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Results for “directed evolution”

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At least 1,153 records · Page 64Linked to original sources
PubMed1980

Chromosomal interrelationship of hamster species of the genus Mesocricetus.

The similarity of chromosomes and the mode by which differences occurred in the chromosomes of the species comprising the genus Mesocricetus, M. auratus (2n = 44), two "cryptic" species of M. brandti (2n = 44 and 2n = 42) and M. newtoni (2n = 38) were determined. Most of the autosomes and the sex chromosomes have either complete or partial G-band correspondence and thus provide definitive evidence for the taxonomic relationship of these species. The karyotypic differences occurred primarily as a result of deletion of sex chromosome heterochromatin and of autosomal translocations that frequently involved chromosomes with heterochromatic short arms or chromosomes bearing NOR's. Only one Robertsonian centric fusion occurred. Despite the conservatism of arrangement of the genetic material, the chromosomal distribution of heterochromatin diverged during the evolution of these species. M. brandti and newtoni each have a metacentric chromosome with a common long arm matching a submetacentric M. auratus autosome, but a short arm corresponding to two different M. auratus chromosomes. These translocations are crucial for explaining the direction of chromosomal evolution of these species and indicate that M. auratus was the commmon ancestral species and that M. brandti and newtoni subsequently evolved independently.

Animals↗
PubMedDate not supplied

[Clinical forms of ischemic heart disease and natural evolution of live information-thermodynamic systems].

Clinical forms of myocardial ischemia are considered in terms of a new approach towards illness formation as a violation of information exchange in a human organism. The latter is suggested to be an open information-thermodynamic system developing to a closed equilibrium stationary thermodynamic system with information as a factor of system stability and direction of the evolution guided by the second thermodynamic law.

Angina Pectoris↗
PubMedDate not supplied

[Origin and evolution of the hamuli in the monogeneans].

The hypothesis of the origin and evolution of the hamuli in monogeneans is proposed. It is suggested that the hamuli originated as the adult attachment organs of protomonogeneans inhabited the gills of the first vertebrates. Primarily they were represented by two lateral pairs of large hooks disposed anterior to the larval haptor. The fundamental direction in the evolution of monogeneans was the concentration of all attachment structures on the growing haptor. It the course of this evolutionary process, the hamuli onchoblasts migrated to the haptor, in which they had reached the position in the hind part of the haptor. The neotenic evolution of the Dactylogyridea and Gyrodactyloidea resulted in the forming new hamuli pairs. The hooks of opposite sides of the haptor are joined in a single complex within each side by the transverse plates (bars). So the presence of 4 hamuli is plesiomorphy for all the monogeneans and the presence of the transverse bars and new hamuli pairs are apomorphy for the Dactylogyridea and Gyrodactyloidea, whose evolution was linked with that of the Teleostei. The origin of the new hamuli pairs and transverse bars in the Dactylogyridea and Gyrodactyloidea appears to be a convergence.

Animals↗
PubMed1999

Novel (CA)n marker DXYS241 on the nonrecombinant part of the human Y chromosome.

The origin of modern humans can be traced by comparing polymorphic sites in either mitochondria or genomic sequences between humans and other primates. The human Y chromosome has both a non-recombining region and X-Y homologous pseudo-autosomal regions. In the nonrecombining region events during evolution can be directly detected. At least a part of homology between Xq21 and Yp11 is a result of rather recent translocations from the X chromosome to the Y chromosome. DNA markers residing in the nonrecombining region of the human Y chromosome are potentially useful in tracing male-specific gene flow in human evolution. However, the number of available markers in the region is limited. Here, we report a novel X-Y homologous (CA)n repeat locus in the nonrecombining region of the Y chromosome. This marker, DXYS241, has several interesting features. Y- and X-chromosome alleles are distinguishable because the Y-chromosome alleles are shorter than the X-chromosome alleles most of the time. We developed 2 primer sets for specific examination of Y- and X-chromosome alleles. The marker should be useful in establishing relationships between populations based on patrilineal gene flow. Sequences homologous to DXYS241 are also found on the X chromosome of primates. Four events during primate evolution that led to the modern human Y chromosome were identified.

