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At least 1,675 records · Page 93Linked to original sources
PubMed2006

Protective effect of agmatine on a reperfusion model after transient cerebral ischemia: Temporal evolution on perfusion MR imaging and histopathologic findings.

BACKGROUND AND PURPOSE: The goal of thrombolytic therapy in patients with acute ischemic stroke is early recanalization, but this may result in delayed reperfusion injury. The purpose of this study was to evaluate the neuroprotective effect of agmatine in a transient ischemic cat model by using MR perfusion imaging and histopathologic analyses. METHOD: One-hour temporary occlusion of the left middle cerebral artery of cats was performed in the control ischemia group (n = 10), and 100 mg/kg of agmatine was intravenously injected immediately after recanalization in the agmatine-treated group (n = 15). MR imaging was performed at 1, 24, and 48 hours after recanalization, and the perfusion patterns were investigated. Terminal-deoxynucleotidyl transferase mediated nick and end-labeling (TUNEL) and hematoxylin-eosin (H&E) stainings were performed at the corresponding sections. RESULTS: In the control ischemia group, the number of TUNEL-positive cells was significantly increased in the areas with reperfusion hyperemia (P < .05). In the agmatine-treated group, no significant increase in the number of TUNEL-positive cells was noted in the areas of reperfusion hyperemia. The difference in the number of TUNEL-positive cells between the control ischemia and agmatine-treated group in the areas of reperfusion hyperemia was significant (P < .05). The total number of TUNEL-positive cells and the area of severe ischemic neuronal damage on H&E stain were also significantly attenuated in the agmatine-treated cats compared with the control ischemia cats (P < .05). CONCLUSION: Our results suggest that agmatine has neuroprotective effects against reperfusion injury and ischemia.

Agmatine↗
PubMed1999

The antibiotic viomycin as a model peptide for the origin of the co-evolution of RNA and proteins.

Viomycin is an RNA-binding peptide antibiotic which inhibits prokaryotic protein synthesis and group I intron self-splicing. This antibiotic enhances the activity of the ribozyme derived from the Neurospora crassa VS RNA, and at sub-inhibitory concentrations it induces the formation of group I intron oligomers. Here, we address the question whether viomycin exerts specificity in the promotion of RNA-RNA interactions. In an in vitro selection experiment we tested the ability of viomycin to specifically select molecules out of an RNA pool. Group I intron RNA was incubated with a pool of random sequence RNA, or with a pool of RNA molecules which had previously been enriched for viomycin-binding RNAs. Viomycin was added in order to select viomycin-binding RNAs and to guide their interaction with the intron RNA resulting in recombinant molecules. Viomycin was indeed capable of specifically selecting RNA molecules which contain viomycin-binding sites promoting recombination. These results suggest that small peptides are able to play the role of selector molecules in a putative 'RNA World' launching the co-evolution of RNA and proteins into an 'RNA-protein World'.

Anti-Bacterial Agents↗
PubMed2004

Combining phylogenetic and hidden Markov models in biosequence analysis.

A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site to the next. These models combine phylogenetic models of molecular evolution, which apply to individual sites, and hidden Markov models, which allow for changes from site to site. Besides improving the realism of ordinary phylogenetic models, they are potentially very powerful tools for inference and prediction--for example, for gene finding or prediction of secondary structure. In this paper, we review progress on combined phylogenetic and hidden Markov models and present some extensions to previous work. Our main result is a simple and efficient method for accommodating higher-order states in the HMM, which allows for context-dependent models of substitution--that is, models that consider the effects of neighboring bases on the pattern of substitution. We present experimental results indicating that higher-order states, autocorrelated rates, and multiple functional categories all lead to significant improvements in the fit of a combined phylogenetic and hidden Markov model, with the effect of higher-order states being particularly pronounced.

Computational Biology↗
PubMed2003

Deletion bias in avian introns over evolutionary timescales.

The role that introns play in the function and evolution of nuclear genomes is not fully understood. Recent models of intron evolution suggest that selection and drift may interact to maintain introns in multicellular organisms. In addition, deletion mutations are more likely to become fixed than insertion mutations. Examination of indel substitutions over macroevolutionary timescales in pigeons and doves (Aves: Columbiformes) reveals that deletion substitutions outnumber insertion substitutions by over six times. The length of indel events is variable.

Animals↗
PubMed2000

The role of the clinical nurse specialist/neonatal nurse practitioner in a breastfeeding clinic: a model of advanced practice.

