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Evolutionary Distance (evolutionary + distance)
Selected AbstractsInterpreting missense variants: comparing computational methods in human disease genes CDKN2A, MLH1, MSH2, MECP2, and tyrosinase (TYR),,HUMAN MUTATION, Issue 7 2007Philip A. Chan Abstract The human genome contains frequent single-basepair variants that may or may not cause genetic disease. To characterize benign vs. pathogenic missense variants, numerous computational algorithms have been developed based on comparative sequence and/or protein structure analysis. We compared computational methods that use evolutionary conservation alone, amino acid (AA) change alone, and a combination of conservation and AA change in predicting the consequences of 254 missense variants in the CDKN2A (n = 92), MLH1 (n = 28), MSH2 (n = 14), MECP2 (n = 30), and tyrosinase (TYR) (n = 90) genes. Variants were validated as either neutral or deleterious by curated locus-specific mutation databases and published functional data. All methods that use evolutionary sequence analysis have comparable overall prediction accuracy (72.9,82.0%). Mutations at codons where the AA is absolutely conserved over a sufficient evolutionary distance (about one-third of variants) had a 91.6 to 96.8% likelihood of being deleterious. Three algorithms (SIFT, PolyPhen, and A-GVGD) that differentiate one variant from another at a given codon did not significantly improve predictive value over conservation score alone using the BLOSUM62 matrix. However, when all four methods were in agreement (62.7% of variants), predictive value improved to 88.1%. These results confirm a high predictive value for methods that use evolutionary sequence conservation, with or without considering protein structural change, to predict the clinical consequences of missense variants. The methods can be generalized across genes that cause different types of genetic disease. The results support the clinical use of computational methods as one tool to help interpret missense variants in genes associated with human genetic disease. Hum Mutat 28(7), 683,693, 2007. Published 2007 Wiley-Liss, Inc. [source] Conservation of DNA methylation in dipteran insectsINSECT MOLECULAR BIOLOGY, Issue 2 2004J. Marhold Abstract DNA methylation is a central mechanism of epigenetic regulation. Whereas vertebrate DNA methylation requires at least four different DNA methyltransferases, Drosophila melanogaster only utilizes a single, Dnmt2-like enzyme. This profound difference has raised the question of the evolutionary significance of the Drosophila methylation system. We have now identified Dnmt2-like open reading frames in the genome sequences of Drosophila pseudoobscura and Anopheles gambiae. These genes represent the only candidate DNA methyltransferases in their respective genomes. Consistent with a catalytic activity of Dnmt2 proteins, we could also demonstrate low but significant levels of DNA methylation in genomic DNA from these species. Lastly, we were also able to detect highly conserved Dnmt2-like open reading frames and concomitant DNA methylation in several additional Drosophila species, which suggests that Dnmt2-mediated DNA methylation has been conserved over a considerable evolutionary distance. [source] TOP: a new method for protein structure comparisons and similarity searchesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2000Guoguang Lu In order to facilitate the three-dimensional structure comparison of proteins, software for making comparisons and searching for similarities to protein structures in databases has been developed. The program identifies the residues that share similar positions of both main-chain and side-chain atoms between two proteins. The unique functions of the software also include database processing via Internet- and Web-based servers for different types of users. The developed method and its friendly user interface copes with many of the problems that frequently occur in protein structure comparisons, such as detecting structurally equivalent residues, misalignment caused by coincident match of C, atoms, circular sequence permutations, tedious repetition of access, maintenance of the most recent database, and inconvenience of user interface. The program is also designed to cooperate with other tools in structural bioinformatics, such as the 3DB Browser software [Prilusky (1998). Protein Data Bank Q. Newslett.84, 3,4] and the SCOP database [Murzin, Brenner, Hubbard & Chothia (1995). J. Mol. Biol.247, 536,540], for convenient molecular modelling and protein structure analysis. A similarity ranking score of `structure diversity' is proposed in order to estimate the evolutionary distance between proteins based on the comparisons of their three-dimensional structures. The function of the program has been utilized as a part of an automated program for multiple protein structure alignment. In this paper, the algorithm of the program and results of systematic tests are presented and discussed. [source] A restoration genetics guide for coral