Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool.

Genome-scale metabolic models (GEMs) are essential tools for in silico phenotype prediction and strain optimisation. The most straightforward GEMs reconstruction approach uses published models as templates to generate the initial draft, requiring further curation. Such an approach is used by BiGG Integration Tool (BIT), available for merlin users. This tool uses models from BiGG Models database as templates for the draft models. Moreover, BIT allows the selection between different template combinations. The main objective of this study is to assess the draft models generated using this tool and compare them BIT, comparing these to CarveMe models, both of which use the BiGG database, and curated models. For this, three organisms were selected, namely Streptococcus thermophilus, Xylella fastidiosa and Mycobacterium tuberculosis. The models' variability was assessed using reactions and genes' metabolic functions. This study concluded that models generated with BIT for each organism were differentiated, despite sharing a significant portion of metabolic functions. Furthermore, the template seems to influence the content of the models, though to a lower extent. When comparing each draft with curated models, BIT had better performances than CarveMe in all metrics. Hence, BIT can be considered a fast and reliable alternative for draft reconstruction for bacteria models.

Exploring synergies between plant metabolic modelling and machine learning.

As plants produce an enormous diversity of metabolites to help them adapt to the environment, the study of plant metabolism is of utmost importance to understand different plant phenotypes. Omics data have been generated at an unprecedented rate for several organisms, including plants, and are widely used to study the central dogma of molecular biology, connecting the genome to phenotypes. Constraint-based modelling (CBM) methods, working over genome-scale metabolic models (GSMMs), have been crucial for organising and analysing omics data by integrating them with biochemical knowledge. In 2009, the first plant GSMM was reconstructed and, since then, several advances have been made, including the creation of context- and multi-tissue models that have supported the study of plant metabolism. Nevertheless, plant metabolic modelling remains very challenging. In parallel, as omics datasets are complex and heterogeneous, machine learning (ML) models have been applied in their interpretation to foster knowledge discovery. Recently, the first studies combining both CBM and ML approaches have emerged and have shown promising results. Here, we present the major advances in plant metabolic modelling and review the main CBM-ML hybrid studies. Finally, we discuss the application of machine learning to address the unique challenges of plant metabolic modelling.

Trophic niche changes associated with the eradication of invasive mammals in an insular lizard: an assessment using isotopes.

Invasive species are a major threat to island biodiversity, and their eradications have substantially contributed to the conservation of island endemics. However, the consequences of eradications on the trophic ecology of native taxa are largely unexplored. Here, we used the eradication of invasive black rats Rattus rattus and European rabbits Oryctolagus cuniculus from the Berlenga Island, in the western coast of Portugal, as a whole-ecosystem experiment to investigate the effects of the eradication of invasive mammals on the trophic niche and body dimensions of the island-restricted Berlenga wall lizard Podarcis carbonelli berlengensis over a 2-year period. Our results suggest an expansion of the isotopic niche and an intensification of the sexual dimorphism of the lizard following mammal eradication. Additionally, we found considerable variability in isotopic niche across the island and detected evidence of sex-specific and season-modulated nutritional requirements of this threatened reptile. Our findings support that the eradication of 2 of the planet's most problematic invasive vertebrates led to changes in the lizard trophic niche and sexual dimorphism in just 2 years. This suggests that the ecological pressures-for example, prey availability and habitat structure-to which lizards are exposed have substantially changed post-eradication. Our study emphasizes the scientific value of island eradications as experiments to address a wide range of ecological questions and adds to the increasing body of evidence supporting substantial conservation gains associated with these restoration interventions.

Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli.

BACKGROUND: A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the genetic diversity of Stx-converting phage genomes (Stx phages), focusing on the lysis-lysogeny decision and lytic cassettes. RESULTS: We show that most STEC isolates belong to non-O157 serotypes (73 %), regardless the sources and geographical regions. While the majority of STEC genomes contain a single stx gene (61 %), strains containing two (35 %), three (3 %) and four (1 %) stx genes were also found, being stx2 the most prevalent gene variant. Their location is exclusively found in intact prophage regions, indicating that they are phage-borne. We further demonstrate that Stx phages can be grouped into four clusters (A, B, C and D), three subclusters (A1, A2 and A3) and one singleton, based on their shared gene content. This cluster distribution is in good agreement with their predicted virion morphologies. Stx phage genomes are highly diverse with a vast number of 1,838 gene phamilies (phams) of related sequences (of which 677 are orphams i.e. unique genes) and, although having high mosaicism, they are generally organized into three major transcripts. While the mechanisms that guide lysis-lysogeny decision are complex, there is a strong selective pressure to maintain the stx genes location close to the lytic cassette composed of predicted SAR-endolysin and pin-holin lytic proteins. The evolution of STEC Stx phages seems to be strongly related to acquiring genetic material, probably from horizontal gene transfer events. CONCLUSIONS: This work provides novel insights on the genetic structure of Stx phages, showing a high genetic diversity throughout the genomes, where the various lysis-lysogeny regulatory systems are in contrast with an uncommon, but conserved, lytic system always adjacent to stx genes.

