Parameter estimation for the distribution of single cell lag times

In Quantitative Microbial Risk Assessment, it is vital to understand how lag times of individual cells are distributed over a bacterial population. Such identified distributions can be used to predict the time by which, in a growth-supporting environment, a few pathogenic cells can multiply to a poisoning concentration level.We model the lag time of a single cell, inoculated into a new environment, by the delay of the growth function characterizing the generated subpopulation. We introduce an easy-to-implement procedure, based on the method of moments, to estimate the parameters of the distribution of single cell lag times. The advantage of the method is especially apparent for cases where the initial number of cells is small and random, and the culture is detectable only in the exponential growth phase.     

Comparing Stochastically Restricted Linear Estimators in a Regression Model

Conditions for superiority of the minimum dispersion estimator over another with respect to the covariance matrix are derived when the vector parameter of a regression model is subject to competing stochastic restrictions. The restrictions may also consist both of a deterministic part and a stochastic part.     

Population dynamics of two small pelagic fish in the central-south area off Chile: delayed density-dependence and biological interaction

It is widely believed that environmental variability is the main cause for fluctuations in commercially exploited small pelagic fish populations around the world. Nevertheless, density-dependent factors also can drive population dynamics. In this paper, we analyzed thirteen years of a relative abundance index of two clupeoids fish populations coexisting in the central-south area off Chile, namely the common sardine, Strangomera bentincki, and anchovy, Engraulis ringens. We applied the classical diagnostic tools of time series analysis to the observed time-series. Also, the realized per capita population growth rate was studied with the aim of detecting the feedback structure that is characterizing the population dynamics of the two species. The analysis suggests that population fluctuations of the two species have an important density-dependent component, displaying first-order (direct density-dependent) and second-order (delayed density-dependent) simultaneously. The density-dependent component explained 70.5 and 55.6 % of the realized per capita population growth rate of common sardine and anchovy, respectively. The deterministic skeleton model showed an asymptotic convergence to equilibrium density. In presence of a stochastic environment, fluctuations were reproduced for the species showing a component of fluctuation with a period of 4 year. The intrinsic dynamics of each species is typical of interacting species resulting from trophic interactions. It is postulated that the second-order dynamics of S. bentincki and E. ringens in central-south Chile, may be the result from interactions with a specialist predator (the fishing fleet), interacting with exogenous environmental factors.     

A stochastic model for the membrane potential of a stimulated neuron

We present a simple model describing the transition between the prefiring, firing and postfiring phases of a single neuron in a large neural net. Using typical values for the physiological parameters that enter the model, we find average interspike times that are close to those reported in experimental measurements.     

Convergence to stationary distributions in two-species stochastic competition models

Two sets of sufficient conditions are given for convergence to stationary distributions, for some general models of two species competing in a randomly varying environment. The models are nonlinear stochastic difference equations which define Markov chains. One set of sufficient conditions involves strong continuity and -irreducibility of the transition probability for the chain. The second set has a much weaker irreducibility condition, but is only applicable to monotonic models. The results are applied to a stochastic two-species Ricker model, and to Chesson's lottery model with vacant space, to illustrate how the assumptions can be checked in specific models.     

Structural adaptations of the femur and humerus to arboreal and terrestrial environments in three species of macaque

One reason to measure cross-sectional structural properties of primate long bones is to define mechanically relevant complexes of traits that describe the adaptation of bone to different biomechanical environments. This can be effectively accomplished when congeneric species having different postural and locomotor behaviors are compared. This paper compares the cross-sectional geometry of the femur and humerus in three behaviorally different macaque species as a basis for defining such patterns. Cross-sectional moments of inertia in the standard anatomical planes were calculated at five locations along the diaphyses of the femur and humerus in Macaca fascicularis, M. nemestrina, and M. mulatta. The data suggest that the "barrel-shaped" femur is associated with behaviors for which long limbs and small body size are an asset. This may be associated with, but is not restricted to, leaping behaviors. The data also suggest that structural rigidity of the femur and humerus is greater per unit body weight in primates that spend significant amounts of time in terrestrial environments than in those that are more restricted to climbing in arboreal environments.     

