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At least 955 records · Page 53Linked to original sources
PubMed2002

Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale.

A comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains. Thirty-four r-protein families are represented in all domains but 33 families are specific to Archaea and Eucarya, providing evidence for specialisation at an early stage of evolution between the bacterial lineage and the lineage leading to Archaea and Eukaryotes. With only one specific r-protein, the archaeal ribosome appears to be a small-scale model of the eukaryotic one in terms of protein composition. However, the mechanism of evolution of the protein component of the ribosome appears dramatically different in Archaea. In Bacteria and Eucarya, a restricted number of ribosomal genes can be lost with a bias toward losses in intracellular pathogens. In Archaea, losses implicate 15% of the ribosomal genes revealing an unexpected plasticity of the translation apparatus and the pattern of gene losses indicates a progressive elimination of ribosomal genes in the course of archaeal evolution. This first documented case of reductive evolution at the domain scale provides a new framework for discussing the shape of the universal tree of life and the selective forces directing the evolution of prokaryotes.

Animals↗
PubMed1998

[Genetic differentiation of Caucasian wood mice: comparison of isozymic, chromosomal and molecular divergence].

Data on the complex genetic analysis of three sympatric species of Caucasian wood mice, Apodemus ponticus, A. fulvipectus, and A. uralensis are presented. A high degree of genetic differentiation at the isozymic, karyological and molecular (nuclear DNA) levels was revealed. The genetic distances between each pair of species varied significantly within a wide range depending on the analyzed level of the organization of genetic material. Mean values of genetic divergence from one species to another were also variable. These findings indicated that evolution of chromosomes was slower than that of isozymes, and the degree of species divergence was similar on cytogenetic and molecular levels. They also suggested that the rates of species evolution could vary in different phyletic lineages and on different levels of organization. Some phyletic lineages of Apodemus could be distinguished by different directions of evolution.

Animals↗
PubMed2005

Animal visual systems and the evolution of color patterns: sensory processing illuminates signal evolution.

Animal color pattern phenotypes evolve rapidly. What influences their evolution? Because color patterns are used in communication, selection for signal efficacy, relative to the intended receiver's visual system, may explain and predict the direction of evolution. We investigated this in bowerbirds, whose color patterns consist of plumage, bower structure, and ornaments and whose visual displays are presented under predictable visual conditions. We used data on avian vision, environmental conditions, color pattern properties, and an estimate of the bowerbird phylogeny to test hypotheses about evolutionary effects of visual processing. Different components of the color pattern evolve differently. Plumage sexual dimorphism increased and then decreased, while overall (plumage plus bower) visual contrast increased. The use of bowers allows relative crypsis of the bird but increased efficacy of the signal as a whole. Ornaments do not elaborate existing plumage features but instead are innovations (new color schemes) that increase signal efficacy. Isolation between species could be facilitated by plumage but not ornaments, because we observed character displacement only in plumage. Bowerbird color pattern evolution is at least partially predictable from the function of the visual system and from knowledge of different functions of different components of the color patterns. This provides clues to how more constrained visual signaling systems may evolve.

Animal Communication↗
PubMed2004

Evolution of seasonal ecological niches in the Passerina buntings (Aves: Cardinalidae).

The evolution of migration has long been considered complex and recent work has demonstrated additional complexity: some species follow the same ecological conditions throughout the year, whereas others 'switch niches' between breeding and wintering ranges. Hypotheses regarding the evolution of migration would generally predict niche-following as primitive, and niche-switching as derived. However, no test has, to our knowledge, yet determined the directionality of evolution of these states within a lineage. We present an analysis of phylogenetic dimensions of seasonal niches in the Passerina buntings that indicates greater evolutionary change in the niches of breeding populations than among those of wintering populations. These results are consistent with hypotheses of (i) niche conservatism (in winter, at least) across a recently speciated lineage; and (ii) the derived state of the breeding (rather than winter) ecological niches of each species.

Animal Migration↗
PubMed1997

Microsatellite evolution--a reciprocal study of repeat lengths at homologous loci in cattle and sheep.

