The manipulation of calcium oscillations by harnessing self-organisation

This paper investigates how self-organisation might be harnessed for the manipulation and control of calcium oscillations. Calcium signalling mechanisms are responsible for a number of important functions within biological systems, such as fertilization, secretion, contraction, neuronal signalling and learning. In this paper, calcium oscillations are investigated as a biological periodic process. Within biological systems such periodic behaviour is one of the outcomes from self-organisation. The understanding of periodic processes in living systems can enable more accurate diagnosis and physiologically suitable clinical therapies to be proposed, for diseases such as cancer, epilepsy, cardiac diseases and other dynamic diseases. In this paper these ideas are investigated by means of the calcium-induced calcium release (CICR) model and a number of representative simulations of intra and inter-cellular calcium oscillations are used to illustrate the manipulation and control of these oscillations in normal and pathological situations.     

Crustal evolution in the early precambrian

Recently published models present highly conflicting views of continental evolution. At one extreme, it is envisaged that continental crust was fully developed by 4000 Myr ago and quantitatively recycled through the mantle throughout geological time without net change of crustal mass (continental steady-state hypothesis). A fundamentally contrasted view is that the earliest continental crust ( 3700 Myr) occurred in small, localised patches, and that once juvenile continental crust is cratonised it cannot be returned to the mantle in bulk. This corresponds to the concept of irreversible chemical differentiation of the mantle with accompanying growth of continental crust through geological time (continental growth hypothesis). In between these extremes, it has been suggested that some relatively minor continental constituents may be selectively recycled into the mantle. This does not involve wholesale recycling of continental crust, and still allows continental growth. Whilst isotopic and trace element modelling imposes important constraints it is not absolutely definitive in deciding between contrasted evolutionary models. Additional criteria for continental evolution must be sought from assorted geological, geophysical, geochemical and geochronological data. As one example, it is important to determine the age and regional extent of exposed early Precambrian continental crust, and also whether exposed crust is underlain by significantly older crust at depth.The use of radiogenic isotopes provides one of the most powerful tools for elucidating the evolution of any given sector of continental crust through geological time, and constraining crustal residence time. This approach, combined with several others, strongly favours the continental growth hypothesis.     

Numerical simulations of microtubule self-organisation by reaction and diffusion

This article addresses the physical chemical processes underlying biological self-organisation by which a homogenous solution of reacting chemicals spontaneously self-organises. Theoreticians have predicted that self-organisation can arise from a coupling of reactive processes with molecular diffusion. In addition, the presence of an external field, such as gravity, at a critical moment early in the process may determine the morphology that subsequently develops. The formation, in-vitro, of microtubules, a constituent of the cellular skeleton, shows this type of behaviour. The preparations spontaneously self-organise by reaction-diffusion and the morphology that develops depends upon the presence of gravity at a critical bifurcation time early in the process. Here, we present numerical simulations of a population of microtubules that reproduce this behaviour. Microtubules can grow from one end whilst shrinking from the other. The shrinking end leaves behind a chemical trail of high tubulin concentration. Neighbouring microtubules preferentially grow into these regions, whilst avoiding regions of low tubulin concentration. The chemical trails produced by individual microtubules thus activate and inhibit the formation of neighbouring microtubules and this progressively leads to self-organisation. Gravity acts by way of its directional interaction with the macroscopic density fluctuations present in the solution arising from microtubule disassembly.     

Find of Tremadocian ostracodes in cherts of Kazakhstan

First late Tremadocian (Early Ordovician) ostracodes were found in cherts of the Burubaital Formation near the “Burultas” deposit in southern Kazakhstan. The preservation of carbonate ostracode shellshells in siliceous environment is discussed. The monotypic ostracode assemblage includes the newly described form, Burultalina nikitinae gen. et sp. nov.     

Female dominance over males in primates: self-organisation and sexual dimorphism

The processes that underlie the formation of the dominance hierarchy in a group are since long under debate. Models of self-organisation suggest that dominance hierarchies develop by the self-reinforcing effects of winning and losing fights (the so-called winner-loser effect), but according to 'the prior attribute hypothesis', dominance hierarchies develop from pre-existing individual differences, such as in body mass. In the present paper, we investigate the relevance of each of these two theories for the degree of female dominance over males. We investigate this in a correlative study in which we compare female dominance between groups of 22 species throughout the primate order. In our study female dominance may range from 0 (no female dominance) to 1 (complete female dominance). As regards 'the prior attribute hypothesis', we expected a negative correlation between female dominance over males and species-specific sexual dimorphism in body mass. However, to our surprise we found none (we use the method of independent contrasts). Instead, we confirm the self-organisation hypothesis: our model based on the winner-loser effect predicts that female dominance over males increases with the percentage of males in the group. We confirm this pattern at several levels in empirical data (among groups of a single species and between species of the same genus and of different ones). Since the winner-loser effect has been shown to work in many taxa including humans, these results may have broad implications.     

