Simulation of Y-chromosomal haplotype data

The non-recombining nature of the Y-chromosome determines the non-independence of alleles between loci. The evolution of short tandem repeat (STR) loci in the Y-chromosome is the result of different factors such as differential mutation rates, mutation modes, gene conversion, selection and demographic processes. The degree of correlation between loci is dependent on the magnitude of these processes. The simulation of data is a routine tool used for testing hypotheses in population and evolutionary studies. The most basic parameters hitherto used in lineage haplotype simulations are the allele frequency distributions and mutation rates, assuming either full independence or linkage between loci. In this study we introduce use of the Spearman correlation coefficient to estimate the degree of dependence between non-recombining loci. Then, both the interdependence between loci and the allele frequency distributions at multi-allelic loci are incorporated in an algorithm for simulating haplotypes. We illustrate the method using published and unpublished Y-chromosome STR data.     

Moving forward with the primate microbiome: Introduction to a special issue of the American Journal of Primatology

Primate microbiome research is a quickly growing field with exciting potential for informing our understanding of primate biology, ecology, and evolution as well as host‐microbe interactions more broadly. This introductory essay to a special section of the American Journal of Primatology provides a cross‐sectional snapshot of current activity in these areas by briefly summarizing the diversity of contributed papers and their relationships to key themes in host‐associated microbiome research. It then uses this survey as a foundation for consolidating a set of key research questions to broadly guide future research. It also argues for the importance of methods standardization to facilitate comparative analyses and the identification of generalizable patterns and relationships. While primatology will benefit greatly from the integration of microbial datasets, it is uniquely positioned to address important questions regarding microbiology and macro‐ecology and evolution more generally. We are eager to see where the primate microbiome leads us.     

Activation of potassium channels by hypoxia and reoxygenation in the human lung adenocarcinoma cell line A549

Active oxygen species are generated in cells during pathophysiologic conditions such as illflammation and postischemic reperfusion. If oxygen radical scavengers are added before reperfusion, then the magnitude of injury is reduced. We inves-tigated whether free radicals generated following exposure to hypoxia and reoxygenation activate voltage-dependent K⁺ ion channels in tumor cells in vitro. Using the technique of whole cell voltage clamping, we recorded currents from two families of potassium (K⁺) channels that were activated following reoxygenation. One of these groups possessed the electrophysical characteristics of a tetraethylammonium (TEA)-sensitive delayed rectifier channel and the other possessed characteristics of a Tea-insensitive slow inactivating channel. We present evidence which suggests that K⁺ channels are activated following reoxygenation but not during the hypoxia phase. The K⁺ currents decayed with time following reoxygenation. The decay characteristics of the K⁺ currents depended on the duration and level of hypoxia to which the cells were exposed. To determine whether activation of K⁺ channels by reoxygenation was initiated by free radicals, we pretreated cells with N-Acetyl L-Cysteine (NAC), a free radical scavenger, and found that this pretreatment abolished the currents induced by reoxygenation. We also present evidence that free radicals do not directly act on the channel itself, but activate a protein kinase which, in turn, activates the K⁺ channels. Taken together, these results indicate that one of the early responses to oxidative stress is the activation of K⁺ currents. © 1993 Wiley-Liss, Inc.     

Rates and Patterns of Scndna and Mtdna Divergence within the Drosophila Melanogaster Subgroup

Levels of DNA divergence among the eight species of the Drosophila melanogaster subgroup and D. takahashii have been determined using the technique of DNA-DNA hybridization. Two types of DNA were used: single-copy nuclear DNA (scnDNA) and mitochondrial DNA (mtDNA). The major findings are: (1) A phylogeny has been derived for the group based on scnDNA which is congruent with chromosomal data, morphology, and behavior. The three homosequential species, simulans, sechellia, and mauritiana, are very closely related; the scnDNA divergence indicate the two island species are a monophyletic group. (2) The rates of change of scnDNA and mtDNA are not greatly different; if anything scnDNA evolves faster than mtDNA. (3) The rates of scnDNA evolution are not closely correlated to chromosomal (inversion) evolution. (4) The Drosophila genome appears to consist of two distinct classes of scnDNA with respect to rate of evolutionary change, a very rapidly evolving fraction and a relatively conservative fraction. (5) The absolute rate of change was estimated to be at least 1.7% nucleotide substitution per one million years. (6) DNA distance estimates based on restriction site variation are correlated with distances based on DNA-DNA hybridization, although the correlation is not very strong.     