The application of microsatellites in evolutionary studies requires an understanding of the patterns governing their evolution in different species. The finding that homologous microsatellite loci are longer, i.e., containing more repeat units, in human and in other primates has been taken as evidence for directional microsatellite evolution and for a difference in the rate of evolution between species. However, it has been argued that this finding is an inevitable consequence of biased selection of longer-than-average microsatellites in human, because cloning procedures are adopted to generate polymorphic and, hence, long markers. As a test of this hypothesis, we conducted a reciprocal comparison of the lengths of microsatellite loci in cattle and sheep using markers derived from the bovine genome as well as the ovine genome. In both cases, amplification products were longer in the focal species, and loci were also more polymorphic in the species from which they were originally cloned. The crossing pattern that we found suggests that interspecific length differences detected at homologous microsatellite loci are the result of biased selection of loci associated with cloning procedures. Hence, comparisons of microsatellite evolution between species are flawed unless they are based on reciprocal analyses or on genuinely random selection of loci with respect to repeat length.

Animals↗
PubMed1998

P-selectin requirement for neutrophil accumulation and injury in the direct passive Arthus reaction.

The aim of this study was to investigate the role of P-selectin in the accumulation of neutrophils in the direct passive Arthus reaction in rat skin. Direct passive Arthus dermal reaction was induced in male Sprague-Dawley (SD) rats by a single i.v. injection of rat anti-sheep globulin (SG) 1 h before i.d. injection of SG antigen. Anti-P-selectin or irrelevant control antibody was given 1 h before rat anti-SG injection. Complement depletion was also performed in a separate group by pretreatment with cobra venom factor (CVF). In all groups dermal swelling was assessed 4 h after antigen challenge. Four hours after antigen challenge, rats treated with control antibody developed skin swelling (2.29 +/- 0.47 mm), prominent complement deposition and neutrophil accumulation. This response was associated with local up-regulation of endothelial P-selectin. Pre-treatment with anti-P-selectin antibody 1 h before passive Arthus induction prevented skin swelling (0.29 +/- 0.06 mm, P < 0.05, cf with control antibody treatment), neutrophil accumulation and up-regulation of endothelial P-selectin despite complement deposition. CVF treatment prevented complement deposition, neutrophil accumulation and skin swelling (0.13 +/- 0.07 mm, P < 0.05, cf with saline treatment). However, endothelial P-selectin expression was still present. Inhibition of skin swelling and neutrophil accumulation in direct passive Arthus by functional inhibition of P-selectin suggest a pivotal role for this adhesion molecule in this inflammatory process. These results also suggest that multiple steps are involved in the evolution of direct passive Arthus, including both P-selectin expression and complement activation. However, while complement activation is essential for neutrophil accumulation and expression of dermal injury, P-selectin up-regulation initiated by antibody/antigen deposition occurs independently of complement activation.

Animals↗
PubMedDate not supplied

[Molecular biology, darwinism and nomogenesis].

The theory of nomogenesis put forward by L. S. Berg in 1922 is discussed. It is shown that side by side with some erroneous anti-darwinian ideas the theory contains a series of important suggestions which anticipate the further development of the synthetic theory of evolution. Berg has foreseen the development of molecular biology. Thus he was the fore-teller of our branch of science. The theory of nomogenesis emphasized the limitations of natural selection which determine the directionality of evolution. Berg treated the speciation as a kind of phase transition. Even the most conscientious critics of Berg have misrepresented the real sense of his works. It is totally groundless to treat nomogenesis as an idealistic of Lamarkian theory. Berg was superior to his critics. However the enthusiasm about nomogenesis in our time shows the inability to separate "the grains from weeds".

Biological Evolution↗
PubMedDate not supplied

Networks of gene regulation, neural development and the evolution of general capabilities, such as human empathy.

A network of gene regulation organized in a hierarchical and combinatorial manner is crucially involved in the development of the neural network, and has to be considered one of the main substrates of genetic change in its evolution. Though qualitative features may emerge by way of the accumulation of rather unspecific quantitative changes, it is reasonable to assume that at least in some cases specific combinations of regulatory parts of the genome initiated new directions of evolution, leading to novel capabilities of the brain. These notions are applied, in this paper, to the evolution of the capability of cognition-based human empathy. It is suggested that it has evolved as a secondary effect of the evolution of strategic thought. Development of strategies depends on abstract representations of one's own possible future states in one's own brain to allow assessment of their emotional desirability, but also on the representation and emotional evaluation of possible states of others, allowing anticipation of their behaviour. This is best achieved if representations of others are connected to one's own emotional centres in a manner similar to self-representations. For this reason, the evolution of the human brain is assumed to have established representations with such linkages. No group selection is involved, because the quality of strategic thought affects the fitness of the individual. A secondary effect of this linkage is that both the actual states and the future perspectives of others elicit vicarious emotions, which may contribute to the motivations of altruistic behaviour.

