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PubMed2006

The ompA gene in Chlamydia trachomatis differs in phylogeny and rate of evolution from other regions of the genome.

Strains of Chlamydia trachomatis are classified into serovars based on nucleotide sequence differences in ompA, the gene that encodes the major outer membrane protein. Phylogenetic characterization of strains based on ompA, however, results in serovar groupings that are inconsistent with the distinguishing features of C. trachomatis pathobiology, e.g., tissue tropisms and disease presentation. We have compared nucleotide sequences at multiple sites distributed around the chlamydial genome from 18 strains representing 16 serovars; sampled regions included genes encoding housekeeping enzymes (totaling 2,073 bp), intergenic noncoding segments (1,612 bp), and a gene encoding a second outer membrane protein (porB; 1,023 bp), with the ompA sequence (1,194 bp) used for reference. These comparative analyses revealed substantial variation in nucleotide substitution patterns among the sampled regions, with average pairwise sequence differences ranging from 0.15% for the housekeeping genes to 12.1% for ompA. Phylogenetic characterization of the sampled genomic sequences yielded a strongly supported tree that divides the strains into groupings consistent with C. trachomatis biology and which has a topology quite distinct from the ompA tree. This phylogenetic incongruity can be accounted for by recombination of the ompA gene between different genomic backgrounds. We found, however, no evidence of recombination within or between any of the sampled regions around the C. trachomatis genome apart from ompA. Parallel analysis of published sequence data on four members of the pmp gene family are consistent with the phylogenetic analyses reported here.

Animals↗
PubMed1983

Factors associated with prognosis in human breast cancer. I. Predictors for rate of evolution and relapse.

The associations of several clinical factors with general survival, percentage of relapse and survival in the group of patients who relapsed were analyzed in a series of 399 Stage II breast cancer patients operated and irradiated at the Institute of Oncology and Radiobiology in Havana. In another series of 187 patients these associations were studied in regard to the presence of estradiol receptors in the tumors. Factors related to the presence of estrogen receptors were unrelated to the percentage of relapse in long term follow-up. Age and menstrual status were related to the presence of estradiol receptors and to survival inside the group of patients who relapsed but were unrelated to the percentage of relapses. Lymph node status was mainly associated with the percentage of relapses but not related to the presence of estradiol receptors. Other factors (parity and age at first childbirth), related to the presence of receptors, did not clearly influence prognosis. Lactation influenced positively survival inside the relapse group without any clear association with hormone receptors. Results are discussed in terms of a model considering particular host--tumor interaction: The probability of relapse and the speed of evolution of the systemic disease, mutually independent, but determining the prognosis.

Adult↗
PubMed2002

Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.

Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.

Algorithms↗
PubMed1993

Concurrent Measurements of Oxygen and Carbon Dioxide Exchange during Lightflecks in Maize (Zea mays L.).

Leaves of maize (Zea mays L.) were enclosed in a temperature-controlled cuvette under 35 Pa (350 [mu]bars) CO2 and 0.2 kPa (0.2%)O2 and exposed to short periods (1-30 s) of illumination (light-flecks). The rate and total amount of CO2 assimilated and O2 evolved were measured. The O2 evolution rate was taken as an indicator of the rate of photosynthetic noncyclic electron transport (NCET). In this C4 species, the response of electron transport during the lightflecks qualitatively mimicked that of C3 species previously tested, whereas the response of CO2 assimilation differed. Under short-duration lightflecks at high photon flux density (PFD), the mean rate of O2 evolution was greater than the steady-state rate of O2 evolution under the same PFD due to a burst of O2 evolution at the beginning of the lightfleck. This O2 burst was taken as indicating a high level of NCET involved in the buildup of assimilatory charge via ATP, NADPH, and reduced or phosphorylated metabolites. However, as lightfleck duration decreased, the amount of CO2 assimilated per unit time of the lightfleck (the mean rate of CO2 assimilation) decreased. There was also a burst of CO2 from the leaf at the beginning of low-PFD lightflecks that further reduced the assimilation during these lightflecks. The results are discussed in terms of the buildup of assimilatory charge through the synthesis of high-energy metabolites specific to C4 metabolism. It is speculated that the inefficiency of carbon uptake during brief light transients in the C4 species, relative to C3 species, is due to the futile synthesis of C4 cycle intermediates.

Journal Article↗
PubMed2005

Allometric scaling of flight energetics in orchid bees: evolution of flux capacities and flux rates.

The evolution of metabolic pathways involved in energy production was studied in the flight muscles of 28 species of orchid bees. Previous work revealed that wingbeat frequencies and mass-specific metabolic rates decline in parallel by threefold as body mass increases interspecifically over a 20-fold range. We investigated the correlated evolution of metabolic rates during hovering flight and the flux capacities, i.e. V(max) values, of flight muscle enzymes involved in substrate catabolism, the Krebs cycle and the electron transport chain. V(max) at the hexokinase (HK) step scales allometrically with an exponent almost identical to those obtained for wingbeat frequency and mass-specific metabolic rate. Analysis of this relationship using phylogenetically independent contrasts supports the hypothesis of correlated evolution between HK activity and mass-specific metabolic rate. Although other enzymes scale allometrically with respect to body mass, e.g. trehalase, glycogen phosphorylase and citrate synthase, no other enzyme activities were correlated with metabolic rate after controlling for phylogenetic relatedness. Pathway flux rates were used with enzyme V(max) values to estimate fractional velocities (fraction of V(max) at which enzymes operate) for various reactions to gain insights into enzyme function and how this varies with body mass. Fractional velocity is highly conserved across species at the HK step, but varied at all other steps examined. These results are discussed in the context of the regulation and evolution of pathways of energy metabolism.

Animals↗
PubMed2006

Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis.

The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be selected to best infer the evolutionary history of the mitochondria within a group of organisms, and what properties of a gene determine its phylogenetic performance? The current study addresses these questions in a Bayesian phylogenetic framework with reference to a phylogeny of plethodontid and related salamanders derived from 27 complete mitochondrial genomes; this topology is corroborated by nuclear DNA and morphological data. Evolutionary rates for each mitochondrial gene and divergence dates for all nodes in the plethodontid mitochondrial genome phylogeny were estimated in both Bayesian and maximum likelihood frameworks using multiple fossil calibrations, multiple data partitions, and a clock-independent approach. Bayesian analyses of individual genes were performed, and the resulting trees compared against the reference topology. Ordinal logistic regression analysis of molecular evolution rate, gene length, and the G-shape parameter a demonstrated that slower rate of evolution and longer gene length both increased the probability that a gene would perform well phylogenetically. Estimated rates of molecular evolution vary 84-fold among different mitochondrial genes and different salamander lineages, and mean rates among genes vary 15-fold. Despite having conserved amino acid sequences, cox1, cox2, cox3, and cob have the fastest mean rates of nucleotide substitution, and the greatest variation in rates, whereas rrnS and rrnL have the slowest rates. Reasons underlying this rate variation are discussed, as is the extensive rate variation in cox1 in light of its proposed role in DNA barcoding.

Animals↗