Microtubule self-organisation by reaction-diffusion processes in miniature cell-sized containers and phospholipid vesicles

Under appropriate conditions, in vitro microtubule preparations self-organise over macroscopic distances by a process of reaction and diffusion. To investigate whether such self-organisation can also occur in objects as small as a cell or an embryo we carried out experiments in miniature containers of cellular dimension. When assembled under self-organising conditions in wells of 120–500 μm, microtubules developed organised structures. Self-organisation is strongly affected by shape, being highly favoured by elongated forms. In wells of more complex shape, geometrical factors may either oppose or strengthen one another and so inhibit or reinforce self-organisation. Microtubules were also assembled within phospholipid vesicles of 2–5 μm diameter. Under self-organising conditions, we observed large shape changes from spheroids to long tubes (50–100 μm) and intertwined coils. We conclude that self-organisation of microtubules by reaction–diffusion processes can occur in containers of cellular dimensions and is capable of strongly deforming the cellular membrane.     

Auxin, self-organisation, and the colonial nature of plants

Evolution has provided at least two particularly successful independent solutions to the problems of multicellularity - animals and higher plants. An obvious requirement for successful multicellularity is communication between different parts of the organism, both locally, for example between neighbouring cells, and over very long distances. Recent advances in understanding hormone signalling networks in plants are beginning to reveal how co-ordination of activity across the whole plant body can be achieved despite the lack of a control centre, typical of animal systems. Of particular importance in this distributed regulatory approach are the self-organising properties of the transport system for the plant hormone auxin. This review examines the integrative role of the auxin transport network in co-ordinating plant growth and development.     

External optimal control of self-organisation dynamics in a chemotaxis reaction diffusion system

Detailed quantitative understanding and specific external control of cellular behaviour are general long-term goals of modem bioscience research activities in systems biology. Pattern formation and self-organisation processes both in single cells and in distributed cell populations are phenomena which are highly significant for the functionality of life, because life requires to maintain a highly organised spatiotemporal system structure. In particular chemotaxis is crucial for various biological aspects of intercellular signalling and cell aggregation. As an example for model based control of self-organising biological systems, we describe numerical optimal control of E. coli bacterial chemotaxis based on a 1-D two-component partial differential equation (PDE) model of reaction diffusion type. We present a numerical scheme to force cell aggregation patterns to particular desired results by applying a boundary influx control of chemoattractant without interfering with the system itself. Optimal controls are numerically computed by using a specially tailored interior point optimisation technique applied to a direct collocation discretisation of the control function and the PDE constraint. The objective to be minimised is the deviation of a desired cell distribution from the cell density, which results from the dynamics of the controlled system.     

Objectivistic views in biology: an obstacle to our understanding of self-organisation processes in aquatic ecosystems

• 1 Ecologists are frequently inspired by the mechanistic view of classical physics in which motion is reduced to the effect of external forces on defined states of observable objects. Accordingly, dynamic events in ecosystems are resolved into environmental influences acting upon given states of an organismic system. In this conceptional scheme, both the environmental influences and the organismic system are assumed to be describable by objectively determinable parameters.
• 2 The present article directs criticism at this objectivistic approach. Accordingly, it is shown that an objectivistic view of living systems does not account for the complexity of organismic interactions which are continuously modified in a directional manner to achieve certain end states. This is exemplified in the physiological adaptation of micro‐organisms to their abiotic and biotic environment. Here, a population of single cells tends towards a ‘multicellular organism’ in which energy utilisation is optimised. During an investigation of this physiological adaptation process the organisms also adapt to the imposed experimental conditions, rendering futile any analysis in mechanistic terms.
• 3 Owing to this property of physiological adaptation a distinct research strategy is called for to establish the nature and ecological significance of this directionality. This strategy must be based on the observation that the sensitivity of living systems to a given environmental stimulus depends on the organismic prehistory with respect to previous exposures to stimuli. Thus, from an analysis of the adaptive response of a natural population to a defined challenge, information about prior environmental conditions may be derived that could not be obtained by other means.
• 4 Examples for the application of this research strategy to environmental problems are given.

     

Pyrolysis of precambrian kerogens: Constraints and capabilities

Summary Precambrian kerogens are currently considered to be the primary candidates for the search of biochemical fossils. Degradation of kerogens by relatively mild pyrolysis techniques, such as under high vacuum, can liberate indicative structural moieties which were incorporated in, and perhaps shielded by, these solid and highly condensed, basically aromatic substances. It is necessary to observe analytical constraints (sample size and shape, temperature, pressure, time, etc.) in order to prevent an overabundant yield of secondary pyrolyzates (inter- and intramolecular rearrangements) which can prevent kerogen characterization. Potential biochemical fossils have been found in Precambrian kerogens. Demonstratable syngenetic biochemical fossils are expected after kerogen diagenesis and catagenesis is understood in sufficient detail, and when pyrolysis is augmented by multiple, improved analytical techniques.Dedicated to the Memory of H.C. Urey (1893–1981)     

The evolution of the early precambrian geobiological systems

Bacterial paleontology provides vast opportunities for the study of all types of sedimentary and volcanic-sedimentary rocks, at any stage of metamorphism and of any age. Bacteria are shown to play an important role in weathering, transfer, sedimentation, and diagenesis of the sediments and in the formation of many minerals that have previously been thought to be abiogenic.     

