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 We illustrate the method using published and unpublished Y-chromosome STR data.     

Effect of microwave treatment on the shear bond strength of different types of commercial teeth to acrylic resin

doi:10.1111/j.1741‐2358.2009.00333.x
Effect of microwave treatment on the shear bond strength of different types of commercial teeth to acrylic resin Objective: The purpose of this study was to verify the effect of microwave treatment on the shear bond strength of commercial types of teeth to acrylic resin, when the glossy ridge laps were unmodified (groups 1 and 5), bur abraded (groups 2 and 6), bur grooved (groups 3 and 7) or etched by monomer (groups 4 and 8). Background: Controversial findings have shown that mechanical or chemical changes in ridge‐lap surface of the tooth increase or decrease the bond strength between tooth and acrylic resin, and the microwave disinfection may cause different changes on this bond strength. Materials and methods: Eighty specimens (n = 10) were made with the acrylic resin bonded to tooth glossy ridge lap, polymerised in water at 74°C for 9 h, and deflasked after flask cooling. Specimens of the groups 5, 6, 7 and 8 were individually immersed in 150 ml of water and submitted to microwave treatment in an oven at 650 W for 3 min. Control specimens (groups 1, 2, 3 and 4) were not microwave treated. Shear bond strength test was performed in an Instron machine with a cross‐speed of 1 mm/min. Collected data were submitted to anova and Tukey’s test (α = 0.05). Results: Microwave treatment decreased the shear bond strength values of the tooth/resin bond. In the microwaved and non‐microwaved procedures, mechanical retention improved the shear bond strength when compared with the control and monomer treatments. Conclusion: Shear bond strength of the tooth/resin bond was influenced by the microwave treatment and different commercial teeth association, and was lower for the Biotone tooth.     

Faunal changes and geographic crypticism indicate the occurrence of a biogeographic transition zone along the southern East Pacific Rise

Aim Deep‐sea hydrothermal vents have now been reported along all active mid‐ocean ridges and back‐arc basins, but the boundaries of biogeographic entities remain questionable owing to methodological issues. Here we examine biogeographic patterns of the vent fauna along the East Pacific Rise (EPR) and determine the relative roles of regional and local factors on the distribution of biodiversity associated with mussel beds along a poorly explored zone, the southern EPR (SEPR). Location East Pacific Rise. Methods A species list of macrobenthic invertebrates along the EPR was compiled from the literature and supplemented with data recovered during the French research cruise BIOSPEEDO carried out in 2004 along the SEPR. Biogeographic patterns were assessed by combining the identification of morphological species with a molecular barcoding approach. A multivariate regression tree (MRT) analysis was performed to identify any geographic breaks, and an empirical distribution of species richness was compared with predictions provided by a mid‐domain effect model. Macrofaunal community structure associated with mussel beds along the SEPR was analysed in relation to environmental factors using cluster and canonical redundancy analyses. Results Sequencing of the cytochrome c oxidase subunit I gene revealed the occurrence of several cryptic species complexes along the EPR, with the equator separating the southern and northern clades. Furthermore, during the BIOSPEEDO cruise at least 10 still unnamed species were collected between 7°25′ S and 21°33′ S. The shift in community structure identified by MRT analysis was located south of 17°34′ S or south of 13°59′ S, depending on the data used, suggesting that the southern part of the SEPR (17°25′–21°33′ S) constitutes a biogeographic transition zone in the vent fauna along the EPR. At a regional scale, latitude combined with the type of venting was significantly correlated with the community structure associated with mussel beds. Main conclusions Together, the molecular data, in situ observations, and the distribution of species suggest that the high diversity of vent fauna species presently observed between 17°25′ S and 21°33′ S is probably a result of the overlap of several distinct biogeographic provinces. We argue that this area thus constitutes a biogeographic vent fauna transition zone along the EPR.     

Sex-specific aggression and sex ratio in wintering finch flocks: serins and siskins differ

Males are dominant over females in many bird species. This may lead to male monopolisation of resources whenever food is scarce or clumped and secondarily to lower female survival rates. As a result of the consequent male-biased sex ratio in the adult population, competition may arise either (1) between males and females, as males attempt to exclude females from feeding patches, or (2) between males because females do not pose a competitive threat. We recorded agonistic interactions between males and females in wintering foraging flocks of serins (Serinus serinus) and siskins (Carduelis spinus) to test for inter-specific differences. Most of the aggressive interactions in serins were between males and females, whereas in siskins they were between males. We also compared sex ratios for each species during the winter, determined from separate trapping efforts over an 11-year period, to test whether the direction of aggression by males (i.e. male/male; male/female) relates to variations in female survival rates. The proportion of females was smaller in winter than in autumn for serins, but differences in siskins were negligible. Results are interpreted in relation to the social organization displayed by both species studied.     

A CUG codon adapted two-hybrid system for the pathogenic fungus Candida albicans

The genetics of the most common human pathogenic fungus Candida albicans has several unique characteristics. Most notably, C. albicans does not follow the universal genetic code, by translating the CUG codon into serine instead of leucine. Consequently, the use of Saccharomyces cerevisiae as a host for yeast two-hybrid experiments with C. albicans proteins is limited due to erroneous translation caused by the aberrant codon usage of C. albicans. To circumvent the need for heterologous expression and codon optimalization of C. albicans genes we constructed a two-hybrid system with C. albicans itself as the host with components that are compatible for use in this organism. The functionality of this two-hybrid system was shown by successful interaction assays with the protein pairs Kis1–Snf4 and Ino4-Ino2. We further confirmed interactions between components of the filamentation/mating MAP kinase pathway, including the unsuspected interaction between the MAP kinases Cek2 and Cek1. We conclude that this system can be used to enhance our knowledge of protein–protein interactions in C. albicans.     

Microplate coagulation assays.

This report describes the development of microplate-based blood coagulation assays. The assays require a kinetic microplate reader to follow changes in absorbance at 405 nm caused by the coagulating plasma. Procedures for performing prothrombin time and activated partial thromboplastin time tests are described with intra- and inter-assay variability of a few percentage points. The prothrombin time of normal plasma was 64.5 +/- 3.6 s, and the activated partial thromboplastin time was 69.8 +/- 3.2 s. Clotting times were prolonged when normal plasma was mixed with plasmas deficient in particular coagulation factors, as expected. These assays take advantage of the microplate format (small sample size and multiple simultaneous assays) and can be customized for specific purposes, such as quantifying purified factor IX or assessing protein C activity in plasma.