Classification of cell signalling in tissue development

The traditional classification of signalling in biological systems is insufficient and outdated and novel efforts must take into account advances in systems theory, information theory and linguistics. We present some of the classification systems currently used both within and outside of the biological field and discuss some specific aspects of the nature of signalling in tissue development. The analytical methods used in understanding non-biological networks provide a valuable vocabulary, which requires integration and a system of classification to further facilitate development.     

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.     

Mechanism of ROS scavenging and antioxidant signalling by redox metallic and fullerene nanomaterials: Potential implications in ROS associated degenerative disorders

BackgroundThe balance between oxidation and anti-oxidation is believed to be critical in maintaining healthy biological systems. However, our endogenous antioxidant defense systems are incomplete without exogenous antioxidants and, therefore, there is a continuous demand for exogenous antioxidants to prevent stress and ageing associated disorders. Nanotechnology has yielded enormous variety of nanomaterials (NMs) of which metallic and carbonic (mainly fullerenes) NMs, with redox property, have been found to be strong scavengers of ROS and antioxidants in preclinical in vitro and in vivo models.Scope of reviewRedox activity of metal based NMs and membrane translocation time of fullerene NMs seem to be the major determinants in ROS scavenging potential exhibited by these NMs. A comprehensive knowledge about the effects of ROS scavenging NMs in cellular antioxidant signalling is largely lacking. This review compiles the mechanisms of ROS scavenging as well as antioxidant signalling of the aforementioned metallic and fullerene NMs.Major conclusionsDirect interaction between NMs and proteins does greatly affect the corona/adsorption formation dynamics but such interaction does not provide the explanation behind diverse biological outcomes induced by NMs. Indirect interaction, however, that could occur via NMs uptake and dissolution, NMs ROS induction and ROS scavenging property, and NMs membrane translocation time seem to work as a central mode of interaction.General significanceThe usage of potential antioxidant NMs in biological systems would greatly impact the field of nanomedicine. ROS scavenging NMs hold great promise in the future treatment of ROS related degenerative disorders.     

ARE WARNING COLORS HANDICAPS?

The handicap theory, in which the cost of waste guarantees honest advertising, is being used increasingly in solutions to the problems of biological signal evolution. However, it is usually applied to systems which are insufficiently understood to allow testing against alternative theories. In particular, the ability of the handicap theory to explain the design of signals has never been properly tested. We test its ability to explain signal design features in an unusually well studied area of biological signalling: warning coloration and mimicry. Since a full handicap model proves immediately unrealistic, we modify the model to incorporate realistic assumptions about predator learning. Using this model we explicitly compare the handicap theory with a purely “conventional” signalling model and with a null model. Predictions relating to three key design features (conspicuousness, pattern similarity, and Batesian mimicry) are compared, and tested against available data. Although many predictions remain to be tested adequately, we conclude that: (i) conspicuousness is most plausibly explained by the conventional signalling theory that ascribes the function of conspicuous coloration to signal efficacy rather than waste; (ii) pattern similarity, within and between species, is unlikely to be the result of the need to produce similar degrees of conspicuousness, as predicted by the handicap theory, but is plausibly explained as the result of pattern generalization amongst discriminating predators, as predicted by the conventional signalling theory; and (iii) Batesian mimicry is predicted by the conventional signalling theory, but not the handicap theory. Therefore the handicap theory fails to provide an adequate explanation of the main design features of at least one major signalling system.     

