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At least 1,297 records · Page 72Linked to original sources
PubMed1989

Structural and evolutionary comparisons of four alleles of the mouse Igk-J locus which encodes immunoglobulin kappa light chain joining (J kappa) segments.

The Igk-J locus of the mouse encodes the immunoglobulin kappa light chain joining (J) segments. Four Igk-J alleles have been described on the basis of restriction enzyme length polymorphisms. The nucleotide sequences of the Igk-Ja allele (type strain, C.C58), Igk-Jc allele (type strain, SJL/J), and Igk-Jd allele (type strain, SK/CamRk) have been determined and are compared with the previously reported Igk-Jb allele sequence (type strain, BALB/c). The mouse sequences are also compared with published sequences for rat and human J kappa sequences. Far more differences were found between the Igk-Ja allele and the other mouse alleles than between any two of the latter. These result in two amino acid substitutions which distinguish the J2 and J3' segments of the Igk-Ja allele from the other three alleles. Use of the Phylogenetic Analysis Using Parsimony program to generate a phylogenetic tree strongly indicates that after divergence from the rat ancestor, there appears to have been an early split between the Igk-Ja allele and the evolutionary precursor of the other mouse alleles. There also appears to have been far less divergence from the ancestral condition in the Igk-Ja allele than in the other alleles. Also, the presence of only one convergent mutation among the four mouse alleles provides strong evidence against any crossing over within the Igk-J locus during the history of these alleles. Finally, the differences in rates of evolution of the Igk-J alleles are in marked contrast to the relatively uniform rates of divergence of four alleles of a mouse V kappa gene, Igk-VSer.

Alleles↗
PubMed2006

Evolution of immunity and host chromosome integration site of P2-like coliphages.

The amount and distribution of variation in the genomic region containing the genes in the lytic-lysogenic genetic switch and the sequence that determines the integration site into the host chromosome were analyzed for 38 P2-like phages from Escherichia coli. The genetic switch consists of two convergent mutually exclusive promoters, Pe and Pc, and two repressors, C and Cox. The immunity repressor C blocks the early Pe promoter, leading to the establishment of lysogeny. The Cox repressor blocks expression of Pc, allowing lytic growth. Phylogenetic analyses showed that the C and Cox proteins were distributed into seven distinct classes. The phylogenetic relationship differed between the two proteins, and we showed that homologous recombination plays a major role in creating alterations in the genetic switch, leading to new immunity classes. Analyses of the host integration site for these phages resulted in the discovery of a previously unknown site, and there were at least four regular integration sites. Interestingly, we found no case where phages of the same immunity class had different host attachment sites. The evolution of immunity and integration sites is complex, since it involves interactions both between the phages themselves and between phages and hosts, and often, both regulatory proteins and target DNA must change.

Amino Acid Sequence↗
PubMed2006

Wagner's canalization model.

Wagner (1996, Does evolutionary plasticity evolve? Evolution 50, 1008-1023.) and Siegal and Bergman, 2002 and Azevedo et al., 2006 have studied a simple model of the evolution of a network of N genes, in order to explain the observed phenomenon that systems evolve to be robust. These authors primarily considered the case N=10 and used simulations to reach their conclusions. Here we investigate this model in more detail, considering systems of different sizes with and without recombination, and with selection for convergence instead of to a specified limit. For the simpler evolutionary model lacking recombination, we analyze the system as a neutral network. This allows us to describe the equilibrium distribution networks within genotype space. Our results show that, given a sufficiently large population size, the qualitative observation that systems evolve to be robust, is itself robust, as it does not depend on the details of the model. In simple terms, robust systems have more viable offspring, so the evolution of robustness is merely selection for increased fecundity, an observation that is well known in the theory of neutral networks.

Biological Evolution↗
PubMed1981

Convergence to equilibrium states for a reaction-diffusion system modelling the spatial spread of a class of bacterial and viral diseases.

