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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 43 (1996), S. 216-223 
    ISSN: 1432-1432
    Keywords: Base composition ; Stop-codon density ; Coding-sequence length ; Compositional heterogeneity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Since base composition of translational stop codons (TAG, TAA, and TGA) is biased toward a low G+C content, a differential density for these termination signals is expected in random DNA sequences of different base compositions. The expected length of reading frames (DNA segments of sense codons flanked by in-phase stop codons) in random sequences is thus a function of GC content. The analysis of DNA sequences from several genome databases stratified according to GC content reveals that the longest coding sequences—exons in vertebrates and genes in prokaryotes—are GC-rich, while the shortest ones are GC-poor. Exon lengthening in GC-rich vertebrate regions does not result, however, in longer vertebrate proteins, perhaps because of the lower number of exons in the genes located in these regions. The effects on coding-sequence lengths constitute a new evolutionary meaning for compositional variations in DNA GC content.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 43 (1996), S. 216-223 
    ISSN: 1432-1432
    Keywords: Key words: Base composition — Stop-codon density — Coding-sequence length — Compositional heterogeneity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Since base composition of translational stop codons (TAG, TAA, and TGA) is biased toward a low G+C content, a differential density for these termination signals is expected in random DNA sequences of different base compositions. The expected length of reading frames (DNA segments of sense codons flanked by in-phase stop codons) in random sequences is thus a function of GC content. The analysis of DNA sequences from several genome databases stratified according to GC content reveals that the longest coding sequences—exons in vertebrates and genes in prokaryotes—are GC-rich, while the shortest ones are GC-poor. Exon lengthening in GC-rich vertebrate regions does not result, however, in longer vertebrate proteins, perhaps because of the lower number of exons in the genes located in these regions. The effects on coding-sequence lengths constitute a new evolutionary meaning for compositional variations in DNA GC content.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 39 (1994), S. 340-346 
    ISSN: 1432-1432
    Keywords: E. coli genome ; VSP repair ; CTAG tetranucleotide ; G+C content ; Contrast vocabularies ; CAI
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract E. coli genes that contain a high frequency of the tetranucleotide CTAG are also rich in the tetramers CTTG, CCTA, CCAA, TTGG, TAGG, and CAAG (group-I tetramers). Conversely, E. coli genes lacking CTAG are rich in the tetranucleotides CCTG, CCAG, CTGG, and CAGG (group-II tetramers). These two gene samples differ also in codon usage, amino acid composition, frequency of Dcm sites, and contrast vocabularies. Group-I tetramers have in common that they are depleted by very-short-patch repair (VSP), while group-II tetramers are favored by VSP activity. The VSP system repairs G:T mismatches to G:C, thereby increasing the overall G+C content of the genome; for this reason the CTAG-rich sample has a lower G+C content than the CTAG-poor sample. This compositional heterogeneity can be tentatively explained by a low level of VSP activity on the CTAG-rich sample. A negative correlation is found between the frequency of group-I tetramers and the level of gene expression, as measured by the Codon Adaptation Index (CAI). A possible link between the rate of VSP activity and the level of gene expression is considered.
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  • 4
    ISSN: 1432-1432
    Keywords: Archaebacteria ; Protein-synthesis inhibition ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The sensitivities to 37 protein-synthesis inhibitors were determined in cell-free translational systems for 13 Archaebacteria species. Multivariate factor analysis by principal components, cluster analysis by the unweighted pair-group clustering algorithm, and compatibility and parsimony methods of constructing phylogenetic trees were used both to infer the genealogical relationships within archaebacteria and to establish their relations with the eubacterial and eukaryotic kingdoms.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 43 (1996), S. 161-163 
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
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  • 6
    ISSN: 1432-1432
    Keywords: Key words:Escherichia coli— G + C content — Intergenic DNA — Transcription-induced mutation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. This paper analyzes correlations in base composition between pairs of neighboring genes in Escherichia coli. The G + C contents of nearby, but convergently or divergently transcribed, genes show weak but significant correlations, and this is attributed to compositional variation among genomic regions. The finding that the base composition varies among intergenic regions, depending upon whether the adjacent genes are transcribed convergently, divergently, or in the same orientation, seems to indicate that transcription affects the patterns of mutation and, therefore, the overall base composition of the region.
