Double-base lesions are produced in DNA by free radicals

Evidence has been accumulating at the oligomer level that free radical-initiated DNA damage includes lesions in which two adjacent bases are both modified. Prominent examples are lesions in which a pyrimidine base is degraded to a formamido remnant and an adjacent guanine base is oxidized. An assay has been devised to detect double-base lesions based on the fact that the phosphoester bond 3' to a nuclesoside bearing the formamido lesion is resistant to hydrolysis by nuclease P1. The residual modified dinucleoside monophosphates obtained from a nuclease P1 (plus acid phosphatase) digest of DNA can be (32)P-postlabeled using T4 polynucleotide kinase. Using this assay the formamido single lesion and the formamido-8-oxoguanine double lesion were detected in calf thymus DNA after X-irradiation in oxygenated aqueous solution. The lesions were measured in the forms d(P(F)pG) and d(P(F)pG(H)), where P(F) stands for a pyrimidine nucleoside having the base degraded to a formamido remnant and G(H) stands for 8-oxo-deoxyguanosine. The yields in calf thymus DNA irradiated 60 Gy were 8.6 and 3.2 pmol/microgram DNA, respectively.     

Recovery of sandy beach and maritime forest vegetation on Phuket Island (Thailand) after the major Indian Ocean tsunami of 2004

Question: How rapidly has the sandy beach and maritime forest vegetation on Phuket recovered and regenerated after the impact of the major Indian Ocean tsunami of 2004? What are the characteristics of sandy beach species for regenerating their populations and the invasion patterns of originally non-sandy beach species or other newcomers after the tsunami? Location: Phuket Island, southern Thailand. Methods: Species composition of beaches was studied on the same research plots 6 months before and 9 months after the tsunami. The changes in individual species cover before and after the tsunami were determined by χ² tests. Change in community composition was analysed by detrended correspondence analysis. The relationship between species and environmental factors was analysed by canonical correspondence analysis. Results: The sites disturbed by the tsunami were often invaded by annuals, especially grasses and asteraceous plants, rather than by perennials. In contrast, species with clonal growth by stolons decreased significantly. Factors determining the species habitat differences were soil hardness (penetration resistance of sandy soil), per cent silt content, soil water content and beach management. Habitat differences among originally non-sandy beach herbaceous species that expanded their population or moved to the coast after the disaster were defined by sand accretion or erosion caused by the tsunami. Many sandy beach herbaceous communities changed into Dactyloctenium aegyptium communities because of the tsunami were originally constituted by non-sandy beach D. aegyptium with Cenchrus echinatus. Although the forest floors of most maritime forests were invaded by originally non-sandy beach Tridax procumbens, Eleusine indica or D. aegyptium because of the tsunami, this did not result in a change in the vegetation unit, because species' loss was restricted to the understorey. In time, these forests will recover their previous community composition. Conclusions: Our results suggest that originally non-sandy beach native species invaded the disturbed beaches rapidly after the tsunami but their habitats differ. Sites where sand accumulated on a beach because of the tsunami were invaded by D. aegyptium and E. indica, whereas soil erosion permitted invasion by Digitania adscendens. Tridax procumbens establishes rapidly on wet sites with hard soil, high per cent silt content and low beach management pressure. Sandy beach species with subterranean long rhizomes are strongly tolerant of such disasters. We concluded that the species composition of the beaches disturbed by a temporary large disaster is determined by dormancy and growth forms, with radicoid form being influential.     

MC1R genotype modifies risk of melanoma in families segregating CDKN2A mutations

Mutations in the exons of the cyclin-dependent kinase inhibitor gene CDKN2A are melanoma-predisposition alleles which have high penetrance, although they have low population frequencies. In contrast, variants of the melanocortin-1 receptor gene, MC1R, confer much lower melanoma risk but are common in European populations. Fifteen Australian CDKN2A mutation-carrying melanoma pedigrees were assessed for MC1R genotype, to test for possible modifier effects on melanoma risk. A CDKN2A mutation in the presence of a homozygous consensus MC1R genotype had a raw penetrance of 50%, with a mean age at onset of 58.1 years. When an MC1R variant allele was also present, the raw penetrance of the CDKN2A mutation increased to 84%, with a mean age at onset of 37.8 years (P=.01). The presence of a CDKN2A mutation gave a hazard ratio of 13.35, and the hazard ratio of 3.72 for MC1R variant alleles was also significant. The impact of MC1R variants on risk of melanoma was mediated largely through the action of three common alleles, Arg151Cys, Arg160Trp, and Asp294His, that have previously been associated with red hair, fair skin, and skin sensitivity to ultraviolet light.     

Double base lesions in DNA X-irradiated in the presence or absence of oxygen

Previously, double lesions in which two adjacent bases are modified were identified in DNA oligomers exposed in solution to ionizing radiation. However, the formation of such lesions in polymer DNA had not been demonstrated. Using reference oligomer containing a specific double lesion and employing liquid chromatography-mass spectrometry (LC-MS), it was possible to show directly that double lesions are formed in irradiated calf thymus DNA. The double lesion in which a pyrimidine base is degraded to a formamido remnant and an adjacent guanine base is oxidized to 8-oxoguanine was detected in DNA X-irradiated in oxygenated aqueous solution. The double lesion in which the methyl carbon atom of a thymine base is covalently linked to carbon at the 8-position of an adjacent guanine base was detected in DNA irradiated in a deoxygenated environment.     