Ground-based methods reproduce space-flight experiments and show that weak vibrations trigger microtubule self-organisation

The effect of weightlessness on physical and biological systems is frequently studied by experiments in space. However, on the ground, gravity effects may also be strongly attenuated using methods such as magnetic levitation and clinorotation. Under suitable conditions, in vitro preparations of microtubules, a major element of the cytoskeleton, self-organise by a process of reaction–diffusion: self-organisation is triggered by gravity and samples prepared in space do not self-organise. Here, we report experiments carried out with ground-based methods of clinorotation and magnetic levitation. The behaviour observed closely resembles that of the space-flight experiment and suggests that many space experiments could be carried out equally well on the ground. Using clinorotation, we find that weak vibrations also trigger microtubule self-organisation and have an effect similar to gravity. Thus, in some in vitro biological systems, vibrations are a countermeasure to weightlessness.     

In vitro CNS tissue analogues formed by self-organisation of reaggregated post-natal brain tissue

In this paper, we report the characterization of 'Hi-Spot' cultures formed by the re-aggregation of dissociated postnatal CNS tissue grown at an air-liquid interface. This produces a self-organised, dense, organotypic cellular network. Western blot, immunohistochemical, viral transfection and electron microscopy analyses reveal neuronal and glial populations, and the development of a synaptic network. Multi-electrode array recordings show synaptically driven network activity that develops through time from single unit spiking activity to global network bursting events. This activity is blocked by tetanus toxin and modified by antagonists of glutamatergic and GABAergic receptors suggesting tonic activity of excitatory and inhibitory synaptic signaling. The tissue-like properties of these cultures has been further demonstrated by their relative insensitivity to glutamate toxicity. Exposure to millimolar concentrations of glutamate for hours is necessary to produce significant excitotoxic neuronal death, as in vivo. We conclude that 'Hi-Spots' are biological analogues of CNS tissue at a level of complexity that allows for detailed functional analyses of emergent neuronal network properties.     

Radiolarian petrographic preservation types in Jurassic to Lower Tertiary cherts of Costa Rica

Radiolarian cherts are locally intercalated, mostly as up to 45 m thick sequences of rhythmically bedded chert, in the Jurassic to Lower Tertiary Nicoya Ophiolite Complex of western and southern Costa Rica (Central America). Additionally, bedded chert is present in some Campanian and Paleocene/Eocene sedimentary series that overly the Nicoya Complex. The ophiolitic cherts may be thermally recrystallized to different grades due to post depositional basaltic magmatism. The radiolarian skeletons mainly consist of microquartz; complete dissolution of the skeletons, i.e. exclusive preservation of the fillings, is rare. The fillings are variable in composition: quartz, length-fast chalcedony, and quartz-pigment mixtures are dominant; opal-CT, clay minerals, chlorite, zeolites, baryte, manganese and iron oxides, epidote and calcite are subordinate. The non-siliceous minerals may locally replace the siliceous phases and/or intergrow with them. Thus, approximately 40 preservation types have been observed in the Costa Rican cherts. In combination with the different preservation grades, a large number of preservation variants is present. However, in the cherts of the Nicoya Complex quartz-rich preservation types are strongly dominant, whereas opal-CT, zeolites and calcite are more important in the cherts of the overlying sedimentary series. Types and grades of radiolarian preservation represent an important aid in the reconstruction of the postdepositional diagenetic and thermal history of the Costa Rican cherts.     

Inorganic polyphosphates in mitochondria

Current data concerning the crucial role of inorganic polyphosphates (polyP) in mitochondrial functions and dysfunctions in yeast and animal cells are reviewed. Biopolymers with short chain length (∼15 phosphate residues) were found in the mitochondria of Saccharomyces cerevisiae. They comprised 7–10% of the total polyP content of the cell. The polyP are located in the membranes and intermembrane space of mitochondria. The mitochondrial membranes possess polyP/Ca²⁺/polyhydroxybutyrate complexes. PolyP accumulation is typical of promitochondria but not of functionally active mitochondria. Yeast mitochondria possess two exopolyphosphatases splitting P_i from the end of the polyP chain. One of them, encoded by the PPX1 gene, is located in the matrix; the other one, encoded by the PPN1 gene, is membrane-bound. Formation of well-developed mitochondria in the cells of S. cerevisiae after glucose depletion is accompanied by decrease in the polyP level and the chain length. In PPN1 mutants, the polyP chain length increased under glucose consumption, and the formation of well-developed mitochondria was blocked. These mutants were defective in respiration functions and consumption of oxidizable carbon sources such as lactate and ethanol. Since polyP is a compound with high-energy bonds, its metabolism vitally depends on the cell bioenergetics. The maximal level of short-chain acid-soluble polyP was observed in S. cerevisiae under consumption of glucose, while the long-chain polyP prevailed under ethanol consumption. In insects, polyP in the mitochondria change drastically during ontogenetic development, indicating involvement of the polymers in the regulation of mitochondrial metabolism during ontogenesis. In human cell lines, specific reduction of mitochondrial polyP under expression of yeast exopolyphosphatase PPX1 significantly modulates mitochondrial bioenergetics and transport.