Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “directed evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60Linked to original sources
PubMed2000

Ribozyme-catalyzed tRNA aminoacylation.

The RNA world hypothesis implies that coded protein synthesis evolved from a set of ribozyme catalyzed acyl-transfer reactions, including those of aminoacyl-tRNA synthetase ribozymes. We report here that a bifunctional ribozyme generated by directed in vitro evolution can specifically recognize an activated glutaminyl ester and aminoacylate a targeted tRNA, via a covalent aminoacyl-ribozyme intermediate. The ribozyme consists of two distinct catalytic domains; one domain recognizes the glutamine substrate and self-aminoacylates its own 5'-hydroxyl group, and the other recognizes the tRNA and transfers the aminoacyl group to the 3'-end. The interaction of these domains results in a unique pseudoknotted structure, and the ribozyme requires a change in conformation to perform the sequential aminoacylation reactions. Our result supports the idea that aminoacyl-tRNA synthetase ribozymes could have played a key role in the evolution of the genetic code and RNA-directed translation.

Acylation↗
PubMed2002

Near-neutrality in evolution of genes and gene regulation.

The nearly neutral theory contends that the interaction of drift and selection is important and occurs at various levels, including synonymous and nonsynonymous substitutions in protein coding regions and sequence turnover of regulatory elements. Recent progress of the theory is reviewed, and the interaction between drift and selection is suggested to differ at these different levels. Weak selective force on synonymous changes is stable, whereas its consequence on nonsynonymous changes depends on environmental factors. Selection on differentiation of regulatory elements is even more dependent on environmental factors than on amino acid changes. Of particular significance is the role of drift in the evolution of gene regulation that directly participates in morphological evolution. The range of near neutrality depends on the effective size of the population that is influenced by selected linked loci. In addition to the effective population size, molecular chaperones such as heat shock protein 90 have significant effects on the range of near neutrality.

Amino Acid Substitution↗
PubMed2006

Conserved phenotypic variation patterns, evolution along lines of least resistance, and departure due to selection in fossil rodents.

Within a group of organisms, some morphologies are more readily generated than others due to internal developmental constraints. Such constraints can channel evolutionary changes into directions corresponding to the greatest intraspecific variation. Long-term evolutionary outputs, however, depend on the stability of these intraspecific patterns of variation over time and from the interplay between internal constraints and selective regimes. To address these questions, the relationship between the structure of phenotypic variance covariance matrices and direction of morphological evolution was investigated using teeth of fossil rodents. One lineage considered here leads to Stephanomys, a highly specialized genus characterized by a dental pattern supposedly favoring grass eating. Stephanomys evolved in the context of directional selection related to the climatic trend of global cooling causing an increasing proportion of grasslands in southwestern Europe. The initial divergence (up to approximately 6.5 mya) was channeled along the direction of greatest intraspecific variation, whereas after 6.5 mya, morphological evolution departed from the direction favored by internal constraints. This departure from the "lines of least resistance" was likely the consequence of an environmental degradation causing a selective gradient strong enough to overwhelm the constraints to phenotypic evolution. However, in a context of stabilizing selection, these constraints actually channel evolution, as exemplified by the lineage of Apodemus. This lineage retained a primitive diet and dental pattern over the last 10 myr. Limited morphological changes occurred nevertheless in accordance with the main patterns of intraspecific variation. The importance of these lines of least resistance directing long-term morphological evolution may explain parallel evolution of some dental patterns in murine evolution.

Animals↗
PubMed2007

Reinforcement of mate preference among hybridizing Heliconius butterflies.

Recent models of mate preference evolution suggest that direct selection on alleles at preference loci and correlated evolution of preference with locally adapted mating cues are more likely to drive the evolution of assortative mate preference than reinforcement. Mate preference evolution in mimetic Heliconius butterflies has been attributed to all three forms of selection, but here we show that reinforcement has been critical. By examining geographical variation in assortative mating and male mate preference among seven populations of three hybridizing Heliconius species from Costa Rica, we found pronounced character displacement of preference such that sexual isolation was enhanced in areas of interspecific contact. Of the different explanations for the evolution of assortative mate preference, only reinforcement is dependent on interspecific contact in this system. Thus, the observed pattern of reproductive character displacement of mate preference is best explained as a product of indirect selection generated by natural selection against nonmimetic hybrids.

