Multiple relational equilibria: Polymorphism,metamorphosis and other possibly similar phenomena

In a preceding paper (Rashevsky, 1969. “Outline of a Unified Approach to Physics, Biology and Sociology.”Bulletin of Mathematical Biophysics,31, 159–198) certain isomorphisms between biological and social systems on the one hand and physical systems on the other were studied. The notion or relational forces, of which ordinary physical forces are a particular case, was introduced. In the present paper an attempt is made to establish analogies between stable equilibria in physical systems, equilibria due to physical forces, and stable equilibria in biological and social systems which are due to purely relational forces. The notion of relational forces causing multiple equilibria similar to multiple equilibria in some physical systems is studied, and it is outlined how this notion may possibly help the understanding of such phenomena as polymorphism, metamorphosis and the existence of rudimentary organs or rudimentary functions.     

Some order-disorder considerations in living systems

Order and disorder in biological systems are considered quantitatively in terms of information and entropy. After discussing the factors contributing to the information content of a living cell, a calculation is made of this parameter. The value for a typical bacterial cell is 4.6×10¹⁰ bits. This value is compared with an experimental value of the heat of growth and entropy production ofE. Coli. A discussion of methods of improving the calculation is also presented.     

Information theory and the ethylene genetic network

The original aim of the Information Theory (IT) was to solve a purely technical problem: to increase the performance of communication systems, which are constantly affected by interferences that diminish the quality of the transmitted information. That is, the theory deals only with the problem of transmitting with the maximal precision the symbols constituting a message. In Shannon''s theory messages are characterized only by their probabilities, regardless of their value or meaning. As for its present day status, it is generally acknowledged that Information Theory has solid mathematical foundations and has fruitful strong links with Physics in both theoretical and experimental areas. However, many applications of Information Theory to Biology are limited to using it as a technical tool to analyze biopolymers, such as DNA, RNA or protein sequences. The main point of discussion about the applicability of IT to explain the information flow in biological systems is that in a classic communication channel, the symbols that conform the coded message are transmitted one by one in an independent form through a noisy communication channel, and noise can alter each of the symbols, distorting the message; in contrast, in a genetic communication channel the coded messages are not transmitted in the form of symbols but signaling cascades transmit them. Consequently, the information flow from the emitter to the effector is due to a series of coupled physicochemical processes that must ensure the accurate transmission of the message. In this review we discussed a novel proposal to overcome this difficulty, which consists of the modeling of gene expression with a stochastic approach that allows Shannon entropy (H) to be directly used to measure the amount of uncertainty that the genetic machinery has in relation to the correct decoding of a message transmitted into the nucleus by a signaling pathway. From the value of H we can define a function I that measures the amount of information content in the input message that the cell''s genetic machinery is processing during a given time interval. Furthermore, combining Information Theory with the frequency response analysis of dynamical systems we can examine the cell''s genetic response to input signals with varying frequencies, amplitude and form, in order to determine if the cell can distinguish between different regimes of information flow from the environment. In the particular case of the ethylene signaling pathway, the amount of information managed by the root cell of Arabidopsis can be correlated with the frequency of the input signal. The ethylene signaling pathway cuts off very low and very high frequencies, allowing a window of frequency response in which the nucleus reads the incoming message as a varying input. Outside of this window the nucleus reads the input message as an approximately non-varying one. This frequency response analysis is also useful to estimate the rate of information transfer during the transport of each new ERF1 molecule into the nucleus. Additionally, application of Information Theory to analysis of the flow of information in the ethylene signaling pathway provides a deeper insight in the form in which the transition between auxin and ethylene hormonal activity occurs during a circadian cycle. An ambitious goal for the future would be to use Information Theory as a theoretical foundation for a suitable model of the information flow that runs at each level and through all levels of biological organization.Key words: information theory, shannon entropy, frequency systems analysis, Arabidopsis thaliana, ethylene signaling systems, plant genetic networks, circadian cycles     

