Blueprint: descrição da complexidade da regulação metabólica através da reconstrução de modelos metabólicos e regulatórios integrados

Tese de doutoramento em Biomedical EngineeringUm modelo metabólico consegue prever o fenótipo de um organismo. No entanto, estes modelos podem obter previsões incorretas, pois alguns processos metabólicos são controlados por mecanismos reguladores. Assim, várias metodologias foram desenvolvidas para melhorar os modelos metabólicos através da integração de redes regulatórias. Todavia, a reconstrução de modelos regulatórios e metabólicos à escala genómica para diversos organismos apresenta diversos desafios. Neste trabalho, propõe-se o desenvolvimento de diversas ferramentas para a reconstrução e análise de modelos metabólicos e regulatórios à escala genómica. Em primeiro lugar, descreve-se o Biological networks constraint-based In Silico Optimization (BioISO), uma nova ferramenta para auxiliar a curação manual de modelos metabólicos. O BioISO usa um algoritmo de relação recursiva para orientar as previsões de fenótipo. Assim, esta ferramenta pode reduzir o número de artefatos em modelos metabólicos, diminuindo a possibilidade de obter erros durante a fase de curação. Na segunda parte deste trabalho, desenvolveu-se um repositório de redes regulatórias para procariontes que permite suportar a sua integração em modelos metabólicos. O Prokaryotic Transcriptional Regulatory Network Database (ProTReND) inclui diversas ferramentas para extrair e processar informação regulatória de recursos externos. Esta ferramenta contém um sistema de integração de dados que converte dados dispersos de regulação em redes regulatórias integradas. Além disso, o ProTReND dispõe de uma aplicação que permite o acesso total aos dados regulatórios. Finalmente, desenvolveu-se uma ferramenta computacional no MEWpy para simular e analisar modelos regulatórios e metabólicos. Esta ferramenta permite ler um modelo metabólico e/ou rede regulatória, em diversos formatos. Esta estrutura consegue construir um modelo regulatório e metabólico integrado usando as interações regulatórias e as ligações entre genes e proteínas codificadas no modelo metabólico e na rede regulatória. Além disso, esta estrutura suporta vários métodos de previsão de fenótipo implementados especificamente para a análise de modelos regulatórios-metabólicos.Genome-Scale Metabolic (GEM) models can predict the phenotypic behavior of organisms. However, these models can lead to incorrect predictions, as certain metabolic processes are controlled by regulatory mechanisms. Accordingly, many methodologies have been developed to extend the reconstruction and analysis of GEM models via the integration of Transcriptional Regulatory Network (TRN)s. Nevertheless, the perspective of reconstructing integrated genome-scale regulatory and metabolic models for diverse prokaryotes is still an open challenge. In this work, we propose several tools to assist the reconstruction and analysis of regulatory and metabolic models. We start by describing BioISO, a novel tool to assist the manual curation of GEM models. BioISO uses a recursive relation-like algorithm and Flux Balance Analysis (FBA) to evaluate and guide debugging of in silico phenotype predictions. Hence, this tool can reduce the number of artifacts in GEM models, decreasing the burdens of model refinement and curation. A state-of-the-art repository of TRNs for prokaryotes was implemented to support the reconstruction and integration of TRNs into GEM models. The ProTReND repository comprehends several tools to extract and process regulatory information available in several resources. More importantly, this repository contains a data integration system to unify the regulatory data into standardized TRNs at the genome scale. In addition, ProTReND contains a web application with full access to the regulatory data. Finally, we have developed a new modeling framework to define, simulate and analyze GEnome-scale Regulatory and Metabolic (GERM) models in MEWpy. The GERM model framework can read a GEM model, as well as a TRN from different file formats. This framework assembles a GERM model using the regulatory interactions and Genes-Proteins-Reactions (GPR) rules encoded into the GEM model and TRN. In addition, this modeling framework supports several methods of phenotype prediction designed for regulatory-metabolic models.I would like to thank Fundação para a Ciência e Tecnologia for the Ph.D. studentship I was awarded with (SFRH/BD/139198/2018)

