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Complete Genome (complete + genome)
Terms modified by Complete Genome Selected AbstractsThe discovery of genes implicated in myocardial infarctionJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 2009W. H. OUWEHAND Summary., The era of Genome-Wide Association Studies (GWAS) commenced in 2007 with the study of the Wellcome Trust Case Control Consortium (WTCCC) which for the first time ever showed that risk loci can be identified by scanning the complete genome for sequence variation in large numbers of cases of disease and healthy controls. We and others have expanded on this effort and successfully identified the first 11 risk loci for myocardial infarction (MI) and coronary artery disease (CAD). Studies on quantitative traits provide an alternative approach to identify MI/CAD risk loci. This review captures the early successes in the emerging field of disease genomics. [source] Genetic stability (in vivo) of the attenuated oral rabies virus vaccine SAD B19MICROBIOLOGY AND IMMUNOLOGY, Issue 1 2009Aline Beckert ABSTRACT The distribution of oral rabies vaccine baits containing replication-competent live viruses poses certain environmental safety risks; among others, the possibility of reversion to or an increase in virulence. Hence, the genetic stability of the complete genome of the most widely used oral rabies vaccine virus, SAD B19, was examined after four and 10 serial i.c. passages in foxes and mice, respectively. It was shown that the consensus strain of SAD B19 was extremely stable in vivo. After 10 consecutive passages in mice not a single mutation was observed. In foxes, seven single nucleotide exchanges were found between the first and fourth passage, of which only one resulted in an amino acid exchange at position 9240 of the L-gene. This mutation was not observed during the first three passages and, furthermore, it was shown that this mutation was not linked to enhanced virulence. [source] Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao: what's new from this old foe?MOLECULAR PLANT PATHOLOGY, Issue 5 2008LYNDEL W. MEINHARDT SUMMARY Moniliophthora perniciosa (=Crinipellis perniciosa) causes one of the three main fungal diseases of Theobroma cacao (cacao), the source of chocolate. This pathogen causes Witches' broom disease (WBD) and has brought about severe economic losses in all of the cacao-growing regions to which it has spread with yield reductions that range from 50 to 90%. Cacao production in South America reflects the severity of this pathogen, as the yields in most of the infected regions have not returned to pre-outbreak levels, even with the introduction of resistant varieties. In this review we give a brief historical account and summarize the current state of knowledge focusing on developments in the areas of systematics, fungal physiology, biochemistry, genomics and gene expression in an attempt to highlight this disease. Moniliophthora perniciosa is a hemibiotrophic fungus with two distinct growth phases. The ability to culture a biotrophic-like phase in vitro along with new findings derived from the nearly complete genome and expression studies clearly show that these different fungal growth phases function under distinct metabolic parameters. These new findings have greatly improved our understanding of this fungal/host interaction and we may be at the crossroads of understanding how hemibiotrophic fungal plant pathogens cause disease in other crops. Historical summary of WBD:, The first WDB symptoms appear to have been described in the diaries of Alexandre Rodrigues Ferreira (described as lagartão; meaning big lizard) from his observations of cacao trees in 1785 and 1787 in Amazonia, which is consistent with the generally accepted idea that M. perniciosa, like its main host T. cacao, evolved in this region. The disease subsequently arrived in Surinam in 1895. WBD moved rapidly, spreading to Guyana in 1906, Ecuador in 1918, Trinidad in 1928, Colombia in 1929 and Grenada in 1948. In each case, cacao production was catastrophically affected with yield reductions of 50,90%. After the arrival of M. perniciosa in Bahia in 1989, Brazil went from being the world's 3rd largest producer of cacao (347 000 tonnes in 1988,1990; c. 15% of the total world production at that time) to a net importer (141 000 tonnes in 1998,2000). Fortunately for chocolate lovers, other regions of the world such as West Africa and South East Asia have not yet been affected by this disease and have expanded production to meet growing world demand (predicted to reach 3 700 000 tonnes by 2010). Classification:,Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: super-kingdom Eukaryota; kingdom Fungi; phylum Basidiomycota; subphylum Agaricomycotina; class Agaricomycetes; subclass Agaricomycetidae; order Agaricales; family Marasmiaceae; genus Moniliophthora. Useful websites:,http://www.lge.ibi.unicamp.br/vassoura/, http://nt.ars-grin.gov/taxadescriptions/keys/TrichodermaIndex.cfm, http://www.worldcocoafoundation.org/info-center/research-updates.asp, http://www.ars.usda.gov/ba/psi/spcl [source] Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignmentsPROTEIN SCIENCE, Issue 11 2000Iddo Friedberg Abstract The PSI-BLAST algorithm has been acknowledged as one of the most powerful tools for detecting remote evolutionary relationships by sequence considerations only. This has been demonstrated by its ability to recognize remote structural homologues and by the greatest coverage it enables in annotation of a complete genome. Although recognizing the correct fold of a sequence is of major importance, the accuracy of the alignment is crucial for the success of modeling one sequence by the structure of its remote homologue. Here we assess the accuracy of PSI-BLAST alignments on a stringent database of 123 structurally similar, sequence-dissimilar pairs of proteins, by comparing them to the alignments defined on a structural basis. Each protein sequence is compared to a nonredundant database of the protein sequences by PSI-BLAST. Whenever a pair member detects its pair-mate, the positions that are aligned both in the sequential and structural alignments are determined, and the alignment sensitivity is expressed as the per-centage of these positions out of the structural alignment. Fifty-two sequences detected their pair-mates (for 16 pairs the success was bi-directional when either pair member was used as a query). The average percentage of correctly aligned residues per structural alignment was 43.5 ± 2.2%. Other properties of the alignments were also examined, such as the sensitivity vs. specificity and the change in these parameters over consecutive iterations. Notably, there is an improvement in alignment sensitivity over consecutive iterations, reaching an average of 50.9 + 2.5% within the five iterations tested in the current study. [source] BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmonANIMAL GENETICS, Issue 1 2010S. Lorenz Summary A better understanding of the genotype,phenotype correlation of Atlantic salmon is of key importance for a whole range of production, life history and conservation biology issues attached to this species. High-density linkage maps integrated with physical maps and covering the complete genome are needed to identify economically important genes and to study the genome architecture. Linkage maps of moderate density and a physical bacterial artificial chromosome (BAC) fingerprint map for the Atlantic salmon have already been generated. Here, we describe a strategy to combine the linkage mapping with the physical integration of newly identified single nucleotide polymorphisms (SNPs). We resequenced 284 BAC-ends by PCR in 14 individuals and detected 180 putative SNPs. After successful validation of 152 sequence variations, genotyping and genetic mapping were performed in eight salmon families comprising 376 individuals. Among these, 110 SNPs were positioned on a previously constructed linkage map containing SNPs derived from expressed sequence tag (EST) sequences. Tracing the SNP markers back to the BACs enabled the integration of the genetic and physical maps by assigning 73 BAC contigs to Atlantic salmon linkage groups. [source] Quantitative trait loci underlying milk production traits in sheepANIMAL GENETICS, Issue 4 2009B. Gutiérrez-Gil Summary Improvement of milk production traits in dairy sheep is required to increase the competitiveness of the industry and to maintain the production of high quality cheese in regions of Mediterranean countries with less favourable conditions. Additional improvement over classical selection could be reached if genes with significant effects on the relevant traits were specifically targeted by selection. However, so far, few studies have been undertaken to detect quantitative trait loci (QTL) in dairy sheep. In this study, we present a complete genome scan performed in a commercial population of Spanish Churra sheep to identify chromosomal regions associated with phenotypic variation observed in milk production traits. Eleven half-sib families, including a total of 1213 ewes, were analysed following a daughter design. Genome-wise multi-marker regression analysis revealed a genome-wise significant QTL for milk protein percentage on chromosome 3. Eight other regions, localized on chromosomes 1, 2, 20, 23 and 25, showed suggestive significant linkage associations with some of the analysed traits. To our knowledge, this study represents the first complete genome scan for milk production traits reported in dairy sheep. The experiment described here shows that analysis of commercial dairy sheep populations has the potential to increase our understanding of the genetic determinants of complex production-related traits. [source] The quest for the mechanisms of lifeBIOTECHNOLOGY & BIOENGINEERING, Issue 7 2003Maria I. Klapa Abstract The genomic revolution, manifested by the sequencing of the complete genome of many organisms, along with technological advances, such as DNA microarrays and developments in high-throughput analysis of proteins, metabolites, and isotopic tracer distribution patterns, challenged the conventional ways in which questions are