Chromosome endoreduplication in endosperm cells of two maize genotypes and their progenies

Summary Chromosome endoreduplication is a very common process in higher plants but its function and genetic control are still to be clarified. In our experiments we analyzed, by Feulgen cytophotometry, chromosome endoreduplication in endosperm cells of two maize genotypes, IHP and ILP, having high and low protein content in their seed, respectively. Chromosome endoreduplication occurs in both lines within 24 days after pollination, attaining a maximum ploidy level of 384C (7 DNA replication rounds) in IHP and of 192C (6 replication rounds) in ILP. In the mature seed, endosperms of the two lines show different mean ploidy level. In reciprocal crosses between IHP and ILP the f₁ endosperms have mean ploidy levels analogous to that of the maternal parent, showing that the difference in ploidy level between the two genotypes is maintained. After selfing of the f₁ plants, the difference in ploidy level between the two F₂ populations is reduced. In F₂ the mean ploidy level is as variable as in f₁, indicating the absence of genetic segregation. From our data, it is apparent that both the genetic constitution (cytoplasmic and nuclear) of the maternal parent and the genotype of the individual endosperms influence the ploidy level. An analysis of the protein content in endosperms carried out on the same seed sample as analyzed cytophotometrically showed that the protein content increases, during seed development, parallel to chromosome endoreduplication and varies, in the two lines, in reciprocal crosses and their progeny, according to the same trend as mean ploidy level, suggesting a correlation between the two parameters.     

Measurement of the relative proportion of symmetrical and asymmetrical chromosome-type interchanges induced by gamma radiation in human-hamster hybrid cells

Using hamster-human hybrid cells and methods for differential staining of the hamster and human chromosomes, the relative proportion of induced chromosome-type symmetrical and asymmetrical interchange aberrations was measured after a 6.5-Gy dose of gamma radiation. The ratio of these aberration types was not significantly different from 1:1, i.e., the proportion of such interchanges that are symmetrical is very near 0.5, in agreement with the conclusion of others (J.A. Heddle, Genetics 52, 1329-1334, 1965; M. Holmberg and J. Jonasson, Hereditas 74, 57-68, 1973; J.R.K. Savage and D.G. Papworth, Mutat. Res. 95, 7-18, 1983). This proportion is important because virtually all estimates of radiation-induced chromosome-type exchange aberrations are based on measurement of the easily observed but unstable and lethal asymmetrical types, while some of the biological effects of concern from the point of view of oncogenesis and mutagenesis are thought to result from production of stable and nonlethal symmetrical types.     

Camponotus ants mine sand for vertebrate urine to extract nitrogen

The ability of some ant species (including Camponotus spp.) to forage on vertebrate urine to extract urea may extend their niche in competitive and strongly nitrogen‐limited environments. We examined the preference of Camponotus terebrans, a sand‐dwelling ant widespread in southern Australia, for baits including urine, and the duration of their foraging on those baits. We baited ants with liquid stains of urine (human and kangaroo), urea in water (2.5%. 3.5%, 7.0%, 10.0%) and sucrose in water (20% and 40%) poured directly on the ground, as well as hard baits in plots drawn on sandy soil (Kangaroo Island, South Australia). We counted individuals of this mostly nocturnal species to determine their attraction to different baits for one month. We checked plant growth on the plots after nine and 13 months. Ants collected insects and meat; they foraged for at least 29 days on stains. Ants were most numerous on 10% urea, followed by 7% urea, 3.5% urea, urine (which contains ~2.5% urea) and 2.5% urea, 40% sucrose and 20% sucrose; sucrose was less attractive to them than equimolar urea bait. Ants were attracted to human, kangaroo, and unidentified urines, and they collected bird guano. Baits and ant foraging did not affect plant recruitment in plots. We observed incidentally Camponotus consobrinus foraging on urine, which may be a common resource for this genus at the site. The remarkable ability of C. terebrans to extract nitrogen from dry sand over weeks explains partly its success on sandy soils. Foraging on urine may be an important strategy to address nitrogen limitation on sandy soils and exploit commensally niches in which hosts are kangaroos, wallabies and other vertebrates. The understanding of plant–vertebrate interactions must factor in the role of ants as commensal organisms. Such ants could also reduce greenhouse gas emissions from urine.