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 theinitial draft, requiring further curation. Such an approachis 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.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. A. Oliveira (DFA/BD/10205/2020), E. Cunha (DFA/BD/8076/2020), F. Cruz (SFRH/BD/139198/2018), J. Sequeira (SFRH/BD/147271/2019), and M. Sampaio (SFRH/BD/144643/2019) hold a doctoral fellowship provided by the FCT. J. Ribeiro hold a fellowship provided by the University of Minho (UMI-NHO/BIM/2020/68). Oscar Dias acknowledge FCT for the Assistant Research contract obtained under CEEC Individual 2018.info:eu-repo/semantics/publishedVersio

Occurrence and Distribution of Fasciolosis in a Cohort of Ovine Livestock Restricted to a Mountain Plateau in Central Portugal

Fasciola hepatica is a parasite that is widespread in Europe, having been reported in ru- minants of several European countries and causing an important economic impact. This study ascertained the occurrence and distribution of fasciolosis in Portuguese ovine livestock by assessing F. hepatica IgG antibodies in a cohort of confined sheep from a high-altitude region of central Portugal in a 2-year period. Positive animals were found in most locations and in both years, with 18 of the 92 an- imals (19.6% [95% confidence interval CI: 12.03–19.15]) and 17 of the same 92 animals (18.5% [95% CI: 11.15–27.93]) showing to be seropositive in the first year and second year, respectively (p = 0.85). Pasture contamination by F. hepatica eggs could be reduced by thorough anthelmintic treatments.info:eu-repo/semantics/publishedVersio

merlin v4: an updated platform for reconstructing genome-scale metabolic models

The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) software is an open source user-friendly Java application developed for Windows and Unix, aimed towards the reconstruction of genome-scale metabolic models. The development of merlin follows a design philosophy of automating time-consuming steps in the reconstruction of genome-scale metabolic models, while allowing users to control the parameters of operations and manually curate the results. All major steps involved in the reconstruction of a metabolic model are implemented in merlin, including genome retrieval and its functional annotation, construction of the reactions set and associated entities, model compartmentalization and conversion to standard SBML formats. The fourth iteration of merlin includes a major overhaul of the user interface, implementation of new features, improvements to existing features, and most notably, the implementation of the object-relational mapping framework Hibernate. The graphical layout has been significantly streamlined, while supporting the latest version of AiBench, providing users with an intuitive and responsive interface. Development was also focused at new quality of life improvements, aimed mainly towards importing, exporting and duplicating merlin user projects. The development of the latest version of merlin followed a modular approach, culminating in the implementation of a plugin manager which simplifies and hastens the process of updating and debugging the various features of merlin. In addition, TranSyT, a state-of-the-art genome-wide transmembrane transport system annotation tool has been implemented to overcome the limitations of the previously available TRIAGE module. Finally, it is noteworthy to mention the implementation of BioISO, a tool aimed at evaluating a genome-scale metabolic network or biomass formulation, based on the previously available COBRA and FBA frameworks.info:eu-repo/semantics/publishedVersio

Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database

First Online: 28 August 2021Genome-Scale metabolic models (GEMs) are a relevant tool in systems biology for in silico strain optimisation and drug discovery. An easier way to reconstruct a model is to use available GEMs as templates to create the initial draft, which can be curated up until a simulation-ready model is obtained. This approach is implemented in merlin's BiGG Integration Tool, which reconstructs models from existing GEMs present in the BiGG Models database. This study aims to assess draft models generated using models from BiGG as templates for three distinct organisms, namely, Streptococcus thermophilus, Xylella fastidiosa and Mycobacterium tuberculosis. Several draft models were reconstructed using the BiGG Integration Tool and different templates (all, selected and random). The variability of the models was assessed using the reactions and metabolic functions associated with the model's genes. This analysis showed that, even though the models shared a significant portion of reactions and metabolic functions, models from different organisms are still differentiated. Moreover, there also seems to be variability among the templates used to generate the draft models to a lower extent. This study concluded that the BiGG Integration Tool provides a fast and reliable alternative for draft reconstruction for bacteria.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. A. Oliveira (DFA/BD/10205/2020), E. Cunha (DFA/BD/8076/2020), F. Cruz (SFRH /BD/139198/2018), J. Sequeira (SFRH/BD/147271/2019), and M. Sampaio (SFRH/BD/144643/2019) hold a doctoral fellowship provided by the FCT. Oscar Dias acknowledge FCT for the Assistant Research contract obtained under CEEC Individual 2018.info:eu-repo/semantics/publishedVersio

