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1

Digitale Medien

Sensitivity of Patterns of Molecular Evolution to Alterations in Methodology: A Critique of Hughes and Yeager (1998)

Smith, Nick G.C. ; Hurst, Laurence D.

Springer

Journal of molecular evolution 47 (1998), S. 493-500

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ISSN: 1432-1432

Schlagwort(e): Key words: Substitution rate estimation — Intron evolution — Synonymous and nonsynonymous correlation — GC composition

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie

Notizen: 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.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/PL00013151

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2

Digitale Medien

Evolutionary Lability of Context-Dependent Codon Bias in Bacteria (2000)

McVean, Gilean A.T. ; Hurst, Gregory D.D.

Springer

Journal of molecular evolution 50 (2000), S. 264-275

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ISSN: 1432-1432

Schlagwort(e): Key words: Codon bias — Bacteria —Escherichia coli— Out-of-frame stop codons — AGG motifs —Haemophilus influenzae—Mycoplasma genitalium

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie

Notizen: 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.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/s002399910031

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3

Digitale Medien

The Genetic Code Is One in a Million (1998)

Freeland, Stephen J. ; Hurst, Laurence D.

Springer

Journal of molecular evolution 47 (1998), S. 238-248

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ISSN: 1432-1432

Schlagwort(e): Key words: Genetic code — Error minimization — Mistranslation — Transition/transversion bias — Evolution — Natural selection

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie

Notizen: 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.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/PL00006381

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4

Digitale Medien

A Quantitative Measure of Error Minimization in the Genetic Code (1999)

Haig, David ; Hurst, Laurence D.

Springer

Journal of molecular evolution 49 (1999), S. 708-708

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ISSN: 1432-1432

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/PL00006591

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5

Digitale Medien

A quantitative measure of error minimization in the genetic code (1991)

Haig, David ; Hurst, Laurence D.

Springer

Journal of molecular evolution 33 (1991), S. 412-417

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ISSN: 1432-1432

Schlagwort(e): Genetic code ; Complementary hydropathy ; Translation

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie

Notizen: 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.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/BF02103132

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6

Digitale Medien

Precipitation in the Venezuelan Andes in the context of regional climate (1998)

Pulwarty, R. S. ; Barry, R. G. ; Hurst, C. M. ; [weitere]

Springer

Meteorology and atmospheric physics 67 (1998), S. 217-237

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ISSN: 1436-5065

Quelle: Springer Online Journal Archives 1860-2000

Thema: Geographie , Physik

Notizen: Summary Rainfall regimes are primarily unimodal in central and eastern Venezuela but bimodal (peaks in May–June and September-October-November with a minimum in July–August) in the northwest. There is a sharp transition across the Andes suggesting a topographic-circulation connection. However, a mid-summer minimum also occurs at other locations in Venezuela and Central America during individual years. This paper addresses the nature and control of the regimes including the role of large-scale circulation features and convection as indicated by outgoing longwave radiation data. Altitudinal characteristics of precipitation in the Andes and their spatial variability are also investigated. The development of the minimum within the rainy season annual cycle is shown to be related to the combined effects of the evolution of sea surface temperatures in the east Pacific warm pool and reinforced in the area of the Andes by enhanced easterlies during July and August.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/BF01277512

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7

Digitale Medien

Uptake of Zn++ and aflatoxin from perlite and liquid culture by Zea mays seedlings (1982)

Llewellyn, G. C. ; Reynolds, J. D. ; Hurst, L. ; [weitere]

Springer

Mycopathologia 77 (1982), S. 111-116

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ISSN: 1573-0832

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie , Medizin

Notizen: 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’.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/BF00437393

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8

Digitale Medien

Book reviews (1988)

Fairbairn, Kenneth J. ; Rogerson, Peter A. ; Metzger, James E. ; [weitere]

Springer

The annals of regional science 22 (1988), S. 91-131

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ISSN: 1432-0592

Quelle: Springer Online Journal Archives 1860-2000

Thema: Architektur, Bauingenieurwesen, Vermessung , Geographie , Wirtschaftswissenschaften

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/BF01286405

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9

Digitale Medien

Laphygma Exigua immigrations into the British Isles, 1947–1963 (1965)

Hurst, G. W.

Springer

International journal of biometeorology 9 (1965), S. 21-28

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ISSN: 1432-1254

Quelle: Springer Online Journal Archives 1860-2000

Thema: Geographie , Physik

Beschreibung / Inhaltsverzeichnis: Zusammenfassung Alle bekannten Einflüge von LAPHYGMA EXIGUA nach England von 1947–1963 wurden in Beziehung zu den vorhergehenden möglichen Fluglinien von der Süd-Biskaya aus untersucht; statistisch wird gezeigt, dass in jedem Fall die Motten aus Südspanien oder jenseits davon kamen. Motten, die zu Beginn des Jahres eintrafen, stammten aus Gebieten südlich 40°N, in den meisten Fällen aus Marokko oder Madeira. Von Mai ab war das Ursprungsland der meisten Motten Nordwestspanien, ausgenommen 1962,als sich die Herkunft einer verhältnismässig grossen Anzahl in Südengland bis Marokko zurückverfolgen liess.

Kurzfassung: Resume Toutes les migrations connues de LAPHYGMA EXIGUA vers l'Angleterre entre 1947 et 1963 ont été étudiées en fonction des lignes de vol possibles à partir du Sud de la Biscaye; il est statistiquement établi que, dans tous les cas, ces mites venaient du Sud de l'Espagne ou d'au-delà. Les arrivées précoces dans l'année sont originaires de régions au Sud du 40 ème degré de Latitude Nord, la plupart du Maroc ou de Madère. A partir du mois de mai, la région d'origine de la plupart des mites a été le Nord-Ouest de l'Espagne, sauf en 1962 où les arrivées dans le Sud de l'Angleterre étaient originaires du Maroc.

Notizen: Abstract All known immigrations of the LAPHYGMA EXIGUA into Britain in the period 1947 to 1963 were examined in relation to preceding potential trajectories from South Biscay and a statistical demonstration is given that in every case moths originated from North Spain or beyond. Arrivals early in the year are shown to have originated from south of 40°N, and in most cases from Morocco or Madeira.From May onwards,however, moths came mainly from North-west Spain, except in 1962 when relatively huge numbers in southern England could also be traced back to Morocco.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/BF02187305

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10

Digitale Medien

The gene for MRC OX-2 membrane glycoprotein is localized on human chromosome 3 (1987)

McCaughan, G. W. ; Clarks, M. J. ; Hurst, J. ; [weitere]

Springer

Immunogenetics 25 (1987), S. 133-135

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ISSN: 1432-1211

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie , Medizin

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/BF00364281

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