approached in the biological sciences: (a) rather than examining a small number of genes and/or reactions at any one time;, we can now analyze gene expression and protein activity in the context of systems of interacting genes and gene products; (b) comprehensive analysis of biological systems requires the integration of all cellular fingerprints: genome sequence, maps of gene expression, protein expression, metabolic output, and in vivo enzymatic activity; and (c) collecting, managing, and analyzing comparable data from various cellular profiles requires expertise from several fields that transcend traditional discipline boundaries. While researchers in systems biology have still to address difficult challenges in both experimental and computational arenas, they possess, for the first time, the opportunity to unravel the mechanisms of life. The enormous impact of these discoveries in diverse areas, such as metabolic engineering, strain selection, drug screening and development, bioprocess development, disease prognosis and diagnosis, gene and other medical therapies, is an obvious motivation for pursuing integrated analyses of cellular systems. © 2003 Wiley Periodicals, Inc. [source] Genomic BLAST: custom-defined virtual databases for complete and unfinished genomesFEMS MICROBIOLOGY LETTERS, Issue 2 2002Leda Cummings Abstract BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes. [source] Cryptococcus neoformans capsule biosynthesis and regulationFEMS YEAST RESEARCH, Issue 8 2004Guilhem Janbon Abstract The capsule is certainly the most prominent virulence factor in Cryptococcus neoformans: acapsular strains are avirulent, and capsular polysaccharides have a deleterious effect on the immune system. Until very recently, very few genes involved in capsule biosynthesis had been identified , and this despite the existence of a detailed body of work concerning the capsule's composition, structure and their regulation by environmental factors. The tremendous development of experimental tools and techniques suited to the study of C. neoformans biology together with the sequencing of three complete genomes have, over the last three years, enabled the identification of a number of proteins which participate directly in biosynthesis of the capsule or which regulate its size. Even though this knowledge is still preliminary, it gives us a clearer picture of the various events needed for biosynthesis of this fascinating structure. [source] Multiple copies of cytochrome oxidase 1 in species of the fungal genus FusariumMOLECULAR ECOLOGY RESOURCES, Issue 2009SCOTT R. GILMORE Abstract Using data from published mitochondrial or complete genomes, we developed and tested primers for amplification and sequencing of the barcode region of cytochrome oxidase 1 (COX1) of the fungal genus Fusarium, related genera of the order Hypocreales, and degenerate primers for fungi in the subdivision Pezizomycotina. The primers were successful for amplifying and sequencing COX1 barcodes from 13 genera of Hypocreales (Acremonium, Beauveria, Clonostachys, Emericellopsis, Fusarium, Gliocladium, Hypocrea, Lanatonectria, Lecanicillium, Metarhizium, Monocillium, Neonectria and Stilbella), 22 taxa of Fusarium, and two genera in other orders (Arthrosporium, Monilochaetes). Parologous copies of COX1 occurred in several strains of Fusarium. In some, copies of the same length were detected either by heterozygous bases in otherwise clean sequences or in different replicates of amplification and sequencing events; this may indicate multiple transcribed copies. Other strains included one or two introns. Two intron insertion sites had at least two nonhomologous intron sequences among Fusarium species. Irrespective of whether the multiple copy issue could be resolved by sequencing RNA transcripts, developing a precise COX1 -based barcoding system for Fusarium may not be feasible. The overall divergence among homologous COX1 sequences obtained so far is rather low, with many species sharing identical sequences. [source] Heterochromatin-mediated control of virulence gene expressionMOLECULAR MICROBIOLOGY, Issue 3 2006Catherine J. Merrick Summary In recent years, the sequencing and annotation of complete genomes, together with the development of genetic and proteomic techniques to study previously intractable eukaryotic microbes, has revealed interesting new themes in the control of virulence gene expression. Families of variantly expressed genes are found adjacent to telomeres in the genomes of both pathogenic and non-pathogenic organisms. This subtelomeric DNA is normally heterochromatic and higher-order chromatin structure has now come to be recognized as an important factor controlling both the evolution and expression dynamics of these multigene families. In eukaryotic cells, higher-order chromatin structure plays a central role in many DNA processes including the control of chromosome integrity and recombination, DNA partitioning during cell division, and transcriptional control. DNA can be packaged in two distinct forms: euchromatin is relatively accessible to DNA binding proteins