An efficient method for calculation of dynamic logarithmic gains in biochemical systems theory

Biochemical systems theory (BST) characterizes a given biochemical system based on the logarithmic gains, rate-constant sensitivities and kinetic-order sensitivities defined at a steady state. This paper describes an efficient method for calculation of the time courses of logarithmic gains, i.e. dynamic logarithmic gains L(Xi, Xj; t), which expresses the percentage change in the value of a dependent variable Xi at a time t in response to an infinitesimal percentage change in the value of an independent variable Xj at t=0. In this method, one first recasts the ordinary differential equations for the dependent variables into an exact canonical nonlinear representation (GMA system) through appropriate transformations of variables. Owing to the structured mathematical form of this representation, the recast system can be fully described by a set of numeric parameters, and the differential equations for the dynamic logarithmic gains can be set up automatically without resource to computer algebra. A simple general-purpose computer program can thus be written that requires only the relevant numeric parameters as input to calculate the time courses of the variables and of the dynamic logarithmic gains for both concentrations and fluxes. Unlike other methods, the proposed method does not require to derive any expression for the partial differentiation of flux expressions with respect to each independent variable. The proposed method has been applied to two kinds of reaction models to elucidate its usefulness.     

A new method for choosing the computational cell in stochastic reaction–diffusion systems

How to choose the computational compartment or cell size for the stochastic simulation of a reaction–diffusion system is still an open problem, and a number of criteria have been suggested. A generalized measure of the noise for finite-dimensional systems based on the largest eigenvalue of the covariance matrix of the number of molecules of all species has been suggested as a measure of the overall fluctuations in a multivariate system, and we apply it here to a discretized reaction–diffusion system. We show that for a broad class of first-order reaction networks this measure converges to the square root of the reciprocal of the smallest mean species number in a compartment at the steady state. We show that a suitably re-normalized measure stabilizes as the volume of a cell approaches zero, which leads to a criterion for the maximum volume of the compartments in a computational grid. We then derive a new criterion based on the sensitivity of the entire network, not just of the fastest step, that predicts a grid size that assures that the concentrations of all species converge to a spatially-uniform solution. This criterion applies for all orders of reactions and for reaction rate functions derived from singular perturbation or other reduction methods, and encompasses both diffusing and non-diffusing species. We show that this predicts the maximal allowable volume found in a linear problem, and we illustrate our results with an example motivated by anterior-posterior pattern formation in Drosophila, and with several other examples.     

An efficient protein complex purification method for functional proteomics in higher eukaryotes

The ensemble of expressed proteins in a given cell is organized in multiprotein complexes. The identification of the individual components of these complexes is essential for their functional characterization. The introduction of the 'tandem affinity purification' (TAP) methodology substantially improved the purification and systematic genome-wide characterization of protein complexes in yeast. The use of this approach in higher eukaryotic cells has lagged behind its use in yeast because the tagged proteins are normally expressed in the presence of the untagged endogenous version, which may compete for incorporation into multiprotein complexes. Here we describe a strategy in which the TAP approach is combined with double-stranded RNA interference (RNAi) to avoid competition from corresponding endogenous proteins while isolating and characterizing protein complexes from higher eukaryotic cells. This strategy allows the determination of the functionality of the tagged protein and increases the specificity and the efficiency of the purification.     

A lipophilic complex with 186Re188Re incorporated in liposomes suitable for radiotherapy

Liposomes with a 70 nm diameter were made by the detergent removal technique on a gel filtration column. The complex oxodichloroethoxy-bis-(triphenylphosphine)rhenium(V) = (Rephos) was irradiated by neutrons in the reactor at PSI. 45 ± 5% of the radioactive complex was incorporated into the bilayer of the liposomes during the liposome formation. The stability of these radioactive liposomes was tested by dialysis: a loss of 40% of the radioactivity identified as perrhenate was observed after 8 days. Addition of the antioxidant ascorbic acid diminished the loss to 20%. Such liposomes carrying the lipophilic radioactive Re-complex can potentially be used in β-radiotherapy. The γ-lines of the two rhenium isotopes are helpful for localizing them in therapy controls by a γ-camera, a big advantage compared to other nuclides proposed for therapy (e.g. ⁹⁰Yttrium).     

Saccharides as efficacious solubilisers for highly lipophilic compounds in aqueous media

The bioavailability of lipophilic substrates is critical for biotransformations with isolated enzymes as well as with whole cells. With the example of a series of lipophilic ketones the suitability of saccharides as potent solubilisers for highly lipophilic substrates was demonstrated. Best results were obtained for d-glucose, which increased substrate solubility up to 50 times. In whole-cell biocatalysis the sugar acts both as solubiliser and as carbon source for which reason this procedure does not impair cell physiology and is unique in being environmentally benign. The capability of saccharides to solubilise lipophilic compounds in aqueous media sources from their ability to form hydrophilic and lipophilic domains at hydrophobic interfaces, thus forming cyclodextrin-like structures around the lipophilic substrate.     

