A Stochastic Phylogenetic Algorithm for Mitochondrial DNA Analysis.

This paper presents an exploratory analysis of the mitochondrial DNA (mtDNA) of 32 species in the subphylum Vertebrata, divided in 7 taxonomic classes. Multiple stochastic parameters, such as the Hurst and detrended fluctuation analysis (DFA) exponents, Shannon entropy, and Chargaff ratio are computed for each DNA sequence. The biological interpretation of these parameters leads to defining a triplet of novel indices. These new functions incorporate the long-range correlations, the probability of occurrence of nucleic bases, and the ratio of pyrimidines-to-purines. Results suggest that relevant regions in mtDNA can be located using the proposed indices. Furthermore, early results from clustering algorithms indicate that the indices introduced might be useful in phylogenetic studies.

Structural thermodynamics of lamellar cationic lipid-DNA complex: DNA compressibility modulus.

We have studied theoretically the compressibility modulus B of DNA and complexation adsorption isotherms of DNA and lipids, as a function of DNA spacing d(DNA) and NaCl electrolyte concentration, respectively, in isoelectric states of lamellar DNA/cationic lipid (CL) self-assemblies. The electrostatic free energy derived from the Poisson-Boltzmann theory predicts partial agreement with measured B values for interhelical separations d(DNA)>33 A when use is made of a fit of hydration repulsion from bulk DNA hexagonal phases in solution. For lower interchain separations the prediction worsens due to the hydration interaction that overcomes the electrostatic contribution. An exact match of the system's counterion electrochemical potentials and the coions of salt in aqueous phase leads to the electrostatic part of the free energy that renders isotherms of d(DNA) versus ionic strength in qualitative consistency with general trends of available experimental data of CL-DNA complexes.

Phase evolution of lamellar cationic lipid-DNA complex: steric effect of an electrolyte.

The complexation isotherms of DNA plus lipids of a symmetric lamellar cationic lipid-DNA system were determined within a mean field free energy. The free energy incorporates the ion's finite size of NaCl simple electrolyte in solution and makes use of known structure data on this complex. The results for the predicted isotherms are in qualitative agreement with the trends of the experimental data for this property.

Uptake and clearance of PCB congeners in Chamaelea gallina: response of oxidative stress biomarkers.

PCB uptake and clearance by clams, Chamaelea gallina, were studied in specially designed flow-through channels. After 8 weeks exposure to 10 ppb Aroclor 1254 in water, clams were depurated for 10 weeks, in the same exposure channel or after transfer to clean systems. Accumulation of the 20 congeners studied depended on its initial abundance and physicochemical properties. A linear relationship was found between log bioconcentration factor and log octanol/water partition coefficient of each form. Clearance of each PCB depended also on its initial load and solubility, being faster in clams transferred to clean systems. Exposure significantly enhanced catalase and 6-P-gluconate dehydrogenase activities, but not other antioxidative enzymes. Superoxide dismutase, low during the exposure phase, increased seven-fold during depuration. Aroclor-treated clams had higher GSH levels than controls, but decreased to 15-35% after 2 days clearance, rose to 150% after 12 days, and declined to low levels by the end of the experience. Biotransformation of PCBs to quinones and redox cycling-promoted oxidative stress might explain the increased antioxidative defenses. The biochemical changes observed at the beginning of clearance could be attributed to clam handling, by adaptation to and recovery from hypoxic/anoxic stress.

Electrostatic correlation force of discretely charged membranes.

The total force between two like charged surfaces is investigated as a function of counterion concentration in aqueous solution and surfaces distance of separation. A smooth and a discrete density of surface charge sigma(s) lead to differences in the force distance curve at high sigma(s), which are negligible for low surface charge. The total force per unit area with divalent counterions is an oscillating function of sigma(s). At fixed surfaces separation and region of attraction (increasing sigma(s)), there is a variation in its strength that results from a competition between the ideal kinetic and ion-ion correlation force components as predicted from the anisotropic hypernetted chain approximation.