Diffusion influences in denaturable insolubilized enzyme catalysts

The influence of diffusion on the apparent thermal stability of a reversibly or irreversibly denaturable enzyme is examined theoretically when he enzyme is uniformly distributed in a porous solid. If the overall reaction rate is influenced by diffusion through the catalyst, the insolubilized catalyst is shown to yield an apparently more thermally stable enzyme even though the maximal velocity V_m, and the Michaelis constant, K_m, are the same for the free and insolubilized forms of enzyme. Brief consideration is given to the experimental conditions needed to clearly demonstrate whether insolubilization does or does not effect the thermal stability of the enzyme.     

Ca2+ induces transbilayer redistribution of all major phospholipids in human erythrocytes.

Elevating cytoplasmic Ca2+ levels in erythrocytes activates a pathway for transbilayer diffusion of plasma membrane phospholipids. The use of spin-labeled and fluorescent phospholipid analogues revealed that the pathway permits diffusion of all the major classes of phospholipids and does not distinguish between the two types of probes. Diffusion was bidirectional, began immediately upon elevation of cytoplasmic [Ca2+] above 50-100 microM, persisted as long as the [Ca2+] remained elevated, and disappeared promptly when Ca2+ levels fell. Diffusion was unaffected by conditions which suppress shedding of vesicles, discounting this event as a requisite for phospholipid reorientation induced by Ca2+.     

Nucleocytoplasmic shuttling of JAZ, a new cargo protein for exportin-5

Exportin-5 is a nuclear export receptor for certain classes of double-stranded RNA (dsRNA), including pre-micro-RNAs, viral hairpin RNAs, and some tRNAs. It can also export the RNA binding proteins ILF3 and elongation factor EF1A. However, the rules that determine which RNA binding proteins are exportin-5 cargoes remain unclear. JAZ possesses an unusual dsRNA binding domain consisting of multiple C2H2 zinc fingers. We found that JAZ binds to exportin-5 in a Ran-GTP- and dsRNA-dependent manner. Exportin-5 stimulates JAZ shuttling, and gene silencing of exportin-5 reduces shuttling. Recombinant exportin-5 also stimulates nuclear export of JAZ in permeabilized cells. JAZ also binds to ILF3, and surprisingly, this interaction is RNA independent, even though it requires the dsRNA binding domains of ILF3. Exportin-5, JAZ, and ILF3 can form a heteromeric complex with Ran-GTP and dsRNA, and JAZ increases ILF3 binding to exportin-5. JAZ does not contain a classical nuclear localization signal, and in digitonin-permeabilized cells, nuclear accumulation of JAZ does not require energy or cytosol. Nonetheless, low temperatures prevent JAZ import, suggesting that nuclear entry does not occur via simple diffusion. Together, these data suggest that JAZ is exported by exportin-5 but translocates back into nuclei by a facilitated diffusion mechanism.     

A Multiple-Relaxation-Time Lattice-Boltzmann Model for Bacterial Chemotaxis: Effects of Initial Concentration,Diffusion, and Hydrodynamic Dispersion on Traveling Bacterial Bands

Bacterial chemotaxis can enhance the bioremediation of contaminants in aqueous and subsurface environments if the contaminant is a chemoattractant that the bacteria degrade. The process can be promoted by traveling bands of chemotactic bacteria that form due to metabolism-generated gradients in chemoattractant concentration. We developed a multiple-relaxation-time (MRT) lattice-Boltzmann method (LBM) to model chemotaxis, because LBMs are well suited to model reactive transport in the complex geometries that are typical for subsurface porous media. This MRT-LBM can attain a better numerical stability than its corresponding single-relaxation-time LBM. We performed simulations to investigate the effects of substrate diffusion, initial bacterial concentration, and hydrodynamic dispersion on the formation, shape, and propagation of bacterial bands. Band formation requires a sufficiently high initial number of bacteria and a small substrate diffusion coefficient. Uniform flow does not affect the bands while shear flow does. Bacterial bands can move both upstream and downstream when the flow velocity is small. However, the bands disappear once the velocity becomes too large due to hydrodynamic dispersion. Generally bands can only be observed if the dimensionless ratio between the chemotactic sensitivity coefficient and the effective diffusion coefficient of the bacteria exceeds a critical value, that is, when the biased movement due to chemotaxis overcomes the diffusion-like movement due to the random motility and hydrodynamic dispersion.     

