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Correlation between respiratory function tests and evolution time in asthmatic patients.

A transversal and prospective study was performed to demonstrate a relationship between the evolution time of asthma episodes and alterations observed in the respiratory function tests (RFT) during asymptomatic periods. Asthmatic patients (n = 80) of both sexes, were studied, we investigated the evolution time of the asthmatic episodes and performed RFTs in the patients during their asymptomatic periods. Respiratory patterns were classified as normal, obstructive, or mixed (obstructive-restrictive), and a Spearman correlation test was performed. Twenty nine patients were male and fifty one female. All were between 5 and 49 years of age. Of the total number of patients, 13.7% fell into a normal pattern, 57.5% into an obstructive pattern and 28.7% in a mixed pattern. In the groups showing the shortest evolution time, the obstructive pattern was more common (75% of patients with less than 5 years of evolution time and 53.8% with an evolution time between five and ten years). The mixed pattern was more common in patients with more years suffering asthma (16.6% in the group of patients having 5 or less years of evolution and 50% in the group with more than 20 years). We found a Spearman value of 0.7, and we can conclude that there is more pulmonary damage associated to a longer evolution period of bronchial asthma.

Adolescent↗

PubMed1993

[Changes in the pancreatic and respiratory functions in cystic fibrosis. The influence of the time of the evolution of the disease].

BACKGROUND: Cystic fibrosis is the most frequent congenital disease in Caucasian and is transmitted by recessive autosomic inheritance. It is characterized by affection of different glands of exocrine secretion, particularly the pancreas and the lung. The aim of this study was to analyze the degree of alteration of pulmonary and pancreatic exocrine function in a group of patients with cystic fibrosis in relation to the time of disease evolution. METHODS: Twenty-one patients between 9 and 31 years of age were studied; 11 with an evolution of lower than or equal to 158 months and 10 with an evolution of higher than 158 months (median of the total patients). To study pancreatic exocrine function the BT-PABA test immunoreactive serum trypsin test were used. To evaluate respiratory function FEV1, FVC, FEV1/FVC ratio and PaO2 were used. RESULTS: The results obtained demonstrated that in the group with a lower time of evolution the diagnosis had been carried out at earlier ages (17 +/- 17 months versus 84 +/- 60 months; p = 0.002) and presented a significantly more altered pancreatic exocrine function (BT-PABA: 13 +/- 12% versus 35 +/- 23%; p = 0.013). However, respiratory function was altered in the group with longer time of evolution (FEV1: 68 +/- 20% versus 36 +/- 23%; p = 0.003; FVC: 74 +/- 9 versus 52 +/- 25%; p = 0.013; FEV1/FEV: 77 +/- 19 versus 50 +/- 9%; p < 0.001; PaO2: 84 +/- 16 versus 58 +/- 11%; p < 0.001). CONCLUSIONS: Pancreatic exocrine function is most intensely affected in patients diagnosed with cystic fibrosis at earlier and with shorter times of evolution while patients who have the longest time of evolution and who were diagnosed later in life presented greater changes in respiratory function.

Adolescent↗

PubMed1998

[Prostate cancer in Isère and Tarn (France) between 1985 and 1995: evolution of therapeutic indications].

The objective is to describe the evolution of therapeutic practices of prostate carcinoma in the departements of Tarn and Isère in France for the 1985-1995 period. This retrospective study is based on patient folders for whom a prostate carcinoma has been diagnosed between 1985 and 1995. A sample of 871 patients have been included after randomisation stratified on the year and the department of the diagnostic in the files of the cancer registries of Tarn and Isère. Therapeutic practices of the prostate cancer have significantly evolved between 1985 and 1989. The rate of radical prostatectomies increased from 1986 whereas the rate of radiotherapy remained stable. This evolution has been made to the detriment of non curative treatments with the decrease of the rate of hormonotherapies. This is due to the important development of diagnostic technics which led to an earlier diagnostic of these cancers; but, the evolution of therapeutic technics and particularly of the radical prostatectomy allowed the evolution of indications for the treatment of this cancer, with the increase of the rate of radical prostatectomies and the decrease of the rate of radiotherapies at the same stage of disease evolution. For 1990 to 1995, there was no major evolution. Some indications are discussed in this disease touching old man, with a slow evolution.

Adenocarcinoma↗

PubMed2025

Phylogenomics Unveils the Complex Evolution of Retroviruses in Birds.

