ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Electronic Resource
    Electronic Resource
    Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 504-510 
    Details
    ISSN: 1432-1432
    Keywords: Human genome ; Amino acids ; Isochores ; Coding sequences ; Introns ; Codon positions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have analyzed the correlation that exists between the GC levels of third and first or second codon position for about 1400 human coding sequences. The linear relationship that was found indicates that the large differences in GC level of third codon positions of human genes are paralleled by smaller differences in GC levels of first and second codon positions. Whereas third codon position differences correspond to very large differences in codon usage within the human genome, the first and second codon position differences correspond to smaller, yet very remarkable, differences in the amino acid composition of encoded proteins. Because GC levels of codon positions are linearly correlated with the GC levels of the isochores harboring the corresponding genes, both codon usage and amino acid composition are different for proteins encoded by genes located in isochores of different GC levels. Furthermore, we have also shown that a linear relationship with a unity slope and a correlation coefficient of 0.77 exists between GC levels of introns and exons from the 238 human genes currently available for this analysis. Introns are, however, about 5% lower in GC, on average, than exons from the same genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102652
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    Silent substitutions in mammalian genomes and their evolutionary implications (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 583-589 
    Details
    ISSN: 1432-1432
    Keywords: Isochores ; Mutation rates ; Mammals ; DNA replication ; DNA repair
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An analysis of silent substitutions in pairwise comparisons of homologous genes from different mammals has shown that, in spite of individual fluctuations, their frequencies (which are very strongly correlated with the frequency of substitutions per synonymous site calculated according to Li et al. 1985) do not vary, on the average, with the GC levels of silent positions. This holds in the general case, in which silent positions of pairs of homologous genes share the same composition, namely in the human/other primates, human/artiodactyls, and in the mouse/rat pairs, as well as in the special cases in which the composition of silent positions are different, namely in the human/rabbit and the human/rat (or human/mouse) pairs. A slightly lower frequency found for low GC values in the human/bovine and human/pig pairs seems to be due to the specific gene samples used. These results contradict the previously claimed existence of differences in mutation rates and of mutational biases in third codon positions of coding sequences located in different isochores of mammalian genomes. They also imply that the variations in nucleotide precursor pools through the cell cycle and the differences in replication timing, or in repair efficiency, which were reported for different isochores, do not lead, as claimed, to differences in mutation rates, not in mutational biases in mammals. The differences claimed appear to be due to using small gene samples when individual fluctuations from gene to gene are relatively large.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00182744
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Compositional patterns in vertebrate genomes: Conservation and change in evolution (1988)
    Springer
    Journal of molecular evolution 28 (1988), S. 7-18 
    Details
    ISSN: 1432-1432
    Keywords: Compositional patterns ; Compositional shifts ; Genome evolution ; Isochores ; Vertebrates ; Selection ; Neutral theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The evolution of vertebrate genomes can be investigated by analyzing their regional compositional patterns, namely the compositional distributions of large DNA fragments (in the 30–100-kb size range), of coding sequences, and of their different codon positions. This approach has shown the existence of two evolutionary modes. In the conservative mode, compositional patterns are maintained over long times (many million years), in spite of the accumulation of enormous numbers of base substitutions. In the transitional, or shifting, mode, compositional patterns change into new ones over much shorter times. The conservation of compositional patterns, which has been investigated in mammalian genomes, appears to be due in part to some measure of compositional conservation in the base substitution process, and in part to negative selection acting at regional (isochore) levels in the genome and eliminating deviations from a narrow range of values, presumably corresponding to optimal functional properties. On the other hand, shifts of compositional patterns, such as those that occurred between cold-blooded and warm-blooded vertebrates, appear to be due essentially to both negative and positive selection again operating at the isochore level, largely under the influence of changes in environmental conditions, and possibly taking advantage of mutational biases in the replication/repair enzymes and/or in the enzyme make-up of nucleotide precursor pools. Other events (like translocations and changes in chromosomal structure) also play a role in the transitional mode of genome evolution. The present findings (1) indicate that isochores, which correspond to the DNA segments of individual or contiguous chromatin domains, represent selection units in the vertebrate genome; and (2) shed new light on the selectionist-neutralist controversy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02143493