A reaction-diffusion system which describes the spatial spread of bacterial diseases is studied. It consists of two nonlinear parabolic equations which concern the evolution of the bacteria population and of the human infective population in an urban community, respectively. Different boundary conditions of the third type are considered, for the two variables. This model is suitable to study oro-faecal transmitted diseases in the European Mediterranean regions. A threshold parameter is introduced such that for suitable values of it the epidemic eventually tends to extinction, otherwise a globally asymptotically stable spatially inhomogeneous stationary endemic state appears. The case in which the bacteria diffuse but the human population does not, has also been considered.

Bacterial Infections↗
PubMed1989

Crystallite orientation discontinuities and the evolution of mammalian enamel--or, when is a prism?

The nature and relationship of crystallite domains have been explored in fossil and extant enamels spanning an evolutionary period of 200 x 10(6) years. Minor crystallite orientation discontinuities, either linear or planar, were found to be consistent characteristics of all specimens examined. The earliest minor discontinuity is linear (convergence line), shown here in Oligokyphus and Eozostrodon. The convergence line would be the result of the occasional development of a conical Tomes' process to the parent ameloblast. An increase in number and regularity of convergence lines, shown here in Haldanodon, marks the appearance of a regular pseudoprismatic enamel structure. The second minor discontinuity to appear is planar (seam), shown here in a dryolestid eupantothere. The seam has previously been deduced to relate developmentally to a central groove on the sloping floor-wall of the Tomes' process pit. Coincident with the appearance of the seam is that of a rudimentary major planar discontinuity which does not enclose a domain to constitute what would normally be acknowledged as a prism. Its developmental basis would be the establishment of a steep wall and floor (however partial in circumference) to the Tomes' process pit. The extent of the major planar discontinuities was found to increase subsequently to enclose a classically recognizable prismatic domain, shown here in Amphiperatherium, Hassianycteris, Smilodon and Felis. This would be consistent with the further development of a definitive floor and wall to the Tomes' process pit. The sequential appearance of minor linear, minor planar and major planar discontinuities in crystallite orientation is seen as fundamental to the evolution of mammalian enamel structure.

Animals↗
PubMed1995

Properties of evolutionarily stable learning rules.

Suppose a strategy for learning the optimal behavior in repeatedly played games is genetically determined. Then the animal is engaged in a learning game as well as the repeatedly played game. Harley (1981, J. theor. Biol. 89, 611-633) considers evolutionarily stable strategies in such learning games, called evolutionarily stable (ES) learning rules. Harley's work, though significant, is limited in that he does not establish the stochastic convergence of ES learning rules. Furthermore, his study of the relative payoff sum (RPS) approximation is limited to simulation experiments. Here, the stochastic convergence of ES learning rules and the RPS approximation is established. The ES learning rules and the RPS approximation were found to converge to the same quality, the so-called matching ratio, with probability one.

Animals↗
PubMed2000

Numerical study of the spherically symmetric gross-pitaevskii equation in two space dimensions

We present a numerical study of the time-dependent and time-independent Gross-Pitaevskii (GP) equation in two space dimensions, which describes the Bose-Einstein condensate of trapped bosons at ultralow temperature with both attractive and repulsive interatomic interactions. Both time-dependent and time-independent GP equations are used to study the stationary problems. In addition the time-dependent approach is used to study some evolution problems of the condensate. Specifically, we study the evolution problem where the trap energy is suddenly changed in a stable preformed condensate. In this case the system oscillates with increasing amplitude and does not remain limited between two stable configurations. Good convergence is obtained in all cases studied.

Journal Article↗
PubMed1982

[Phylogenetic aspect of human pathology].

In human diseases, the appearing signs of organisms more or less remote from man phylogenetically are usually considered to be atavisms which do not reflect the thesis of similarities in the evolutionary process. Phylogenetic similarities in human pathology represent recapitulations, parallelisms, and convergences. Since recapitulation was dealt with one of the previously published articles, this paper analyses parallelisms and convergences in pathology. By the examples of uterus malformations, gene and chromosome mutations, tumors, and tuberculosis it is shown that parallel development of a pathological sign consists in repetition in man of a species sign of an animal, in the emergence of phenotypically and genotypically homologous hereditary diseases, and in similar manifestations of modification changes of cells and tissues of man and other mammals. Convergent similarities even under pathological conditions develop in unrelated organisms. The subdivision of similarities existing in diseases into recapitulations, parallelisms, and convergences requires that the data of comparative anatomy and physiology, embryology and paleontology be taken into consideration.