Exploring oxidative modifications of tyrosine: An update on mechanisms of formation,advances in analysis and biological consequences

Abstract

Protein oxidation is increasingly recognised as an important modulator of biochemical pathways controlling both physiological and pathological processes. While much attention has focused on cysteine modifications in reversible redox signalling, there is increasing evidence that other protein residues are oxidised in vivo with impact on cellular homeostasis and redox signalling pathways. A notable example is tyrosine, which can undergo a number of oxidative post-translational modifications to form 3-hydroxy-tyrosine, tyrosine crosslinks, 3-nitrotyrosine and halogenated tyrosine, with different effects on cellular functions. Tyrosine oxidation has been studied extensively in vitro, and this has generated detailed information about the molecular mechanisms that may occur in vivo. An important aspect of studying tyrosine oxidation both in vitro and in biological systems is the ability to monitor the formation of oxidised derivatives, which depends on a variety of analytical techniques. While antibody-dependent techniques such as ELISAs are commonly used, these have limitations, and more specific assays based on spectroscopic or spectrometric techniques are required to provide information on the exact residues modified and the nature of the modification. These approaches have helped understanding of the consequences of tyrosine oxidation in biological systems, especially its effects on cell signalling and cell dysfunction, linking to roles in disease. There is mounting evidence that tyrosine oxidation processes are important in vivo and can contribute to cellular pathology.     

Advances in methods for the determination of biologically relevant lipid peroxidation products

Abstract

Lipid peroxidation is recognized to be an important contributor to many chronic diseases, especially those of an inflammatory pathology. In addition to their value as markers of oxidative damage, lipid peroxidation products have also been shown to have a wide variety of biological and cell signalling effects. In view of this, accurate and sensitive methods for the measurement of lipid peroxidation products are essential. Although some assays have been described for many years, improvements in protocols are continually being reported and, with recent advances in instrumentation and technology, highly specialized and informative techniques are increasingly used. This article gives an overview of the most currently used methods and then addresses the recent advances in some specific approaches. The focus is on analysis of oxysterols, F₂-isoprostanes and oxidized phospholipids by gas chromatography or liquid chromatography mass spectrometry techniques and immunoassays for the detection of 4-hydroxynonenal.     

CTGF facilitates cell‐cell communication in chondrocytes via PI3K/Akt signalling pathway

PurposesGap junction intercellular communication (GJIC) is essential for articular cartilage to respond appropriately to physical or biological stimuli and maintain homeostasis. Connective tissue growth factor (CTGF), identified as an endochondral ossification genetic factor, plays a vital role in cell proliferation, migration and adhesion. However, how CTGF regulates GJIC in chondrocytes is still unknown. This study aims to explore the effects of CTGF on GJIC in chondrocytes and its potential biomechanism.Materials and methodsqPCR was performed to determine the expression of gene profile in the CCN family in chondrocytes. After CTGF treatment, CCK‐8 assay and scratch assay were performed to explore cell proliferation and migration. A scrape loading/dye transfer assay was adopted to visualize GJIC in living chondrocytes. Western blot analysis was done to detect the expression of Cx43 and PI3K/Akt signalling. Immunofluorescence staining was used to show protein distribution. siRNA targeting CTGF was used to detect the influence on cell‐cell communication.ResultsThe CTGF (CCN2) was shown to be the highest expressed member of the CCN family in chondrocytes. CTGF facilitated functional gap junction intercellular communication in chondrocytes through up‐regulation of Cx43 expressions. CTGF activated PI3K/Akt signalling to promote Akt phosphorylation and translocation. Suppressing CTGF also reduced the expression of Cx43. The inhibition of PI3K/Akt signalling decreased the expressions of Cx43 and thus impaired gap junction intercellular communication enhanced by CTGF.ConclusionsFor the first time, we provide evidence to show CTGF facilitates cell communication in chondrocytes via PI3K/Akt signalling pathway.     