reef conservationMOLECULAR ECOLOGY, Issue 12 2008ILIANA B. BAUMS Abstract Worldwide degradation of coral reef communities has prompted a surge in restoration efforts. They proceed largely without considering genetic factors because traditionally, coral populations have been regarded as open over large areas with little potential for local adaptation. Since, biophysical and molecular studies indicated that most populations are closed over shorter time and smaller spatial scales. Thus, it is justified to re-examine the potential for site adaptation in corals. There is ample evidence for differentiated populations, inbreeding, asexual reproduction and the occurrence of ecotypes, factors that may facilitate local adaptation. Discovery of widespread local adaptation would influence coral restoration projects mainly with regard to the physical and evolutionary distance from the source wild and/or captive bred propagules may be moved without causing a loss of fitness in the restored population. Proposed causes for loss of fitness as a result of (plant) restoration efforts include founder effects, genetic swamping, inbreeding and/or outbreeding depression. Direct evidence for any of these processes is scarce in reef corals due to a lack of model species that allow for testing over multiple generations and the separation of the relative contributions of algal symbionts and their coral hosts to the overall performance of the coral colony. This gap in our knowledge may be closed by employing novel population genetic and genomics approaches. The use of molecular tools may aid managers in the selection of appropriate propagule sources, guide spatial arrangement of transplants, and help in assessing the success of coral restoration projects by tracking the performance of transplants, thereby generating important data for future coral reef conservation and restoration projects. [source] New chloroplast primers for intraspecific variation in Dicranum scoparium Hedw. (Dicranaceae) and amplification success in other bryophyte speciesMOLECULAR ECOLOGY RESOURCES, Issue 4 2010A. LANG Abstract Primers for four loci that amplify cpDNA regions have been designed for population genetic analyses in Dicranum scoparium Hedw. and compared with trnL(UAA)5,exon- trnF. All loci showed intraspecific variation with a number of haplotypes ranging between two and six. trnH- psbADic showed an intercontinental disjunction, but no variability within the four Swiss populations surveyed, whereas the three remaining loci displayed intrapopulation variability in at least one population (rps19- rpl2, rpoB, trnT- rps4). These primers were additionally tested on 22 bryophytes and three fern species. The primers amplified mostly in mosses and liverworts, but less well in ferns, pointing to their evolutionary distance from the bryophytes. [source] A bacterial conjugation machinery recruited for pathogenesisMOLECULAR MICROBIOLOGY, Issue 5 2003Anja Seubert Summary Type IV secretion systems (T4SS) are multicomponent transporters of Gram-negative bacteria adapted to functions as diverse as DNA transfer in bacterial conjugation or the delivery of effector proteins into eukaryotic target cells in pathogenesis. The generally modest sequence conservation between T4SS may reflect their evolutionary distance and/or functional divergence. Here, we show that the establishment of intraerythrocytic parasitism by Bartonella tribocorum requires a putative T4SS, which shares an unprecedented level of sequence identity with the Trw conjugation machinery of the broad-host-range antibiotic resistance plasmid R388 (up to 80% amino acid identity for individual T4SS components). The highly conserved T4SS loci are collinear except for the presence of numerous tandem gene duplications in B. tribocorum, which mostly encode variant forms of presumed surface-exposed pilus subunits. Conservation is not only structural, but also functional: R388 mutated in either trwD or trwH encoding essential T4SS components could be trans -complemented for conjugation by the homologues of the B. tribocorum system. Conservation also includes the transcription regulatory circuit: both T4SS loci encode a highly homologous and interchangeable KorA/KorB repressor system that negatively regulates the expression of all T4SS components. This striking example of adaptive evolution reveals the capacity of T4SS to assume dedicated functions in either DNA transfer or pathogenesis over rather short evolutionary distance and implies a novel role for the conjugation systems of widespread broad-host-range plasmids in the evolution of bacterial pathogens. [source] Use of specific PCR primers to identify three important industrial species of Saccharomyces genus: Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces pastorianusLETTERS IN APPLIED MICROBIOLOGY, Issue 2 2010G.V. De Melo Pereira Abstract Aim:, To develop species-specific primers capable of distinguishing between three important yeast species in alcoholic fermentation: Saccharomyces bayanus, Saccharomyces cerevisiae and Saccharomyces pastorianus. Methods