Animals↗
PubMed2003

[Role of horizontal gene transfer by bacteriophages in the origin of pathogenic bacteria].

The review considers the involvement of bacteriophages in transferring genes, which determine bacterial pathogenicity, and the increasing role of comparative genomics and genetics of bacteria and bacteriophages in detecting new cases of horizontal gene transfer. Examples of phage participation in this process proved to a different extent are described. Emphasis is placed on the original work carried out in Russia and focused on bacteriophages (temperate transposable phages and giant virulent phi KZ-like phages) of conditional pathogen Pseudomonas aeruginosa. Consideration is given to the possible lines of further research of the role of bacteriophages in the infection process and, in particular, the role of virulent phages, whose products are similar to those of pathogenic bacteria, in modification of clinical signs of infectious diseases and in evolution. An attempt is made to predict the possible direction of pathogen evolution associated with development of new treatment strategies and generation of new specific niches.

Animals↗
PubMed1987

Directional fixation of mutations in vertebrate evolution.

We have made pairwise comparisons between the coding sequences of 21 genes from cold-blooded vertebrates and 41 homologous sequences from warm-blooded vertebrates. In the case of 12 genes, GC levels were higher, especially in third codon positions, in warm-blooded vertebrates compared to cold-blooded vertebrates. Six genes showed no remarkable difference in GC level and three showed a lower level. In the first case, higher GC levels appear to be due to a directional fixation of mutations, presumably under the influence of body temperature (see Bernardi and Bernardi 1986b). These GC-richer genes of warm-blooded vertebrates were located, in all cases studied, in isochores higher in GC than those comprising the homologous genes of cold-blooded vertebrates. In the third case, increases appear to be due to a limited formation of GC-rich isochores which took place in some cold-blooded vertebrates after the divergence of warm-blooded vertebrates. The directional changes in the GC content of coding sequences and the evolutionary conservation of both increased and unchanged GC levels are in keeping with the existence of compositional constraints on the genome.

Animals↗
PubMed2004

Evolution of insomnia: current status and future direction.

Traditional epidemiologic studies of insomnia provide valid but fairly rudimentary information regarding the presence, frequency, duration and evolution of sleep problems. Standardized tools such as validated questionnaires (e.g., Pittsburgh Sleep Quality Index and sleep logs) help assess the presence and severity of sleep problems, while other methods (e.g., SLEEP L system) address insomnia diagnoses. Other instruments (e.g., Structured Clinical Interview for DSM-IV [SCID], Short-Form 36 [SF-36], Epworth Sleepiness Scale [ESS]) provide insights into insomnia consequences and co-morbidities. Sleep laboratory studies using polysomnography (PSG) have also provided useful findings (e.g., relating to sleep apnea and excessive daytime sleepiness) in experimental and population-based patient samples containing subgroups enriched for certain variables under investigation. These methods have significantly increased our knowledge about insomnia. Critically, longitudinal studies are needed to further our understanding of the pathophysiology and morbidity of insomnia, defining roles for risk factors, hyperarousal and co-morbidities and the effects of treatment in long-term disease progression. This review summarizes the current available data on the evolution of insomnia and proposes a model that warrants further research attention and discussion.

Comorbidity↗
PubMed1981

Turnover of mouse intestinal brush border membrane proteins and enzymes in organ culture. A direct evaluation from studies on the evolution of enzyme activities during the culture.