Differential scanning calorimetry as a complementary diagnostic tool for the evaluation of biological samples

BackgroundDifferential scanning calorimetry (DSC) is a tool for measuring the thermal stability profiles of complex molecular interactions in biological fluids. DSC profiles (thermograms) of biofluids provide specific signatures which are being utilized as a new diagnostic approach for characterizing disease but the development of these approaches is still in its infancy.MethodsThis article evaluates several approaches for the analysis of thermograms which could increase the utility of DSC for clinical application. Thermograms were analyzed using localized thermogram features and principal components (PCs). The performance of these methods was evaluated alongside six models for the classification of a data set comprised of 300 systemic lupus erythematosus (SLE) patients and 300 control subjects obtained from the Lupus Family Registry and Repository (LFRR).ResultsClassification performance was substantially higher using the penalized algorithms relative to localized features/PCs alone. The models were grouped into two sets, the first having smoother solution vectors but lower classification accuracies than the second with seemingly noisier solution vectors.ConclusionsCoupling thermogram technology with modern classification algorithms provides a powerful diagnostic approach for analysis of biological samples. The solution vectors from the models may reflect important information from the thermogram profiles for discriminating between clinical groups.General significanceDSC thermograms show sensitivity to changes in the bulk plasma proteome that correlate with clinical status. To move this technology towards clinical application the development of new approaches is needed to extract discriminatory parameters from DSC profiles for the comparison and diagnostic classification of patients. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.     

Extracellular phosphoprotein regulation is affected by culture system scale-down

BackgroundPhosphorylated proteins are known to be present in multiple body fluids in normal conditions, and abnormally accumulated under some pathological conditions. The biological significance of their role in the extracellular space has started being elucidated only recently, for example in bone mineralization, neural development, and coagulation. Here, we address some criticalities of conventional culture systems for the study of the extracellular regulation of phosphorylation.MethodsWe make use of microfluidics to scale-down the culture volume to a size comparable to the interstitial spaces occurring in vivo. The phosphoprotein content of conditioned media was analyzed by a colorimetric assay that detects global phosphorylation.ResultsWe found that miniaturization of the culture system increases phosphoprotein accumulation. Moreover, we demonstrated that in conventional culture systems dilution affects the extent of the phosphorylation reactions occurring within the extracellular space. On the other hand, in microfluidics the phosphorylation status was not affected by addition of adenosine triphosphate (ATP) and FAM20C Golgi Associated Secretory Pathway Kinase (FAM20C) ectokinase, as if their concentration was already not limiting for the phosphorylation reaction to occur.ConclusionsThe volume of the extracellular environment plays a role in the process of extracellular phosphorylation due to its effect on the concentration of substrates, enzymes and co-factors.General significanceThus, the biological role of extracellular phosphoregulation may be better appreciated within a microfluidic culture system.     

Getting the most out of Shannon information

Shannon information is commonly assumed to be the wrong way in which to conceive of information in most biological contexts. Since the theory deals only in correlations between systems, the argument goes, it can apply to any and all causal interactions that affect a biological outcome. Since informational language is generally confined to only certain kinds of biological process, such as gene expression and hormone signalling, Shannon information is thought to be unable to account for this restriction. It is often concluded that a richer, teleosemantic sense of information is needed. I argue against this view, and show that a coherent and sufficiently restrictive theory of biological information can be constructed with Shannon information at its core. This can be done by paying due attention some crucial distinctions: between information quantity and its fitness value, and between carrying information and having the function of doing so. From this I construct an account of how informational functions arise, and show that the “subject matter” of these functions can easily be seen as the natural information dealt with by Shannon’s theory.     

Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information

Background  

Most of the existing in silico phosphorylation site prediction systems use machine learning approach that requires preparing a good set of classification data in order to build the classification knowledge. Furthermore, phosphorylation is catalyzed by kinase enzymes and hence the kinase information of the phosphorylated sites has been used as major classification data in most of the existing systems. Since the number of kinase annotations in protein sequences is far less than that of the proteins being sequenced to date, the prediction systems that use the information found from the small clique of kinase annotated proteins can not be considered as completely perfect for predicting outside the clique. Hence the systems are certainly not generalized. In this paper, a novel generalized prediction system, PPRED (Phosphorylation PREDictor) is proposed that ignores the kinase information and only uses the evolutionary information of proteins for classifying phosphorylation sites.     

Error-prone signalling.

