The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias

Genes sequences from Escherichia coli, Salmonella typhimurium, and other members of the Enterobacteriaceae show a negative correlation between the degree of synonymous-codon usage bias and the rate of nucleotide substitution at synonymous sites. In particular, very highly expressed genes have very biased codon usage and accumulate synonymous substitutions very slowly. In contrast, there is little correlation between the degree of codon bias and the rate of protein evolution. It is concluded that both the rate of synonymous substitution and the degree of codon usage bias largely reflect the intensity of selection at the translational level. Because of the high variability among genes in rates of synonymous substitution, separate molecular clocks of synonymous substitution might be required for different genes.      

The mode of action of Vibrio cholerae cytolysin. The influences on both erythrocytes and planar lipid bilayers.

The interaction with erythrocytes of cholera cytolysin (CC) obtained from a non-01 Vibrio cholerae strain results in the osmotic rupture of target cells upon formation by CC of the waterfilled pores in their membranes. The aggregation of several toxin monomers is required for the formation of one CC channel with a radius of 0.9-1.0 nm. The investigations using planar bilayer lipid membranes suggest that the CC-induced pore is an interprotein anion selective channel carrying a fixed positive charge. The role of the charge was supported by the influence of pH on the selectivity, single conductance and voltage gating of the CC channels. The ability of the CC to modify both model and natural membranes has a maximum at pH 6.0-7.0. It was found that CC channels insert into the membrane asymmetrically. The effect of proteolytic treatment of the channel by papain also indicates that the two entrances of the channel protrude from the plane of the membrane into the solution for different distances. It is proposed that the biological effects of the non-01 V. cholera cytolysin are based on its channel-forming activity.     

Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes

Restriction enzymes produced by bacteria serve as a defense against invading bacteriophages, and so phages without other protection would be expected to undergo selection to eliminate recognition sites for these enzymes from their genomes. The observed frequencies of all restriction sites in the genomes of all completely sequenced DNA phages (T7, lambda, phi X174, G4, M13, f1, fd, and IKe) have been compared to expected frequencies derived from trinucleotide frequencies. Attention was focused on 6-base palindromes since they comprise the typical recognition sites for type II restriction enzymes. All of these coliphages, with the exception of lambda and G4, exhibit significant avoidance of the particular sequences that are enterobacterial restriction sites. As expected, the sequenced fraction of the genome of phi 29, a Bacillus subtilis phage, lacks Bacillus restriction sites. By contrast, the RNA phage MS2, several viruses that infect eukaryotes (EBV, adenovirus, papilloma, and SV40), and three mitochondrial genomes (human, mouse, and cow) were found not to lack restriction sites. Because the particular palindromes avoided correspond closely with the recognition sites for host enzymes and because other viruses and small genomes do not show this avoidance, it is concluded that the effect indeed results from natural selection.      

Increased variation in sex organ positions can increase reciprocity and pollination success in heterostylous plant populations

The reciprocal position of sexual organs in complementary floral morphs is central to our understanding of heterostyly. Reciprocity indices are used to quantify the spatial match between complementary sex organs, but previous indices fail to appropriately account for intra-population variation in sex organ positions. In this study, we examine how an increase in intra-population variation in sex organ heights affects reciprocity and consequently reproductive success. We formulated a reciprocity index that incorporates this variation and asked if estimates of reciprocity can predict reproductive success in naturally occurring heterostylous populations. We developed a reciprocity index that assumed pollen transfer success equalled one for a perfectly matched stigma–anther pair, and decreased to zero with increasing mismatch. We examined the relationship between intra-population variation in organ position and reciprocity, compared previously proposed indices using simulated populations and empirical data from natural populations, and tested the ability of the indices to predict reproductive success. We observed that when differences between mean complementary sex-organ heights are small, increasing intra-population variation in heights resulted in a decrease in reciprocity. However, when this difference is larger, reciprocity increased, reached a peak, and then decreased with increasing variation. Previous indices failed to capture this behavior. Seed set was positively related to reciprocity for our index. These results challenge the current understanding that increasing variation in sex-organ heights will always decrease reciprocity in heterostylous populations. This may help explain why heterostylous systems exhibit and tolerate high amounts of intra-population variation in sex organ heights.     

Theory of intermolecular electron transfer in nanoscale biological structures

Macromolecular biological systems performing directed electron transfer are nano-sized structures. The distance between carrier molecules (cofactors), which represent practically isolated electron localization centers, reaches tens of angstroms. The electron transfer theory based on the concept of delocalized electron states, which is conventionally used in biophysics, is unable to adequately interpret the results of concrete observations in many cases. On the basis of the theory of electronic transitions in the case of localized states, developed in the physics of disordered matter, a mechanism of long-distance electron transfer in biological systems is suggested. The molecular relaxation of the microenvironment of electron localization centers that accompanies the electron transfer process is also considered.     

Efficiency of the Human Visual System in Recognition of Moving Objects

The relationships studied between the efficiency of the human visual system for recognition of moving objects in the presence of dynamic additive quasi-white Gaussian noise and the duration of object presentation are studied. Different conditions of observation and the parameters of moving objects were analyzed. The efficiency-presentation duration relationship was shown to be a function with two extrema (a minimum and a maximum, at 120 and 400 ms, respectively). The study offers an interpretation of the findings and a functional model to explain this phenomenon.     

On the influence of local molecular environment on the redox potential of electron transfer cofactors in bacterial photosynthetic reaction centers

The addition of cryosolvents (glycerol, dimethylsulfoxide) to a water solution containing bacterial photosynthetic reaction centers changes the redox potential of the bacteriochlorophyll dimer but does not affect the redox potential of the quinone primary acceptor. It is shown that the change in redox potential can be due to variation of the electrostatic interactions between cofactors and the local molecular environment, which is modified by solvent additives. The degree of influence of a solvent on the redox potential of various cofactors is determined by their solvent accessibility, i.e. on their arrangement in the structure of reaction centers.