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  • Articles  (59)
  • Springer  (52)
  • Institute of Physics  (7)
  • American Geophysical Union
  • Biology  (59)
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  • Articles  (59)
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  • 1
    Electronic Resource
    Electronic Resource
    Sensitivity of Patterns of Molecular Evolution to Alterations in Methodology: A Critique of Hughes and Yeager (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 493-500 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Substitution rate estimation — Intron evolution — Synonymous and nonsynonymous correlation — GC composition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Employing a set of 43 othologous mouse and rat genes, Hughes and Yeager (J. Mol. Evol. 45:125–130, 1997) reported (1) no correlation between synonymous and nonsynonymous rates of nucleotide substitution, (2) a positive correlation between intronic GC contents (GC i) and intronic substitution rates (K i), (3) that the average K i value was very similar to the average K s value, and (4) that the compositional correlation between the rat and the mouse genes is stronger at the third codon position (GC3) than at the first and second codon positions (GC12). We have examined the robustness of these results to alterations in substitution rate estimation protocol, alignment protocol, and statistical procedure. We find that a significant correlation between K a and K s is observed either if a rank correlation statistic is used instead of regression analysis, if one outlier is excluded from the analysis, or if a regression weighted by gene size is employed. The correlation between K i and GC i we find to be sensitive to changes in alignment protocol and disappears on the use of weighted means. The finding that K s and K i are approximately the same is dependent on the method for estimating K s values. Finally, the variance around the regression line of rat GC3 versus mouse GC3 we find to be significantly higher than that in GC12. The source of the discrepancy between this and Hughes and Yeager's result is unclear. The variance around the line for GC4 is higher still, as might be expected. Using a methodology that may be considered preferable to that of Hughes and Yeager, we find that all four of their results are contradicted. More importantly this analysis reinforces the need for caution in assembling and analyzing data sets, as the degree of sensitivity to what many might consider minor methodological alterations is unexpected.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00013151
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  • 2
    Electronic Resource
    Electronic Resource
    Evolutionary Lability of Context-Dependent Codon Bias in Bacteria (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 264-275 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Codon bias — Bacteria —Escherichia coli— Out-of-frame stop codons — AGG motifs —Haemophilus influenzae—Mycoplasma genitalium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered. Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably between genomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910031
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  • 3
    Electronic Resource
    Electronic Resource
    The Genetic Code Is One in a Million (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 238-248 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Genetic code — Error minimization — Mistranslation — Transition/transversion bias — Evolution — Natural selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation: erroneous codons are either synonymous or code for an amino acid with chemical properties very similar to those of the one that would have been present had the error not occurred. This work has suggested that the second base of codons is less efficient in this respect, by about three orders of magnitude, than the first and third bases. These results are based on the assumption that all forms of error at all bases are equally likely. We extend this work to investigate (1) the effect of weighting transition errors differently from transversion errors and (2) the effect of weighting each base differently, depending on reported mistranslation biases. We find that if the bias affects all codon positions equally, as might be expected were the code adapted to a mutational environment with transition/transversion bias, then any reasonable transition/transversion bias increases the relative efficiency of the second base by an order of magnitude. In addition, if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006381
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  • 4
    Electronic Resource
    Electronic Resource
    A Quantitative Measure of Error Minimization in the Genetic Code (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 708-708 
    Details
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006591
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  • 5
    Electronic Resource
    Electronic Resource
    A quantitative measure of error minimization in the genetic code (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 412-417 
    Details
    ISSN: 1432-1432
    Keywords: Genetic code ; Complementary hydropathy ; Translation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have calculated the average effect of changing a codon by a single base for all possible single-base changes in the genetic code and for changes in the first, second, and third codon positions separately. Such values were calculated for an amino acid's polar requirement, hydropathy, molecular volume, and isoelectric point. For each attribute the average effect of single-base changes was also calculated for a large number of randomly generated codes that retained the same level of redundancy as the natural code. Amino acids whose codons differed by a single base in the first and third codon positions were very similar with respect to polar requirement and hydropathy. The major differences between amino acids were specified by the second codon position. Codons with U in the second position are hydrophobic, whereas most codons with A in the second position are hydrophilic. This accounts for the observation of complementary hydropathy. Single-base changes in the natural code had a smaller average effect on polar requirement than all but 0.02% of random codes. This result is most easily explained by selection to minimize deleterious effects of translation errors during the early evolution of the code.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02103132
