ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

Electronic Resource

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

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

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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

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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3

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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

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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4

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Comparison of allozyme and mitochondrial DNA spatial differentiation in the limpet Patella vulgata (1995)

Hurst, C. D. ; Skibinski, D. O. F.

Springer

Marine biology 122 (1995), S. 257-263

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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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5

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Activation of Maxi-K Channels by Parathyroid Hormone and Prostaglandin E2 in Human Osteoblast Bone Cells (1996)

Moreau, R. ; Hurst, A.M. ; Lapointe, J-Y. ; [et al.]

Springer

The journal of membrane biology 150 (1996), S. 175-184

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ISSN: 1432-1424

Keywords: Key words: Patch clamp — Calcium activated K channel — Osteoblast — PTH — PGE2

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Chemistry and Pharmacology

Notes: Abstract. Patch clamp experiments were performed on two human osteosarcoma cell lines (MG-63 and SaOS-2 cells) that show an osteoblasticlike phenotype to identify and characterize the specific K channels present in these cells. In case of MG-63 cells, in the cell-attached patch configuration (CAP) no channel activity was observed in 2 mm Ca Ringer (control condition) at resting potential. In contrast, a maxi-K channel was observed in previously silent CAP upon addition of 50 nm parathyroid hormone (PTH), 5 nm prostaglandin E2 (PGE2) or 0.1 mm dibutyryl cAMP + 1 μm forskolin to the bath solution. However, maxi-K channels were present in excised patches from both stimulated and nonstimulated cells in 50% of total patches tested. A similar K channel was also observed in SaOS-2 cells. Characterization of this maxi-K channel showed that in symmetrical solutions (140 mm K) the channel has a conductance of 246 ± 4.5 pS (n = 7 patches) and, when Na was added to the bath solution, the permeability ratio (PK/PNa) was 10 and 11 for MG-63 and SaOS-2 cells respectively. In excised patches from MG-63 cells, the channel open probability (P o ) is both voltage- (channel opening with depolarization) and Ca-dependent; the presence of Ca shifts the P o vs. voltage curve toward negative membrane potential. Direct modulation of this maxi-K channel via protein kinase A (PKA) is very unlikely since in excised patches the activity of this channel is not sensitive to the addition of 1 mm ATP + 20 U/ml catalytic subunit of PKA. We next evaluated the possibility that PGE2 or PTH stimulated the channel through a rise in intracellular calcium. First, calcium uptake (45Ca++) by MG-63 cells was stimulated in the presence of PTH and PGE2, an effect inhibited by Nitrendipine (10 μm). Second, whereas PGE2 stimulated the calcium-activated maxi-K channel in 2 mm Ca Ringer in 60% of patches studied, in Ca-free Ringer bath solution, PGE2 did not open any channels (n = 10 patches) nor did cAMP + forskolin (n = 3 patches), although K channels were present under the patch upon excision. In addition, in the presence of 2 mm Ca Ringer and 10 μm Nitrendipine in CAP configuration, PGE2 (n = 5 patches) and cAMP + forskolin (n = 2 patches) failed to open K channels present under the patch. As channel activation by phosphorylation with the catalytic subunit of PKA was not observed, and Nitrendipine addition to the bath or the absence of calcium prevented the opening of this channel, it is concluded that activation of this channel by PTH, PGE2 or dibutyryl cAMP + forskolin is due to an increase in intracellular calcium concentration via Ca influx.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002329900042

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6

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Kinship and social tolerance among female and juvenile wild house mice: kin bias but not kin discrimination (1995)

Hurst, Jane L. ; Barnard, C. J.

Springer

Behavioral ecology and sociobiology 36 (1995), S. 333-342

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ISSN: 1432-0762

Keywords: Mus domesticus ; Kin bias ; Aggression Group territoriality ; Territory invasion

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract Kin-biased social tolerance among house mice has been interpreted in terms of kin discrimination. However, several lines of evidence suggest it may instead be an incidental artifact of group member discrimination. This leads to very different predictions about the social consequences of relatedness within and between social groups. Social interactions between wild-stock adult female and juvenile house mice (Mus domesticus) established in neighbouring territorial groups within enclosures reveal relatedness to dominant males within groups as the major factor determining social tolerance of juveniles by females. Relatedness to the female herself had no significant independent effect on responses indicating tolerance. Females were generally more aggressive toward neighbouring-group juveniles (all unrelated to females) compared with those from their own group (all related to females), but were most aggressive toward neighbouring juveniles sired by the neighbouring dominant male. They were also more aggressive toward their own-group juveniles that had been sired by the neighbouring dominant but only when encountered in the neighbouring territory and with a greater bias against female juveniles. Females were least aggressive toward own-group juveniles sired by their own-group dominant male. The sire-bias in tolerance among females is similar to that reported among the dominant males themselves in an earlier study. As a result of the combined sire-bias in tolerance by adult males and females, juveniles sired by their own-group dominant males become less likely to intrude into a neighbouring territory with time. Overall, the results suggest that differences in social tolerance reflect discrimination on the basis of social group membership rather than relatedness between interactants and thus provide strong experimental evidence in support of incidental kin bias rather than kin discrimination.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00167794

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7

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Kinship and social tolerance among female and juvenile wild house mice: kin bias but not kin discrimination (1995)

Hurst, J. L. ; Barnard, C. J.