Animals↗
PubMed1993

Molecular evidence that the spiny mouse (Acomys) is more closely related to gerbils (Gerbillinae) than to true mice (Murinae).

Spiny mice of the genus Acomys traditionally have been classified as members of the Murinae, a subfamily of rodents that also includes rats and mice with which spiny mice share a complex set of morphological characters, including a unique molar pattern. The origin and evolution of this molar pattern, documented by many fossils from Southern Asia, support the hypothesis of the monophyly of Acomys and all other Murinae. This view has been challenged by immunological studies that have suggested that Acomys is as distantly related to mice (Mus) as are other subfamilies (e.g., hamsters: Cricetinae) of the muroid rodents. We present molecular evidence derived from DNA.DNA hybridization data that indicate that the spiny mouse Acomys and two African genera of Murinae, Uranomys and Lophuromys, constitute a monophyletic clade, a view that was recently suggested on the basis of dental characters. However, our DNA.DNA hybridization data also indicate that the spiny mice (Acomys) are more closely related to gerbils (Gerbillinae) than to the true mice and rats (Murinae) with which they have been classified. Because Acomys and the brush-furred mice Uranomys and Lophuromys share no derived morphological characters with the Gerbillinae, their murine morphology must have evolved by convergence, including the molar pattern previously considered to support the monophyly of the Murinae.

Animals↗
PubMed2000

Evolution in the high Andes: the phylogenetics of Muscisaxicola ground-tyrants.

Phylogenetic relationships within the genus Muscisaxicola, a primarily Andean group of tyrant-flycatchers, were studied using complete sequences of the mitochondrial genes COII and ND3. Relationships among Muscisaxicola species were found to differ substantially from those of previous views, suggesting convergence in traditional avian taxonomic characters within the genus. The 11 species of large, gray, "typical" Muscisaxicola flycatchers (including M. grisea, newly restored to species status) formed a distinct clade, consisting of two major groups: a clade of 6 species breeding primarily in the central Andes and a clade of 5 species breeding primarily in the southern Andes. The other 2 species traditionally placed in this genus, M. fluviatilis, an Amazonian species, and M. maculirostris, were both rather divergent genetically from the typical species, although M. maculirostris may be the sister taxon to the typical clade. The patterns of sympatry exhibited by Muscisaxicola species in the high Andes appear to be the consequence of speciation and secondary contact within regions of the Andes, rather than a result of dispersal between regions. Diversification of the typical Muscisaxicola species appears to have occurred during the middle and late Pleistocene, suggesting generally that taxa of the high Andes and Patagonia may have been greatly influenced by mid-to-late Pleistocene events. There were likely several independent developments of migration within this genus, but migration is probably ancestral in the southern clade, with subsequent loss of migration in two taxa.

Animals↗
PubMed1995

Evolution of the NH2- and COOH-terminal extensions of chloroplast ribosomal protein S18. Nucleotide sequence of pea and rye chloroplast rps 18 genes.

An unusual, variably repeated heptapeptide motif is present in most chloroplast ribosomal protein S18 sequences (Weglöhner and Subramanian, FEBS Lett. 269, 193-197, 1991), whereas it is absent in bacterial, cyanelle, and in the chloroplast S18 of the lower plant liverwort. In order to understand the evolution of this higher plant-specific motif, we have cloned and sequenced chloroplast rps18 genes from pea, a dicot plant of the large legume family and rye, a monocot plant with temperature-sensitive chloroplast ribosome formation. The derived amino acid sequence of pea S18 protein shows two and that of rye seven repeats of this motif. We also show that a different heptapeptide motif is discernible in the recently published chloroplast S18 sequence of Pinus thunbergii (a gymnosperm), which can however be derived convergently from a putative progenitor of angiosperm-gymnosperm chloroplast S18. The presence of a 3-fold repeat of an asparagine-rich heptapeptide in the C-terminal extensions of all cereal S18 is also shown here. The results are further discussed in terms of possible origin of these repeats and the ribosomal protein evolution in general.