The solution structure of a lasalocid A metal complex in lipophilic solvents

Lasalocid A (LasNa), a common antibiotic in veterinary medicine, is a polyetheral ionophore, disrupting cation equilibria through the cell wall. By means of circular dichroism (in the UV and in the near-IR), paramagnetic NMR, and with the aid of the program PERSEUS, we determined the solution geometry of the 1:1 Las-Yb3+ complex in CD3CN and CDCl3, following a protocol similar to the one successfully used for the anthracycline-metal adduct. The resulting structure is in full agreement with the expectation of the ligand wrapping around the cation in a horseshoe shape. The oxygen atoms participate in the coordination either through a direct, first sphere, or a longer range interaction.     

A rapid and efficient PCR-based mutagenesis method applicable to cell physiology study

PCR-based mutagenesis is a cornerstone of molecular biology and protein engineering studies. Herein we describe a rapid and highly efficient mutagenesis method using type IIs restriction enzymes. A template gene is amplified into two separate PCR fragments using two pairs of anchor and mutagenic primers. Mutated sequences are located near the recognition site of a type IIs restriction enzyme. After digestion of two fragments with a type IIs enzyme, exposed cohesive ends that are complementary to each other are then ligated together to generate a mutated gene. We applied this method to introduce multiple site-directed mutations in EGFP and Bcl-2 family genes and observed perfect mutagenesis efficiency at the desired sites. This efficient and cost-effective mutagenesis method can be applied to a wide variety of structural and functional studies in cell physiology. Type IIs restriction enzyme; enhanced green fluorescent protein; Bcl-2     

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.     

A diffusion model and optimal cell loading for immobilized cell biocatalysts

A diffusion model based on the random pore model is derived for immobilized cell biocatalysts and verified with 19 sets of experimental diffusion data. The predicted effective diffusivity relative to that for the support matrix reflects a quadratic dependence on the cell loading and contains a single parameter that depends on the intracellular diffusivity and the chemical partitioning coefficient. The model is used to predict optimal cell loadings that maximize the total reaction rate in an immobilized cell biocatalyst. A rule of thumb based on the diffusion model is obtained to the effect that the cell loading should be at least (1/3) for single reactions regardless of the kinetics and diffusional resistances. A means of calculating improved lower bounds is provided for cases where the cellular diffusional resistance is known but the kinetics are not. The optimal cell loadings for reversible first-order and for Michaelis-Menten kinetics are presented and demonstrated to be within the range of conditions of practical interest.     

The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem

A new approach to the long-standing local minimum problem of molecular energy minimization is proposed. The approach relies upon a field of computer mathematics known as combinatorial optimization, together with methods of conformational analysis derived from distance geometry. The advantages over the usual numerical techniques of optimization are, first, that the algorithms derived are globally convergent, and second, that the mathematical problems involved are well-posed and suitable for study within the modern theory of computational complexity. In this paper we introduce the approach, and describe a computer program based on it.     

Ethanol injection method for hydrophilic and lipophilic drug-loaded liposome preparation

In this article, a hydrophobic (beclomethasone dipropionate; BDP) and a hydrophilic (cytarabine; Ara-C) drugs have been encapsulated in liposomes in order to be administered via the pulmonary route. For this aim, a liposome preparation method, which is easy to scale up, the ethanol injection method, has been selected. The effects of critical process and formulation parameters have been investigated. The drug-loaded liposomes were prepared and characterized in terms of size, zeta potential, encapsulation efficiency, release study, cell uptake, and aerodynamic behavior. Small multilamellar vesicles, with sizes ranging from about 80 to 170?nm, were successfully obtained. Results indicated a significant influence of phospholipid and cholesterol amounts on liposome size and encapsulation efficiency. The higher encapsulation efficiencies were about 100% for the hydrophobic drug (BDP) and about 16% for the hydrophilic one (Ara-C). The in vitro release study showed a prolonged release profile for BDP, in contrast with Ara-C, which was released more rapidly. The cell-uptake test revealed that fluorescent liposomes have been well internalized into the cytoplasm of SW-1573 human lung carcinoma cells, confirming the possibility to use liposomes for lung cell targeting. Nebulized Ara-C and BDP liposomes presented aerodynamic diameters compatible with deep lung deposition. In conclusion, the elaborated liposomes seem to be promising carriers for both Ara-C and BDP pulmonary delivery.     

A simple and efficient method for raising steroid antibodies in rabbits

The production of estradiol antibodies by two immunization procedures was monitored by means of an enzyme-immunoassay. Procedure A consisted of three intramuscular injections given at two-week intervals, followed by five intravenous booster injections and procedure B consisted of multiple intradermal injections given once. Procedure A gave much higher antibody titer. In both procedures the sensitivities of assays using the antisera increased initially and reached a plateau after three to four months of immunization. Consistent changes in specificities were observed. A shortened procedure A is proposed as a simple and efficient procedure for raising steroid antibodies in rabbits.     

Use of lipophilic anions for estimation of biomass and cell viability

A method is described to estimate the microbial biomass of a sample, to enumerate the cells, and to distinguish the portion of metabolically active cells in the population by measuring the binding of phenyldicarbaundecaborane (PCB(-)) to the cells. This method can also be used for the analysis of a complex population of microorganisms if the cells composing the sample are sensitive to different biocidal agents. In addition, the analysis of PCB(-) binding is useful for the enumeration of the phage-infected cells and phage particles.