Prevalence of Toxoplasma gondii Antibodies and Risk Factor Investigation in Portuguese Veterinarians: A Matched Case–Control Study

Toxoplasma gondii is a widespread zoonotic agent that greatly impacts Public Health, being responsible for one of the most important parasitic zoonosis worldwide. T. gondii has a heteroxenous life cycle, with cats being the definitive hosts and all warm-blooded animals, including humans, being intermediate hosts. Veterinary practitioners (VP) may be at a higher risk than the general population for T. gondii infection, as they have direct and daily contact with many animal species. The aim of the present study was to ascertain if VP were more likely to be anti-T. gondii IgG seropositive than the general population, as well as to understand if age, accidents with blood-contaminated sharps (cross-blood contamination), gender, working years, and geographic regions play a role as risk factors for T. gondii infection. For this purpose, a case–control study using archived samples was performed. (2) Methods: A total of 350 veterinary practitioners were tested using a commercial semiquantitative enzyme immunoassay for anti-T. gondii IgG. From the general population, 175 anonymous volunteers (matched with cases by region, age, and gender) were studied for anti-T. gondii IgG. (3) Results: There was no statistical difference found between the presence of anti-T. gondii IgG in practitioners (26%; CI = 21.40–30.60%) and the general population (33.14%; CI = 26.17–40.12%) (p = 0.108). Univariate and multivariate analysis showed that only age (older groups) was found to be associated with a higher prevalence of anti-T. gondii IgG, with significant p values (p < 0.05) for both univariate and multivariate analysis. (4) Conclusions: To the best of our knowledge, this is the first case–control study fully focused on the prevalence of anti-T. gondii IgG in VP in Portugal, showing that there was no significant risk for T. gondii infection in veterinarians exposed daily and repeatedly to different species of animals.info:eu-repo/semantics/publishedVersio

PISCIS: multiple autonomous underwater vehicles for environmental and oceanographic field studies

In this paper we describe the envisaged utilization of autonomous underwater vehicles (AUVs) underthe PISCIS project. The aim of the project is to develop an integrated system for underwater datacollection, particularly suited for environmental and oceanographic field studies. The UnderwaterSystems and Technology Lab (LSTS) at the University of Porto accumulated wide experience in thedevelopment and operation of small-size underwater robotic vehicles. Built upon this experience, thePISCIS project will be focused on the development of new technologies and methodologies tobroaden the range of addressable operational scenarios

Walkability Index for Elderly Health: A Proposal

Nowadays, the elderly tend to make more trips: Health benefits resulting from their daily walking routines are an important topic in the context of urban renewal processes. Many health organizations and researchers have demonstrated the influence of the urban environment on walkability levels. This article aims to design a multifactor Walkability Index for Elderly Health (WIEH), capable of associating both the adequacy level of public spaces to elderly walkability, and physical exercise benefits while walking. The methodological approach comprised two main parts: Firstly, a literature review of main reports, legislation, and scientific articles was conducted at the intersection of 'gerontology and physical exercise' with 'urban design and mobility', leading to the selection of four aging-related studies as main contributors to the design of the WIEH; and, secondly, the development of the WIEH was undertaken, based on two premises and designed according to four steps. The first premise defined three systematic areas (urban tissue, urban scene, and safety), variables, and criteria to classify the pedestrian network; and the second premise focused on slopes and stairs in public spaces. The WIEH is divided in four steps: (1) Analyzing public spaces and characterizing their quality for walking, (2) considering the existence of slopes and stairs, (3) calculating different routes for the elderly in their daily routines, or when going to points of interest, and (4) selecting the "heart-friendly route" for elderly people. Adequate walking paths for the elderly can be identified through this innovative approach, with the aim of achieving direct health benefits during their daily routines. Ultimately, the WIEH is capable of supporting decision makers and designers in creating inclusive and age-friendly spaces