The rise of birds represents one of the major evolutionary transitions in the history of life. Yet, much remains obscure about the origins and diversification of viruses in birds. Endogenous retroviruses (ERVs), relics of past retroviral infections, provide molecular fossils for interrogating the evolution and ecology of retroviruses. Here, we perform phylogenomic mining of ERVs within the genomes of 758 bird species and identify more than 470,000 ERVs, revealing a highly diverse and complex retrovirus repertoire in birds. These ERVs greatly expand the diversity of retroviruses in birds, indicating that exogenous retroviruses characterized in birds to date are highly underestimated. The evolution of retroviruses in birds is shaped by both coevolution and cross-species transmission. Tens of retrovirus lineages originated during the early evolution of birds, four of which contribute to more than 90% of complete ERVs in birds. We also observe recent ERV activity across the bird phylogeny (particularly in Passeriformes). Moreover, we find that ERVs can mediate genome rearrangements, potentially facilitating the genome evolution of birds. Many bird retroviruses recruited genes of cellular provenience, which might drive the evolution of the genome complexity of retroviruses. Together, these results unveil a diverse and complex retrovirosphere in birds and provide insights into the intricate evolution of retrovirus-bird interaction.

Animals↗

PubMed2002

Diversifying selection of the tumor-growth promoter angiogenin in primate evolution.

Diversifying selection drives the rapid differentiation of gene sequences and is one of the main forces behind adaptive evolution. Most genes known to be shaped by diversifying selection are those involved in host-pathogen or male-female interactions characterized as molecular "arms races." Here we report the unexpected detection of diversifying selection in the evolution of a tumor-growth promoter, angiogenin (ANG). A comparison among 11 primate species demonstrates that ANG has a significantly higher rate of nucleotide substitution at nonsynonymous sites than at synonymous sites, a hallmark of positive selection acting at the molecular level. Furthermore, we observed significant charge diversity at the molecular surface, suggesting the presence of selective pressures in the microenvironment of ANG, including its binding molecules. A population survey of ANG in chimpanzees, however, reveals no polymorphism, which may have resulted from a recent selective sweep of a charge-altering substitution in chimpanzee evolution. Functional assays of recombinant ANGs from the human and owl monkey indicate that primate ANGs retain angiogenic activity despite rapid evolution. Our study, together with findings of similar selection in the primate breast cancer suppressor gene, BRCA1, reveals an intriguing phenomenon of unusual selective pressures on, and adaptive evolution of, cancer-related genes in primate evolution.

Amino Acid Sequence↗

PubMed2000

Evolution of vertebrate immunoglobulin variable gene segments.

Evolution of Ig V gene segments are generally characterized by (a) evolution by "the birth and death process" and (b) diversifying selection. However, the detailed evolutionary pattern of V gene segments varies among species due to the fact that the humoral immune system itself has changed during vertebrate evolution. The change in somatic diversification system coupled with the change in lymphocyte development has imposed a significant impact on the evolution of Ig genes. In order to understand the evolution of immunological genes it is important to view it in the context of the evolution of the entire immune system itself.

Animals↗

PubMed1993

Characterization of the cow stomach lysozyme genes: repetitive DNA and concerted evolution.

Cow stomach lysozyme genes have evolved in a mosaic pattern. The majority of the intronic and flanking sequences show an amount of sequence difference consistent with divergent evolution since duplication of the genes 40-50 million years ago. In contrast, exons 1, 2, and 4 and immediately adjacent intronic sequences differ little between genes and show evidence of recent concerted evolution. Exon 3 appears to be evolving divergently. The three characterized genes vary from 5.6 to 7.9 kilobases in length. Different distributions of repetitive DNA are found in each gene, which accounts for the majority of length differences between genes. The different distributions of repetitive DNA in each gene suggest the repetitive elements were inserted into each gene after the duplications that give rise to these three genes and provide additional support for divergent evolution for the majority of each gene. The observation that intronic and flanking sequences are evolving divergently suggests that the concerted evolution events involved in homogenizing the coding regions of lysozyme genes involve only one exon at a time. This model of concerted evolution would allow the shuffling of exon-sized pieces of information between genes, a phenomenon that may have aided in the early adaptive evolution of stomach lysozyme.

Animals↗

PubMed1993

The D/H ratio and the evolution of water in the terrestrial planets.