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  • 7
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The structure, genomic organization and transcription of the gene encoding histone H2B in the protozoan parasite Trypanosoma cruzi have been studied. This gene consists of a 746-nucleotlde unit, tandemly repeated at least 18 times in each of two clusters. DNA probes corresponding to histones H2B and H3 hybridized to different chromosomes revealing that the genes coding for these two histones are not physically linked in the genome of T. cruzi. The primary transcription product of the H2B gene is processed by trans-splicing and polyadenylation. Inhibition of DNA synthesis with aphidicolin resulted in the reduction of histone H2B mRNA to undetectable levels in about two hours, suggesting that its abundance is regulated throughout the cell cycle as it occurs in other eukaryotes. in addition, a concomitant inhibition of translation by cycloheximide reverted this effect indicating that de novo protein synthesis is required for RNA instability. Histone mRNA abundance was dependent on the life-cycle stage of T. cruzi: abundant in amastigotes and epimastigotes, the dividing forms in the host cell and the insect vector, respectively, white undetected in trypomastigotes, the parasite's non-dividing life stage.
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  • 8
    ISSN: 1432-0886
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The electrophoretic patterns of esterase (E-1), alcohol dehydrogenase (ADH), and glutamate oxaloacetate transaminase (GOT) isozymes were studied in two Spanish populations of the lily Scilla autumnalis with B-chromosome carrying individuals. The E-1 isozyme activity appears only in those individuals with B-chromosomes. None of the bulbs free of B's show it. Five bulbs, mosaic for B-content, were identified. Electrophoretic analysis shows that these bulbs are characterised by mosaicism for E-1 isozyme activity. An analysis of individual roots by both electrophoretic and cytological methods shows that tissue mosaicism for B-content correlates with tissue mosaicism for E-1 isozyme activity. The electrophoretic analysis of different roots from bulbs heterozygous for the Est-1 locus indicates that the structural gene for E-1 is not located on the B-chromosome itself. Rather there is a derepressor effect of Bs on E-1 isozyme activity. Since ADH and GOT patterns are unaffected by the presence of B-chromosomes it is clear that they do not exhibit a generalised derepressor effect.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Plant systematics and evolution 148 (1984), S. 1-18 
    ISSN: 1615-6110
    Keywords: Angiosperms ; Solanaceae ; Solanum tuberosum ; Allozyme variability ; polyploidy ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Gene frequencies at 13 isozyme loci were determined in three South American taxa of cultivated potatoes [the diploid group (gp.) Stenotomum, the diploid subgroups (subgp.) Goniocalyx, and the tetraploid gp. Andigena ofS. tuberosum], in the diploid weed speciesS. sparsipilum, and in most of the main cultivars now raised in the Northern Hemisphere (the tetraploid gp. Tuberosum ofS. tuberosum). High levels of genetic variability (mean number of alleles per locus, percentage of polymorphic loci, and mean heterozygosity) were detected, being higher in tetraploid potatoes. An equilibrium among the evolutionary factors which increase genetic variability and artificial selection for maximum yield would explain the high uniformity of heterozygosity values we observed in both Andigena (0.36 ± 0.02) and Tuberosum (0.38 ± 0.01) cultivars.—The low value of genetic distance (D = 0.044) between Stenotomum and Goniocalyx does not support the status of species forS. goniocalyx.—In most isozyme loci, the electromorphs of gp. Andigena were a combination of those found in both gp. Stenotomum andS. sparsipilum, suggesting an amphidiploid origin of gp. Andigena from that two diploid taxa. The presence in Andigena of unique electromorphs, which were lacking in both gp. Stenotomum andS. sparsipilum, suggests that other diploid species could be also implied in the origin of tetraploid Andean potatoes. Furthermore, since Andigena were more related to Stenotomum (D = 0.052) than toS. sparsipilum (D = 0.241), the autopolyploidization of Stenotomum individuals and the subsequent hybridization with gp. Andigena may also have occurred. Thus, our study suggests a multiple origin (amphidiploidy, autoploidy, and hybridization at tetraploid level) of gp. Andigena.—Most of the electromorphs of gp. Tuberosum were also found in gp. Andigena; both the direct derivation of that group from the Andean tetraploid potatoes and the repeated introgression provided by breeding programmes could explain this result. However, the allele c of Pgm-B, present in 30 out of 76 Tuberosum cultivars from Northern Hemisphere as well as in 3 Chilean Tuberosum cultivars, lacks in the 258 Andigena genotypes sampled, suggesting that Chilean germplasm could have taken part in the origin of at least the 39% of the potato cultivars from Europe and North America analyzed here.—The distanceWagner procedure provides an estimate of a 30% of heterogeneity in the evolutionary divergence shown by different groups of cultivated potatoes. Diploid groups show a higher (22.5%) evolutionary rate than tetraploids, which can be attributed to both tetrasomic inheritance and facultative autofecundation that exists in Andigena and Tuberosum groups. Thus, artificial selection acting since 10000 years has not resulted in a higher rate of molecular evolution at the isozyme level in the tetraploids.
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  • 10
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