Models of growth, self-reproduction and autoregulation based on consideration of reaction vessels with distensible, semipermeable walls]

We constructed non-equilibrium thermodynamics of the open physical-chemical irreversible processes in reactors with the strain semipermeable walls. This thermodynamics does not use the reciprocal relations of Onsager, so it may be applied when the stability stationary state is far from equilibrium. One of a general consequences of this thermodynamics is the statement: coordinated growth and self-reproduction are possible near the absolute equilibrium of the dissolvent and near the absolute stability stationary state of all chemicals with the absolute conservation of the differential equations of chemical kinetics. The supposition of ideal mixing is unnecessary; this condition is fulfilled automatically with diffusion. Growth and self-reproduction are not connected with positive eigenvalue of the differential equation of chemical kinetics. It is possible to construct a model of autoregulation and differentiation with this thermodynamics. The uniquness of such autoregulation follows from the mathematical theory [1]. The mathematical foundation of this thermodynamics is given in [1].     

Starvation Driven Diffusion as a Survival Strategy of Biological Organisms

The purpose of this article is to introduce a diffusion model for biological organisms that increase their motility when food or other resource is insufficient. It is shown in this paper that Fick’s diffusion law does not explain such a starvation driven diffusion correctly. The diffusion model for nonuniform Brownian motion in Kim (Einstein’s random walk and thermal diffusion, preprint http://amath.kaist.ac.kr/papers/Kim/31.pdf, 2013) is employed in this paper and a Fokker–Planck type diffusion law is obtained. Lotka–Volterra type competition systems with spatial heterogeneity are tested, where one species follows the starvation driven diffusion and the other follows the linear diffusion. In heterogeneous environments, the starvation driven diffusion turns out to be a better survival strategy than the linear one. Various issues such as the global asymptotic stability, convergence to an ideal free distribution, the extinction and coexistence of competing species are discussed.     

Cuticular hydrocarbon profiles differ between ant body parts: implications for communication and our understanding of CHC diffusion

Insect cuticular hydrocarbons (CHCs) serve as communication signals and protect against desiccation. They form complex blends of up to 150 different compounds. Due to differences in molecular packing, CHC classes differ in melting point. Communication is especially important in social insects like ants, which use CHCs to communicate within the colony and to recognize nestmates. Nestmate recognition models often assume a homogenous colony odor, where CHCs are collected, mixed, and redistributed in the postpharyngeal gland (PPG). Via diffusion, recognition cues should evenly spread over the body surface. Hence, CHC composition should be similar across body parts and in the PPG. To test this, we compared CHC composition among whole-body extracts, PPG, legs, thorax, and gaster, across 17 ant species from 3 genera. Quantitative CHC composition differed between body parts, with consistent patterns across species and CHC classes. Early-melting CHC classes were most abundant in the PPG. In contrast, whole body, gaster, thorax, and legs had increasing proportions of CHC classes with higher melting points. Intraindividual CHC variation was highest for rather solid, late-melting CHC classes, suggesting that CHCs differ in their diffusion rates across the body surface. Our results show that body parts strongly differ in CHC composition, either being rich in rather solid, late-melting, or rather liquid, early-melting CHCs. This implies that recognition cues are not homogenously present across the insect body. However, the unequal diffusion of different CHCs represents a biophysical mechanism that enables caste differences despite continuous CHC exchange among colony members.     

Instability in diffusing fluid layers

A small perturbation analysis is carried out to determine the stability of a fluid containing two layers of diffusing solutes in a common solvent and acted upon by a uniform gravitational field. It is found that instability can arise even though the unperturbed diffusion does not lead to the formation of a density inversion within the fluid.     

