Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

All different or all the same? Exploring the diversity of professional practices in Portuguese school psychology

"Published online: 29 March 2016"

The construction of professional identities in the contexts of work

This chapter identifies and analyzes some characteristics of working situations that are important in the construction of professional identities. It is claimed that professional identity presumes a dynamic process and is constructed and reconstructed in social situations and interactions. Work has a central place in the life of individuals and societies. The contexts of work are places par excellence for investment, expression, negotiation and recognition of the actor themselves and of others. They are, thus, situations for the attribution offeelings about work, ofrelational transactions, oflearning and production of professional know ledge, which are fundamental elements in the (re )construction of professional identity and which are emphasized here below.

The role of monocarboxylate transporters in 3-bromopyruvate effect in cancer cells

Tese de Doutoramento em Biologia Molecular e Ambiental (área de especialização em Biologia Molecular e Saúde).