The presence of liquid water at the surface of the Earth has played a major role in the biological evolution of the Earth. None of the other terrestrial planets--Mercury, Venus and Mars--has liquid water at its surface. However, it has been suggested, since the early seventies, from both geological and atmospheric arguments that, although Venus and Mars are presently devoid of liquid water, their surfaces could have been partially or completely covered by water at some time of their evolution. There are many possible diagnostics of the long-term evolution of the planets, either from the present characteristics of their surfaces or from their present atmospheric compositions. Among them, the present value of the D/H ratio is of particular interest, although its significance in terms of long term evolution has been challenged by some authors. Recent progress has been made in this field. We now have evidence for higher D/H ratios on Mars and Venus than on Earth, with an enrichment factor of the order of 5 on Mars, and about 100 on Venus. Any scenario for the evolution of these planets must take this into The most recent models on the evolution of Mars and Venus are reviewed in light of these new measurements.

Atmosphere↗

PubMed1981

Simulation of protein evolution by random fixation of allowed codons.

Computer simulation of protein evolution is based on a simple model consisting of random fixation of allowed codons (RFAC). Random replacement of single nucleotides occurs in a DNA sequence. If this results in any of the synonomous codons for allowed amino acids the mutation is fixed, if not, there is no change in the DNA and the cycle is repeated. Multiple fixations at the same nucleotide site, back mutations, degenerate fixations and coincidental identity of amino acids all occur. RFAC simulation begins with a single DNA sequence and follows a phylogeny based on the fossil record. The rate of fixation at the level of DNA is constant. The model upon which RFAC simulation is based is the same as the neutral theory of molecular evolution. The simulation is therefore a test of this theory. The results of simulated and real evolution are compared for fibrinopeptides A in mammals and cytochromes C and hemoglobin alpha and beta chains in vertebrates. In each case the allowed variation at each site has been set equal to that observed, twice that observed and all protein amino acids. Rates of fixation vary from 2.4 X 10(-10) to 10(-8) accepted nucleotide fixations per codon per year. There is some, although never excellent, agreement between real and simulated evolution, the better fits are obtained in the cases of fibrinopeptides A and cytochromes C. The major source of discrepancy between real evolution and simulation is irregularities in the rates of real evolution. RFAC simulation is compared with the random evolutionary hit (REH) model, augmented maximum parsimony and the accepted point mutations (PAM) approach.

Amino Acids↗

PubMed1991

Elements in microbial evolution.

Spontaneous mutation, selection, and isolation are key elements in biological evolution. Molecular genetic approaches reveal a multitude of different mechanisms by which spontaneous mutants arise. Many of these mechanisms depend on enzymes, which often do not act fully at random on the DNA, although a large number of sites of action can be observed. Of particular interest in this respect are DNA rearrangement processes, e.g., by transposition and by site-specific recombination systems. The development of gene functions has thus to be seen as the result of both DNA rearrangement processes and sequence alterations brought about by nucleotide substitutions and small local deletions, insertions, and duplications. Prokaryotic microorganisms are particularly appropriate for studying the effects of spontaneous mutation and thus microbial evolution, as they have haploid genomes, so that genetic alterations become rapidly apparent phenotypically. In addition, bacteria and their viruses and plasmids have relatively small genomes and short generation times, which also facilitate research on evolutionary processes. Besides the strategy of development of gene functions in the vertical transmission of genomes from generation to generation, the acquisition of short DNA segments from other organisms appears to be an important strategy in microbial evolution. In this process of horizontal evolution natural vector DNA molecules are often involved. Because of acquisition barriers, the acquisition strategy works best for relatively small DNA segments, hence at the level of domains, single genes, or at most operons. Among the many enzymes and functional systems involved in vertical and horizontal microbial evolution, some may serve primarily for essential life functions in each individual and only secondarily contribute to evolution.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1996

A theory of evolution that includes prebiotic self-organization and episodic species formation.

A theory has been proposed that encompasses pre-replication changes in RNA synthesis and non-gradual variant formation, in addition to competitive replication. Using a fundamental theorem of natural selection and maximum principle scaled to nucleotide condensation, evolution in vitro was demonstrated to maximally damp both kinetic and thermodynamic forces driving this reaction, from its pre-replication stage. This led to the finding that evolution follows a path of least action. These principles form the framework for a general theory of evolution, whose scope extends beyond evolution modeled by synthesis of non-interacting RNA molecules. It applies, in particular, to standard processes, such as competitive crystallization. In calculations simulating de novo formation of self-replicating RNA molecules in the Qbeta replicase system, spontaneous changes in strand secondary structure promoted the transition from random copolymerization to template-directed polymerization. This finding indicates selection preceded genome self-propagation. Non-gradual species formation was attributed to the presence of heterogeneous thermodynamic forces. Growth unconstrained by competition follows mutation to a variant able to utilize a free energy source alien to its progenitors. Evolution in a heterogeneous system can, therefore, exhibit discontinuous rates of species formation and spawn new species populations. Natural selection among competing self-propagators thus gives way to a principle of wider scope stating that evolution optimally damps the physicochemical forces causing change within an evolving system.