Autoavaliação e justiça social na avaliação das escolas em portugal / Self-evaluation and social justice on portugals schools evaluation / Autoevaluación y justicia social en la evaluación de las escuelas en portugal / Auto-évaluation et justice sociale dans lévaluation des écoles au portugal

Resumo Partindo da crença de que o envolvimento das escolas em processos de autoavaliação pode contribuir para que melhor se conheçam e, em função desse conhecimento, tomem decisões que contribuam para a concretização da justiça social, foi desenvolvido um estudo que analisou duas políticas de educação em Portugal justificadas por essa intenção e que exigem o recurso à autoavaliação. Os dados, recolhidos por entrevistas semi-directivas a diretores(as) de escolas, professores(as) de equipes de autoavaliação e ex-ministro da educação responsável pela lei de avaliação, permitem concluir que a autoavaliação, pelo conhecimento que fornece das situações vividas, pode apoiar práticas de justiça curricular promotoras de justiça social. No entanto, para isso, a autoavaliação não pode se esgotar na atenção a resultados obtidos em exames e em lógicas de performatividade.

Abstract Based on the belief that the involvement of schools in self-assessment processes allow them to better know each other and, based on this knowledge, make decisions that contribute to social justice, a study was developed focused on two education policies in Portugal, both justified in this intention and which require the use of self-evaluation. The data collected from semi-directive interviews with school principals, teachers, self-evaluation team coordinators and the ex-minister of education responsible for the evaluation law allows concluding that self-evaluation, due to the knowledge it provides from situations experienced and the effects generated, can support curricular justice practices that promote social justice. However, to do so, it must not be limited to the results obtained in national exams and on performative logic.

Resumen Partiendo de la creencia de que la involucración de las escuelas en procesos de autoevaluación puede contribuir para que estas se conozcan mejor y, en función de este conocimiento, tomen decisiones que contribuyan para la concreción de la justicia social, fue elaborado un estudio que analizó dos políticas de educación en Portugal justificadas en esta intención y que exigen el recurso de la autoevaluación. Los datos, recolectados mediante entrevistas semidirigidas con directores/as de escuelas, profesores/as de equipos de autoevaluación y un ex Ministro de Educación responsable por la ley de evaluación, permiten concluir que la autoevaluación, por los conocimientos que suministra de las situaciones vividas, puede apoyar a prácticas de justicia, en los planes de estudios, promotoras de la justicia social. Aun considerando esto, la finalidad propuesta no se debe agotar en la atención a resultados obtenidos en exámenes ni en lógicas de desempeño.

Résumé En partant de la conviction que l'implication des écoles dans les processus d'auto-évaluation peut les aider à mieux se connaître pour, prendre des décisions d´après ces constats qui contribuent à réaliser la justice sociale, une étude menée au Portugal a analysé deux politiques éducatives fondées sur ces conceptions qui ont recours à l'auto-évaluation. Les données récoltées à travers des entretiens semi-directifs auprès de directeurs d'école, de professeures des équipes d'auto-évaluation et de l'ancien ministre de l'Éducation chargé de la loi d'évaluation nous permettent de conclure que l'auto-évaluation, grâce aux connaissances qu'elle fournit sur les situations vécues, peut promouvoir les pratiques de justice en milieu scolaire favorisant la justice sociale. Néanmoins, pour cela, notre attention ne doit pas se limiter aux résultats obtenus dans les examens et aux logiques de performativité.

Predicting promoters in phage genomes using PhagePromoter.

SUMMARY: The growing interest in phages as antibacterial agents has led to an increase in the number of sequenced phage genomes, increasing the need for intuitive bioinformatics tools for performing genome annotation. The identification of phage promoters is indeed the most difficult step of this process. Due to the lack of online tools for phage promoter prediction, we developed PhagePromoter, a tool for locating promoters in phage genomes, using machine learning methods. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs. AVAILABILITY AND IMPLEMENTATION: This tool was integrated in the Galaxy framework and it is available online at: https://bit.ly/2Dfebfv. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Staphylococci phages display vast genomic diversity and evolutionary relationships.

BACKGROUND: Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator-prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, typically characterized by highly mosaic genomes and no universal genes. To better understand the diversity and relationships among phages infecting human pathogens, we have analysed the complete genome sequences of 205 phages of Staphylococcus sp. RESULTS: These are predicted to encode 20,579 proteins, which can be sorted into 2139 phamilies (phams) of related sequences; 745 of these are orphams and possess only a single gene. Based on shared gene content, these phages were grouped into four clusters (A, B, C and D), 27 subclusters (A1-A2, B1-B17, C1-C6 and D1-D2) and one singleton. However, the genomes have mosaic architectures and individual genes with common ancestors are positioned in distinct genomic contexts in different clusters. The staphylococcal Cluster B siphoviridae are predicted to be temperate, and the integration cassettes are often closely-linked to genes implicated in bacterial virulence determinants. There are four unusual endolysin organization strategies found in Staphylococcus phage genomes, with endolysins predicted to be encoded as single genes, two genes spliced, two genes adjacent and as a single gene with inter-lytic-domain secondary translational start site. Comparison of the endolysins reveals multi-domain modularity, with conservation of the SH3 cell wall binding domain. CONCLUSIONS: This study provides a high-resolution view of staphylococcal viral genetic diversity, and insights into their gene flux patterns within and across different phage groups (cluster and subclusters) providing insights into their evolution.