Realized climatic niches of deciduous trees: comparing western Eurasia and eastern North America

Aim  Assessment of cross-continental similarities and differences in climatic limiting values for deciduous tree species and of the possible deterministic influence of past and present climatic differences on the modern tree flora in two regions.
Location  The deciduous forest regions of western Eurasia and eastern North America.
Methods  Based on species distribution data (range maps) and climate site data, the realized climatic niches of 137 deciduous tree species from the two regions were quantified using climatic envelopes. To compare these envelopes on the two continents, a hierarchical cluster analysis was performed, and principal components analysis was used to check cluster consistency.
Results  Significant differences do exist for upper limits of winter temperatures and for lower limits of summer temperatures between Western Eurasia and eastern North America. Lower limits for the annual water balance also appear different, suggesting that the deciduous trees may be more drought-tolerant in western Eurasia than in eastern North America. Climatic range types generated by the cluster analysis can be characterized, according to the distribution of the species, as boreal-temperate, northern temperate, temperate, southern temperate, and Appalachian. Five of the eight clusters contain trees from both regions, but three groups consist only of American species that have no European counterparts.
Main conclusions  Differences in temperature limitations can be explained by location on the east versus west side of the continents and by the almost complete lack of warm moist areas in western Eurasia. The difference in drought tolerance, on the other hand, is more likely to be the product of a deterministic sorting process that occurred during the Plio-Pleistocene.     

Three deeply divided lineages of the freshwater mussel genus <Emphasis Type="Italic">Anodonta</Emphasis> in western North America

The surprising diversity and recent dramatic decline of freshwater mussels in North America have been well documented, although inventory efforts to date have been concentrated in the eastern United States. Unlike their eastern counterparts, western freshwater mussels have received comparatively little attention. The accurate identity of western lineages is a necessary component for future inventory, monitoring, and ecological work involving these taxa. Here we initiate a study involving the most speciose genus (Anodonta) in western North America, incorporating information about type localities and type specimen morphology and describing the discovery of three highly divergent lineages among four western Anodonta species. In a limited phylogenetic analysis, we find (1) that A. californiensis/nuttalliana and A.oregonensis/kennerlyi are distinct, highly divergent clades, and (2) that A. beringiana is more closely allied with A. woodiana, an Asian species, than either of the other two western North American clades. We were largely unable to resolve the placement of these three clades with respect to other anodontines, and suggest the need for a broader phylogenetic framework. We recommend, however, that the existence of these three deeply divergent groups be considered in the development of regional monitoring, conservation and research plans despite the taxonomic uncertainty.     

A polymorphism study of the human Agouti gene and its association with MC1R

To determine whether the Agouti Signalling Protein (ASP) gene is associated with skin and hair coloration in humans, the complete coding region of ASP was screened for polymorphisms. Analysis of ASP in Caucasian, African-American, Spanish Basque, Hispanic, Apache and Australian Aboriginal populations revealed no amino acid substitutions. A single polymorphism in the 3' untranslated region occurred at a frequency of 0.2 in African-Americans. Variants of the Melanocortin 1 Receptor (MC1R) gene have been found to be associated with red hair and fair skin in humans. Red hair individuals are usually compound heterozygotes or homozygous for one of a number of MC1R polymorphisms associated with red hair. Some individuals however are heterozygous for only one of these polymorphisms and dizygotic twins can be concordant for MC1R variants but discordant for hair colour. A recent study has also identified rare redheads carrying no MC1R variants indicating that polymorphisms of the human MC1R gene are required but not sufficient for the red hair phenotype. To address the question of whether ASP also contributes to the red hair phenotype, individuals previously identified as having unexpected MC1R genotypes were screened for polymorphisms at the ASP locus. No polymorphisms were found in any of these individuals. Results indicate that the human ASP gene is unlikely to function in normal human pigmentation in the same way as MC1R.     

The Role of Melanocortin‐1 Receptor Polymorphism in Skin Cancer Risk Phenotypes

We have examined melanocortin‐1 receptor (MC1R) variant allele frequencies in the general population and in a collection of adolescent dizygotic and monozygotic twins to determine statistical associations of pigmentation phenotypes with increased skin cancer risk. This included hair and skin color, freckling, mole count and sun exposed skin reflectance. Nine variants were studied and designated as either strong R (OR = 63; 95% CI 32–140) or weak r (OR = 5; 95% CI 3–11) red hair alleles. Penetrance of each MC1R variant allele was consistent with an allelic model where effects were multiplicative for red hair but additive for skin reflectance. To assess the interaction of the brown eye color gene BEY2/OCA2 on the phenotypic effects of variant MC1R alleles we imputed OCA2 genotype in the twin collection. A modifying effect of OCA2 on MC1R variant alleles was seen on constitutive skin color, freckling and mole count. In order to study the individual effects of these variants on pigmentation phenotype we have established a series of human primary melanocyte strains genotyped for the MC1R receptor. These include strains which are MC1R wild‐type consensus, variant heterozygotes, and homozygotes for strong R alleles Arg151Cys and Arg160Trp. Ultrastructural analysis demonstrated that only consensus strains contained stage III and IV melanosomes in their terminal dendrites whereas Arg151Cys and Arg160Trp homozygous strains contained only immature stage I and II melanosomes. Such genetic association studies combined with the functional analysis of MC1R variant alleles in melanocytic cells should provide a link in understanding the association between pigmentary phototypes and skin cancer risk.