The handicap principle of Zahavi is potentially of great importance to the study of biological communication. Existing models of the handicap principle, however, make the unrealistic assumption that communication is error free. It seems possible, therefore, that Zahavi's arguments do not apply to real signalling systems, in which some degree of error is inevitable. Here, we present a general evolutionarily stable strategy (ESS) model of the handicap principle which incorporates perceptual error. We show that, for a wide range of error functions, error-prone signalling systems must be honest at equilibrium. Perceptual error is thus unlikely to threaten the validity of the handicap principle. Our model represents a step towards greater realism, and also opens up new possibilities for biological signalling theory. Concurrent displays, direct perception of quality, and the evolution of 'amplifiers' and 'attenuators' are all probable features of real signalling systems, yet handicap models based on the assumption of error-free communication cannot accommodate these possibilities.     

Organismic supercategories and qualitative dynamics of systems

The representation of biological systems by means of organismic supercategories, developed in previous papers (Bull. Math. Biophysics,30, 625–636;31, 59–71;32, 539–561), is further discussed. The different approaches to relational biology, developed by Rashevsky, Rosen and by Băianu and Marinescu, are compared with Qualitative Dynamics of Systems which was initiated by Henri Poincaré (1881). On the basis of this comparison some concrete result concerning dynamics of genetic system, development, fertilization, regeneration, analogies, and oncogenesis are derived.     

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.     

Is metabolic rate a universal ‘pacemaker’ for biological processes?

A common, long‐held belief is that metabolic rate drives the rates of various biological, ecological and evolutionary processes. Although this metabolic pacemaker view (as assumed by the recent, influential ‘metabolic theory of ecology’) may be true in at least some situations (e.g. those involving moderate temperature effects or physiological processes closely linked to metabolism, such as heartbeat and breathing rate), it suffers from several major limitations, including: (i) it is supported chiefly by indirect, correlational evidence (e.g. similarities between the body‐size and temperature scaling of metabolic rate and that of other biological processes, which are not always observed) – direct, mechanistic or experimental support is scarce and much needed; (ii) it is contradicted by abundant evidence showing that various intrinsic and extrinsic factors (e.g. hormonal action and temperature changes) can dissociate the rates of metabolism, growth, development and other biological processes; (iii) there are many examples where metabolic rate appears to respond to, rather than drive the rates of various other biological processes (e.g. ontogenetic growth, food intake and locomotor activity); (iv) there are additional examples where metabolic rate appears to be unrelated to the rate of a biological process (e.g. ageing, circadian rhythms, and molecular evolution); and (v) the theoretical foundation for the metabolic pacemaker view focuses only on the energetic control of biological processes, while ignoring the importance of informational control, as mediated by various genetic, cellular, and neuroendocrine regulatory systems. I argue that a comprehensive understanding of the pace of life must include how biological activities depend on both energy and information and their environmentally sensitive interaction. This conclusion is supported by extensive evidence showing that hormones and other regulatory factors and signalling systems coordinate the processes of growth, metabolism and food intake in adaptive ways that are responsive to an organism's internal and external conditions. Metabolic rate does not merely dictate growth rate, but is coadjusted with it. Energy and information use are intimately intertwined in living systems: biological signalling pathways both control and respond to the energetic state of an organism. This review also reveals that we have much to learn about the temporal structure of the pace of life. Are its component processes highly integrated and synchronized, or are they loosely connected and often discordant? And what causes the level of coordination that we see? These questions are of great theoretical and practical importance.     

Visualizing phosphatidylcholine via mass spectrometry imaging: relevance to human health

ABSTRACT

Introduction: Mass spectrometry imaging (MSI) techniques are nowadays widely used to obtain spatially resolved metabolite information from biological tissues. Since (phospho)lipids occur in all animal tissues and are very sensitively detectable, they are often in the focus of such studies. This particularly applies for phosphatidylcholines (PC) which are very sensitively detectable as positive ions due to the permanent positive charge of their choline headgroup.