Alleles↗
PubMed2005

Intensity of malaria transmission and the evolution of drug resistance.

The intensity of malaria transmission varies both naturally and as a consequence of human public health intervention. The relationship between transmission intensity and the rate at which antimalarial drug resistance evolves affects the design of surveillance programmes, and the likely impact of malaria control programmes. Several theoretical studies have investigated this relationship and their key results are summarised and interpreted. The most important result is that transmission intensity does not directly affect the evolution of resistance. It exerts its influence through three clinical/epidemiological "mediators" (clonal multiplicity, the threat of infection, level of human immunity) which ultimately determine the dynamics of resistance via five "effector" variables: sexual recombination, intrahost dynamics, community drug use, proportion of malaria infections treated, and the number of parasites per host. We argue that the evolution of resistance is likely to be a two-stage process: mutations encoding drug tolerance preceding those encoding resistance. The evolution of drug tolerance is determined solely by the level of drug use in the community which is likely to have an extremely weak relationship with transmission intensity. The evolution of resistance is more complex and affected by all five effectors. The most likely scenarios are that resistance evolves faster in areas of high transmission if encoded by a single gene but if encoded by two or more genes it evolves fastest in areas of high or low transmission, with a minimum at intermediate levels of transmission.

Animals↗
PubMed2001

The outlook for cosmic company.

The last 100 million years or so has seen a continued increase in encephalization for several terrestrial species. Intelligence has survival value. Developments in astrobiology suggest that what was once considered enormously improbable, namely life, is now suspected of being ubiquitous. It may be that the evolution of intelligence is unlikely, but in a finite, breathtakingly large universe (10(22) stars) small probability likely does not matter. Even if nature is indifferent to producing intelligence, SETI might still succeed. Biological intelligence may be rare, but it has the potential for creating engineered synthetic intelligence, capable of rapid and directed self-evolution. The galaxy could be rife with such long-lived, communicating devices, even if intelligent protoplasm is both rare and fleeting. SETI is looking for narrow-band, microwave signals that are not produced naturally. Ultimately, SETI is more exploration than experimentation.

Artificial Intelligence↗
PubMed2002

Gene duplication and divergence in the early evolution of vertebrates.

The duplication-degeneration-complementation model of duplicate gene preservation by subfunctionalisation is currently the best explanation for the high level of retention of duplicate genes in early vertebrate evolution. But a direct test of the applicability of this model to such ancient evolutionary events may be difficult. More likely, recent duplications in other lineages will allow us to establish general principles concerning the fate of genes of different types that are duplicated in different ways. These principles may be then extrapolated to understanding the early evolution of the vertebrates.

Animals↗
PubMed1995

[A modern view of the evolution of virulence].

According to the prevailing, traditional view parasites should develop reduced virulence towards their hosts, because more virulent pathogens are more likely to drive the hosts, and thus themselves to extinction. Virulence is considered to be a primitive stage of a parasitive-host association. However the usefulness and validity of this view have been questioned. Recent studies suggest that parasites need not necessarily evolve towards reduced virulence. The points of view of Darwinian medicine in the direction of the evolution of virulence there may be many possible coevolutionary trajectories, depending on the details of the parasite's life-history, the host's behavior and the transmissibility of the parasite. Theoretical and epidemiological evidences indicate that pathogens transmitted by arthropod vectors are significantly more lethal to humans than those transmitted by personal contact. Water borne enteric pathogens are less virulent after purification of water supplies. Recent experiments also support the emerging theory that parasitism can evolve to be either more or less virulent in a long-term host, depending on the way the parasite is transmitted to the host and on the environment in which they live.

Animals↗
PubMed2005

Divergence, recombination and retention of functionality during protein evolution.