X-ray and model-building studies on the specificity of the active site of proteinase K

Proteinase K, the extracellular serine endopeptidase (E.C. 3.4.21.14) from the fungus Tritirachium album limber, is homologous to the bacterial subtilisin proteases. The binding geometry of the synthetic inhibitor carbobenzoxy-Ala-Phechloromethyl Ketone to the active site of proteinase K was the first determined from a Fourier synthesis based on synchrotron X-ray diffraction data between 1.8 Å and 5.0 Å resolution. The protein inhibitor complexes was refined by restrained least-squares minimization with the data between 10.0 and 1.8 Å. The final R factor was 19.1% and the model contained 2,018 protein atoms, 28 inhibitors atoms, 125 water molecules, and two Ca²⁺ ions. The peptides portion of the inhibitor is bound to the active center of proteinase K by means of a three-stranded antiparallel pleated sheet, with the side chain of the phenylalanine located in the P1 site. Model building studies, with lysine replacing phenylalanine in the inhibitor, explain the relatively unspecific catalytic activity of the enzyme.     

Stochastic simulation of clonal growth in the tall goldenrod,Solidago altissima

Summary As clonal plants grow they move through space. The movement patterns that result can be complex and difficult to interpret without the aid of models. We developed a stochastic simulation model of clonal growth in the tall goldenrod, Solidago altissima. Our model was calibrated with field data on the clonal expansion of both seedlings and established clones, and model assumptions were verified by statistical analyses.When simulations were based on empirical distributions with long rhizome lengths, there was greater dispersal, less leaf overlap, and less spatial aggregation than when simulations were based on distributions with comparatively short rhizome lengths. For the field data that we utilized, variation in rhizome lengths had a greater effect than variation for either branching angles or rhizome initiation points (see text). We also found that observed patterns of clonal growth in S. altissima did not cause the formation of fairy rings. However, simulations with an artificial distribution of branching angles demonstrate that fairy rings can result solely from a plant's clonal morphology.Stochastic simulation models that incorporated variation in rhizome lengths, branching angles, and rhizome initiation points produced greater dispersal and less leaf overlap than deterministic models. Thus, variation for clonal growth parameters may increase the efficiency of substrate exploration by increasing the area covered and by decreasing the potential for intraclonal competition. We also demonstrated that ramet displacements were slightly, but consistently lower in stochastic simulation models than in random-walk models. This difference was due to the incorporation of details on rhizome bud initiation into stochastic simulation models, but not random-walk models. We discuss the advantages and disadvantages of deterministic, stochastic simulation, and random-walk models of clonal growth.     

A method for determining overall protein fold from NMR distance restraints

Summary We describe a simple method for determining the overall fold of a polypeptide chain from NOE-derived distance restraints. The method uses a reduced representation consisting of two particles per residue, and a force field containing pseudo-bond and pseudo-angle terms, an electrostatic term, but no van der Waals or hard shell repulsive terms. The method is fast and robust, requiring relatively few distance restraints to approximate the correct fold, and the correct mirror image is readily determined. The method is easily implemented using commercially available molecular modeling software.     

Prospective theoretical and experimental study towards electrochemically grafted poly(N-vinyl-2-pyrrolidone) films on metallic surfaces

Quantum chemistry calculations of equilibrium geometry, atomic charges, dipole moment, and frontier orbital energies are carried out on model N-vinyl-2-pyrrolidone, its radical anion and cation, and three protonated derivatives. Attempts to obtain poly(N-vinyl-2-pyrrolidone) films grafted on nickel and platinum electrodes, respectively by cathodic and anodic polarizations, are reported. A thin, covering and insulating film is obtained on the Pt anode, as indicated by surface characterizations carried out with UPS and IRRAS spectroscopies. The fact that the film remains adherent to the metallic surface in spite of a permanent contact with an acetonitrile solution in which poly(N-vinyl-2-pyrrolidone) is soluble suggests that chemisorption has indeed been achieved.