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Codon usage changes and sequence dissimilarity between human and rat (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 81-91 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Evolutionary rate ; Isochores ; Silent dissimilarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary This paper reports on the relationship between the number of silent differences and the codon usage changes in the lineages leading to human and rat. Examination of 102 pairs of homologous genes gives rise to four main conclusions: (1) We have previously demonstrated the existence of a codon usage change (called the minor shift) between human and rat; this was confirmed here with a larger sample. For genes with extreme C+G frequencies, the C+G level in the third codon position is less extreme in rat than in human. (2) Protein similarity and percentage of positive differences are the two main factors that discriminate homologous genes when characterized by differences between rat and human. By definition, positive differences result from silent changes between A or T and C or G with a direction implying a C+G content variation in the same direction as the overall gene variation. (3) For genes showing both codon usage change and low protein similarity, a majority of amino acid replacements contributes to C+G level variation in positions I and II in the same direction as the variation in position III. This is thus a new example of protein evolution due to constraints acting at the DNA level. (4) In heavy isochores (high C+G content) no direct correlation exists between codon usage change (measured by the dissymmetry of differences) and silent dissimilarity. In light isochores the opposite situation is observed: modification of codon usage is associated with a high synonymous dissimilarity. This result shows that, in some cases, modification of constraints acting at the DNA level could accelerate divergence between genomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02109477
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 107-113 
    Details
    ISSN: 1432-1432
    Keywords: DNA repair ; DNA replication ; DNA transcription ; Isochores
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The frequencies of synonymous substitutions of mammalian genes cover a much wider range than previously thought. We report here that the different frequencies found in homologous genes from a given mammalian pair are correlated with those in the same homologous genes from a different mammalian pair. This indicates that the frequencies of synonymous substitutions are gene-specific (as are the frequencies of nonsynonymous substitutions), or, in other words, that “fast” and “slow” genes in one mammal are fast and slow, respectively, in any other one. Moreover, the frequencies of synonymous substitutions are correlated with the frequencies of nonsynonymous substitution in the same genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00166602
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 6
    Electronic Resource
    Electronic Resource
    The compositional distribution of coding sequences and DNA molecules in humans and murids (1988)
    Springer
    Journal of molecular evolution 27 (1988), S. 311-320 
    Details
    ISSN: 1432-1432
    Keywords: Genome composition ; Coding sequences ; Isochores ; Humans ; Murids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The compositional distributions of coding sequences and DNA molecules (in the 50-100-kb range) are remarkably narrower in murids (rat and mouse) compared to humans (as well as to all other mammals explored so far). In murids, both distributions begin at higher and end at lower GC values. A comparison of homologous coding sequences from murids and humans revealed that their different compositional distributions are due to differences in GC levels in all three codon positions, particularly of genes located at both ends of the distribution. In turn, these differences are responsible for differences in both codon usage and amino acids. When GC levels at first+second codon positions and third codon positions, respectively, of murid genes are plotted against corresponding GC levels of homologous human genes, linear relationships (with very high correlation coefficients and slopes of about 0.78 and 0.60, respectively) are found. This indicates a conservation of the order of GC levels in homologous genes from humans and murids. (The same comparison for mouse and rat genes indicates a conservation of GC levels of homologous genes.) A similar linear relationship was observed when plotting GC levels of corresponding DNA fractions (as obtained by density gradient centrifugation in the presence of a sequence-specific ligand) from mouse and human. These findings indicate that orderly compositional changes affecting not only coding sequences but also noncoding sequences took place since the divergence of murids. Such directional fixations of mutations point to the existence of selective pressures affecting the genome as a whole.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101193
