Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2 > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.     

Stress-induced effects on feeding behavior and growth performance of the sea bass (<Emphasis Type="Italic">Dicentrarchus labrax</Emphasis>): a self-feeding approach

Repetitive aquaculture-related protocols may act as cyclic stressors that induce chronic stress in cultured fish. The sea bass is particularly sensitive to stressful conditions and the mere presence of humans will disturb feeding behavior. In this paper, we study whether chronic stress induced by repetition of acute stress protocols affects long-term feeding behavior and growth performance in sea bass and whether exogenous cortisol may induce stress-like changes in these parameters. We demonstrate that both chronic stress and dietary cortisol decrease food intake and have a negative effect on feed conversion efficiency, severely impairing sea bass performance. Both experimental approaches induced changes in the daily feeding activity by lengthening the active feeding periods. Fish subjected to a cyclic stressor modify their daily feeding pattern in an attempt to avoid interference with the time of the stressor. The delay in feeding when fish are acutely and repeatedly stressed could be of substantial adaptive importance.     

Interaction between clonal plasma cells and the immune system in plasma cell dyscrasias

The term "monoclonal gammopathy" (MG) includes a group of clonal plasma cell disorders, which show heterogeneous clinical behavior. While multiple myeloma (MM) and plasma cell leukemia (PCL) are incurable malignant diseases, most patients with MG of undetermined significance (MGUS) show an indolent/benign clinical course. Evidence has accumulated which supports the role of the bone marrow microenvironment in MG. Accordingly, the survival, drug-resistance and proliferation of MM cells have been shown to be largely dependent on a supportive microenvironment. Among the different environment-associated parameters, those related to the status/activity of the immune system are particularly relevant. This review focuses on the different ways clonal plasma cells (PC) interact with the immune system in different models of MG, to characterize crucial events in the development and progression of MG. These advances may support the design of novel therapeutic approaches in patients with MG.     

Mechanisms maintaining biodiversity in Mediterranean pine-oak forests: insights from a spatial simulation model

Recurrent anthropogenic and natural perturbations, resource limitations and heterogeneous environments contribute to the maintenance of a remarkable biodiversity in Mediterranean plant communities. Yet, the essential mechanisms of community assembly in these systems remain largely unexplored. In the current paper we investigate the coexistence of Aleppo pine (Pinus halepensis Mill.) and Holm oak (Quercus ilex L.), two of the most widely distributed species in the Iberian Peninsula, in relation to gradients in water availability and disturbance. A spatial model of landscape forest dynamics was implemented, calibrated with experimental data, with stands arranged on a heterogeneous lattice and coupled by dispersal. It was found that pine population persistence in the landscape can be explained independently by a competition-colonization tradeoff (in mesic homogeneous environments) and by a tradeoff between shade and drought tolerance (in heterogeneous low disturbed environments). Both mechanisms reinforce mutually to maintain a shifting mosaic of both taxa along disturbance and aridity gradients. This view is consistent with palynological, historical and forest inventory records. In turn, equilibrium theories of vegetation dynamics (phytosociological), that neglect the role of heterogeneity and disturbances may be inadequate for Mediterranean forests, and have been shown to result in mismanagement practices. We claim that biologically informed models of forest dynamics are desperately needed as diagnosis tools for sustainable forest management.     

Sensitive and specific molecular detection of Burkholderia pseudomallei, the causative agent of melioidosis, in the soil of tropical northern Australia

Burkholderia pseudomallei, the cause of the severe disease melioidosis in humans and animals, is a gram-negative saprophyte living in soil and water of areas of endemicity such as tropical northern Australia and Southeast Asia. Infection occurs mainly by contact with wet contaminated soil. The environmental distribution of B. pseudomallei in northern Australia is still unclear. We developed and evaluated a direct soil B. pseudomallei DNA detection method based on the recently published real-time PCR targeting the B. pseudomallei type III secretion system. The method was evaluated by inoculating different soil types with B. pseudomallei dilution series and by comparing B. pseudomallei detection rate with culture-based detection rate for 104 randomly collected soil samples from the Darwin rural area in northern Australia. We found that direct soil B. pseudomallei DNA detection not only was substantially faster than culture but also proved to be more sensitive with no evident false-positive results. This assay provides a new tool to detect B. pseudomallei in soil samples in a fast and highly sensitive and specific manner and is applicable for large-scale B. pseudomallei environmental screening studies or in outbreak situations. Furthermore, analysis of the 104 collected soil samples revealed a significant association between B. pseudomallei-positive sites and the presence of animals at these locations and also with moist, reddish brown-to-reddish gray soils.     

Characteristics of loci and individuals are associated with germline microsatellite mutation rates in lesser kestrels (Falco naumanni)

Although microsatellites are one of the most popular tools in genetic studies, their mutational dynamics and evolution remain unclear. Here, we apply extensive pedigree genotyping to identify and analyze the patterns and factors associated with de novo germline mutations across nine microsatellite loci in a wild population of lesser kestrels (Falco naumanni). A total of 10 germline mutations events were unambiguously identified in four loci, yielding an average mutation rate of 2.96x10(-3). Across loci, mutation rate was positively correlated with locus variability and average allele size. Mutations were primarily compatible with a stepwise mutation model, although not exclusively involved single-step changes. Unexpectedly, we found an excess of maternally transmitted mutations (male-to-female ratio of 0.1). One of the analyzed loci (Fn2.14) resulted hypermutable (mutation rate=0.87%). This locus showed a size-dependent mutation bias, with longer alleles displaying deletions or additions of a small number of repeat than shorter alleles. Mutation probability at Fn2.14 was higher for females and increased with parental (maternal) age but was not associated with individual physical condition, multilocus heterozygosity, allele length or allele span. Overall, our results do not support the male-biased mutation rate described in other organisms and suggest that mutation dynamics at microsatellite loci are a complex process which requires further research.