The turnover of mouse intestinal brush border membrane enzymes has been studied by kinetic analysis of the evolution of enzyme activities during organ culture. By comparing the results obtained in these studies with the predictions from a mathematical model of enzyme synthesis and degradation in organ cultures, it has been possible to reach the following conclusions: (1) There is no degradation of brush border membrane enzymes during culture and the rate of synthesis of each enzyme is directly measurable from the kinetics of total enzyme accumulation (tissue + media). (2) Brush border membrane enzymes are released in culture media by two complementary processes. The first one involves a differential solubilization of enzymes but its exact nature cannot be exactly stated. The second one involves a microvesiculation of brush border membranes, the importance of which in vivo is seen in the possible conciliation between urinary membrane synthesis and heterogeneous turnover of membrane components.

Alkaline Phosphatase↗
PubMed2003

The role of phenotypic plasticity in driving genetic evolution.

Models of population divergence and speciation are often based on the assumption that differences between populations are due to genetic factors, and that phenotypic change is due to natural selection. It is equally plausible that some of the differences among populations are due to phenotypic plasticity. We use the metaphor of the adaptive landscape to review the role of phenotypic plasticity in driving genetic evolution. Moderate levels of phenotypic plasticity are optimal in permitting population survival in a new environment and in bringing populations into the realm of attraction of an adaptive peak. High levels of plasticity may increase the probability of population persistence but reduce the likelihood of genetic change, because the plastic response itself places the population close to a peak. Moderate levels of plasticity arise whenever multiple traits, some of which are plastic and others not, form a composite trait involved in the adaptive response. For example, altered behaviours may drive selection on morphology and physiology. Because there is likely to be a considerable element of chance in which behaviours become established, behavioural change followed by morphological and physiological evolution may be a potent force in driving evolution in novel directions. We assess the role of phenotypic plasticity in stimulating evolution by considering two examples from birds: (i) the evolution of red and yellow plumage coloration due to carotenoid consumption; and (ii) the evolution of foraging behaviours on islands. Phenotypic plasticity is widespread in nature and may speed up, slow down, or have little effect on evolutionary change. Moderate levels of plasticity may often facilitate genetic evolution but careful analyses of individual cases are needed to ascertain whether plasticity has been essential or merely incidental to population differentiation.

Adaptation, Biological↗
PubMed1990

[Evolution of the locomotor-sensory systems].

Among directing physical factors of evolution of the locomotor-sensory system (LSS) gravitation, photons energy, oscillations of water and air media, ligands play the main role. At the molecular level the LSS elements are formed on the base of synthesizing genes that bring about development of protein molecules of tubulin and specific protonizing proteins in composition of the locomotor apparatus in Procariota flagellas. Tubulin and dinein with ATPh-ase activity are included in the flagella composition of LSS in Eukaryota, actin and miozin--with a high ATPh-ase activity--in composition of LSS myofilaments in ameboid Eukaryota and locomotor musculature in Metazoa. Simultaneously, in Pro- and Eukaryota in the same cell sensory molecules of rhodopsin, mechanoreceptors, chemoreceptors and so on can be synthesized. As a rule they localize in the flagellar membranes. In Metazoa single receptory flagellar cells are differentiated; they realize conservatively some receptive molecules that are already prepared by their ancessors--Eukaryota. The molecules also preserve their localization in the flagellar membranes. In Metazoa two types of locomotion take place according to the function of regulatory genes: initial flagellar and muscular definitive apparatus. Both types of locomotion are directed and regulated by the organs of sense and CNS; they form a strict spatial model of fixated synaptic connections of LSS. For the first time it was discovered in Ctenophora. This model, despite a complicated organization, is conservatively preserved in its general form in all Proto- and Denterostomia.

Animals↗
PubMed1975

A theory of evolution above the species level.

Gradual evolutionary change by natural selection operates so slowly within established species that it cannot account for the major features of evolution. Evolutionary change tends to be concentrated within speciation events. The direction of transpecific evolution is determined by the process of species selection, which is analogous to natural selection but acts upon species within higher taxa rather than upon individuals within populations. Species selection operates on variation provided by the largely random process of speciation and favors species that speciate at high rates or survive for long periods and therefore tend to leave many daughter species. Rates of speciation can be estimated for living taxa by means of the equation for exponential increase, and are clearly higher for mammals than for bivalve mollusks.

