An analysis of determinants of amino acids substitution rates in bacterial proteins

The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated in comparative analyses. To this aim, we made regression analyses combining data available on these variables and on evolutionary rates, in two well-documented model bacteria, Escherichia coli and Bacillus subtilis. In both bacteria, the level of expression of the protein in the cell was by far the most important driving force constraining the amino acids substitution rate. Subsequent inclusion in the analysis of the other variables added little further information. Furthermore, when the rates of synonymous substitutions were included in the analysis of the E. coli data, only the variable expression levels remained statistically significant. The rate of nonsynonymous substitution was shown to correlate with expression levels independently of the rate of synonymous substitution. These results suggest an important direct influence of expression levels, or at least codon usage bias for translation optimization, on the rates of nonsynonymous substitutions in bacteria. They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes.     

Colour polymorphism in birds: causes and functions

We studied polymorphism in all species of birds that are presently known to show intraspecific variation in plumage colour. At least three main mechanisms have been put forward to explain the maintenance of polymorphism: apostatic, disruptive and sexual selection. All of them make partly different predictions. Our aims were to investigate evolutionary causes and adaptive functions of colour polymorphism by taking into account a number of ecological and morphological features of polymorphic species. Overall, we found 334 species showing colour polymorphism, which is 3.5% of all bird species. The occurrence of colour polymorphism was very high in Strigiformes, Ciconiiformes, Cuculiformes and Galliformes. Phylogenetically corrected analysis using independent contrasts revealed that colour polymorphism was maximally expressed in species showing a daily activity rhythm extended to day/night, living in both open and closed habitats. All these findings support the hypothesis that colour polymorphism probably evolved under selective pressures linked to bird detectability as affected by variable light conditions during activity period. Thus, we conclude that selective agents may be prey, predators and competitors, and that colour polymorphism in birds may be maintained by disruptive selection.     

The effect of high protein diet on urea and guanidino compound levels in renal insufficient mice

Summary. Nephrectomy in mice provokes a decrease in creatinine clearance (CTN_Cl) and an increase in urea and specific guanidino compound (GC) concentrations in blood and other tissues. Our purpose was to investigate the influence of high protein diet (HPD) on CTN_Cl, urea and GC levels in NX mice. Mice were nephrectomized or sham-operated and subdivided in groups to study five diet conditions. At the end of each experiment, 10 days and 30 days postsurgery, urine and blood were collected for determination of urea and GCs, including creatinine. HPD resulted in significantly higher CTN_Cl values in sham-operated mice than those observed in mice under normal protein diet, 10 days as well as 30 days postnephrectomy. HPD induced significant increases in plasma urea, guanidinosuccinic acid, argininic acid and α-keto-δ-guanidinovaleric acid concentration 10 days postsurgery but not 30 days postsurgery. HPD coincided with significantly higher excretion of urea, guanidinosuccinic acid, α-keto-δ-guanidinovaleric acid, creatine, argininic acid and γ-guanidinobutyric acid in sham-operated and nephrectomized mice 10 days postsurgery. Our results show that HPD induces supplementary (to nephrectomy) increases of urea and GCs in the early postsurgery period but not in the later phase. Received June 13, 2000 Accepted January 9, 2001     

The role of Mg2+ in the regulation of the structural and functional steady-states in rat liver mitochondria

A possible relationship between mitochondrial Mg²⁺ levels, structural configurations, and functional steady states has been studied in rat liver mitochondria. The results show that the concentration of mitochondrial Mg²⁺ in respiratory state 4 is definitely higher than in respiratory state 3. The metabolic transition from state 3 to state 4 and vice-versa is associated with reversible influx-efflux of about 10 nmol of Mg²⁺ per mg protein. The net uptake of this aliquot of Mg²⁺ is a necessary condition in order for the metabolic transition to state 4, both structurally and functionally, to occur. This process requires a threshold concentration of external Mg²⁺ greater than 5 mM. The phosphorylative mechanism does not appear to depend on the presence or absence of external Mg²⁺. The role of Mg²⁺ on the attainment and maintenance of the structural and functional steady state 4 seems to be correlated with its regulatory effect on the concentration of the mitochondrial P_i.     