We have only a vague idea of precisely how protein sequences evolve in the context of protein structure and function. This is primarily because structural and functional contexts are not easily predictable from the primary sequence, and evaluating patterns of evolution at individual residue positions is also difficult. As a result of increasing biodiversity in genomics studies, progress is being made in detecting context-dependent variation in substitution processes, but it remains unclear exactly what context-dependent patterns we should be looking for. To address this, we have been simulating protein evolution in the context of structure and function using lattice models of proteins and ligands (or substrates). These simulations include thermodynamic features of protein stability and population dynamics. We refer to this approach as 'ab initio evolution' to emphasise the fact that the equilibrium details of fitness distributions arise from the physical principles of the system and not from any preconceived notions or arbitrary mathematical distributions. Here, we present results on the retention of functionality in homologous recombinants following population divergence. A central result is that protein structure characteristics can strongly influence recombinant functionality. Exceptional structures with many sequence options evolve quickly and tend to retain functionality--even in highly diverged recombinants. By contrast, the more common structures with fewer sequence options evolve more slowly, but the fitness of recombinants drops off rapidly as homologous proteins diverge. These results have implications for understanding viral evolution, speciation and directed evolutionary experiments. Our analysis of the divergence process can also guide improved methods for accurately approximating folding probabilities in more complex but realistic systems.

Evolution, Molecular↗
PubMed1990

The involucrin genes of pig and dog: comparison of their segments of repeats with those of prosimians and higher primates.

The involucrin genes of the dog and the pig have been cloned and sequenced. Like the corresponding genes of the prosimians, each contains a homologous segment of short tandem repeats at the same position in the coding region. However, the codon sequence of the repeats in the prosimians differs significantly from that of the nonprimate mammals. This evolution has been brought about by a combination of genetic modifications (selective deletions, mutations, and gene conversions). In the anthropoids, this segment of repeats was replaced by a modern one differing in location, sequence, and repeat length. In several of its properties the modern segment has continued the prosimian trend away from the nonprimates. The overall direction of the evolution of this segment has therefore been maintained even though there have been sudden changes in the evolutionary processes acting on the gene.

Animals↗
PubMed2004

Detection of BCR/ABL fusion product in normoblasts in a case of chronic myelogenous leukemia.

Erythroblast phase of chronic myelogenous leukemia (CML) and Philadelphia chromosome-positive acute erythroid leukemia are rare events. The distinction between these two entities is poorly defined. The World Health Organization (WHO) classification requires the presence of more than 50% of erythroblasts in the bone marrow for the diagnosis of both the erythroid/myeloid or pure erythroid subtypes of acute erythroid leukemia. However, in previous studies of erythroblast crisis CML, the percentage of erythroid series in the bone marrow is seldom mentioned and the direct relationship of the erythroblasts and the Philadelphia chromosome has never been established. We report a well-documented case of acute erythroid leukemia transformed from CML. The studies in morphology, immunohistochemistry, and flow cytometry fulfill the WHO criteria for the diagnosis of acute erythroid leukemia, and yet the complex karyotype containing Philadelphia chromosome indicates genetic evolution. Finally, the direct demonstration of the BCR/ABL fusion product by fluorescence in situ hybridization in the erythroblasts provides concrete evidence that the erythroblasts are part of the leukemic process and not an innocent bystander.

Erythroblasts↗
PubMed1995

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming.

BACKGROUND: An important prerequisite for computational structure-based drug design is prediction of the structures of ligand-protein complexes that have not yet been experimentally determined by X-ray crystallography or NMR. For this task, docking of rigid ligands is inadequate because it assumes knowledge of the conformation of the bound ligand. Docking of flexible ligands would be desirable, but requires one to search an enormous conformational space. We set out to develop a strategy for flexible docking by combining a simple model of ligand-protein interactions for molecular recognition with an evolutionary programming search technique. RESULTS: We have developed an intermolecular energy function that incorporates steric and hydrogen-bonding terms. The parameters in this function were obtained by docking in three different protein systems. The effectiveness of this method was demonstrated by conformationally flexible docking of the inhibitor AG-1343, a potential new drug against AIDS, into HIV-1 protease. For this molecule, which has nine rotatable bonds, the crystal structure was reproduced within 1.5 A root-mean-square deviation 34 times in 100 simulations, each requiring eight minutes on a Silicon Graphics R4400 workstation. The energy function correctly evaluates the crystal structure as the global energy minimum. CONCLUSIONS: We believe that a solution of the docking problem may be achieved by matching a simple model of molecular recognition with an efficient search procedure. The necessary ingredients of a molecular recognition model include only steric and hydrogen-bond interaction terms. Although these terms are not necessarily sufficient to predict binding affinity, they describe ligand-protein interactions faithfully enough to enable a docking program to predict the structure of the bound ligand. This docking strategy thus provides an important tool for the interdisciplinary field of rational drug design.