Dimensional analysis in mathematical biology. II

The application of dimensional analysis in biology is further illustrated by functional equations composed of dimensionless numbers and dealing with renal physiology, lung physiology and plant leaf shape. Dimensional variables and dimensionless numbers are examined from the viewpoint of numerical invariant properties of a certain physical system. Utilization of the method for problems such as design of an artificial kidney is considered briefly. A tabulation of variables useful in biology is given, with suggestions for a number of new dimensional entities. A continuation of the list of dimensionless invariants from Part I (Bull. Math. Biophysics,23, 355–376, 1961) is provided and includes terms pertaining to general physiology, geometric growth, metabolism, ecological interactions, muscle kinetics and other areas. It is pointed out that use of dimensionless ratios (similarity criteria) makes possible a direct comparison of form or shape factors and relative growth ratios with a variety of physical ratios, through the use of functional equations containing only dimensionless entities. Organismal similarity during growth and development, and between genetically related species, may be analyzed in terms of “automodel” or “self-similar” systems governed by certain dimensionless invariants. Tables of biological variables and dimensionless groupings are included.     

Analysis of tracer experiments: IV. The kinetics of generalN compartment systems

The methods of C. W. Sheppard and A. S. Householder (Jour. App. Physcis,22, 510–20, 1951), H. D. Landahl (Bull. Math. Biophysics,16, 151–54, 1954) and H. E. Hart (Bull. Math. Biophysics,17, 87–94, 1955;ibid.,19, 61–72, 1957;ibid.,20, 281–87, 1958) are employed in studying the kinetics of generalN compartment systems. It is shown that the nature of the transfer processes occurring in fluid flow systems and the chemical processes occurring in quadratic systems and in catalyzed quadratic systems can in principle be completely determined for all polynomial dependencies. Systems involving three-body and higher-order interactions can be completely solved, however, only if supplementary information is available. Research supported by the Atomic Energy Commission, Contract AT (30-1)-1551.     

Bioassays for risk assessment of coal conversion products

Traditional as well as biotechnological processing of coal leads to complex mixtures of products. Besides chemical and physical characterization, which provides the information for product application, there is a need for bioassays to monitor properties that are probably toxic, mutagenic or cancerogenic. Investigations carried out focused on the selection, adaptation and validation of bioassays for the sensitive estimation of toxic effects. Organisms like bacteria, Daphnia magna and Scenedesmus subspicatus, representing different complexities in the biosphere, were selected as test systems for ecotoxicological and mutagenicity studies. The results obtained indicate that bioassays are, in principle, suitable tools for characterization and evaluation of coal-derived substances and bioconversion products. Using coal products, coal-relevant model compounds and bioconversion products, data for risk assessment are presented. Received: 17 June 1998 / Received revison: 21 October 1998 / Accepted: 24 October 1998     

Some considerations on relational equilibria

A previous study (Bull. Math. Biophysics,31, 417–427, 1969) on the definitions of stability of equilibria in organismic sets determined byQ relations is continued. An attempt is made to bring this definition into a form as similar as possible to that used in physical systems determined byF-relations. With examples taken from physics, biology and sociology, it is shown that a definition of equilibria forQ-relational systems similar to the definitions used in physics can be obtained, provided the concept of stable or unstable structures of a system determined byQ-relations is considered in a probabilistic manner. This offers an illustration of “fuzzy categories,” a notion introduced by I. Bąianu and M. Marinescu (Bull. Math. Biophysics,30, 625–635, 1968), in their paper on organismic supercategories, which is designed to provide a mathematical formalism for Rashevsky's theory of Organismic Sets (Bull. Math. Biophysics,29, 389–393, 1967;30, 163–174, 1968;31, 159–198, 1969). A suggestion is made for a method of mapping the abstract discrete space ofQ-relations on a continuum of variables ofF-relations. Problems of polymorphism and metamorphosis, both in biological and social organisms, are discussed in the light of the theory.     