Springer

Behavioral ecology and sociobiology 36 (1995), S. 333-342

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ISSN: 1432-0762

Keywords: Key wordsMus domesticus ; Kin bias ; Aggression ; Group territoriality ; Territory invasion

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract Kin-biased social tolerance among house mice has been interpreted in terms of kin discrimination. However, several lines of evidence suggest it may instead be an incidental artifact of group member discrimination. This leads to very different predictions about the social consequences of relatedness within and between social groups. Social interactions between wild-stock adult female and juvenile house mice (Mus domesticus) established in neighbouring territorial groups within enclosures reveal relatedness to dominant males within groups as the major factor determining social tolerance of juveniles by females. Relatedness to the female herself had no significant independent effect on responses indicating tolerance. Females were generally more aggressive toward neighbouring-group juveniles (all unrelated to females) compared with those from their own group (all related to females), but were most aggressive toward neighbouring juveniles sired by the neighbouring dominant male. They were also more aggressive toward their own-group juveniles that had been sired by the neighbouring dominant but only when encountered in the neighbouring territory and with a greater bias against female juveniles. Females were least aggressive toward own-group juveniles sired by their own-group dominant male. The sire-bias in tolerance among females is similar to that reported among the dominant males themselves in an earlier study. As a result of the combined sire-bias in tolerance by adult males and females, juveniles sired by their own-group dominant males become less likely to intrude into a neighbouring territory with time. Overall, the results suggest that differences in social tolerance reflect discrimination on the basis of social group membership rather than relatedness between interactants and thus provide strong experimental evidence in support of incidental kin bias rather than kin discrimination.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00167794

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8

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Ligands of Urinary Lipocalins from the Mouse: Uptake of Environmentally Derived Chemicals (1998)

Robertson, Duncan ; Hurst, Jane ; Hubbard, Simon ; [et al.]

Springer

Journal of chemical ecology 24 (1998), S. 1127-1140

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ISSN: 1573-1561

Keywords: Major urinary protein ; menadione ; olfactory communication ; scent marking ; mouse

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Chemistry and Pharmacology

Notes: Abstract Mouse urine contains large quantities of proteins (major urinary proteins, MUPs) that are thought to function by binding lipophilic and volatile semiochemicals in a central calyx of the MUP. Two notable semiochemicals are 2-sec-butyl-4,5-dihydrothiazole and a brevicomin (3,4-dehydro-exo-brevicomin). MUPs derived from deposits of urine from wild caught mice contain neither of these ligands, but are replete with menadione. The menadione is probably incorporated in vitro from the environment, although some incorporation in vivo can also be demonstrated. These data show that the calyx of MUPs can bind other hydrophobic molecules derived from the environment, which may influence longevity of signal and deposition patterns of urinary scent marks. The ability to displace, rapidly and completely, the natural ligands by menadione also provides a new tool in the analysis of MUP function.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1022434300449

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9

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Identity, prevalence and intensity of infestation with wing feather mites on birds (Passeriformes) from the Setubal Peninsula of Portugal (1995)

Behnke, Jerzy M. ; McGregor, Peter K. ; Shepherd, Mike ; [et al.]

Springer

Experimental and applied acarology 19 (1995), S. 443-458

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ISSN: 1572-9702

Keywords: Birds ; feather mites ; prevalence ; intensity of infection ; Proctophyllodes ; P. pinnatus ; P. troncatus ; P. serini ; P. clavatus ; P. stylifer ; Pteronyssoides obscurus

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The results of a 4 year project investigating species of mites infesting wing primary feathers on 21 species of Passeriformes are reported. The majority of species were identified as belonging to the genus Proctophyllodes Robin, 1877 with one new host record. In addition Pteronyssoides obscurus Berlese 1884 was found on European swallows, also a new host record. A novel method to enable quantification of mite intensities without causing harm to the birds was devised and evaluated. This relied on visual inspection of wing primary feathers and assignment of subjective infestation scores to individual feathers, the sum of the individual scores comprising the primary feather total mite infestation score (PTMIS). Comparisons between species revealed that birds could be grouped into four categoris depending on their infestation intensity with mites. Swallows, sand martins and greenfinches showed the highest prevalence and most intense infestations (mean PTMIS ≥ 6.8). Blackbirds, blackcaps, serins, goldfinches, Cetti's warblers, great tits and house sparrows showed moderate levels of infestation with prevalence in the range 60–90.9% but a mean PTMIS lower than in the former group (1.6–5.8). The third group comprised Sardinian warblers, nightingales and short-toed tree creepers and was characterized by a prevalence of mites ≥ 40% and a mean PTMIS of 0.6–1.4. The final group, representing wrens, chiffchaffs, fan-tailed warblers and waxbills were without detectable mites, the only exception being wrens on which mites were identified in only three birds of the 32 sampled. These results are interpreted in the light of published information and possible explanations for the observations are discussed.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00048263

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