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  • 1
    Electronic Resource
    Electronic Resource
    Biased biological functions of horizontally transferred genes in prokaryotic genomes (2004)
    [s.l.] : Nature Publishing Group
    Nature genetics 36 (2004), S. 760-766 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Horizontal gene transfer is one of the main mechanisms contributing to microbial genome diversification. To clarify the overall picture of interspecific gene flow among prokaryotes, we developed a new method for detecting horizontally transferred genes and their possible donors by Bayesian ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/ng1381
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  • 2
    Electronic Resource
    Electronic Resource
    FGFR-related gene nou-darake restricts brain tissues to the head region of planarians (2002)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 419 (2002), S. 620-624 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The study of planarian regeneration may help us to understand how we can rebuild organs and tissues after injury, disease or ageing. The robust regenerative abilities of planarians are based upon a population of totipotent stem cells (neoblasts), and among the organs regenerated by these ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature01042
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  • 3
    Electronic Resource
    Electronic Resource
    Multiple class I loci expressed by the quail Mhc (1999)
    Springer
    Immunogenetics 49 (1999), S. 456-460 
    Details
    ISSN: 1432-1211
    Keywords: Key words Antigen processing ; Evolution ; Cell surface molecules ; Mhc ; Class I antigens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050519
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  • 4
    Electronic Resource
    Electronic Resource
    Slow Evolutionary Rate of GB Virus C/Hepatitis G Virus (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 383-389 
    Details
    ISSN: 1432-1432
    Keywords: Key words: GBV-C/HGV — GBV-A — Phylogenetic tree — Substitution rate — Divergence time
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. With the aim of elucidating evolutionary features of GB virus C/hepatitis G virus (GBV-C/HGV), molecular evolutionary analyses were conducted using the entire coding region of this virus. In particular, the rate of nucleotide substitution for this virus was estimated to be less than 9.0 × 10−6 per site per year, which was much slower than those for other RNA viruses. The phylogenetic tree reconstructed for GBV-C/HGV, by using GB virus A (GBV-A) as outgroup, indicated that there were three major clusters (the HG, GB, and Asian types) in GBV-C/HGV, and the divergence between the ancestor of GB- and Asian-type strains and that of HG-type strains first took place more than 7000–10,000 years ago. The slow evolutionary rate for GBV-C/HGV suggested that this virus cannot escape from the immune response of the host by means of producing escape mutants, implying that it may have evolved other systems for persistent infection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006482
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  • 5
    Electronic Resource
    Electronic Resource
    Constrained Evolution with Respect to Gene Overlap of Hepatitis B Virus (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S083 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Hepatitis B virus — Genetic classification — Constrained evolution — Overlapping gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. With the aim of elucidating the evolution of a hepadnavirus family, we constructed molecular phylogenetic trees for 27 strains of hepatitis B virus (HBV) using both the unweighted pair-grouping and neighbor-joining methods. All five gene regions, P, C, S, X, and preS, were used to construct the phylogenetic trees. Using the phylogenetic trees obtained, we classified these strains into five major groups in which the strains were closely related to each other. Our classification reinforced our previous view that genetic classification is not always compatible with conventional classification determined by serological subtypes. Moreover, constraints on the evolutionary process of HBV were analyzed for amino-acid-altering (nonsynonymous) and silent (synonymous) substitutions, because two-thirds of the open reading frame (ORF), P, contains alternating overlapping ORFs. In our unique analysis of this interesting gene structure of HBV, the most frequent synonymous substitutions were observed in the nonoverlapped parts of the P and C genes. On the other hand, the number of synonymous substitutions per nucleotide site for the S gene was quite low and appeared a strongly constrained evolution. Because the P gene overlaps the S gene in a different frame, the low rate of synonymous substitution for the S gene can be explained by the evolutionary constraints which are imposed on the overlapping gene region. In other words, synonymous substitutions in the S gene can cause amino acid changes in its overlapping region in a different frame. Thus, the evolution of HBV is constrained evolutionarily by the overlapping genes. We propose calling this mode of viral evolution ``constrained evolution.'' The evolution of HBV represents a typical constrained evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000061
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  • 6
    Electronic Resource
    Electronic Resource
    Inter-RNA homology and possible roles of small RNAs (1981)
    Springer
    Journal of molecular evolution 17 (1981), S. 245-250 
    Details
    ISSN: 1432-1432
    Keywords: Small RNAs ; mRNA ; 18S rRNA ; Sequence homology ; Transcription ; mRNA processing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequence of a segment of U1 and U3b small RNAs (sRNAs) is shown to have a high complementarity with the nucleotide sequence of a part of the leader region of almost all eukaryotic genes studied so far. The complementary region of U3b is located in the unpaired segment of the secondary structure of U3b constructed by Reddy et al. (1979). A similar complementarity is also observed between these RNAs and the leader regions of eukaryotic viruses, but the complementary region is not always identical with that for eukaryotic genes. Complementarity is also observed between the 3′ end of 18S rRNA and a segment of U1 or U3b which is almost contiguous to the region complementary with mRNA. These observations suggest that U1 and U3b may be involved in mRNA processing and transport in the nucleus or in translation in the cytoplasm. In addition to U1 and U3b, another sRNA, i.e., 4.5S RNAI, is shown to have segments which are homologous to the Hogness box of the flanking region of gene and the Proudfoot-Brownlee (PB) box of mRNA near the poly(A) attachment site. The two segments which are complementary with these boxes are located almost contiguously on a co-joined loop of the secondary structure of 4.5S RNAI constructed by Ro-Choi et al. (1972). Since the Hogness box and PB box are both considered as a recognition site by the RNA polymerase, it is possible that 4.5S RNAI is involved in mediating gene transcription.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01732762