Amino Acid Sequence↗
PubMed2004

Evolution of robusta green coffee redox enzymatic activities with maturation.

Oxidation reactions in coffee involve redox-sensitive polyphenols and appear to control the fragmentation of coffee storage proteins both in solution and during roasting. Coffee-specific nitrogenous flavor precursors may derive from this process. Accordingly, data converge to suggest that the redox status of the green bean before roasting might control the development of subsequent redox reactions during roasting. Consequently, we decided to identify biological events that may trigger or prevent oxidation during maturation of the coffee cherry and set the final redox status of the green bean. In a previous study, we observed that the sensitivity of green coffee to oxidative processes decreased along maturation. By using the very same samples originating from open-pollinated Robusta clones, we followed the activity of three essential redox enzymes: catalase (CAT), peroxidase (POD) and polyphenoloxidase (PPO). While CAT and POD activities increased with maturation, PPO activities decreased. Thanks to the identification of an atypical immature subclass, it appeared that CAT might be an essential factor in setting the final redox status of the green bean before the roasting event.

Catalase↗
PubMed2004

Release of gold-bearing fluids in convergent margin magmas prompted by magnetite crystallization.

A relationship between convergent margin magmas and copper-gold ore mineralization has long been recognized. The nature of the genetic link is controversial, particularly whether the link is due to high-oxygen-fugacity (fO2) melts and fluids released from subducted slabs or to brine exsolution during magmatic evolution. For submarine, subduction-related volcanic glasses from the eastern Manus basin, Papua New Guinea, we here report abrupt decreases in gold and copper abundances, coupled with a switch in the behaviour of titanium and iron from concentration increases to decreases as SiO2 rises. We propose that the abrupt depletion in gold and copper results from concurrent sulphur reduction as a result of fO2 buffering, causing enhanced formation of copper-gold hydrosulphide complexes that become scavenged from crystallizing melts into cogenetic magmatic aqueous fluids. This process is particularly efficient in oxidized arc magmas with substantial sulphate. We infer that subsequent migration and cooling of exsolved aqueous fluids create links between copper-gold mineralization and arc magmatism in the Manus basin, and at convergent margins in general.

Journal Article↗
PubMedDate not supplied

Development and evolution of the mammalian limb: adaptive diversification of nails, hooves, and claws.

Paleontological evidence indicates that the evolutionary diversification of mammals early in the Cenozoic era was characterized by an adaptive radiation of distal limb structures. Likewise, neontological data show that morphological variation in distal limb integumentary appendages (e.g., nails, hooves, and claws) can be observed not only among distantly related mammalian taxa but also among closely related species within the same clade. Comparative analysis of nail, claw, and hoof morphogenesis reveals relatively subtle differences in mesenchymal and epithelial patterning underlying these adult differences in distal limb appendage morphology. Furthermore, studies of regulatory gene expression during vertebrate claw development demonstrate that many of the signaling molecules involved in patterning ectodermal derivatives such as teeth, hair, and feathers are also involved in organizing mammalian distal limb appendages. For example, Bmp4 signaling plays an important role during the recruitment of mesenchymal cells into the condensations forming the terminal phalanges, whereas Msx2 affects the length of nails and claws by suppressing proliferation of germinal epidermal cells. Evolutionary changes in the form of distal integumentary appendages may therefore result from changes in gene expression during formation of mesenchymal condensations (Bmp4, posterior Hox genes), induction of the claw fold and germinal matrix (shh), and/or proliferation of epidermal cells in the claw matrix (Msx1, Msx2). The prevalence of convergences and parallelisms in nail and claw structure among mammals underscores the existence of multiple morphogenetic pathways for evolutionary change in distal limb appendages.