Biological Evolution↗
PubMed1999

Involvement of gene products in bacterial evolution.

Three strategies of different quality contribute in parallel to the natural formation of genetic variants in bacteria: (1) small local alterations of DNA sequences; (2) recombinational reshuffling of segments of the genome; and (3) acquisition of DNA sequences by horizontal gene transfer. Key enzymes involved in these processes often act as variation generators by making use of structural flexibilities of biological macromolecules and of the effect of random encounter. In the theory of molecular evolution, genetic determinants of variation generators as well as of modulators of the frequency of genetic variation are defined as evolutionary genes. This postulate is consistent with the notion that spontaneous mutagenesis is in general not adaptive and that the direction of evolution depends on natural selection exerted on populations of genetic variants.

Bacteria↗
PubMed2004

A new intrinsic thermal parameter for enzymes reveals true temperature optima.

Two established thermal properties of enzymes are the Arrhenius activation energy and thermal stability. Arising from anomalies found in the variation of enzyme activity with temperature, a comparison has been made of experimental data for the activity and stability properties of five different enzymes with theoretical models. The results provide evidence for a new and fundamental third thermal parameter of enzymes, T(eq), arising from a subsecond timescale-reversible temperature-dependent equilibrium between the active enzyme and an inactive (or less active) form. Thus, at temperatures above its optimum, the decrease in enzyme activity arising from the temperature-dependent shift in this equilibrium is up to two orders of magnitude greater than what occurs through thermal denaturation. This parameter has important implications for our understanding of the connection between catalytic activity and thermostability and of the effect of temperature on enzyme reactions within the cell. Unlike the Arrhenius activation energy, which is unaffected by the source ("evolved") temperature of the enzyme, and enzyme stability, which is not necessarily related to activity, T(eq) is central to the physiological adaptation of an enzyme to its environmental temperature and links the molecular, physiological, and environmental aspects of the adaptation of life to temperature in a way that has not been described previously. We may therefore expect the effect of evolution on T(eq) with respect to enzyme temperature/activity effects to be more important than on thermal stability. T(eq) is also an important parameter to consider when engineering enzymes to modify their thermal properties by both rational design and by directed enzyme evolution.

Acid Phosphatase↗
PubMed2001

Multiplicative versus additive selection in relation to genome evolution: a simulation study.

The evolution of molecular quantitative traits, such as codon usage bias or base frequencies, can be explained as the result of mutational biases alone, or as the result of mutation and selection. Whereas mutation models can be investigated easily, realistic modelling of selection-directed genome evolution is analytically intractable, and numerical calculations require substantial computer resources. We investigated the evolution of optimal codon frequency under additive and multiplicative effects of selected linked codons. We show that additive selective effects of many linked sites cannot be effective in genomes when the number of selected sites is greater than the effective population size, a realistic assumption according to current molecular data. We then discuss the implications of these results for isochore evolution in vertebrates.

Codon↗
PubMed2005

Structural anisotropy and internal magnetic fields in trabecular bone: coupling solution and solid dipolar interactions.

We investigate the use of intermolecular multiple-quantum coherence to probe structural anisotropy in trabecular bone. Despite the low volume fraction of bone, the bone-water interface produces internal magnetic field gradients which modulate the dipolar field, depending on sample orientation, choice of dipolar correlation length, correlation gradient direction, and evolution time. For this system, the probing of internal magnetic field gradients in the liquid phase permits indirect measurements of the solid phase dipolar field. Our results suggest that measurements of volume-averaged signal intensity as a function of gradient strength and three orthogonal directions could be used to non-invasively measure the orientation of structures inside a sample or their degree of anisotropy. The system is modeled as having two phases, solid and liquid (bone and water), which differ in their magnetization density and magnetic susceptibility. A simple calculation using a priori knowledge of the material geometry and distribution of internal magnetic fields verifies the experimental measurements as a function of gradient strength, direction, and sample orientation.

Anisotropy↗
PubMed2004

Should names reflect the evolution of bacterial species?