A commitment to quality health care requires the development of innovative models of care. An example of such a model is the Clinical Nurse Specialist/Neonatal Nurse Practitioner in the role as consultant to Lactation Consultants in a large breastfeeding clinic. The role of the Clinical Nurse Specialist/Neonatal Nurse Practitioner in this ambulatory setting encompasses all the dimensions of the advanced practice model including research, leadership, education, and clinical practice. The evolution of this model of care is described. A conceptual framework of this advanced practice model is presented, supported by examples of the role in the clinic.

Adult↗
PubMed2004

Networking the seceder model: Group formation in social and economic systems.

The seceder model illustrates how the desire to be different from the average can lead to formation of groups in a population. We turn the original, agent based, seceder model into a model of network evolution. We find that the structural characteristics of our model closely match empirical social networks. Statistics for the dynamics of group formation are also given. Extensions of the model to networks of companies are also discussed.

Journal Article↗
PubMed2005

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence patterns is the comparative analysis of orthologous intergenic regions of related species. This analysis is complicated by various factors. First, one needs to take the phylogenetic relationship between the species into account in order to distinguish conservation that is due to the occurrence of functional sites from spurious conservation that is due to evolutionary proximity. Second, one has to deal with the complexities of multiple alignments of orthologous intergenic regions, and one has to consider the possibility that functional sites may occur outside of conserved segments. Here we present a new motif sampling algorithm, PhyloGibbs, that runs on arbitrary collections of multiple local sequence alignments of orthologous sequences. The algorithm searches over all ways in which an arbitrary number of binding sites for an arbitrary number of transcription factors (TFs) can be assigned to the multiple sequence alignments. These binding site configurations are scored by a Bayesian probabilistic model that treats aligned sequences by a model for the evolution of binding sites and "background" intergenic DNA. This model takes the phylogenetic relationship between the species in the alignment explicitly into account. The algorithm uses simulated annealing and Monte Carlo Markov-chain sampling to rigorously assign posterior probabilities to all the binding sites that it reports. In tests on synthetic data and real data from five Saccharomyces species our algorithm performs significantly better than four other motif-finding algorithms, including algorithms that also take phylogeny into account. Our results also show that, in contrast to the other algorithms, PhyloGibbs can make realistic estimates of the reliability of its predictions. Our tests suggest that, running on the five-species multiple alignment of a single gene's upstream region, PhyloGibbs on average recovers over 50% of all binding sites in S. cerevisiae at a specificity of about 50%, and 33% of all binding sites at a specificity of about 85%. We also tested PhyloGibbs on collections of multiple alignments of intergenic regions that were recently annotated, based on ChIP-on-chip data, to contain binding sites for the same TF. We compared PhyloGibbs's results with the previous analysis of these data using six other motif-finding algorithms. For 16 of 21 TFs for which all other motif-finding methods failed to find a significant motif, PhyloGibbs did recover a motif that matches the literature consensus. In 11 cases where there was disagreement in the results we compiled lists of known target genes from the literature, and found that running PhyloGibbs on their regulatory regions yielded a binding motif matching the literature consensus in all but one of the cases. Interestingly, these literature gene lists had little overlap with the targets annotated based on the ChIP-on-chip data. The PhyloGibbs code can be downloaded from http://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/phylogibbs.cgi or http://www.imsc.res.in/~rsidd/phylogibbs. The full set of predicted sites from our tests on yeast are available at http://www.swissregulon.unibas.ch.

Algorithms↗
PubMed1986

[Various characteristics of gene localization in eukaryotic chromosomes. Formulation of a problem and analysis of non-random localization of mating type loci in fungi].

We have denoted two possible models of gene order evolution as the "card" and "chess" models. The first suggests random shuffling of genes during evolution, the second--non-random gene transposition, gene order being checked by natural selection. We discuss here localization of the mating type locus in fungal genomes. In 8 of 10 genetically well studied species of ascomycetous fungi, the mating type locus is linked to a centromere; in one species, it segregates regularly during the second meiotic division, and only one species does not show any regularity in the mating type locus segregation. Centromeric linkage of the mating type locus maintains heterozygosity of all centromeric genome regions during intratetrad fertilization observed in some fungi. Non-random localization of mating type locus can be considered as the means for conservation of heterozygosity.

Chromosome Mapping↗
PubMed2001

A study of the simulated evolution of the spectral sensitivity of visual agent receptors.