Disciplinary reporting affects the interpretation of climate change impacts in global oceans

Climate change is affecting marine ecosystems, but different investigative approaches in physical, chemical, and biological disciplines may influence interpretations of climate‐driven changes in the ocean. Here, we review the ocean change literature from 2007 to 2012 based on 461 of the most highly cited studies in physical and chemical oceanography and three biological subdisciplines. Using highly cited studies, we focus on research that has shaped recent discourse on climate‐driven ocean change. Our review identified significant differences in spatial and temporal scales of investigation among disciplines. Physical/chemical studies had a median duration of 29 years (n = 150) and covered the greatest study areas (median 1.41 × 10⁷ km², n = 148). Few biological studies were conducted over similar spatial and temporal scales (median 8 years, n = 215; median 302 km², n = 196), suggesting a more limited ability to separate climate‐related responses from natural variability. We linked physical/chemical and biological disciplines by tracking studies examining biological responses to changing ocean conditions. Of the 545 biological responses recorded, a single physical or chemical stressor was usually implicated as the cause (59%), with temperature as the most common primary stressor (44%). The most frequently studied biological responses were changes in physiology (31%) and population abundance (30%). Differences in disciplinary studies, as identified in this review, can ultimately influence how researchers interpret climate‐related impacts in marine systems. We identified research gaps and the need for more discourse in (1) the Indian and other Southern Hemisphere ocean basins; (2) research themes such as archaea, bacteria, viruses, mangroves, turtles, and ocean acidification; (3) physical and chemical stressors such as dissolved oxygen, salinity, and upwelling; and (4) adaptive responses of marine organisms to climate‐driven ocean change. Our findings reveal that highly cited biological studies are rarely conducted on scales that match those of physical and chemical studies. Rather, we suggest a need for measuring responses at biologically relevant scales.     

Die Beziehungen zwischen molekularen Informationsgrö\en und den dazugehörigen molaren thermodynamischen Grö\en

Summary Information Theory is applied to chemical reactions involving selection processes. It turns out that the information entropy S _I is closely related to the corresponding entropy function S _T as used in chemical thermodynamics. The change of the molecular information entropy for 1 mol of uniformly synthesized substance is given in moldit where S _I= S_T/R. With n decision in the course of synthesis of a single molecule and z possibilities for each decision there is S _I =n lg z. (E.g. The number of possibilities z is 2 if one special optical isomer has to be selected out of the two existing kinds with any decision.) The entropy change is calculated for various selective processes as, for instance, the replication of polymers with a certain lenght in the case of uniform subunits or with a certain composition on sequence; in the case of different subunits. The replication processes require additional selection work that can be derived from the calculated entropy changes.     

Organismic supercategores: II. On multistable systems

The representation of biological systems in terms of organismic supercategories, introduced in previous papers (Bull. Math. Biophysics,30, 625–636;31, 59–70) is further discussed. To state more clearly this representation some new definitions are introduced. Also, some necessary changes in axiomatics are made. The conclusion is reached that any organismic supercategory has at least one superpushout, and this expresses the fact that biological systems are multistable. This way a connection between some results of Rashevsky’s theory of organismic sets and our results becomes obvious.     

Identifying the dominant process (physical versus biological) in pelagic marine ecosystems from field estimates of chlorophyll a and phytoplankton production

A new approach is described to identify the dominant process (physical versus biological) in a pelagic marine ecosystem, from simple biological oceanographic field variables. The approach is based on quantification of the matching (M) between phytoplankton production (P) and losses, from field estimates of chlorophyll a(Chl) and P. Coefficient M is estimated for a wide range of oceanic and coastal environments and of trophic characteristics, using dat from the literature. Results show that M characterizes the dominance of physical versus biological processes in pelagic systems. The coefficient may be especially useful as a means for extracting process information on pelagic marine ecosystems from large data sets of Chl and P, e.g. recorded by moored instruments or provided by satellite images of ocean colour.      