Biological Evolution↗

PubMed1997

Rapid rate of control-region evolution in Pacific butterflyfishes (Chaetodontidae).

Sequence differences in the tRNA-proline (tRNApro) end of the mitochondrial control-region of three species of Pacific butterflyfishes accumulated 33-43 times more rapidly than did changes within the mitochondrial cytochrome b gene (cytb). Rapid evolution in this region was accompanied by strong transition/transversion bias and large variation in the probability of a DNA substitution among sites. These substitution constraints placed an absolute ceiling on the magnitude of sequence divergence that could be detected between individuals. This divergence "ceiling" was reached rapidly and led to a decay in the relative rate of control-region/cytb b evolution. A high rate of evolution in this section of the control-region of butterflyfishes stands in marked contrast to the patterns reported in some other fish lineages. Although the mechanism underlying rate variation remains unclear, all taxa with rapid evolution in the 5'-end of the control-region showed extreme transition biases. By contrast, in taxa with slower control-region evolution, transitions accumulated at nearly the same rate as transversions. More information is needed to understand the relationship between nucleotide bias and the rate of evolution in the 5'-end of the control-region. Despite strong constraints on sequence change, phylogenetic information was preserved in the group of recently differentiated species and supported the clustering of sequences into three major mtDNA groupings. Within these groups, very similar control-region sequences were widely distributed across the Pacific Ocean and were shared between recognized species, indicating a lack of mitochondrial sequence monophyly among species.

Animals↗

PubMed2003

Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution.

Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds, determining that an extended neutral network in sequence space is associated with each of them. Within our model, neutral evolution leads to a non-Poissonian substitution process, due to the broad distribution of connectivities in neutral networks. The observation that the substitution process has non-Poissonian statistics has been used to argue against the original Kimura neutral theory, while our model shows that this is a generic property of neutral evolution with structural conservation. Our model also predicts that the substitution rate can strongly fluctuate from one branch to another of the evolutionary tree. The average sequence similarity within a neutral network is close to the threshold of randomness, as observed for families of sequences sharing the same fold. Nevertheless, some positions are more difficult to mutate than others. We compare such structurally conserved positions to positions conserved in protein evolution, suggesting that our model can be a valuable tool to distinguish structural from functional conservation in databases of protein families. These results indicate that a synergy between database analysis and structurally based computational studies can increase our understanding of protein evolution.

Amino Acid Sequence↗

PubMed1997

Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven.

Mammalian evolution is believed to be male driven because the greater number of germ cell divisions per generation in males increases the opportunity for errors in DNA replication. Since the Y Chromosome (Chr) replicates exclusively in males, its genes should also evolve faster than X or autosomal genes. In addition, estimating the overall male-to-female mutation ratio (alpha m) is of great importance as a large alpha m implies that replication-independent mutagenic events play a relatively small role in evolution. A small alpha m suggests that the impact of these factors may, in fact, be significant. In order to address this problem, we have analyzed the rates of evolution in the homologous X-Y common SMCX/SMCY genes from three different species--mouse, human, and horse. The SMC genes were chosen because the X and Y copies are highly homologous, well conserved in evolution, and in all probability functionally interchangeable. Sequence comparisons and analysis of synonymous substitutions in approximately 1kb of the 5' coding region of the SMC genes reveal that the Y-linked copies are evolving approximately 1.8 times faster than their X homologs. The male-to-female mutation ratio alpha m was estimated to be 3. These data support the hypothesis that mammalian evolution is male driven. However, the ratio value is far smaller than suggested in earlier works, implying significance of replication-independent mutagenic events in evolution.

Amino Acid Sequence↗

PubMed1989

Codon evolution and conservation of the reading phase in genetic code translation.

The description of the optimized evolution of a code based on 4 nucleotides involves a sequential transition of codons, formed firstly by monomers evolving to dimers and then to triplets, in accordance with the progressive increase of the number of amino acids to be coded. The successive increase in the size of these codons during evolution implies changes in the phase reading of the genetic message, which could become chaotic. In order to overcome this constraint, this paper proposes a codon evolution where two things occur simultaneously: codons change in size and there is an alternation of the molecule which holds the information. For example, the nucleotides of the original oligonucleotide are read as monomers when they are translated to an oligopeptide, but further on, this oligopeptide which is read as amino acid dimers, is translated to a nucleotide form (oligonucleotide). Finally, amino acids conforming a peptide are translated from this oligonucleotide, through a reading of triplets. Although plausible, this evolution is a low-probability process due to the fact that it requires a singular sequence of the oligonucleotide and oligopeptide involved. An alternative hypothesis of evolution is also discussed. It proposes that with the exclusion of the establishment of monomer and dimer codons, there is a direct generation of a code of trinucleotides which arises only when a certain number of amino acids has already been generated. Both hypotheses are discussed in terms of the development of a code in which an optimized hardware is maintained through out its evolution.

