitive properties are identified as relevant to the current problem: the ability to respond differently against different configurations of the environment (discriminability of cognition), and the ability to make an appropriate response to maintain a particular relation with the environment (selectivity of cognition). A basic framework bridging the two features of living systems, probabilistic disposition and the cognitive properties, is presented towards a general theory explaining the process generating probabilities of biological events. In this framework, a deterministic model of a system of entities is developed, in which objects are described as subjects that cognize events (i.e. entities as cognizers). Cognition is used in a wider sense, including not only biotic but also abiotic, and cognizers are conceptually distinguished from the meta-observer who describes the system externally. Based on this perspective, this paper seeks to explicate how events can occur in an uncertain, probabilistic manner, if observed from a cognizer viewpoint, even under a deterministic system. Each cognizer is identified with both the set of states that are actually taken, and its motion function which maps its state uniquely to a successor state depending on the current states of itself and of the rest of cognizers constituting the system. The model analysis reveals that the cognitive properties, discriminability and selectivity, of a cognizer can contribute to determining the probability of an event encountered by the cognizer itself-in particular, discrimination reducing the uncertainty in events occurrence for the cognizer. Biological implication of this result is discussed focusing on the concept of the probability of survival and reproduction.