Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences.

The chaos game representation (CGR) is a scatter plot derived from a DNA sequence, with each point of the plot corresponding to one base of the sequence. If the DNA sequence were a random collection of bases, the CGR would be a uniformly filled square; conversely, any patterns visible in the CGR represent some pattern (information) in the DNA sequence. In this paper, patterns previously observed in a variety of DNA sequences are explained solely in terms of nucleotide, dinucleotide and trinucleotide frequencies.     

Nitrogen and phosphorus dynamics and retention in ecotones of Lake Titicaca,Bolivia/Peru

We are studying present conditions and consequences of material movement from land to water in the Lake Titicaca basin, and how fluxes are affected by human activities. The principal objective of this research is to describe and explain the variability in the Andean Altiplano of (a) water, nutrient and sediment fluxes from land and (b) composition, nutrient limitation and other important features of nearshore lake communities, and compare the effects of different agricultural practices (especially traditional and modern) on these factors. We are focusing on a comparison of the impacts of two forms of agriculture in this region: ancient raised fields currently under rehabilitation, and flat pastures and fields, which are more common. Results of the first year of study indicate there is substantial variability in nitrogen and phosphorus dynamics in relation to ecotone complexity (simple vs. intermediate vs. complex). Raised field sites have the beneficial effect of reducing high available nutrient concentrations (nitrate and soluble reactive phosphorus) and sediment load (measured as turbidity) as the water passes through them enroute to the lake. Aquatic vegetation (algae and macrophytes) reflect well ambient total nitrogen and phosphorus concentrations. Experimental nutrient limitation bioassays indicate that nitrogen is the most important limiting nutrient, though there is important spatial variability within the landscape, and phosphorus as well as nitrogen can be limiting.     

Statistical tests of models of DNA substitution

Summary Penny et al. have written that The most fundamental criterion for a scientific method is that the data must, in principle, be able to reject the model. Hardly any [phylogenetic] tree-reconstruction methods meet this simple requirement. The ability to reject models is of such great importance because the results of all phylogenetic analyses depend on their underlying models—to have confidence in the inferences, it is necessary to have confidence in the models. In this paper, a test statistics suggested by Cox is employed to test the adequacy of some statistical models of DNA sequence evolution used in the phylogenetic inference method introduced by Felsentein. Monte Carlo simulations are used to assess significance levels. The resulting statistical tests provide an objective and very general assessment of all the components of a DNA substitution model; more specific versions of the test are devised to test individual components of a model. In all cases, the new analyses have the additional advantage that values of phylogenetic parameters do not have to be assumed in order to perform the tests.     

Association between heart rate variability and training response in sedentary middle-aged men

The effect of exercise training on heart rate variability (HRV) and improvements in peak oxygen consumption ( _peak) was examined in sedentary middle-aged men. The HRV and absolute and relative _peak of training (n = 19) and control (n = 15) subjects were assessed before and after a 24-session moderate intensity exercise training programme. Results indicated that with exercise training there was a significantly increased absolute and relative _peak (P < 0.005) for the training group (12% and 11% respectively) with no increase for the control group. The training group also displayed a significant reduction in resting heart rate; however, HRV remained unchanged. The trained subjects were further categorized into high (n = 5) and low (n = 5) HRV groups and changes in _peak were compared. Improvements in both absolute and relative _peak were significantly greater (P > 0.005) in the high HRV group (17% and 20% respectively) compared to the low HRV group (6% and 1% respectively). The groups did not differ in mean age, pretraining oxygen consumption, or resting heart rate. These results would seem to suggest that a short aerobic training programme does not alter HRV in middle-aged men. Individual differences in HRV, however, may be associated with _peak response to aerobic training.     

Compatibility of Phloxine B, an Insecticidal Photoactive Dye, with Selected Biocontrol Fungi

The incorporation of the photoactive red food dye, phloxine B, into integrated pest management strategies has been suggested for the control of various insect pests. Inclusion of such a chemical pest control agent may interfere with a microbial pest control agent. Thus, representative fungi with potential for biocontrol were tested for their responses to phloxine B (0.01%) at different temperatures. Growth rates at selected temperatures were inhibited by dye in the presence of light for Coniothyrium minitans and Verticillium lecanii. Trichoderma virens growth was inhibited in light and dark. At optimal growth temperatures, Beauveria bassiana growth was inhibited only by the photoactivated dye species, while growth of Stilbella erythrocephala was not affected by the dye even in the presence of light.     