Systematics is the process of characterizing and arranging bacterial diversity in an orderly manner, recognizing groups of similar organisms in a hierarchical scheme whose basic entity is the species. To allow the exchange of scientific knowledge, taxa have to be named. Taxa are not static entities since they are subject to evolution, the direction of which can be inferred by using a wide range of techniques targeting specific traits. However, it is not clear how this dynamism should be reflected in taxonomic nomenclature. In the present report, several considerations are presented that deal with the relationship between the evolution of taxa and their nomenclature; an example is given which concerns the nomenclature of the species Lactobacillus delbrueckii.

Bacteria↗
PubMed1992

RNA virus populations as quasispecies.

RNA virus mutation frequencies generally approach maximum tolerable levels, and create complex indeterminate quasispecies populations in infected hosts. This usually favors extreme rates of evolution, although periods of relative stasis or equilibrium, punctuated by rapid change may also occur (as for other life forms). Because complex quasispecies populations of RNA viruses arise probabilistically and differentially in every host, their compositions and exact roles in disease pathogenesis are indeterminate and their directions of evolution, and the nature and timing of "new" virus outbreaks are unpredictable.

Biological Evolution↗
PubMed1992

Phenotypic evolution under gene-culture transmission in structured populations.

I consider a simple model for the evolution of a quantitative character is structured populations when an offspring's phenotype is determined partly by his or her genetic constitution and partly by cultural transmission of the parental phenotype. Analysis of the model indicates that when individual and group selection are in the same direction, phenotypic evolution always proceeds faster under gene-culture vs. purely genetic transmission. When individual and group selection are countervailing, altruistic characters evolve faster under gene-culture transmission when individual selection is weak and migration among groups is limited, with increased individual selection and migration tending to decrease the advantage of gene-culture transmission over purely genetic transmission. Given the prevalence of cultural transmission in higher species, these results suggest that contrary to what is often assumed, group selection may indeed by a potent evolutionary force in the evolution of altruistic characters.

Altruism↗
PubMed2001

Generation of a broad esterolytic subtilisin using combined molecular evolution and periplasmic expression.

Concomitant activity improvement of an evolved enzyme toward two very different ester substrates was achieved when a unique combination of functional periplasmic enzyme expression in Escherichia coli, random mutagenesis, DNA shuffling and cell-based kinetic screenings was applied. Specifically, we focused on the conversion of subtilisin E into an enzyme with broader esterase activity as opposed to its native amidase activity. Cell-based microtiter assays were performed on N-acetyl-D,L-phenylalanine p-nitrophenyl ester (Phe-NPE) and sucrose 1'-adipate (S1'A), as well as on the tetrapeptide amide substrate N-succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide. After a single modified cycle of directed molecular evolution, we isolated a number of clones exhibiting increased activity toward Phe-NPE. In the following rounds of screenings, mutants with improved activity on Phe-NPE were also tested on S1'A. Three mutants were identified with increased esterolytic activity on Phe-NPE and S1'A, while having similar amidase activity to that of the parental enzymes. Because the two ester substrates are structurally distinct, we have evolved a more general esterolytic subtilisin and this may have important applications in synthesis.

Amidohydrolases↗
PubMed2001

Network analysis provides insights into evolution of 5S rDNA arrays in Triticum and Aegilops.

We have used network analysis to study gene sequences of the Triticum and Aegilops 5S rDNA arrays, as well as the spacers of the 5S-DNA-A1 and 5S-DNA-2 loci. Network analysis describes relationships between 5S rDNA sequences in a more realistic fashion than conventional tree building because it makes fewer assumptions about the direction of evolution, the extent of sexual isolation, and the pattern of ancestry and descent. The networks show that the 5S rDNA sequences of Triticum and Aegilops species are related in a reticulate manner around principal nodal sequences. The spacer networks have multiple principal nodes of considerable antiquity but the gene network has just one principal node, corresponding to the correct gene sequence. The networks enable orthologous groups of spacer sequences to be identified. When orthologs are compared it is seen that the patterns of intra- and interspecific diversity are similar for both genes and spacers. We propose that 5S rDNA arrays combine sequence conservation with a large store of mutant variations, the number of correct gene copies within an array being the result of neutral processes that act on gene and spacer regions together.

Algorithms↗