Bayesian Mixture Models for Assessment of Gene Differential Behaviour and Prediction of pCR through the integration of copy number and gene expression data

We consider modeling jointly microarray RNA expression and DNA copy number data. We propose Bayesian mixture models that define latent Gaussian probit scores for the DNA and RNA, and integrate between the two platforms via a regression of the RNA probit scores on the DNA probit scores. Such a regression conveniently allows us to include additional sample specific covariates such as biological conditions and clinical outcomes. The two developed methods are aimed respectively to make inference on differential behaviour of genes in patients showing different subtypes of breast cancer and to predict the pathological complete response (pCR) of patients borrowing strength across the genomic platforms. Posterior inference is carried out via MCMC simulations. We demonstrate the proposed methodology using a published data set consisting of 121 breast cancer patients

Governing with Ignorance: Understanding the Australian Food Regulator’s Response to Nano Food

This paper examines regulatory responses to the presence of previously undetected and unlabelled nanoparticles in the Australian food system. Until 2015, the Australian regulatory body Food Standards Australia New Zealand (FSANZ) denied that nanoparticles were present in Australian food. However, and despite repeated claims from Australia’s food regulator, research commissioned by civil society group Friends of the Earth has demonstrated that nanoparticles are deliberately included as ingredients in an array of food available for sale in Australia. This paper critically examines how nanoparticles have come to be integrated into Australia’s food system under the radar of Australia’s food regulator. Our case study of FSANZ—including its responses to the civil society-led science that determined the existence of nanoparticles in Australian food—raises a number of important questions about the governance of risk in relation to emerging technologies such as nanotechnology. In this paper, we argue that FSANZ’ response to the presence of nanotechnology in Australia’s food system is an example of ‘governing with ignorance’. This is demonstrated via the denial and dismissal of science claims as a basis for limited regulatory intervention. FSANZ’ response intersects with the centrality of commercial interests in shaping science research and commercialisation, alongside the ‘hands off’ approach to regulation that is characteristic of neoliberal governance approaches. We conclude by arguing that in the current food governance framework, and alongside a paucity of impact science, civil society plays a vital role in attempts to democratise the Australian food system. © 2017, Springer Science+Business Media B.V., part of Springer Nature

Protein markers and seed size variation in common bean segregating populations

18 páginas, 7 tablas.Selection and random genetic drift are the two main forces affecting allele frequencies in common bean breeding programs. Therefore, knowledge on allele frequency changes attributable to these forces is of fundamental importance for breeders. The changes in frequencies of alleles of biochemical markers were examined in F2 to F7 populations derived from crosses between cultivated Mesoamerican and Andean common bean accessions (Phaseolus vulgaris L.). Biochemical markers included the seed proteins phaseolin, lectin and other seed polypeptides, and six isozymes. The Schaffer’s test detected a high significant linear trend of the 63% of the polymorphic loci studied, meaning that directional selection was acting on those loci. Associations between seed size traits, phaseolin seed-storage protein and isozyme markers were detected based on the comparisons of the progeny genotypic means. In the interracial populations the intermediate form PhaH/T, b6, and Rbcs 98 alleles had a positive effect on seed size. In the inter-gene pool populations, a higher transmission of Mesoamerican alleles in all loci was showed, although the Andean alleles PhaT, Skdh 100 , Rbcs 98 , and Diap 100 showed positive effects on seed weight. Our results suggest that phaseolin and other seed proteins markers are linked to loci affecting seed size. These markers have good potential for improving the results of the selection and should be considered as a strategy for germplasm enhancement and to avoid the reduced performance of the inter-gene pool populations.Research was supported by the projects AGF97-0324 and AGL2005-01268/AGR from the Spanish Government, PGIDIT02RAG40301PR from the Galician Government (Spain), and EU-FEDER Funds. A. M. González thanks her fellowship to Ministry of Education, Culture and Sports of Spain. M. De la Fuente is grateful to the Xunta de Galicia for awarding her a fellowship grant.Peer reviewe