Inferring epidemic contact structure from phylogenetic trees

Contact structure is believed to have a large impact on epidemic spreading and consequently using networks to model such contact structure continues to gain interest in epidemiology. However, detailed knowledge of the exact contact structure underlying real epidemics is limited. Here we address the question whether the structure of the contact network leaves a detectable genetic fingerprint in the pathogen population. To this end we compare phylogenies generated by disease outbreaks in simulated populations with different types of contact networks. We find that the shape of these phylogenies strongly depends on contact structure. In particular, measures of tree imbalance allow us to quantify to what extent the contact structure underlying an epidemic deviates from a null model contact network and illustrate this in the case of random mixing. Using a phylogeny from the Swiss HIV epidemic, we show that this epidemic has a significantly more unbalanced tree than would be expected from random mixing.     

Lineages-through-time plots of neutral models for speciation

Drawing inferences about macroevolutionary processes from phylogenetic trees is a fundamental challenge in evolutionary biology. Understanding stochastic models for speciation is an essential step in solving this challenge. We consider a neutral class of stochastic models for speciation, the constant rate birth-death process. For trees with n extant species - which might be derived from bigger trees via random taxon sampling - we calculate the expected time of the kth speciation event (k=1,...,n-1). Further, for a tree with n extant species, we calculate the density and expectation for the number of lineages at any time between the origin of the process and the present. With the developed methods, expected lineages-through-time (LTT) plots can be drawn analytically. The effect of random taxon sampling on LTT plots is discussed.     

Fluoreszenz-in-situ-Hybridisierung in der humangenetischen Diagnostik

The field of genetic diagnostics incorporates a variety of methods that complement each other. Therefore, the development of new methods calls for a review of the advantages and limitations of established and new technologies. Fluorescence in situ hybridization (FISH) is routinely applied in genetics. Custom-designed and commercially available probes allow for nearly unlimited and targeted visualization of genomic DNA using either metaphase spreads, interphase nuclei, tissue sections, or living cells. FISH applications are particularly important for the detection of structural rearrangements such as microdeletions, translocations, inversions, and insertions, as well as for identification of marker chromosomes, characterization of chromosome breakpoints, and prenatal aneuploidy testing. Furthermore, the analysis of genetic heterogeneity, including mosaicism, is accomplished by evaluating single cells. FISH may also be combined with fluorescent antibodies against cell surface markers and correlated to specific morphologic features of cells and tissues.     

Importance of ascospore ornamentation in the taxonomy of Daldinia

Representative specimens of fifteen Daldinia spp. were studied for ultrastructural characteristics of their ascospores by scanning electron microscopy (SEM). The ornamentation of their outermost spore layers was found to be species-consistent, confirming the results of concurrent studies on the morphology of their teleomorphs and anamorphs, secondary metabolite profiles and PCR-based genetic fingerprints. Daldinia spp. may either show smooth or transversally striated ascospores. The spores of the species within the latter group are always ellipsoid-equilateral to ellipsoid-inequilateral with narrowly rounded ends. Smooth, broadly ellipsoid to cylindrical ascospores were observed in all species (D. caldariorum, D. fissa and D. loculata) that are known to produce their stromata on substrates damaged by fire. The ascospores of D. concentrica differed from those of D. childiae (i.e., the cosmopolitan taxon previously regarded as D. concentrica ss. auct.) and other Daldinia spp. in showing a very faint ornamentation, which only became visible at 10000× magnification by SEM. A specimen collected on the isle of Jersey (Channel Islands, UK) showed morphological similarities to the pantropical D. eschscholzii, but its ascospores appeared smooth by SEM, and it may therefore represent a previously undescribed species. Dedicated to Professor Yoshinori Asakawa, Tokushima, Japan, on the occasion of his 60^th birthday PH-R Life Science Center Natural Products     

Cornicle length in Macrosiphini aphids: a comparison of ecological traits

Abstract 1. Aphids often emit cornicle droplets when attacked by predators. While the function of cornicle droplets has long been debated (i.e. mechanical protection vs. chemical signalling), it is not understood why aphid species have cornicles of different lengths.
2. It was hypothesised that aphids living in more scattered colonies have longer cornicles to scent-mark predators with cornicle droplets containing alarm pheromone, so that clone-mates are provided with advanced warning of a threat, even if not at the predation site. To test this hypothesis, multiple regression analyses were used, due to a lack of phylogenetic information on these taxa, to address which ecological traits (amount of wax on an aphid, degree of colony aggregation, feeding shelter, ant attendance) are correlated with cornicle length.
3. Aphids living in dense colonies tended to have shorter cornicles than aphids living in more scattered colonies. Also, aphids with more protection (i.e. wax) on their bodies had shorter cornicles. Aphids also tended to have shorter cornicles when tended by ants. The presence of a feeding shelter was not a good predictor of cornicle length.
4. It is suggested that longer cornicles function to scent-mark predators with alarm pheromone to increase the inclusive fitness of a clone; however the negative correlation between the amount of individual protection, and also ant attendance, and cornicle length argues for a trade-off between different forms of defence.     

Effect of an interferon inhibitor on the antiproliferative signal of interferon-alpha.

We have described a nonantibody type inhibitor of interferons (IFN) in the blood of patients with AIDS, advanced neoplastic disorders, and lupus erythematosus in earlier reports (1,2). In the present study we show that the semipurified inhibitor blocks the antiproliferative signal of IFN-alpha in Daudi cells and the membrane potential shifting ability of IFN-alpha is modulated by the interferon inhibitor preparation (IFI).