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  • 7
    Electronic Resource
    Electronic Resource
    Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide (1982)
    Springer
    Journal of molecular evolution 18 (1982), S. 414-422 
    Details
    ISSN: 1432-1432
    Keywords: Molecular evolution ; Nucleotide substitution ; Evolutionary distance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A formal mathematical analysis of Kimura's (1981) six-parameter model of nucleotide substitution for the case of unequal substitution rates among different pairs of nucleotides is conducted, and new formulae for estimating the number of nucleotide substitutions and its standard error are obtained. By using computer simulation, the validities and utilities of Jukes and Cantor's (1969) one-parameter formula, Takahata and Kimura's (1981) four-parameter formula, and our sixparameter formula for estimating the number of nucleotide substitutions are examined under three different schemes of nucleotide substitution. It is shown that the one-parameter and four-parameter formulae often give underestimates when the number of nucleotide substitutions is large, whereas the six-parameter formula generally gives a good estimate for all the three substitution schemes examined. However, when the number of nucleotide substitutions is large, the six-parameter and four-parameter formulae are often inapplicable unless the number of nucleotides compared is extremely large. It is also shown that as long as the mean number of nucleotide substitutions is smaller than one per nucleotide site the three formulae give more or less the same estimate regardless of the substitution scheme used.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01840889
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  • 8
    Electronic Resource
    Electronic Resource
    Evolutionary origin of a Kunitz-type trypsin inhibitor domain inserted in the amyloid β precursor protein of Alzheimer's disease (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 536-543 
    Details
    ISSN: 1432-1432
    Keywords: Serine protease inhibitor ; Kunitz type ; Evolutionary origin ; Alzheimer's disease ; Insertion sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The Kunitz-type protease inhibitor is one of the serine protease inhibitors. It is found in blood, saliva, and all tissues in mammals. Recently, a Kunitz-type sequence was found in the protein sequence of the amyloid β precursor protein (βAPP). It is known that βAPP accumulates in the neuritic plaques and cerebrovascular deposits of patients with Alzheimer's disease. Collagen type VI in chicken also has an insertion of a Kunitz-type sequence. To elucidate the evolutionary origin of these insertion sequences, we constructed a phylogenetic tree by use of all the available sequences of Kunitz-type inhibitors. The tree shows that the ancestral gene of the Kunitz-type inhibitor appeared about 500 million years ago. Thereafter, this gene duplicated itself many times, and some of the duplicates were inserted into other protein-coding genes. During this process, the Kunitz-type sequence in the present βAPP gene diverged from its ancestral gene about 270 million years ago and was inserted into the gene soon after duplication. Although the function of the insertion sequences is unknown, our molecular evolutionary analysis shows that these insertion sequences in βAPP have an evolutionarily close relationship with the inter-α-trypsin inhibitor or trypstatin, which inhibits the activity of tryptase, a novel membrane-bound serine protease in human T4+ lymphocytes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160466
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular evolution and phylogeny of the human AIDS viruses LAV, HTLV-III, and ARV (1987)
    Springer
    Journal of molecular evolution 24 (1987), S. 330-336 
    Details
    ISSN: 1432-1432
    Keywords: Human AIDS viruses ; Molecular evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A phylogenetic tree for the human lymphadenopathy-associated virus (LAV), the human T-cell lymphotrophic virus type III (HTLV-III), and the acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV) has been constructed from comparisons of the amino acid sequences of their gag proteins. A method is proposed for estimating the divergence times among these AIDS viruses and the rates of nucleotide substitution for their RNA genomes. The analysis indicates that the LAV and HTLV-III strains diverged from one another after 1977 and that their common ancestor diverged from the ARV virus no more than 10 years earlier. Hence, the evolutionary diversity among strains of the AIDS viruses apparently has been generated within the last 20 years. It is estimated that the genome of the AIDS virus has a nucleotide substitution rate on the order of 10−3 per site per year, with the rate in the second half of the genome being double that in the first half.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02134131
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  • 10
    Electronic Resource
    Electronic Resource
    Different evolutionary histories of kringle and protease domains in serine proteases: A typical example of domain evolution (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 331-336 
    Details
    ISSN: 1432-1432
    Keywords: Kringle domain ; Protease domain ; Serine protease ; Domain evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract With the aim of elucidating the evolutionary processes of the kringle and protease domains in serine proteases which are involved with the system of blood coagulation and fibrinolysis, we constructed phylogenetic trees for the kringle and protease domains, separately, by use of amino acid sequence data. The phylogenetic trees constructed clearly showed that the topologies were different between the kringle and protease domains. Because both domains are coded by single peptides of serine proteases, this strongly suggests that the kringle and protease domains must have undergone different evolutionary processes. Thus, these observations imply that serine proteases evolve in a way such that each domain is a unit of evolution, exemplifying a typical mode of domain evolution. A possible relationship between the domain evolution and the exon shuffling theory is also discussed from the viewpoint of gene evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163238
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