Biotests with phytoplankton assemblages. Growth limitation along temporal and spatial gradients

The development of eight different species (populations) along temporal and vertical gradients in several lakes was studied. Many populations had an exponential growth phase and a decline phase. The growth rate was often high during the exponential phase. Some species, e.g. Oscillatoria spp. and Synedra cf. acus, often also had a long stationary phase. The growth rate and the sinking rate of these populations were often very low. Laboratory batch experiments with dilute phytoplankton populations were carried out to estimate the degree of growth limitation (L) for different populations sample from different lakes during the three growth phases. L was always low and often zero for populations initially in the exponential phase and always high for populations initially in the decline phase. The biotests also gave results that can help to explain the vertical distribution of Oscillatoria or Asterionella in three lakes investigated. The results indicate that the growth rates and the development of the populations were dependent on the external chemical and physical conditions. The transition between the different growth phases seemed often to be dependent on the external nutrient conditions. P, N, Si and Fe were probably the most growth-limiting nutrients. The growth rate of some diatoms was probably limited directly or indirectly at high pH. Laboratory biotests with natural populations may give valuable information on the growth-properties of different populations in the lakes. The biotests should, however, be carried out in combination with chemical and physical measurements and quantitative determinations of population densities.     

果胶杆菌(Pectobacterium aroidearum) WNH的筛选及其汉麻生物脱胶效果

【背景】麻类生物脱胶与化学法脱胶相比具有环保优势。【目的】获得用于汉麻生物脱胶的高效果胶酶菌株。【方法】使用以果胶为唯一碳源的培养基,采用平板稀释法进行菌株筛选,通过生理生化实验和16s rRNA基因序列比对鉴定目标菌株。采用单因素试验优化产酶条件,并验证该条件下汉麻生物脱胶效果。【结果】获得一株具备高活性果胶的酶菌株,归类为果胶杆菌(Pectobacterium aroidearum) WNH。在培养温度27 °C、转速160 r/min、接种量10%、初始pH 7.0的条件下培养16 h后,果胶杆菌WNH的粗酶液果胶酶活力达155.03 U/mL。按上述条件对汉麻韧皮进行二次脱胶处理,处理后脱胶率为27.18%,较对照组提高了6.93%。【结论】果胶杆菌WNH具备汉麻生物脱胶的潜力。     

Alghe di acque correnti e loro impiego come bioindicatori

Abstract

Algae of running waters and their employment as bioindicators. The longitudinal distribution of the algal flora and vegetation of the running waters of Central Apennine is examined. This distribution, in addition to temperature, flow velocity, pH, dissolved oxygen and other physical and chemical parameters, seems to be strongly conditioned by the amount of organic matter coming from industries (dairies, paper-mills, sugar-refineries, tanneries, alimentary preserves industries, ecc.) and built-up areas. The system of saprobic organisms and some quantitative methods from it derived and directed to the estimation of the water quality from a biological point of view, are therefore succinctly discussed. The importance of the biological analysis, absolutely necessary to verify the effects of the pollution in the aquatic environment, is lastly underlined.     

草菇热激蛋白60基因(Vvhsp60)生物信息学分析及低温下的表达

【背景】生物受到温度胁迫时,热激蛋白被诱导并在短时间内大量产生,可以使受损的蛋白质恢复正常构象,增强生物对逆境胁迫的耐受性。【目的】初步探究草菇热激蛋白60(Vvhsp60)与低温耐受性的关系,为深入开展草菇不耐低温特性的遗传改良奠定理论基础。【方法】对Vvhsp60进行生物信息学分析,以低温敏感型草菇菌株V23及耐低温菌株VH3为实验材料,利用实时荧光定量PCR技术分析低温胁迫及热激诱导后在低温下草菇菌丝体中Vvhsp60基因的表达水平。【结果】草菇Vvhsp60编码蛋白不存在信号肽,不属于分泌蛋白,在线粒体和细胞质内发挥生物学作用,属于双向跨膜蛋白。低温处理显著提高了V23与VH3菌丝体中Vvhsp60基因的表达量,而且VH3中的表达量显著高于V23,推测Vvhsp60基因的表达量高可能有助于增强草菇对低温胁迫的耐受性。经热激处理后两菌株Vvhsp60基因的表达量显著高于各自未热激处理的对照组,表明热激处理可诱导Vvhsp60基因的表达。【结论】Vvhsp60与草菇低温耐受性相关,并且热激可以诱导Vvhsp60基因的表达。     