Biological Evolution↗
PubMed2003

Engineering evolution to study speciation in yeasts.

The Saccharomyces 'sensu stricto' yeasts are a group of species that will mate with one another, but interspecific pairings produce sterile hybrids. A retrospective analysis of their genomes revealed that translocations between the chromosomes of these species do not correlate with the group's sequence-based phylogeny (that is, translocations do not drive the process of speciation). However, that analysis was unable to infer what contribution such rearrangements make to reproductive isolation between these organisms. Here, we report experiments that take an interventionist, rather than a retrospective approach to studying speciation, by reconfiguring the Saccharomyces cerevisiae genome so that it is collinear with that of Saccharomyces mikatae. We demonstrate that this imposed genomic collinearity allows the generation of interspecific hybrids that produce a large proportion of spores that are viable, but extensively aneuploid. We obtained similar results in crosses between wild-type S. cerevisiae and the naturally collinear species Saccharomyces paradoxus, but not with non-collinear crosses. This controlled comparison of the effect of chromosomal translocation on species barriers suggests a mechanism for the generation of redundancy in the S. cerevisiae genome.

Aneuploidy↗
PubMed2006

The stepwise evolution of early life driven by energy conservation.

Two main theories have emerged for the origin and early evolution of life based on heterotrophic versus chemoautotrophic metabolisms. With the exception of a role for CO, the theories have little common ground. Here we propose an alternative theory for the early evolution of the cell which combines principal features of the widely disparate theories. The theory is based on the extant pathway for conversion of CO to methane and acetate, largely deduced from the genomic analysis of the archaeon Methanosarcina acetivorans. In contrast to current paradigms, we propose that an energy-conservation pathway was the major force which powered and directed the early evolution of the cell. We envision the proposed primitive energy-conservation pathway to have developed sometime after a period of chemical evolution but prior to the establishment of diverse protein-based anaerobic metabolisms. We further propose that energy conservation played the predominant role in the later evolution of anaerobic metabolisms which explains the origin and evolution of extant methanogenic pathways.

Acetates↗
PubMed1998

Assembly of exons from unitary transposable genetic elements: implications for the evolution of protein-protein interactions.

The discovery of "genes-in pieces" provided the first evidence that modern proteins evolved through the assembly and shuffling of simpler building blocks-generally equated with exons. In the theoretical model presented here, it is suggested that exons were created from even smaller modules that have been termed duplication units. Furthermore, these segments may represent the ultimate building blocks for protein assembly. The nucleotide sequences of the duplication units to appear to resemble those mobile genetic elements such as transposons or insertion sequences, i.e. they possess direct repeats at each end and inverted sequences extending 15-25 base pairs from these direct repeats. During evolution, these transposable exons (trexons) would have been replicated and dispersed in the genome thereby promoting homologous recombination and further duplication. Thus, the transposition and splicing of these gene segments gave rise to increasingly complex proteins as well as multi-gene families of proteins. It has been proposed that peptides encoded by the first trexons were predisposed to form dimers or oligomers. Detailed structural analysis of various protein-protein complexes has revealed a tendency for the duplication units to self-associate. Self-binding peptides could have ultimately led to the evolution of protein ligands and receptors with high affinity.

Amino Acid Sequence↗