Evolution at a multiallelic locus under migration and uniform selection

The semilinear parabolic system that describes the evolution of the gene frequencies in the diffusion approximation for migration and selection at a multiallelic locus is investigated. The population occupies a finite habitat of arbitrary dimensionality and shape. The drift and diffusion coefficients may depend on position, but the selection coefficients do not. It is established that if p is a uniform equilibrium point under pure selection, then p is a migration-selection equilibrium, and that generically the introduction of migration does not change the stability of p. It is also proved that if p is a uniform, globally asymptotically stable, internal equilibrium point under pure selection, then the gene frequencies converge to p when both migration and selection are present. Thus, in this case, after a sufficiently long time, there is no genetic indication of the spatial distribution of the population.     

Two techniques for evaluating small molecule-macromolecule binding in complex system

Two techniques are proposed for the evaluation of multiple binding in complex systems. These techniques can be applied to reactions where more than one class of binding sites is present or where there are interactions between equivalent sites. The first technique employs a Klotz or Scatchard plot to evaluate three stoichiometric binding constants and the total number of sites. Furthermore the individual site binding parameters can be determined for several very important systems such as a macromolecule with two classes of independent sites or a macromolecule with three sites that are equivalent but not independent. For a system with many classes of independent sites, a second technique employs a continuous distribution of binding constants to analyze the reaction. This method does not require the assumption of a functional form for the distribution or a knowledge of the number of classes.     

Turing instabilities in a mathematical model for signaling networks

GTPase molecules are important regulators in cells that continuously run through an activation/deactivation and membrane-attachment/membrane-detachment cycle. Activated GTPase is able to localize in parts of the membranes and to induce cell polarity. As feedback loops contribute to the GTPase cycle and as the coupling between membrane-bound and cytoplasmic processes introduces different diffusion coefficients a Turing mechanism is a natural candidate for this symmetry breaking. We formulate a mathematical model that couples a reaction–diffusion system in the inner volume to a reaction–diffusion system on the membrane via a flux condition and an attachment/detachment law at the membrane. We present a reduction to a simpler non-local reaction–diffusion model and perform a stability analysis and numerical simulations for this reduction. Our model in principle does support Turing instabilities but only if the lateral diffusion of inactivated GTPase is much faster than the diffusion of activated GTPase.     

Turing bifurcations with a temporally varying diffusion coefficient

This paper is concerned with the possibility of Turing bifurcations in a reaction-diffusion system in which the diffusion coefficient of one species varies periodically in time. This problem was introduced and investigated numerically by Timm and Okubo (J. Math. Biol. 30, 307, 1992) in the context of predator-prey interactions in plankton populations. Here, I consider the simple case in which the temporal variation in diffusivity has a square-tooth form, alternating between two constant values, with a period that is long compared with the time scale of the kinetics. The analysis is valid for any set of reaction kinetics. I derive explicit expressions for the Floquet multipliers that determine the stability of the steady state, and thereby obtain the conditions for diffusion driven instability to occur. These conditions imply that, depending on the kinetics, the homogeneous equilibrium may be either more or less stable than when the diffusion coefficient is a constant equal to the mean of the variable diffusivity. I go on to consider the form of the solution when diffusion driven instability does occur, and I use perturbation theory to determine the effect of a small temporal variation in the diffusion coefficient on the spatial wavelength of the pattern that results from diffusion driven instability.     

Synthesis and characterization of new beta-diketo derivatives with iron chelating ability

Here we report the synthesis, the characterization and a theoretical study on new glycosylated phenyl substituted beta-diketones; two classes of compounds are obtained according to the condensation reaction: central and side derivatives. Their iron(III) chelating ability is tested by means of UV-visible (UV-vis), potentiometric and NMR techniques. The conformation of central derivatives does not allow any metal chelation, while side derivatives bind iron(III) through the beta-dioxo moiety. The glycosyl moiety does not interact with metal ion but it helps to stabilize metal/ligand (1/3) complexes by means of hydrophylic interactions. The pK(a) of the ligands and the stability constants of their Fe(III) complexes are evaluated by means of UV-vis spectroscopy and potentiometry. A comparison with other iron-chelating agents, on the basis of lipophilicity and the pFe(III), is finally reported.     

Color vision: putting it together

Color vision depends on the visual system comparing signals that originate in different classes of cone photoreceptors. New work shows that the different classes of cones are not only distributed irregularly, but in different individuals they are present in very variable proportions. Surprisingly, this does not affect color vision.     