Application of ITC in foods: A powerful tool for understanding the gastrointestinal fate of lipophilic compounds

BackgroundIsothermal titration calorimetry (ITC) is a biophysical technique widely used to study molecular interactions in biological and non-biological systems. It can provide important information about molecular interactions (such as binding constant, number of binding sites, free energy, enthalpy, and entropy) simply by measuring the heat absorbed or released during an interaction between two liquid solutions.Scope of the reviewIn this review, we present an overview of ITC applications in food science, with particular focus on understanding the fate of lipids within the human gastrointestinal tract. In this area, ITC can be used to study micellization of bile salts, inclusion complex formation, the interaction of surface-active molecules with proteins, carbohydrates and lipids, and the interactions of lipid droplets.Major conclusionsITC is an extremely powerful tool for measuring molecular interactions in food systems, and can provide valuable information about many types of interactions involving food components such as proteins, carbohydrates, lipids, surfactants, and minerals. For systems at equilibrium, ITC can provide fundamental thermodynamic parameters that can be used to establish the physiochemical origin of molecular interactions.General significanceIt is expected that ITC will continue to be utilized as a means of providing fundamental information about complex materials such as those found in foods. This knowledge may be used to create functional foods designed to behave in the gastrointestinal tract in a manner that will improve human health and well-being. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.     

Some biologically active oxovanadium(IV) complexes of triazole derived Schiff bases: their synthesis,characterization and biological properties

A series of biologically active oxovanadium(IV) complexes of triazole derived Schiff bases L₁–L₅ have been synthesized and characterized by their physical, analytical, and spectral data. The synthesized ligands potentially act as bidentate, in which the oxygen of furfural and nitrogen of azomethine coordinate with the oxovanadium atom to give a stoichiometry of vanadyl complexes 1:2 (M:L) in a square-pyramidal geometry. In vitro antibacterial and antifungal activities on different species of pathogenic bacteria (E. coli, S. flexneri, P. aeruginosa, S. typhi, S. aureus, and B. subtilis) and fungi (T. longifusus, C. albicans, A. flavus, M. canis, F. solani, and C. glabrata) have been studied. All compounds showed moderate to significant antibacterial activity against one or more bacterial strains and good antifungal activity against most of the fungal strains. The brine shrimp bioassay was also carried out to check the cytotoxicity of coordinated and uncoordinated synthesized compounds.     

Germinability and fungal occurrence in seeds of Abies alba Mill. populations in southern Italy

Abstract

Germination tests were carried out on seeds from three Italian populations of Abies alba. Seed germinability was up to 38%. HgCl₂, NaClO and plant preservative mixture were used as seed‐sterilising agents. Despite chemical treatments, Papulaspora rubida and Chaetomium globosum were isolated. The possible role of these fungi in the physiology of silver fir seed germination process was discussed.     

Some remarks on topological biology

With reference to several recent papers by the author, it is pointed out that within the principle of biotopological mapping a choice of a primordial graph and of a particular transformation defines a system of abstract biology, similar to systems of abstract geometries. The study of such abstract systems is necessary before one can be found which is isomorphic to the actual biological world. A brief survey of the structure and properties of the system based on the choice of the primordial graph and of the transformationT defined in a previous paper (Bull. Math. Biophysics,16, 317–48, 1954) is made. Two more topological theorems are demonstrated, which, interpreted biologically, lead to the conclusion that the higher an organism, the more adaptable it is. Finally a criticism of that particular system of abstract biology is made, and its inadequacy for the representation of the actual biological phenomena pointed out, and a suggestion is made for a possible point set topological approach to biology.