and generally contains active genes, while heterochromatin is densely packaged, relatively inaccessible and usually transcriptionally silent. These features of chromatin are epigenetically inherited from cell cycle to cell cycle. This review will focus on the epigenetic mechanisms used to control expression of virulence genes in medically important microbial pathogens. Examples of such control have now been reported in several evolutionarily distant species, revealing what may be a common strategy used to regulate many very different families of genes. [source] New insertion sequences of Sulfolobus: functional properties and implications for genome evolution in hyperthermophilic archaeaMOLECULAR MICROBIOLOGY, Issue 1 2005Zachary D. Blount Summary Analyses of complete genomes indicate that insertion sequences (ISs) are abundant and widespread in hyperthermophilic archaea, but few experimental studies have measured their activities in these hosts. As a way to investigate the impact of ISs on Sulfolobus genomes, we identified seven transpositionally active ISs in a widely distributed Sulfolobus species, and measured their functional properties. Six of the seven were found to be distinct from previously described ISs of Sulfolobus, and one of the six could not be assigned to any known IS family. A type II ,Miniature Inverted-repeat Transposable Element' (MITE) related to one of the ISs was also recovered. Rates of transposition of the different ISs into the pyrEF region of their host strains varied over a 250-fold range. The Sulfolobus ISs also differed with respect to target-site selectivity, although several shared an apparent preference for the pyrEF promoter region. Despite the number of distinct ISs assayed and their molecular diversity, only one demonstrated precise excision from the chromosomal target region. The fact that this IS is the only one lacking inverted repeats and target-site duplication suggests that the observed precise excision may be promoted by the IS itself. Sequence searches revealed previously unidentified partial copies of the newly identified ISs in the Sulfolobus tokodaii and Sulfolobus solfataricus genomes. The structures of these fragmentary copies suggest several distinct molecular mechanisms which, in the absence of precise excision, inactivate ISs and gradually eliminate the defective copies from Sulfolobus genomes. [source] Brief communication: Mitochondrial haplotype C4c confirmed as a founding genome in the AmericasAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2010Ripan S. Malhi Abstract Mitochondrial DNA analysis of 31 unrelated Shuswap speakers from a previously poorly sampled region of North America revealed two individuals with haplogroups rarely found in the Americas, C4c and C1d. Comparison of the complete genomes of the two individuals with others found in the literature confirms that C4c is a founding haplotype and gives insight into the evolution of the C1d haplotype. This study demonstrates the importance of collecting and analyzing data from Native North Americans when addressing hypotheses about the peopling of the Americas. Am J Phys Anthropol, 2010. © 2009 Wiley-Liss, Inc. [source] Strong associations between gene function and codon usageAPMIS, Issue 9 2003ANDERS FUGLSANG The association between codon usage and gene function was analyzed in the complete genomes of Eschericia coli, Bacillus subtilis, Lactococcus lactis and Campylobacter jejuni, using the functional annotation provided by NCBI. Two distinctly different ways of quantifying codon usage were used in the analysis. By using contingency tables it was found that for most amino acids a highly significant association with gene function exists for all species, indicating that codon usage at the level of individual amino acids is generally closely coordinated with gene function. By computing the effective number of codons in the annotated genes and comparing the median values in groups of different gene functions it was shown for all species that codon bias gene by gene also differs. [source] Genomic Analyses and the Origin of the EukaryotesCHEMISTRY & BIODIVERSITY, Issue 11 2007Maria Abstract The availability of whole-genome data has created the extraordinary opportunity to reconstruct in fine details the ,tree of life'. The application of such comprehensive effort promises to unravel the enigmatic evolutionary relationships between prokaryotes and eukaryotes. Traditionally, biologists have represented the evolutionary relationships of all organisms by a bifurcating phylogenetic tree. But recent analyses of completely sequenced genomes using conditioned reconstruction (CR), a newly developed gene-content algorithm, suggest that a cycle graph or ,ring' rather than a ,tree' is a better representation of the evolutionary relationships between prokaryotes and eukaryotes. CR is the first phylogenetic-reconstruction method to provide precise evidence about the origin of the eukaryotes. This review summarizes how the CR analyses of complete genomes provide evidence for a fusion origin of the eukaryotes. [source] | ||||||||||||||||