and Results:, Two sets of primers with sequences complementary to the HO genes from Saccharomyces sensu stricto species were used. The use of the ScHO primers produced a single amplificon of c. 400 or 300 bp with species S. cerevisiae and S. pastorianus, respectively. The second pair of primers (LgHO) was also constructed, within the HO gene, composed of perfectly conserved sequences common for S. bayanus species, which generate amplicon with 700 bp. No amplification product was observed in the DNA samples from non- Saccharomyces yeasts. Saccharomyces species have also been characterized via electrophoretic karyotyping using pulsed-field gel electrophoresis to demonstrate chromosomal polymorphisms and to determine the evolutionary distances between these species. Conclusions:, We conclude that our novel species-specific primers could be used to rapidly and accurately identify of the Saccharomyces species most commonly involved in fermentation processes using a PCR-based assay. Significance and Impact of the Study:, The method may be used for routine identification of the most common Saccharomyces sensu stricto yeasts involved in industrial fermentation processes in less than 3 h. [source] A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genomeANIMAL GENETICS, Issue 4 2009C. H. Wu Summary Ovis aries chromosome one (OAR1) is the largest submetacentric chromosome in the sheep genome and is homologous to regions on human chromosomes 1, 2, 3 and 21. Using the USUoRH5000 ovine whole-genome radiation hybrid (RH) panel, we have constructed a RH map of OAR1 comprising 102 framework and 75 placed/binned markers across five linkage groups spanning 3759.43 cR5000, with an average marker density of 21.2 cR5000/marker. The alignment of our OAR1 RH map shows good concordance with the recently developed virtual sheep genome, with fewer than 1.86% discrepancies. A comparative map of OAR1 was constructed by examining the location of RH-mapped orthologues in sheep within the genomes of cow, human, horse and dog. Analysis of the comparative map indicates that conserved syntenies within the five ovine RH linkage groups underwent internal chromosomal rearrangements which, in general, reflect the evolutionary distances between sheep and each of these four species. The ovine RH map presented here integrates all available mapping data and includes new genomic information for ovine chromosome 1. [source] The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networksBIOESSAYS, Issue 7 2007S. Balaji Studies on the conservation of the inferred transcriptional regulatory network of prokaryotes have suggested that specific transcription factors are less-widely conserved in comparison to their target genes. This observation implied that, at large evolutionary distances, the turnover of specific transcription factors through loss and non-orthologous displacement might be a major factor in the adaptive radiation of prokaryotes. However, the recent work of Hershberg and Margalit1 suggests that, at shorter phylogenetic scales, the evolutionary dynamics of the bacterial transcriptional regulatory network might exhibit distinct patterns. The authors find previously unnoticed relationships between the regulatory mode (activation or repression), the number of regulatory interactions and their conservation patterns in ,-proteobacteria. These relationships might be shaped by the differences in the adaptive value and mode of operation of different regulatory interactions. BioEssays 29:625,629, 2007. © 2007 Wiley Periodicals, Inc. [source] Evolution of species-specific cuticular hydrocarbon patterns in Formica antsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2008STEPHEN J. MARTIN A comparison of the cuticular hydrocarbon profiles of thirteen sympatric species of Formica ants from Finland, along with a subset of five species from the British Isles, was conducted. This permitted a comparison of the evolution of these profiles within a single genus and the stability of these profiles over large geographical and evolutionary distances. The study indicated that species-specific hydrocarbon profiles remained remarkably stable between Finland and the British Isles and were not influenced by ecological factors such as soil or vegetation types. This stability allowed candidate cuticular hydrocarbons or groups of hydrocarbons to be identified that may constitute species-specific recognition cues in these ants. In Formica, cuticular hydrocarbon composition has evolved down two distinct paths, either elevated production of Z -9-alkenes or the production of various dimethylalkanes. Evolution of hydrocarbons can be predicted for the other five Formica species for which the cuticular profiles are known. The Z -9-alkenes, dienes, and various distinctive combinations of dimethylalkanes can be used as unique species recognition cues in the Formica ants and this parallels the evolution of species-specific cuticular hydrocarbon composition in the Drosophila flies. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 131,140. [source] | ||||||||||