Animals↗
PubMed2003

Epidemiological modeling in a branching population. Particular case of a general SIS model with two age classes.

This paper covers the elaboration of a general class of multitype branching processes for modeling in a branching population, the evolution of a disease with horizontal and vertical transmissions. When the size of the population may tend to infinity, normalization must be carried out. As the initial size tends to infinity, the normalized model converges a.s. to a dynamical system the solution of which is the probability law of the state of health for an individual ancestors line. The focal point of this study concerns the transient and asymptotical behaviors of a SIS model with two age classes in a branching population. We will compare the asymptotical probability of extinction on the scale of a finite population and on the scale of an individual in an infinite population: when the rates of transmission are small compared to the rate of renewing the population of susceptibles, the two models lead to a.s. extinction, giving consistent results, which no longer applies to the opposite situation of important transmissions. In that case the size of the population plays a crucial role in the spreading of the disease.

Age Factors↗
PubMed2004

Stability in negotiation games and the emergence of cooperation.

Consider a two-player game in which each player contributes a costly resource to the common good of the pair. For such contests, the Nash equilibrium contribution, x*, is one for which neither player can increase its pay-off by unilaterally altering its contribution from x*. We study an elaboration of this game, which allows the players to exchange x-offers back and forth in a negotiation phase until they converge to a final pair of contributions, x1 and x2. A significant feature of such negotiation games, hitherto unrecognized, is the existence of a set of neutrally stable equilibrium points in negotiation phase space. To explore the long-term evolutionary outcome of such games, we simulate populations containing various mixtures of negotiation strategies and, contrary to previous results, we often find convergence to a contribution that is more cooperative than the Nash equilibrium. Mathematical analysis suggests why this might be happening, and provides a novel and robust explanation for cooperation, that negotiation can facilitate the evolution of cooperative behaviour.

Biological Evolution↗
PubMed2001

Geographic variation in female preference functions and male songs of the field cricket Teleogryllus oceanicus.

Male crickets (Teleogryllus oceanicus) produce a complex call consisting of two elements, the long chirp (three to eight sound pulses) followed by a series of short chirps (each with two sound pulses). There is significant geographic variation in the temporal structure of calls, and the long chirp is selected against by acoustically orienting parasitoids in some populations. Here we examine geographic variation in female preference functions for the amount of long chirp. In general, females prefer calls with greater proportions of long chirp, although the strength and nature of selection varied across populations. Variation in preference functions did not match variation in call structure. There was a mismatch between the proportion of long chirp produced by males in a population and the proportion of long chirp preferred by females. The convergent preferences of predators and females are likely to maintain genetic variation in song traits in parasitized populations. The apparent mismatch between preference and trait is discussed in relation to theoretical models of preference evolution.

Animals↗
PubMed2005

Interactive volume reconstruction and measurement on the Grid.

OBJECTIVES: To prove the advantages of integrating grid computing within medical image analysis software, and to discuss the technological, sociological and health care-related issues. METHODS: Presentation of an instant volume reconstruction and measurement tool (PTM3D) used in clinical practice, including percutaneous nephrolithotomy examples; description of a parallel implementation of volume reconstruction, evaluation of this implementation on lung and body reconstruction, presentation of the technical limitations for clinical use and description and discussion of a prototype grid implementation. RESULTS: Volume reconstruction can broaden its medical scope and use by accessing high-performance computing systems; interactive exploration of medical images can co-exist with the usual batch workload of grid systems; the EGEE grid middleware offers some of the required core services; a fully adequate computing environment needs further evolution to integrate realtime constraints. CONCLUSIONS: Clinical experiments of a grid-enabled PTM3D become possible. Widespread adoption of grid technology in the medical images analysis field will benefit from this "early user" project. Convergences appear between two broadly different fields, high energy physics and medical image, towards the need of a smooth integration of the new resources offered by grid systems into the everyday tools of their respective end-users. It can be expected that the convergence will mature towards truly interactive grids, able to serve the needs of the medical community.

Algorithms↗