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  • 6
    Electronic Resource
    Electronic Resource
    Uptake of Zn++ and aflatoxin from perlite and liquid culture by Zea mays seedlings (1982)
    Springer
    Mycopathologia 77 (1982), S. 111-116 
    Details
    ISSN: 1573-0832
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The present paper reports our attempts to determine whether the inclusion of 0.0014 mM Zn++ within a hydroponic culture medium affects the ability of 12-day-old Zea mays, cv. ‘SS-522’ to take-up [3H]-aflatoxin B1. Data from the corollary experiment, i.e., whether inclusion of aflatoxin affects the ability of Zea mays, cvs. ‘Truckers White’, ‘X-Sweet’ and ‘Merit’ to take-up 65ZnCl2 are presented also. This report is a preliminary to one regarding an in-progress analysis of whether pollutant levels of Zn++ affect aflatoxin uptake and distribution. In the absence of irrigating seedlings, which were grown in Perlite containing 65ZnCl2, with a solution containing mixed aflatoxins, the stem contained the greatest amount of label with root plus seed the next highest and the leaf the least for each of the cvs. In contrast, when the seedlings were irrigated with a solution containing mixed aflatoxins, the root plus seed contained either an amount nearly identical to (cv. ‘Truckers White’) or in excess of that within the stem (cvs. ‘X-Sweet’ and ‘Merit’). Calculation of the percentages of aflatoxin-induced diminutions in leaf, stem and root label suggested that the aflatoxins interfered with the translocation of 65ZnCl2 from the root to the stem and leaf, at least for cvs ‘X-Sweet’ and ‘Merit’. When 0.0014mM Zn++ as ZnSO4 was added to an incubation medium in which 12-day-old seedlings were suspended and plant growth assessed over 72 hours, a 15% increase (significant at 0.05 level) in seedling height over that of Zn++-deficient plants was observed. No differences in [3H]-aflatoxin B1 uptake were noted between those seedlings which were grown in either Zn++-containing or lacking media. Less than one % of the[3H]-aflatoxin B1 which was taken-up was recovered within chloroform extracts of the seedlings. The distributions of radioactivity from [3H]-aflatoxin B1 for leaf, stem, seed and root were 0, 57, 26 and 19% and 0, 26, 58 and 18% for Zn++-containing and -lacking media, ‘respectively’.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00437393
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  • 7
    Electronic Resource
    Electronic Resource
    The gene for MRC OX-2 membrane glycoprotein is localized on human chromosome 3 (1987)
    Springer
    Immunogenetics 25 (1987), S. 133-135 
    Details
    ISSN: 1432-1211
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00364281
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  • 8
    Electronic Resource
    Electronic Resource
    Comparison of allozyme and mitochondrial DNA spatial differentiation in the limpet Patella vulgata (1995)
    Springer
    Marine biology 122 (1995), S. 257-263 
    Details
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Allozyme and restriction enzyme analysis of mtDNA was used to study variation in samples from British populations of the marine limpet Patella vulgata in two regions. South Wales and Northeast England. Allozyme analysis revealed significant differences in allele frequencies among samples. However F ST (population differentiation) values were no higher between than within regions, indicating that genetic heterogeneity was localised and not related to geographic separation. For mtDNA, samples from South Wales exhibited higher haplotype diversity values than samples from Northeast England. In addition there were substantial differences in the haplotype distribution between regions. The value of θ, the haploid analogoue of F ST , was low within regions (θ=0.09) but high between regions (θ=0.44). The estimated difference in migration rate for allozymes and mtDNA exceed the neutral expectation, unless it is assumed that there are influential differences in the magnitude of female and male gametic dispersal.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00348938
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  • 9
    Electronic Resource
    Electronic Resource
    The effects of freeze-thaw cycles and leaching on the loss of soluble carbohydrates from leaf material of two subantarctic plants (1985)
    Springer
    Polar biology 4 (1985), S. 27-31 
    Details
    ISSN: 1432-2056
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Leaves and litter of two phanerogams (Acaena magellanica (Lam.) Vahl and Poa flabellata (Lam.) Hook. f.) were collected in spring on the subantarctic island of South Georgia. Leaves immersed in water lost up to 80% of their total available soluble carbohydrates after 6–8 h. The loss of K+ and PO 4 3- followed a similar pattern to that shown by the carbohydrates. Up to 9 daily freeze/thaw cycles gave no increase in metabolite loss for senescent leaves. GLC analysis showed sucrose to be the principal leachate from Acaena. Sucrose, glucose and fructose were the main leachates from Poa. A significant proportion of the soluble carbohydrates in standing dead leaves was trehalose. The relationship of such leachates to microbial decomposition is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00286814
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  • 10
    Electronic Resource
    Electronic Resource
    The effect of temperature on the growth ofCandida saké isolated from the leaves of a subantarctic grass (1984)
    Springer
    Microbial ecology 10 (1984), S. 89-93 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract During a survey of microfungi on the subantarctic island of South Georgia, large numbers of phylloplane yeasts were isolated in late spring from leaves of a tussock grass. The dominant yeast was identified asCandida saké, this being the first record for the Antarctic region. Isolates in liquid culture had a temperature optimum for growth of 20–25°C. It was capable of assimilation of a range of simple carbohydrates, similar to those found in leachates from new leaves of the tussock grass. The seasonal decline of yeasts on the phylloplane is discussed in terms of the availability of leachate and the growth of filamentous microfungi on new leaves.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02011415
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