In this article we study a model for the evolution of the spectral sensitivity of visual receptors for agents in a continuous virtual environment. The model uses a genetic algorithm (GA) to evolve the agent sensors along with the control of the agents by requiring the agents to solve certain tasks in the simulation environment. The properties of the evolved sensors are analyzed for different scenarios. In particular, it is shown that the GA is able to find a balance between sensor costs and agent performance in such a way that the spectral sensor sensitivity reflects the emission spectrum of the target objects and that the capability of the sensors to evolve can help the agents significantly in adapting to their task.

Algorithms↗
PubMed1996

Development and testing of a quality of life model for long-term female cancer survivors.

This research resulted in the evolution of a model depicting the quality of life of long-term female cancer survivors. The foundation for this model's development was Ferrell's (1993) breast cancer model, which incorporates physical, social, psychological and spiritual domains of life. The Ferrell model was adapted following focus-group discussions with 11 long-term female cancer survivors. The adjusted model included new categories, within each of Ferrell's initial domains, that were specific to the focus group participants. Administration of a new instrument, the Long-Term Quality of Life (LTQL), to 187 long-term female cancer survivors produced a final model that included the interaction of all four domains in six major concepts of quality of life. This new model, which reflects the complexity of life in long-term female cancer survivors, may be useful to health professionals in designing interventions to meet the unique needs of these women.

Activities of Daily Living↗
PubMed2004

Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways.

Ralstonia eutropha JMP134 (pJP4) is a useful model for the study of bacterial degradation of substituted aromatic pollutants. Several key degrading capabilities, encoded by tfd genes, are located in the 88 kb, self-transmissible, IncP-1 beta plasmid pJP4. The complete sequence of the 87,688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is reported. Most of the coding sequence corresponds to a well-conserved IncP-1 beta backbone and the previously reported tfd genes. In addition, we found hypothetical proteins putatively involved in the transport of aromatic compounds and short-chain fatty acid oxidation. ORFs related to mobile elements, including the Tn501-encoded mercury resistance determinants, an IS1071-based composite transposon and a cryptic class II transposon, are also present in pJP4. These mobile elements are inefficient in transposition and are located in two regions of pJP4 that are rich in remnants of lateral gene transfer events. pJP4 plasmid was able to capture chromosomal genes and form hybrid plasmids with the IncP-1 alpha plasmid RP4. These observations are integrated into a model for the evolution of pJP4, which reveals mechanisms of bacterial adaptation to degrade pollutants.

Adaptation, Physiological↗
PubMed2003

A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships.

Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 species representing all extant eutherian mammal orders for a new molecular phylogenetic marker, a 1.3kb portion of exon 26 of the apolipoprotein B (APOB) gene. In addition, we analyzed a multigene concatenation that included APOB sequences and a previously published data set (Murphy et al., 2001b) of three mitochondrial and 19 nuclear genes, resulting in an alignment of over 17kb for 42 placentals and two marsupials. Due to computational difficulties, previous maximum likelihood analyses of large, multigene concatenations for placental mammals have used quartet puzzling, less complex models of sequence evolution, or phylogenetic constraints to approximate a full maximum likelihood bootstrap. Here, we utilize a Unix load sharing facility to perform maximum likelihood bootstrap analyses for both the APOB and concatenated data sets with a GTR+Gamma+I model of sequence evolution, tree-bisection and reconnection branch-swapping, and no phylogenetic constraints. Maximum likelihood and Bayesian analyses of both data sets provide support for the superordinal clades Boreoeutheria, Euarchontoglires, Laurasiatheria, Xenarthra, Afrotheria, and Ostentoria (pangolins+carnivores), as well as for the monophyly of the orders Eulipotyphla, Primates, and Rodentia, all of which have recently been questioned. Both data sets recovered an association of Hippopotamidae and Cetacea within Cetartiodactyla, as well as hedgehog and shrew within Eulipotyphla. APOB showed strong support for an association of tarsier and Anthropoidea within Primates. Parsimony, maximum likelihood and Bayesian analyses with both data sets placed Afrotheria at the base of the placental radiation. Statistical tests that employed APOB to examine a priori hypotheses for the root of the placental tree rejected rooting on myomorphs and hedgehog, but did not discriminate between rooting at the base of Afrotheria, at the base of Xenarthra, or between Atlantogenata (Xenarthra+Afrotheria) and Boreoeutheria. An orthologous deletion of 363bp in the aligned APOB sequences proved phylogenetically informative for the grouping of the order Carnivora with the order Pholidota into the superordinal clade Ostentoria. A smaller deletion of 237-246bp was diagnostic of the superordinal clade Afrotheria.

