In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

Background: Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Results: Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56. 7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average HE of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (FST = 0.747 between gene pools), 0. 440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (FST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was~88 kbp, while for the Andean gene pool was~395 kbp, and for the Mesoamerican was ~ 130 kbp. Conclusions: For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches

Comparison of pharmacopeial statistical methods applied in microbiological assay for antibiotics potency determination using parallel lines and three-dose level

Pharmaceutical equivalence studies, useful for checking the interchangeability of generic medicines and their respective innovator medicines, have been carried out in Brazil since 1999, as a consequence of the establishment of the generic medicine policy. For medicines containing antibiotics, microbiological assays are often the most appropriate method. However, the statistical methods applied in these assays are not widely known due to the difficult access to official codes and/or little knowledge of the statistical tools of analysis. Thus, the aim of this work was to compare the statistical methods for determining the potency of antibiotics through the cylinder-plate method using parallel lines and a three-dose level model, as described in the Brazilian Pharmacopeia (4th edition, 1988), British Pharmacopoeia 2011, European Pharmacopoeia (7th edition), The International Pharmacopoeia (4th edition), and United States Pharmacopeia (34th edition). The assay is illustrated with the antibiotic ofloxacin, and details on orthogonal coefficients, normality test, homogeneity of variance test, and detection of outliers are discussed. The calculations obtained by statistical analyses from different pharmacopeias lead to the same final interpretation. In practice, with the availability of alternative pharmacopeial methods, the analyst can choose the most appropriate statistical calculation to be used.Os estudos de equivalência farmacêutica, úteis na verificação da intercambialidade entre os medicamentos genéricos e respectivos medicamentos de referência, têm sido realizados no Brasil desde 1999, como consequência do estabelecimento da política de medicamentos genéricos. Para medicamentos contendo antibióticos, os ensaios microbiológicos são, muitas vezes, o método mais adequado. Entretanto, os métodos estatísticos aplicados nesses ensaios não são amplamente conhecidos devido à dificuldade de acesso aos compêndios oficiais e/ou pouca compreensão das ferramentas estatísticas de análises. Portanto, o objetivo desse trabalho foi comparar os métodos estatísticos para determinação de potência de antibióticos pelo delineamento por retas paralelas e três níveis de doses, descritos nas farmacopeias Brasileira 4. ed. (1988), Britânica 2011, Europeia 7. ed., Internacional 4. ed. e na Farmacopeia dos Estados Unidos 34. ed. (2011). O ensaio é exemplificado com o antibiótico ofloxacino e detalhes sobre coeficientes ortogonais, teste de normalidade, teste de homogeneidade de variância e detecção de outliers são discutidos. Os cálculos obtidos pelas análises estatísticas segundo as diferentes farmacopeias resultaram na mesma interpretação final. Na prática, métodos farmacopéicos alternativos permitem ao analista a escolha do cálculo estatístico mais apropriado a ser utilizado

Germline DNA copy number variation in familial and early-onset breast cancer

Introduction: Genetic factors predisposing individuals to cancer remain elusive in the majority of patients with a familial or clinical history suggestive of hereditary breast cancer. Germline DNA copy number variation (CNV) has recently been implicated in predisposition to cancers such as neuroblastomas as well as prostate and colorectal cancer. We evaluated the role of germline CNVs in breast cancer susceptibility, in particular those with low population frequencies (rare CNVs), which are more likely to cause disease." Methods: Using whole-genome comparative genomic hybridization on microarrays, we screened a cohort of women fulfilling criteria for hereditary breast cancer who did not carry BRCA1/BRCA2 mutations. Results: The median numbers of total and rare CNVs per genome were not different between controls and patients. A total of 26 rare germline CNVs were identified in 68 cancer patients, however, a proportion that was significantly different (P = 0.0311) from the control group (23 rare CNVs in 100 individuals). Several of the genes affected by CNV in patients and controls had already been implicated in cancer. Conclusions: This study is the first to explore the contribution of germline CNVs to BRCA1/2-negative familial and early-onset breast cancer. The data suggest that rare CNVs may contribute to cancer predisposition in this small cohort of patients, and this trend needs to be confirmed in larger population samples.Brazilian National Institute of Science and Technology in Oncogenomics [FAPESP 2008/57887-9, CNPq 573589/08-9, FAPESP (2009/00898-1)]Brazilian National Institute of Science and Technology in Oncogenomic

From sea monsters to charismatic megafauna: changes in perception and use of large marine animals

Marine megafauna has always elicited contrasting feelings. In the past, large marine animals were often depicted as fantastic mythological creatures and dangerous monsters, while also arousing human curiosity. Marine megafauna has been a valuable resource to exploit, leading to the collapse of populations and local extinctions. In addition, some species have been perceived as competitors of fishers for marine resources and were often actively culled. Since the 1970s, there has been a change in the perception and use of megafauna. The growth of marine tourism, increasingly oriented towards the observation of wildlife, has driven a shift from extractive to non-extractive use, supporting the conservation of at least some species of marine megafauna. In this paper, we review and compare the changes in the perception and use of three megafaunal groups, cetaceans, elasmobranchs and groupers, with a special focus on European cultures. We highlight the main drivers and the timing of these changes, compare different taxonomic groups and species, and highlight the implications for management and conservation. One of the main drivers of the shift in perception, shared by all the three groups of megafauna, has been a general increase in curiosity towards wildlife, stimulated inter alia by documentaries (from the early 1970s onwards), and also promoted by easy access to scuba diving. At the same time, environmental campaigns have been developed to raise public awareness regarding marine wildlife, especially cetaceans, a process greatly facilitated by the rise of Internet and the World Wide Web. Currently, all the three groups (cetaceans, elasmobranchs and groupers) may represent valuable resources for ecotourism. Strikingly, the economic value of live specimens may exceed their value for human consumption. A further change in perception involving all the three groups is related to a growing understanding and appreciation of their key ecological role. The shift from extractive to non-extractive use has the potential for promoting species conservation and local economic growth. However, the change in use may not benefit the original stakeholders (e.g. fishers or whalers) and there may therefore be a case for providing compensation for disadvantaged stakeholders. Moreover, it is increasingly clear that even non-extractive use may have a negative impact on marine megafauna, therefore regulations are needed.SFRH/BPD/102494/2014, UID/MAR/04292/2019, IS1403info:eu-repo/semantics/publishedVersio