Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Background  

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence.     

Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size

The distributions of allele sizes at eight simple-sequence repeat (SSR) or microsatellite loci in chimpanzees are found and compared with the distributions previously obtained from several human populations. At several loci, the differences in average allele size between chimpanzees and humans are sufficiently small that there might be a constraint on the evolution of average allele size. Furthermore, a model that allows for a bias in the mutation process shows that for some loci a weak bias can account for the observations. Several alleles at one of the loci (Mfd 59) were sequenced. Differences between alleles of different lengths were found to be more complex than previously assumed. An 8-base-pair deletion was present in the nonvariable region of the chimpanzee locus. This locus contains a previously unrecognized repeated region, which is imperfect in humans and perfect in chimpanzees. The apparently greater opportunity for mutation conferred by the two perfect repeat regions in chimpanzees is reflected in the higher variance in repeat number at Mfd 59 in chimpanzees than in humans. These data indicate that interspecific differences in allele length are not always attributable to simple changes in the number of repeats.      

Aggregation and emergence in hierarchically organized systems: population dynamics

The aim of this work is to present aggregation methods of hierarchically organized systems allowing one to replace the initial micro-system by a macro-system described by a few global variables. We also study the relations between the fast micro-dynamics and the slow macro-dynamics which can produce global properties. Emergence corresponds to a bottom-up coupling that is the result effected by a micro-level at a macro-level. As an example, we present prey-predator models with different time scales in an heterogeneous environment. A fast time scale is associated to the migration process on spatial patches and a slow time scale is associated to growth and interactions between the populations. Preys must go on spatial patches where resources are located and where predators can attack them. The efficiency of the predators to catch preys is patch dependent. Perturbation methods allow us to aggregate the initial system of differential equations for the patch sub-populations into a macro-system of two differential equations governing the total population densities. We study the case of density independent and density dependent migrations. In the latter case, we show that different functional responses can emerge in the macro prey-predator model as a result of the coupling between the slow and fast systems.     

A kinetic inhibition mechanism for maintenance

To fulfil their maintenance costs, most species use mobile pools of metabolites (reserve) in favourable conditions, but can also use less mobile pools (structure) under food-limiting conditions. While some empirical models always pay maintenance costs from structure, the presence of reserve inhibits the use of structure for maintenance purposes. The standard dynamic energy budgets (DEB) model captures this by simply supplementing all costs that could not be paid from reserve with structure. This is less realistic at the biochemical level, and involves a sudden use of structure that can complicate the analysis of the model properties. We here propose a new inhibition formulation for the preferential use of reserve above structure in maintenance that avoids sudden changes in the metabolites use. It is based on the application of the theory for synthesizing units, which can easily become rather complex for demand processes, such as the maintenance. We found, however, a simple explicit expression for the use of reserve and structure for maintenance purposes and compared the numerical behaviour with that of a classical model in oscillating conditions, by using parameters values from a fit of the models to data on yeasts in a batch culture. We conclude that our model can better handle variable environments. This new inhibition formulation has a wide applicability in modelling metabolic processes.     

Effect of predator density dependent dispersal of prey on stability of a predator-prey system

This work presents a predator-prey Lotka-Volterra model in a two patch environment. The model is a set of four ordinary differential equations that govern the prey and predator population densities on each patch. Predators disperse with constant migration rates, while prey dispersal is predator density-dependent. When the predator density is large, the dispersal of prey is more likely to occur. We assume that prey and predator dispersal is faster than the local predator-prey interaction on each patch. Thus, we take advantage of two time scales in order to reduce the complete model to a system of two equations governing the total prey and predator densities. The stability analysis of the aggregated model shows that a unique strictly positive equilibrium exists. This equilibrium may be stable or unstable. A Hopf bifurcation may occur, leading the equilibrium to be a centre. If the two patches are similar, the predator density dependent dispersal of prey has a stabilizing effect on the predator-prey system.     

Structure and organization of the bovine beta-globin genes

Genomic clones spanning the entire cow beta-globin gene locus have been isolated and characterized. These clones demonstrate that the linkage of embryonic-like (epsilon) genes and pseudogenes (psi) to the previously described fetal (gamma) and adult (beta) genes is as follows: 5'-epsilon 3-epsilon 4-psi 3-beta-epsilon 1-epsilon 2-psi 1- psi 2-gamma-3'. Present data indicate that, like that of the goat, the fetal and adult genes arose via block duplication of an ancestral four- gene set: epsilon-epsilon-psi-beta. This duplication event preceded the divergence of cows and goats, which occurred greater than or equal to 18-20 Myr ago. However, cows do not have the additional four-gene block containing a preadult/stress globin gene (beta C). Furthermore, the cow fetal cluster contains an extra beta-like pseudogene, which apparently arose by a small-scale duplication. The fixation of this duplication may indicate a possible evolutionary role for pseudogenes.