Amino Acid Sequence↗
PubMed2006

The population genetics of adaptation on correlated fitness landscapes: the block model.

Several recent theoretical studies of the genetics of adaptation have focused on the mutational landscape model, which considers evolution on rugged fitness landscapes (i.e., ones having many local optima). Adaptation in this model is characterized by several simple results. Here I ask whether these results also hold on correlated fitness landscapes, which are smoother than those considered in the mutational landscape model. In particular, I study the genetics of adaptation in the block model, a tunably rugged model of fitness landscapes. Considering the scenario in which adaptation begins from a high fitness wild-type DNA sequence, I use extreme value theory and computer simulations to study both single adaptive steps and entire adaptive walks. I show that all previous results characterizing single steps in adaptation in the mutational landscape model hold at least approximately on correlated landscapes in the block model; many entire-walk results, however, do not.

Adaptation, Physiological↗
PubMed1999

The role of population size in molecular evolution.

The results of a computer simulation study of the role of population size in population genetical models of molecular evolution are presented. If the mutation rate and strength of selection are held fixed and the population size increased, the eight models examined fall into three domains based on their rates of substitution. In the Ohta domain, the rate of substitution decreases with increasing population size; in the Kimura domain, the rate of substitution remains close to the mutation rate; in the Darwin domain, the rate of substitution increases without bound. In the Kimura and Darwin domains, the rate of substitution is much less sensitive to the population size than suggested by two-allele theories. Remarkably, the overdominance model converges to the neutral model with increasing N. The variation at a neutral locus linked to a selected locus is found to be insensitive to the population size for certain models of selection. A selected locus can actually cause the rate of substitution of deleterious alleles at a linked locus to increase with increasing population size. These unexpected results illustrate that intuition based on two-allele theory is often misleading.

Animals↗
PubMed2002

Evolution and physics in comparative protein structure modeling.

From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.

Biophysical Phenomena↗
PubMed1997

Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history.

The complex evolutionary process of human immunodeficiency virus type 1 (HIV-1) is marked by a high level of genetic variation. It has been shown that the HIV-1 genome is characterized by variable and more constant regions, unequal nucleotide frequencies, and preference for G-to-A substitutions. However, this knowledge has largely been neglected in phylogenetic analyses of HIV-1 nucleotide sequences, even though these analyses are applied to a number of important biological questions. The purpose of this study was to identify a realistic model of HIV-1 evolution and to statistically test if the application of such a model significantly improves the accuracy of phylogenetic analyses. A unique and recently reported HIV-1 transmission cluster consisting of nine infected individuals, for whom the direction and time for each transmission were exactly known, formed the basis for the analyses which were performed under a general model of nucleotide substitution using population sequences from the env V3 and p17gag regions of the HIV-1 genome. Examination of seven different substitution models by maximum-likelihood methods revealed that the fit of the general reversible (REV) model was significantly better than that of simpler models, indicating that it is important to account for the asymmetric substitution pattern of HIV-1 and that the nucleotide substitution rate varied significantly across sites. The shape parameter alpha, which describes the variation across sites by a gamma distribution, was estimated to be 0.38 and 0.25 for env V3 and p17gag, respectively. In env V3, the estimated average transition/transversion rate ratio was 1.42. Thus, the REV model with variable rates across sites (described by a gamma distribution) provides the best description of HIV-1 evolution, whereas simple models are unrealistic and inaccurate. It is likely that the accuracy of phylogenetic studies of HIV-1 and many other viruses would improve substantially by the use of more realistic nucleotide substitution models. This is especially true when attempts are made to estimate the age of distant viral ancestors from contemporary viral sequences.

Base Sequence↗
PubMed2006

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

A recent phylogenomic study reported that the animal phylogeny was unresolved despite the use of 50 genes. This lack of resolution was interpreted as "a positive signature of closely spaced cladogenetic events." Here, we propose that this lack of resolution is rather due to the mutual cancellation of the phylogenetic signal (historical) and the nonphylogenetic signal (due to systematic errors) that results from inadequate taxon sampling and/or model of sequence evolution. Starting with a data set of comparable size, we use 3 different strategies to reduce the nonphylogenetic signal: 1) increasing the number of species; 2) replacing a fast-evolving species by a slowly evolving one; and 3) using a better model of sequence evolution. In all cases, the phylogenetic resolution is markedly improved, in agreement with our hypothesis that the originally reported lack of resolution was artifactual.

Algorithms↗