A Matched Case–Control Study

Funding Information: This study was supported by FCT—Foundation for Science and Technology, I.P., through research grant PTDC/CVT-CVT/0228/2020 and by funds from the Global Health and Tropical Medicine (GHTM, UID/04413/2020), the Research Centre for Endogenous Resource Valorization (VALORIZA, UIDB/05064/2020), the Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB, UIDB/04033/2020) and the Centre for Natural Resources, Environment and Society (CERNAS, UIDB/00681/2020). This work was supported by national funds, through Fundação para a Ciência e Tecnologia (FCT, Portuguese Foundation for Science and Technology), under projects UIDB/04750/2020 and LA/P/0064/2020. Publisher Copyright: © 2022 by the authors.(1) Background: Toxoplasma gondii is a widespread zoonotic agent that greatly impacts Public Health, being responsible for one of the most important parasitic zoonosis worldwide. T. gondii has a heteroxenous life cycle, with cats being the definitive hosts and all warm-blooded animals, including humans, being intermediate hosts. Veterinary practitioners (VP) may be at a higher risk than the general population for T. gondii infection, as they have direct and daily contact with many animal species. The aim of the present study was to ascertain if VP were more likely to be anti-T. gondii IgG seropositive than the general population, as well as to understand if age, accidents with blood-contaminated sharps (cross-blood contamination), gender, working years, and geographic regions play a role as risk factors for T. gondii infection. For this purpose, a case–control study using archived samples was performed. (2) Methods: A total of 350 veterinary practitioners were tested using a commercial semiquantitative enzyme immunoassay for anti-T. gondii IgG. From the general population, 175 anonymous volunteers (matched with cases by region, age, and gender) were studied for anti-T. gondii IgG. (3) Results: There was no statistical difference found between the presence of anti-T. gondii IgG in practitioners (26%; CI = 21.40–30.60%) and the general population (33.14%; CI = 26.17–40.12%) (p = 0.108). Univariate and multivariate analysis showed that only age (older groups) was found to be associated with a higher prevalence of anti-T. gondii IgG, with significant p values (p < 0.05) for both univariate and multivariate analysis. (4) Conclusions: To the best of our knowledge, this is the first case–control study fully focused on the prevalence of anti-T. gondii IgG in VP in Portugal, showing that there was no significant risk for T. gondii infection in veterinarians exposed daily and repeatedly to different species of animals.publishersversionpublishe

A 2-Year Longitudinal Seroepidemiological Evaluation of Toxoplasma gondii Antibodies in a Cohort of Autochthonous Sheep from Central Portugal

Background: Toxoplasma gondii is an important zoonosis and one of the major causes of abortion in sheep worldwide. (2) Methods: We performed a 2-year longitudinal serological antiT. gondii IgG screening on a cohort of a spatially confined population of a Portuguese autochthonous sheep breed in central Portugal. (3) Results: From the screening of the 2015 and 2016 sera, an increase of seroprevalence was observed (57.7% (95% CI: 49.9–65.3%) versus 69.1% (95% CI: 61.5–75.9), from 2015 and 2016, respectively) (p = 0.031). (4) Conclusions The present study is the first to provide prospective data on the anti-T. gondii serological status of a sheep cohort in Portugal, showing an increase in the occurrence of T. gondii. There is a need to provide a clearer understanding of T. gondii epidemiology in Portugal, ideally by implementing monitoring programs on sentinel herds, not only due to the high impact of T. gondii on animal health but also for it being a zoonosis.info:eu-repo/semantics/publishedVersio