Adaptation, Biological↗
PubMed2002

[CT-colonography: current status and future directions in consideration of the technical evolution].

Computertomography and with it CT-colonography evolves technically and also possibilities of data processing proceed rapidly. The current status of CTC can be summarized as follows:The method represents a true alternative to barium enema if technical conditions are given.CTC can be performed with excellent results immediately following an incomplete colonoscopy. In pretherapeutic diagnosis of colorectal carcinoma, CTC can be combined with a staging CT of the abdomen. The recent technical advances with new 16 row technology in image quality and data acquisition - mainly concerning the spatial and temporal resolution - are very promising. Developments in postprocessing of CT data can also contribute to a higher efficiency of labor. Alternative preparation schemata can lead to a more comfortable bowel cleansing and stool labeling can even avoid this procedure, resulting both in an even improved compliance. Radiation exposure in low dose technique is comparable to a double contrast barium enema and can be still reduced by optimisation of scanning parameters.The aim of the following article is (1 to give an overview of the current status of patient preparation, image acquisition and data processing; (2) to review recent clinical trials and experimental studies and to show future directions of CTC with regard to the clinical development.

Colonic Polyps↗
PubMed2006

Evolution of cytokine responses: IL-1beta directly affects intracellular Ca2+ concentration of teleost fish leukocytes through a receptor-mediated mechanism.

In this work we studied the biological activities of recombinant IL-1beta from the teleosts sea bass (Dicentrarchus labrax) and rainbow trout (Oncorhynchus mykiss) by investigating the effects induced on intracellular Ca2+ concentrations ([Ca2+]i) of spleen leucocytes. Splenocytes were loaded with the Ca2+-permeant Fura-2AM, and then stimulated with rIL-1beta. The emitted fluorescence was read for 5 min at 1 min intervals on a dual excitation fluorescence fluorimeter. Results showed that rIL-1beta induced in both species a rise in [Ca2+]i, and a subsequent decrease until 5 min after stimulation. The stimulating effect was dose-dependent in both species reaching a plateau at 200 ng/ml of rIL-1beta, was abolished by heat-treatment of rIL-1beta, and affected in a dose-dependent fashion by treatment of leucocytes with trypsin. These features suggested a functional IL-1 receptor was involved in the binding. The observed rise in [Ca2+]i was not detected in human PBMC and was species-specific, since rIL-1beta from sea bass, trout, and human were unable to interfere each other in the assay. Moreover, incubation of splenocytes with rIL-1beta induced a rapid tyrosine phosphorylation of a 24 kDa polypeptide in both species. This work represents the first evidence of a direct effect on [Ca2+]i induced by IL-1beta and suggests that in the evolution of IL-1 activities, teleost fishes display a peculiar IL-1-associated behaviour that is lacking in mammals.

Animals↗
PubMed2001

In vitro evolution suggests multiple origins for the hammerhead ribozyme.

The hammerhead ribozyme was originally discovered in a group of RNAs associated with plant viruses, and has subsequently been identified in the genome of the newt (Notophthalamus viridescens), in schistosomes and in cave crickets (Dolichopoda species). The sporadic occurrence of this self-cleaving RNA motif in highly divergent organisms could be a consequence of the very early evolution of the hammerhead ribozyme, with all extant examples being descended from a single ancestral progenitor. Alternatively, the hammerhead ribozyme may have evolved independently many times. To better understand the observed distribution of hammerhead ribozymes, we used in vitro selection to search an unbiased sample of random sequences for comparably active self-cleaving motifs. Here we show that, under near-physiological conditions, the hammerhead ribozyme motif is the most common (and thus the simplest) RNA structure capable of self-cleavage at biologically observed rates. Our results suggest that the evolutionary process may have been channelled, in nature as in the laboratory, towards repeated selection of the simplest solution to a biochemical problem.

Base Sequence↗