Amino Acids↗

PubMed2002

Evolution of enzymes in metabolism: a network perspective.

Several models have been proposed to explain the origin and evolution of enzymes in metabolic pathways. Initially, the retro-evolution model proposed that, as enzymes at the end of pathways depleted their substrates in the primordial soup, there was a pressure for earlier enzymes in pathways to be created, using the later ones as initial template, in order to replenish the pools of depleted metabolites. Later, the recruitment model proposed that initial templates from other pathways could be used as long as those enzymes were similar in chemistry or substrate specificity. These two models have dominated recent studies of enzyme evolution. These studies are constrained by either the small scale of the study or the artificial restrictions imposed by pathway definitions. Here, a network approach is used to study enzyme evolution in fully sequenced genomes, thus removing both constraints. We find that homologous pairs of enzymes are roughly twice as likely to have evolved from enzymes that are less than three steps away from each other in the reaction network than pairs of non-homologous enzymes. These results, together with the conservation of the type of chemical reaction catalyzed by evolutionarily related enzymes, suggest that functional blocks of similar chemistry have evolved within metabolic networks. One possible explanation for these observations is that this local evolution phenomenon is likely to cause less global physiological disruptions in metabolism than evolution of enzymes from other enzymes that are distant from them in the metabolic network.

Databases, Protein↗

PubMed1999

Mosquito genomes: structure, organization, and evolution.

A great deal of information has been accumulated on chromosome numbers and heterochromatin distribution as well as on genome size and organization in the mosquito family Culicidae. A number of trends in genome evolution emerge when these data are reviewed in light of recent cladistic phylogenies of Culicidae and its sister families. Anophelinae have heteromorphic sex chromosomes and a small genome size, and repetitive elements are distributed in a long-period interspersion pattern. In contrast, Culicinae have homomorphic sex chromosomes, and repetitive DNA is organized in a short-period interspersion pattern. There has been a general increase in genome size during the evolution of culicine tribes. The organization of the ancestral culicid genome remains uncertain awaiting studies on genome organization in Chaoboridae-Corethrellidae taxa. The most parsimonious hypothesis for the evolution of sex chromosomes and genome organization in Culicidae would be that homomorphic sex chromosomes and a long-period interspersion pattern was ancestral in lineages leading to Toxorhynchitinae and Culcinae. Larger genomes developed in subsequent culicine lineages through accumulation of short-period interspersed repetitive elements. Heteromorphic sex chromosomes evolved early in the evolution of Anophelinae, and a long-period interspersion pattern was retained. The alternative scenario proposed by Rao and Rai (1987a) is that Culicidae arose from a chaoborid Mochlonyx-like ancestor with heteromorphic sex chromosomes and possibly short-period interspersion. This scenario would require the loss of heteromorphic sex chromosomes in the lineage leading to Toxorhynchitinae and Culicinae and the "shedding" of repetitive elements in the lineage leading to Anophelinae. Several interesting patterns have emerged from studies of C-banding, and the distribution of heterochromatin in Culicidae and phylogenies derived from these studies are supported by the modern cladistic analyses. Recent intensive multipoint linkage map studies suggest that recombination frequencies per genome have remained relatively constant over the course of culicid evolution such that Anophelinae, with a relatively small genome size, has a linkage map of similar size to Aedini. As a consequence, taxa in Anophelinae have higher amounts of recombination per haploid genome size than Culicinae. Although several key questions have yet to be addressed, the Culicidae remain one of the best-studied systems of genome evolution in animals.

Animals↗

PubMed1998

The evolution of plant development.

There has been much recent interest in the evolution of plant development and especially in trying to understand the developmental genetic basis of morphological evolution. Significant progress has been made in understanding the evolution of floral organization and the mechanisms that might underlie the evolution of compound leaves and inflorescence morphology. These advances are reinforcing the idea that phenotypic evolution can proceed via changes at few loci of large effect and that promoter evolution may be an important and frequent mechanism.

Evolution, Molecular↗