Areas covered: After a short introduction of lipid species occurring in biological systems and approaches normally used to obtain spatially resolved mass spectra (with the focus on matrix-assisted laser desorption/ionization coupled to time-of-flight (MALDI-TOF) MSI) a survey will be given which diseases have so far been characterized by changes of the PC composition.

Expert commentary: Since PC species are very sensitively detectable by MS, sensitivity is not a major issue. However, spatial resolution is still limited and cellular dimensions can be hardly resolved by MALDI-TOF MSI, which is a critical point of the available approaches. Due to lacks of reproducibility and standardization further development is required.     

Evolution of floral scent in relation to self-incompatibility and capacity for autonomous self-pollination in the perennial herb Arabis alpina

Background and AimsThe transition from outcrossing to selfing is a frequent evolutionary shift in flowering plants and is predicted to result in reduced allocation to pollinator attraction if plants can self-pollinate autonomously. The evolution of selfing is associated with reduced visual floral signalling in many systems, but effects on floral scent have received less attention. We compared multiple populations of the arctic–alpine herb Arabis alpina (Brassicaceae), and asked whether the transition from self-incompatibility to self-compatibility has been associated with reduced visual and chemical floral signalling. We further examined whether floral signalling differ between self-compatible populations with low and high capacity for autonomous self-pollination, as would be expected if benefits of signalling decrease with reduced dependence on pollinators for pollen transfer.MethodsIn a common garden we documented flower size and floral scent emission rate and composition in eight self-compatible and nine self-incompatible A. alpina populations. These included self-compatible Scandinavian populations with high capacity for autonomous self-pollination, self-compatible populations with low capacity for autonomous self-pollination from France and Spain, and self-incompatible populations from Italy and Greece.Key ResultsThe self-compatible populations produced smaller and less scented flowers than the self-incompatible populations. However, flower size and scent emission rate did not differ between self-compatible populations with high and low capacity for autonomous self-pollination. Floral scent composition differed between self-compatible and self-incompatible populations, but also varied substantially among populations within the two categories.ConclusionsOur study demonstrates extensive variation in floral scent among populations of a geographically widespread species. Contrary to expectation, floral signalling did not differ between self-compatible populations with high and low capacity for autonomous self-pollination, indicating that dependence on pollinator attraction can only partly explain variation in floral signalling. Additional variation may reflect adaptation to other aspects of local environments, genetic drift, or a combination of these processes.     

Information content of chemical structures and some possible biological applications

The purpose of this paper is to calculate the amount of information contained in a chemical or biological structure, and to estimate the energy needed for obtaining an organization unit. The first problem is solved by applying H. J. Morowitz's reasoning (Bull. Math. Biophysics,17, 81–86, 1955) and, for the second one, calculations based upon bond formation heat are carried out.Information content theoretical physical entropy, real physical entropy, informational entropy or negentropy entropic information or neginformation, heat amount, as well as relationships between these system parameters, are defined and used. The investigation covers 63 chemical substances (inorganic and organic compounds). The numerical results should show that common organized systems happen to be between two extreme kinds of systems: highly disordered systems and ideally organized systems. Some speculative numerical applications are carried out regarding chlorophyllian photosynthesis and information amount accumulated through biological growth. It seems that Information Theory may predict some biocalorimetric results.     

Dendrimer-based fluorescent indicators: in vitro and in vivo applications

BackgroundThe development of fluorescent proteins and synthetic molecules whose fluorescence properties are controlled by the environment makes it possible to monitor physiological and pathological events in living systems with minimal perturbation. A large number of small organic dyes are available and routinely used to measure biologically relevant parameters. Unfortunately their application is hindered by a number of limitations stemming from the use of these small molecules in the biological environment.ConclusionWe believe that the proposed architecture can represent a useful and novel tool in fluorescence imaging that can be widely applied in conjunction with a broad range of sensing dyes and experimental setups.