Microtubules: dissipative structures formed by self-assembly

Microtubules are hollow fibres that form the track upon which chromosomes or proteins, such as kinesins, are transported in the cell. They are formed by the self-assembly of the protein tubulin both in vitro and in vivo. In the cell, their appearance in time and space is strictly controlled by the presence of nucleation centres. Microtubules are very dynamic structures, a property that is obtained by coupling the self-assembly process to the hydrolysis of the nucleotide, guanosine 5′-triphosphate, (GTP). After assembly, GTP is hydrolysed and guanosine 5′-diphosphate, (GDP)-microtubule structure is formed which, although intrinsically very unstable, is stabilised by a small remaining tubulin-GTP-cap at both ends. As such, the ends of microtubules can be considered as gates for entry into the polymeric state. These gates can be blocked by sub-stoichiometric amounts of drugs such as colchicine.

As biological devices, microtubules differ considerably from man-made devices: they are dynamic dissipative structures, made by spontaneous self-assembly. It has been suggested that microtubules could play a role in the conduction and dynamic storage of information. This implies the existence of different conformational states of tubulin.     

Spatial dissipative structures formed by spontaneous molecular aggregation at interfaces

Interfacial processes as well as formation of dissipative structures have been suggested to play a key role in early pre-biotic evolutionary stages, mainly due to the ability of such processes to induce aggregation and spatial structuring. In this context we would like to draw attention to our recent findings regarding a remarkably wide collection of interfacial chemical reactions which form dissipative spatial structures. Three types of interfacial processes were found to yield this phenomenon: photochemical oxidations at liquid/air and liquid/liquid interfaces; gas/solution reactions; and reactions at membrane surfaces. The phenomenon we describe is the first major example of a network of chemical reactions that develop into macroscopic far-from-equilibrium concentration patterns.     

Spatial dissipative structures formed by spontaneous molecular aggregation at interfaces

Interfacial processes as well as formation of dissipative structures have been suggested to play a key role in early pre-biotic evolutionary stages, mainly due to the ability of such processes to induce aggregation and spatial structuring. In this context we would like to draw attention to our recent findings regarding a remarkably wide collection of interfacial chemical reactions which form dissipative spatial structures. Three types of interfacial processes were found to yield this phenomenon: photochemical oxidations at liquid/air and liquid/liquid interfaces; gas/solution reactions; and reactions at membrane surfaces. The phenomenon we describe is the first major example of a network of chemical reactions that develop into macroscopic far-from-equilibrium concentration patterns.     

Characterization of structures in biofilms formed by a Pseudomonas fluorescens isolated from soil

Background  

Microbial biofilms represent an incompletely understood, but fundamental mode of bacterial growth. These sessile communities typically consist of stratified, morphologically-distinct layers of extracellular material, where numerous metabolic processes occur simultaneously in close proximity. Limited reports on environmental isolates have revealed highly ordered, three-dimensional organization of the extracellular matrix, which may hold important implications for biofilm physiology in vivo.     

Instability of waves formed by motile bacteria

Abstract Cell-free enzyme preparations of the obligately anaerobic halophilic eubacterium Haloanaerobium praevalens synthesize fatty acids from malonyl-CoA. The reaction is stimulated by NaCl and KCl at a concentration of 1 M, and only slightly inhibited by salt concentrations as high as 3 M. Thus, the fatty acid synthetase of H. praevalens is expected to the fully active at the high intracellular salt concentrations present, and it is the first fatty acid synthetase reported to be active in the presence of high salt concentrations.     

Spatial patterns formed by chemotactic bacteria Escherichia coli

In certain experimental conditions, bacteria form complex spatial-temporal patterns. A striking example of such kind was reported by Budrene and Berg (1991), who observed a wide variety of different colony structures ranging from arrays of spots to radially oriented stripes or arrangements of more complex elongated spots, formed by Escherichia coli. We discuss the relevant mechanisms of intercellular regulation in bacterial colony which may cause pattern formation, and formulate the corresponding mathematical model. In numerical experiments a variety of patterns, observed in real systems, is reproduced. The dynamics of their formation is investigated.     

Concentration-dependent diffusion coefficient and dissipative structures

A theoretical study of the Brusselator model with non-uniform distribution of component A and a concentration-dependent diffusion coefficient has been performed. Numerical simulation reveals that a variable diffusion coefficient alters the bifurcation pattern and the stability properties of the steady-state as well as periodic solutions. A simple approximate method, based on one-point collocation, has been proposed to analyze the bifurcation phenomena for the case of fixed boundary conditions and low system size.     

Oscillating dissipative structures in mitochondrial suspensions

The occurrence of spatial structures in the unstirred layer of an oscillating mitochondrial suspension is reported. The structures are detected by photo camera by light scattering in the unstirred layer of suspension. The spatial structures observed are shown to oscillate with the same period as that of mitochondrial oscillations in the bulk phase. Patterning is not affected by the layer depth within the range 0.3-3.0 mm. Various types of oscillatory states of mitochondria are characterized by the corresponding patterns. Patterning is effectively suppressed by the inhibitors of the respiratory chain (antimycin A or CN-).     