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 7
    Electronic Resource
    Electronic Resource
    The compositional properties of human genes (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 493-503 
    Details
    ISSN: 1432-1432
    Keywords: Human genome ; Gene localization ; Isochores ; Coding sequences ; Introns ; Codon positions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The present work represents the first attempt to study in greater detail previously proposed compositional correlations in genomes, based on a body of additional data relating to gene localizations as well as to extended flanking sequences extracted from gene banks. We have investigated the correlations that exist between (1) the GC levels of exons of human genes, and (2) the GC levels of either intergenic sequences or introns associated with the genes under consideration. In both cases, linear relationships with slopes close to unity were found. The similarity of the linear relationships indicates similar GC levels in intergenic sequences and introns located in the same isochores. Moreover, both intergenic sequences and introns showed GC levels 5–10% lower than the corresponding exons. The above findings considerably strengthen the previously drawn conclusion that coding and noncoding sequences (both inter- and intragenic) from the same isochores of the human genome are compositionally correlated. In addition, we find linear correlations between the GC levels of codon positions and of the intergenic sequences or introns associated with the corresponding genes, as well as among the GC levels of codon positions of genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102651
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 8
    Electronic Resource
    Electronic Resource
    Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 308-317 
    Details
    ISSN: 1432-1432
    Keywords: Introns ; Exons ; Gene structure ; Repetitive DNA ; Isochore ; Vertebrate ; Database bias ; Microsatellites ; SINES ; LINES
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We compared the exon/intron organization of vertebrate genes belonging to different isochore classes, as predicted by their GC content at third codon position. Two main features have emerged from the analysis of sequences published in GenBank: (1) genes coding for long proteins (i.e., ≥500 aa) are almost two times more frequent in GC-poor than in GC-rich isochores; (2) intervening sequences (=sum of introns) are on average three times longer in GC-poor than in GC-rich isochores. These patterns are observed among human, mouse, rat, cow, and even chicken genes and are therefore likely to be common to all warm-blooded vertebrates. Analysis of Xenopus sequences suggests that the same patterns exist in cold-blooded vertebrates. It could be argued that such results do not reflect the reality because sequence databases are not representative of entire genomes. However, analysis of biases in GenBank revealed that the observed discrepancies between GC-rich and GC-poor isochores are not artifactual, and are probably largely underestimated. We investigated the distribution of microsatellites and interspersed repeats in introns of human and mouse genes from different isochores. This analysis confirmed previous studies showing that Ll repeats are almost absent from GC-rich isochores. Microsatellites and SINES (Alu, B1, B2) are found at roughly equal frequencies in introns from all isochore classes. Globally, the presence of repeated sequences does not account for the increased intron length in GC-poor isochores. The relationships between gene structure and global genome organization and evolution are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163235
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 9
    Electronic Resource
    Electronic Resource
    Independent regulation of mobile element copy number in Drosophila melanogaster inbred lines (1988)
    Springer
    Chromosoma 96 (1988), S. 291-294 
    Details
    ISSN: 1432-0886
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Using data from in situ hybridization of the giant chromosomes from salivary glands, we have studied hobo mobile element copy numbers in 17 genomes of highly inbred lines of Drosophila melanogaster. A high number of insertions in the 3R arm and a high variance in total copy number characterize the hobo element. The genomic control of copy number (a compensatory effect among chromosome arms) detected previously for mdg-1, I and copia but not for P, was not found for hobo either, and there is no relation between the P and hobo copy numbers per line. From the DNA structure and putative mechanisms of transposition of each element, we suggest that the mechanism of transposition, involving either a reverse transcriptase or a transposase, is a good criterion for determining the way the copy number is regulated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00286916
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 10
    facet.materialart.
    Unknown
    Hybrid viability is correlated with the I and P mobile element copy numbers of the maternal inbred line in Drosophila melanogaster (1989)
    Springer Nature
    Details
    Publication Date: 1989-06-01
    Print ISSN: 0018-067X
    Electronic ISSN: 1365-2540
    Topics: Biology
    Published by Springer Nature
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...