Physical properties of the E. coli 4.5S RNA: first results suggest a hairpin helix of unusual thermal stability.

Hyperchromicity measurements and quasi-elastic laser light scattering (QELS) have been used to assess the solution structure of the metabolically stable E. coli 4.5S RNA. Results from thermal denaturation measurements revealed the 4.5S species to be markedly more stable than most other RNAs characterized thus far. Optical Tm's range from 79 degrees to 88 degrees with transitions approximately 25 degrees C wide. The Tm values show little dependence on ionic strength, but stability is enhanced considerably by Mg+2. In the QELS experiments the diffusion coefficient does not decrease until T greater than 70 degrees C. Neither the diffusive melting nor the diffusion coefficient at infinite dilution (D0(20,w)) show dependencies on ionic strength but both are influenced by Mg+2. The diffusion behavior is in agreement with that predicted for a rigid cylindrical molecule 125 to 160 A long and 37 to 26 A in diameter. Taken together these results are consistent with the more stable hypothetical secondary structures that can be formed, in which 70-75% of the 114 bases are paired to form a single extended hairpin helix.     

On the stability of separable solutions of a sexual age-structured population dynamics model

The Sharpe-Lotka-McKendrick-von Foerster equations for non-dispersing age-sex-structured populations with a harmonic mean type mating law are considered and their separable solutions are analysed. For certain forms of the demographic rates the underlying evolution equations are reduced to systems of ODEs, the long time behavior of their solutions is studied, and the stability of separable solutions is discussed. It is found that for the constant death rates and constant sex ratio of newborns with stationary birth rates this model admits one one-parameter class of separable solutions, two such classes (repeated or different) or no such ones. In the case of special forms of age-dependent birth rates, solutions of one of these two different classes corresponding to the greater root of the characteristic equation are locally stable, solutions of the other one corresponding to the smaller root are unstable, and the population dies out if the model does not admit separable solutions or if initial densities of newborns are small enough in the case of the existence of separable solutions. In the case of constant vital rates, the model has no separable solutions or admits only one class of such ones that are globally stable.     

Diffusional constraints on energy metabolism in skeletal muscle

Aerobic metabolic flux depends on the diffusion of high-energy phosphate molecules (e.g., ATP and phosphocreatine) from the mitochondria to cellular ATPases, as well as the diffusion of other molecules (e.g., ADP, Pi) back to the mitochondria. Here, we develop an approach for evaluating the influence of intracellular metabolite diffusion on skeletal muscle aerobic metabolism through the application of the effectiveness factor (η). This parameter provides an intuitive and informative means of quantifying the extent to which diffusion limits metabolic flux. We start with the classical approach assuming an infinite supply of substrate at the fiber boundary, and we expand this model to ultimately include nonlinear boundary and homogeneous reactions. Comparison of the model with experimental data from a wide range of skeletal muscle types reveals that most muscle fibers are not substantially limited by diffusion (η close to unity), but many are on the brink of rather substantial diffusion limitation. This implies that intracellular metabolite diffusion does not dramatically limit aerobic metabolic flux in most fibers, but it likely plays a role in limiting the evolution of muscle fiber design and function.     

Diffusion in Pseudomonas aeruginosa biofilms: a pulsed field gradient NMR study

A Pseudomonas aeruginosa biofilm is studied with pulsed field gradient echo nuclear magnetic resonance. Although not all spectral components are assigned yet, the experimental results show that a biofilm consists of components with very different diffusion coefficients. The various biofilm components that give motionally narrowed 1H NMR signals, can be grouped into five classes with diffusion coefficients, ranging from 2 x 10(-9) to 1 x 10(-13) m2 s-1. Investigation of the diffusion behavior of water in the biofilm shows three fractions with different diffusion coefficients. Besides the highly mobile bulk water at least two other fractions with much lower diffusion coefficients are detected. It is shown that one of the fractions with the low diffusion coefficient probably arises from intracellular water. Also for another component of the biofilm, glycerol, three fractions with diffusion coefficients that differ more than a factor ten are detected. Also a group of signals exists which result from practically immobile components.