Formation and stability of dissipative structures

The nonlinear interaction of the disturbed wave packet modes has been analysed within nonlinear parabolic equation. There has also been designed the approach to a limit cycle regime of an isolated mode, the analytical stability criterion of the obtained solutions having separated the existance spheres of isolated and multimode regimes. Stochastization and self-organization processes taking place during the formation of dissipative structures have been studied by methods of random function theory.     

On the formation of unique dissipative structures

We consider a simple model for the formation of dissipative structures. In general there exists a multitude of stable final states. We show, however, that when the diffusion constant increases during the development of the system, a stationary state is reached which does not depend on the choice of initial conditions. We also show that a uniquely defined final state builds up when the system is initially strongly excited on one side.     

Oxidation of ethylene by soil bacteria

The course of the biological oxidation of ethylene by soil was dependent on the type of soil used as well as on other factors. As evidenced from an increase in oxidation rate, the ethylene-consuming microorganisms in soil could grow at the expense of ethylene, even when the gas was present at concentrations of 50 ppm or less. Five strains of bacteria strongly resembling each other were isolated from different soils. These pleomorphic, gram-positive, acid-fast, obligate aerobic, ethylene-oxidizing bacteria grew also on saturated alkanes and on ordinary carbon sources. An apparent K_m for ethylene of approximately 40 ppm was estimated for whole-cell suspensions of strain E20 by following the disappearance of the gas from the atmosphere.     

Spectroscopic comparison of different DNA structures formed by oligonucleotides

Six different nucleic acid structures including duplex, triplex and quadruplex are formed by oligonucleotides. Their structural properties are studied in detail by four spectroscopic techniques, i.e. CD, UV, NMR and fluorescence. Results are: CD Spectra: The common characteristics is a negative band at 240 nm, and the spectra are different from each other in the range 260-300 nm. Many factors such as chain direction, sugar puckering, orientation of the glycosyl bond, base stacking and sequence can effect their conformation and then show diversity and complexity in the spectra. UV Spectra: The UV spectra of all forms are quite similar, all of them exhibit a sharp positive peak around 210 nm and a broad positive band in the region of 240-280 nm. Although the bands are different in absorbance, the spectra are not characteristic enough to distinguish these forms. In addition, their thermal denaturation is also observed by UV spectrum, different melting curves and points are shown and some thermodynamic information is provided. NMR Spectra: Since the G residues in the six samples all participate in hydrogen bond, the imino proton can not exchange with the solvent freely so as to allow an observable resonance to arise. The resonance number and chemical shift will vary with the change in base-pairing number and mode as well as the whole geometry of its molecule. Fluorescence Spectra: The interaction mechanisms between EB and these structures are different. B type duplex and triplex adopt an intercalative mode in which the efficiency of energy transfer is relatively high and the fluorescence of EB can not be quenched easily. While for the parallel duplex, outside binding is predominant in which energy transfer can hardly happen and most of its fluorescence can be quenched. As for the quadruplex, groove binding is possible, so the efficiency of energy transfer is higher than that in outside binding, but lower than that in intercalative binding, and fluorescence is quenched partly.     

Conspicuous veils formed by vibrioid bacteria on sulfidic marine sediment

We describe the morphology and behavior of a hitherto unknown bacterial species that forms conspicuous veils (typical dimensions, 30 by 30 mm) on sulfidic marine sediment. The new bacteria were enriched on complex sulfidic medium within a benthic gradient chamber in oxygen-sulfide countergradients, but the bacteria have so far not been isolated in pure culture, and a detailed characterization of their metabolism is still lacking. The bacteria are colorless, gram-negative, and vibrioid-shaped (1.3- to 2.5- by 4- to 10- micro m) cells that multiply by binary division and contain several spherical inclusions of poly-beta-hydroxybutyric acid. The cells have bipolar polytrichous flagella and exhibit a unique swimming pattern, rotating and translating along their short axis. Free-swimming cells showed aerotaxis and aggregated at ca. 2 micro M oxygen within opposing oxygen-sulfide gradients, where they were able to attach via a mucous stalk, forming a cohesive whitish veil at the oxic-anoxic interface. Bacteria attached to the veil kept rotating and adapted their stalk lengths dynamically to changing oxygen concentrations. The joint action of rotating bacteria on the veil induced a homogeneous water flow from the oxic water region toward the veil, whereby the oxygen uptake rate could be enhanced up to six times, as shown by model calculations. The veils showed a pronounced succession pattern. New veils were generated de novo within 24 h and had a homogeneous whitish translucent appearance. Bacterial competitors or eukaryotic predators were apparently kept away by the low oxygen concentration prevailing at the veil surface. Frequently, within 2 days the veil developed a honeycomb pattern of regularly spaced holes. After 4 days, most veils were colonized by grazing ciliates, leading to the fast disappearance of the new bacteria. Several-week-old veils finally developed into microbial mats consisting of green, purple, and colorless sulfur bacteria.