Polymorphisms in DNA-repair genes in a cohort of prostate cancer patients from different areas in Spain: heterogeneity between populations as a confounding factor in association studies

Background: Differences in the distribution of genotypes between individuals of the same ethnicity are an important confounder factor commonly undervalued in typical association studies conducted in radiogenomics. Objective: To evaluate the genotypic distribution of SNPs in a wide set of Spanish prostate cancer patients for determine the homogeneity of the population and to disclose potential bias. Design, Setting, and Participants: A total of 601 prostate cancer patients from Andalusia, Basque Country, Canary and Catalonia were genotyped for 10 SNPs located in 6 different genes associated to DNA repair: XRCC1 (rs25487, rs25489, rs1799782), ERCC2 (rs13181), ERCC1 (rs11615), LIG4 (rs1805388, rs1805386), ATM (rs17503908, rs1800057) and P53 (rs1042522). The SNP genotyping was made in a Biotrove OpenArrayH NT Cycler. Outcome Measurements and Statistical Analysis: Comparisons of genotypic and allelic frequencies among populations, as well as haplotype analyses were determined using the web-based environment SNPator. Principal component analysis was made using the SnpMatrix and XSnpMatrix classes and methods implemented as an R package. Non-supervised hierarchical cluster of SNP was made using MultiExperiment Viewer. Results and Limitations: We observed that genotype distribution of 4 out 10 SNPs was statistically different among the studied populations, showing the greatest differences between Andalusia and Catalonia. These observations were confirmed in cluster analysis, principal component analysis and in the differential distribution of haplotypes among the populations. Because tumor characteristics have not been taken into account, it is possible that some polymorphisms may influence tumor characteristics in the same way that it may pose a risk factor for other disease characteristics. Conclusion: Differences in distribution of genotypes within different populations of the same ethnicity could be an important confounding factor responsible for the lack of validation of SNPs associated with radiation-induced toxicity, especially when extensive meta-analysis with subjects from different countries are carried out.

Allozyme variation in natural populations of Picea asperata

Abstract

Testing differentiation in diploid populations.

We examine the power of different exact tests of differentiation for diploid populations. Since there is not necessarily random mating within populations, the appropriate hypothesis to construct exact tests is that of independent sampling of genotypes. There are two categories of tests, FST-estimator tests and goodness of fit tests. In this latter category, we distinguish "allelic statistics", which account for the nature of alleles within genotypes, from "genotypic statistics" that do not. We show that the power of FST-estimator tests and of allelic goodness of fit tests are similar when sampling is balanced, and higher than the power of genotypic goodness of fit tests. When sampling is unbalanced, the most powerful tests are shown to belong to the allelic goodness of fit group.

L'évaluation et les populations migrantes: Tenir compte des différences culturelles dans le conseil

Difficile de concevoir une évaluation psychologique indépendante des critères culturels ou d'en tenir compte de manière adéquate. C'est pourquoi la globalisation des économies et les mouvements migratoires impliquent de repenser l'évaluation psychologique dans le domaine du conseil et de l'orientation d'un point de vue théorique et pratique. Cette nouvelle situation pose des défis inédits

On the evolution of harming and recognition in finite panmictic and infinite structured populations.

Natural selection may favor two very different types of social behaviors that have costs in vital rates (fecundity and/or survival) to the actor: helping behaviors, which increase the vital rates of recipients, and harming behaviors, which reduce the vital rates of recipients. Although social evolutionary theory has mainly dealt with helping behaviors, competition for limited resources creates ecological conditions in which an actor may benefit from expressing behaviors that reduce the vital rates of neighbors. This may occur if the reduction in vital rates decreases the intensity of competition experienced by the actor or that experienced by its offspring. Here, we explore the joint evolution of neutral recognition markers and marker-based costly conditional harming whereby actors express harming, conditional on actor and recipient bearing different conspicuous markers. We do so for two complementary demographic scenarios: finite panmictic and infinite structured populations. We find that marker-based conditional harming can evolve under a large range of recombination rates and group sizes under both finite panmictic and infinite structured populations. A direct comparison with results for the evolution of marker-based conditional helping reveals that, if everything else is equal, marker-based conditional harming is often more likely to evolve than marker-based conditional helping.

Interrogating eleven fast-evolving genes for signatures of recent positive selection in worldwide human populations

Different signatures of natural selection persist over varying time scales in our genome, revealing possible episodes of adaptative evolution during human history. Here, we identify genes showing signatures of ancestral positive selection in the human lineage and investigate whether some of those genes have been evolving adaptatively in extant human populations. Specifically, we compared more than 11,000 human genes with their orthologs inchimpanzee, mouse, rat and dog and applied a branch-site likelihood method to test for positive selection on the human lineage. Among the significant cases, a robust set of 11 genes were then further explored for signatures of recent positive selection using SNP data. We genotyped 223 SNPs in 39 worldwide populations from the HGDP Diversity panel and supplemented this information with available genotypes for up to 4,814 SNPs distributed along 2 Mb centered on each gene. After exploring the allele frequency spectrum, population differentiation and the maintainance of long unbroken haplotypes, we found signals of recent adaptative phenomena in only one of the 11 candidate gene regions. However, the signal ofrecent selection in this region may come from a different, neighbouring gene (CD5) ratherthan from the candidate gene itself (VPS37C). For this set of positively-selected genes in thehuman lineage, we find no indication that these genes maintained their rapid evolutionarypace among human populations. Based on these data, it therefore appears that adaptation forhuman-specific and for population-specific traits may have involved different genes.