The response of stomata to CO2 relates to its effect on respiration and ATP level

External ATP enhanced stomatal opening of Commelina communis L. differently from EDTA. ATP was more effective in opening stomata than EDTA, when both were applied in amounts yielding equivalent free Ca²⁺ concentration. The stimulation by ATP depended upon its de-phosphorylation and was not due to the P₁ released. Hence an energetical contribution of external ATP appears possible. Increase in CO₂ concentration increased the stimulation of stomatal opening by ATP and diminished the internal ATP level, ATP/(ADP+AMP) ratio and respiration rate.     

Introduction: Plant–herbivore interactions

This special feature resulted from a symposium entitled "Interactions Between Plants and Their Herbivores," held during the Meeting of the Society of Population Ecology in Ohmi-Shirahama, Shiga, Japan, in October 1999 (Chairperson of Symposium: Professor Emeritus E. Kuno of Kyoto University). This theme emerged from discussions by the organizing committee for this symposium: N. Yamamura, J. Takabayashi, T. Nishida, and N. Ohsaki. Professor Mark D. Rausher of Duke University was invited as a special lecturer. In this series of reports, five of the seven participants illustrate the variation found in plant–herbivore interactions and address some problems inherent in current theory.     

Comparison of Linear,Nonlinear and Semiparametric Mixed‐effects Models for Estimating HIV Dynamic Parameters

The potency of antiretroviral agents in AIDS clinical trials can be assessed on the basis of an early viral response such as viral decay rate or change in viral load (number of copies of HIV RNA) of the plasma. Linear, parametric nonlinear, and semiparametric nonlinear mixed‐effects models have been proposed to estimate viral decay rates in viral dynamic models. However, before applying these models to clinical data, a critical question that remains to be addressed is whether these models produce coherent estimates of viral decay rates, and if not, which model is appropriate and should be used in practice. In this paper, we applied these models to data from an AIDS clinical trial of potent antiviral treatments and found significant incongruity in the estimated rates of reduction in viral load. Simulation studies indicated that reliable estimates of viral decay rate were obtained by using the parametric and semiparametric nonlinear mixed‐effects models. Our analysis also indicated that the decay rates estimated by using linear mixed‐effects models should be interpreted differently from those estimated by using nonlinear mixed‐effects models. The semiparametric nonlinear mixed‐effects model is preferred to other models because arbitrary data truncation is not needed. Based on real data analysis and simulation studies, we provide guidelines for estimating viral decay rates from clinical data. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Ecdysteroid levels and integument changes in post-embryonic stages of Anastrepha suspensa

Ecdysteroid levels in larvae and pupae of Anastrepha suspensa (Diptera: Tephritidae) were measured by radioimmunoassay. These levels were correlated with histological changes throughout the development of the post-embryonic stages. Ecdysteroid levels increase rapidly throughout the last-larval instar and on the last day of this stage are 283 pg equivalents of 20-hydroxyecdysone per insect (14.5 ng/g) when wandering behaviour is initiated. At the end of this period the puparium is formed and within 24 h, the ecdysteroid rises to its highest peak (625 pg equivalents of 20-hydroxyecdysone/insect). Larval-pupal apolysis is initiated within 24 h later and the pupal cuticle is then secreted. Two days later, the ecdysteroids reach their lowest levels (75 pg equivalents of 20-hydroxyecdysone/insect or 0.6 ng/g) and most of the larval fat body and other tissues have been histolysed. In 5- to 10-day old pupae ecdysteroid levels again increase and remain relatively high throughout. During this period the larval epidermis is replaced by imaginal epidermis, imaginal discs begin to proliferate and the adult cuticle is secreted. Ecdysteroid levels finally fall 2 days prior to adult emergence. HPLC determinations indicate that 20-hydroxyecdysone is the predominant free ecdysteroid, and along with ecdysone, is readily detectable in all postembryonic stages of this species. An unusually high and unexplained peak of 20-hydroxyecdysone occurs in the pharate adult. This peak probably consists of ecdysone metabolites with retentions similar to that of 20-hydroxyecdysone and to which the antiserum is sensitive.