Domain structure analysis of elongation factor-3 from Saccharomyces cerevisiae by limited proteolysis and differential scanning calorimetry.

Elongation-factor-3 (EF-3) is an essential factor of the fungal protein synthesis machinery. In this communication the structure of EF-3 from Saccharomyces cerevisiae is characterized by differential scanning calorimetry (DSC), ultracentrifugation, and limited tryptic digestion. DSC shows a major transition at a relatively low temperature of 39 degrees C, and a minor transition at 58 degrees C. Ultracentrifugation shows that EF-3 is a monomer; thus, these transitions could not reflect the unfolding or dissociation of a multimeric structure. EF-3 forms small aggregates, however, when incubated at room temperature for an extended period of time. Limited proteolysis of EF-3 with trypsin produced the first cleavage at the N-side of Gln775, generating a 90-kDa N-terminal fragment and a 33-kDa C-terminal fragment. The N-terminal fragment slowly undergoes further digestion generating two major bands, one at approximately 75 kDa and the other at approximately 55 kDa. The latter was unusually resistant to further tryptic digestion. The 33-kDa C-terminal fragment was highly sensitive to tryptic digestion. A 30-min tryptic digest showed that the N-terminal 60% of EF-3 was relatively inaccessible to trypsin, whereas the C-terminal 40% was readily digested. These results suggest a tight structure of the N-terminus, which may give rise to the 58 degrees C transition, and a loose structure of the C-terminus, giving rise to the 39 degrees C transition. Three potentially functional domains of the protein were relatively resistant to proteolysis: the supposed S5-homologous domain (Lys102-Ile368), the N-terminal ATP-binding cassette (Gly463-Lys622), and the aminoacyl-tRNA-synthase homologous domain (Glu820-Gly865). Both the basal and ribosome-stimulated ATPase activities were inactivated by trypsin, but the ribosome-stimulated activity was inactivated faster.     

Impermeability of the rat placenta to insulin during organogenesis

The cause of the embryopathy associated with diabetes mellitus is uncertain. To examine whether exogenously administered insulin may be teratogenic, tracer amounts of radiolabelled insulin were infused for two hours during organogenesis (day 12 1/2 of gestation) into three groups of pregnant rats: control (n = 8), diabetic (n = 5), and hyperinsulinemic (n = 4). For maternal plasma, no differences were found among the three study groups in the percentage of the protein-precipitable (insulin-containing) radioactivity. Tissue radioactivities were expressed relative to the two-hour maternal plasma sample. Maternal kidney samples had the highest total and protein precipitable counts followed in descending order by the maternal plasma, maternal liver, placenta, and embryo. No differences in radioactivities were noted among the three study groups for specific tissues studied. Protein-precipitable radioactivities in the embryo were more than 100-fold less than the maternal plasma values. In 11 of the 17 litters, the acid-insoluble fractions of the embryos were not distinguishable from background counts, and none of the remaining six were greater than twice background. These studies demonstrate that during the period of organogenesis, the rat embryo is protected from maternal insulin by the placenta, and hence, maternal insulin is an unlikely teratogen.     

Spontaneous phase variation in Bordetella pertussis is a multistep non-random process.

Pathogenic strains of Bordetella pertussis undergo spontaneous phase variation and become non-pathogenic upon culturing in vitro. Spontaneous variants of the Tohama and #165 pathogenic strains of B. pertussis were selected by their ability to grow on synthetic and semi-synthetic solid media. The frequency of these variants was between 10(-6) and 10(-7). About 250 variant strains were screened for the presence of virulence-associated traits, such as production of hemolysin, pertussis toxin and filamentous hemagglutinin (FHA). Only four different combinations of the traits were found: 7-11% of the variants displayed all traits, 17% of the variants carried the toxin and FHA, 5-11% carried FHA only and 66% were devoid of all virulence traits. The strains which had at least one virulence trait also demonstrated some adenylate cyclase activity. The disappearance of hemolysin quantitatively affected the other traits. These results suggest that phase variation in B. pertussis is a non-random process, involving multistep disappearance of virulence factors in the following order: hemolysin, pertussis toxin and FHA. In contrast, all 300 variants of strain #18323 of B. pertussis, which were able to grow on the selective solid media, carried all the virulence traits. This is in accordance with the strain's unique intracerebral growth capability.