Genetic variability of rice recurrent selection populations as affected by male sterility or manual recombination

The objective of this work was to determine the effect of male sterility or manual recombination on genetic variability of rice recurrent selection populations. The populations CNA-IRAT 4, with a gene for male sterility, and CNA 12, which was manually recombined, were evaluated. Genetic variability among selection cycles was estimated using14 simple sequence repeat (SSR) markers. A total of 926 plants were analyzed, including ten genitors and 180 individuals from each of the evaluated cycles (1, 2 and 5) of the population CNA-IRAT 4, and 16 genitors and 180 individuals from each of the cycles (1 and 2) of CNA 12. The analysis allowed the identification of alleles not present among the genitors for both populations, in all cycles, especially for the CNA-IRAT 4 population. These alleles resulted from unwanted fertilization with genotypes that were not originally part of the populations. The parameters of Wright's F-statistic (F IS and F IT) indicated that the manual recombination expands the genetic variability of the CNA 12 population, whereas male sterility reduces the one of CNA-IRAT 4.

Inventory of sparse forest populations using adaptive cluster sampling

Abstract

Popping expansion and yield responses of popcorn cultivars under different row spacings and plant populations

The objective of this work was to evaluate the agronomic traits and the popping expansion index of three Brazilian popcorn cultivars under different row spacings and plant populations. The trials were performed during two crop seasons, under field conditions. The experimental design used was a randomized complete block, in a split-split plot, with 27 treatments and four replicates. Treatments were represented in a triple factorial arrangement: three row spacings (0.40, 0.60, and 0.80 m), three plant populations (40,000, 60,000, and 80,000 plants per hectare), and three popcorn cultivars (IAC-TC 01, IAC 12, and Zelia). The increase in plant population causes a reduction in the number of grains per ear, lower prolificacy, and grain weight loss. Cultivar grain yield is affected by row spacing and popcorn plant population. Cultivar IAC 12 shows highest grain yield under row spacings of 0.40 and 0.60 m and plant population between 60,000 and 80,000 plants per hectare. The popping expansion index is not affected by row spacing or plant population.

Interacting populations in heterogeneous environments

To optimally manage a metapopulation, managers and conservation biologists can favor a type of habitat spatial distribution (e.g. aggregated or random). However, the spatial distribution that provides the highest habitat occupancy remains ambiguous and numerous contradictory results exist. Habitat occupancy depends on the balance between local extinction and colonization. Thus, the issue becomes even more puzzling when various forms of relationships - positive or negative co-variation - between local extinction and colonization rate within habitat types exist. Using an analytical model we demonstrate first that the habitat occupancy of a metapopulation is significantly affected by the presence of habitat types that display different extinction-colonization dynamics, considering: (i) variation in extinction or colonization rate and (ii) positive and negative co-variation between the two processes within habitat types. We consequently examine, with a spatially explicit stochastic simulation model, how different degrees of habitat aggregation affect occupancy predictions under similar scenarios. An aggregated distribution of habitat types provides the highest habitat occupancy when local extinction risk is spatially heterogeneous and high in some places, while a random distribution of habitat provides the highest habitat occupancy when colonization rates are high. Because spatial variability in local extinction rates always favors aggregation of habitats, we only need to know about spatial variability in colonization rates to determine whether aggregating habitat types increases, or not, metapopulation occupancy. From a comparison of the results obtained with the analytical and with the spatial-explicit stochastic simulation model we determine the conditions under which a simple metapopulation model closely matches the results of a more complex spatial simulation model with explicit heterogeneity.

Measuring discrepancies between knowledge, preoccupation and fear of aids in populations.

A simple tool to quantify discrepancies between knowledge, preoccupation and fear regarding hiv and aids is presented. This tool is based on standard questions available in health surveys. Some results using recent Swiss data are presented, and the method is discussed.

Calreticulin levels determine onset of early muscle denervation by fast motoneurons of ALS model mice.

Although the precise signaling mechanisms underlying the vulnerability of some sub-populations of motoneurons in ALS remain unclear, critical factors such as metallo-proteinase 9 expression, neuronal activity and endoplasmic reticulum stress have been shown to be involved. In the context of SOD1(G93A) ALS mouse model, we previously showed that a two-fold decrease in calreticulin (CRT) is occurring in the vulnerable fast motoneurons. Here, we asked to which extent the decrease in CRT levels was causative to muscle denervation and/or motoneuron degeneration. Toward this goal, a hemizygous deletion of the crt gene in SOD1(G93A) mice was generated since the complete ablation of crt is embryonic lethal. We observed that SOD1(G93A);crt(+/-) mice display increased and earlier muscle weakness and muscle denervation compared to SOD1(G93A) mice. While CRT reduction in motoneurons leads to a strong upregulation of two factors important in motoneuron dysfunction, ER stress and mTOR activation, it does not aggravate motoneuron death. Our results underline a prevalent role for CRT levels in the early phase of muscle denervation and support CRT regulation as a potential therapeutic approach.

Observations de populations marquées de la musaraigne aquatique Neomys fodiens (Insectivora, Mammalia)

Three populations of the European water shrew Neomy fodiens have been observed by live-trapping, one of them during twelve months. During highest populations density a local maximum of 21 individuals have been caught. Recapture frequency from month to month was less than 50%, probably due to a weak trappability and an important dispersal behaviour. During the winter all three populations disappeared. Change in habitat or change in behaviour might be responsible for the lack of trapping siccess in the cold period.