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Reconstruction of genome-scale metabolic models of microalgae for exploration o...
Cunha, Emanuel RodriguesAs microalgas oferecem oportunidades significativas para a produção de compostos de alto valor nos setores alimentar, farmacêutico, cosmético e de biocombustíveis. Entre elas, Dunaliella salina, Nannochloropsis gaditana e Pavlova lutheri têm sido amplamente estudadas devido à sua capacidade de sintetizar lípidos e pigmentos com valor económico. No entanto, a aplicação industrial em larga escala ainda enfrenta d...
diel_models: a python package for systematic integration of daynight cycles int...
Martins, Luciana; Capela, João; Cunha, Emanuel Rodrigues; Sampaio, Marta; Dias, OscarIn recent years, genome-scale metabolic models have become indispensable tools for studying complex metabolic processes occurring within living organisms. Understanding plants metabolic behaviour under diel cycles (24-h daynight cycles) is essential to explain their adaptive strategies to different light conditions. However, integrating these cycles in plant GEMs is complex, laborious, time-consuming, and not s...
FROG analysis ensures the reproducibility of genome scale metabolic models
Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V NGenome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting a...
Exploring methane mitigation strategies in photosynthetic microorganisms throug...
Apolinário, Gonçalo; Gonçalves, Joana Oliveira; Cunha, Emanuel Rodrigues; Madureira, Leandro Filipe Feiteira; Maciel, José Filipe GonçalvesThe problematic of greenhouse gas (GHG) emissions is a global environmental challenge that has raised concerns in the past few decades. Particularly, the increase in atmospheric concentrations of carbon dioxide, methane, and other damaging gases can lead to catastrophic repercussions to life as we know it. Therefore, reducing GHG emissions and fomenting strategies for their mitigation are crucial steps that nee...
Towards a genome-scale metabolic model of Dunaliella salina
Cunha, Emanuel Rodrigues; Sousa, Vítor; Vicente, A. A.; Geada, Pedro Miguel Macedo; Dias, OscarDunaliella salina is a green algae known for its ability to produce carotenoids. However, maximizing its production while achieving significant biomass yields remains challenging, which can be addressed through systems biology tools like genome-scale metabolic models. This work presents the first genome-scale metabolic model for D. salina, enabling an in silico analysis and optimization of -carotene and lutein ...
The first multi-tissue genome-scale metabolic model of a woody plant highlights...
Cunha, Emanuel Rodrigues; Silva, Miguel; Chaves, Inês; Demirci, Huseyin; Lagoa, Davide Rafael Santos; Lima, Diogo; Rocha, Miguel; Rocha, IsabelOver the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871). Th...
TranSyT, an innovative framework for identifying transport systems
Cunha, Emanuel Rodrigues; Lagoa, Davide Rafael Santos; Faria, José P.; Liu, Filip; Henry, Christopher S.; Dias, OscarThe importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGEâs release, software development for the automatic integration of transport reactions into models has stalled.Here, we present the Transport Systems Tracker (TranSyT). Unlike other transpor...
Exploring Xylella fastidiosas metabolic traits using a GSM model of the phytopa...
Oliveira, Alexandre Rafael Machado; Cunha, Emanuel Rodrigues; Silva, Miguel; Faria, Cristiana Silva; Dias, OscarXylella fastidiosa is a gram-negative phytopathogenic bacterium able to infect over 500 plant species, with devastating consequences for agricultural and forest-based economies. In the last decade, genome-scale metabolic (GSM) models have become important systems biology tools for studying the metabolic behaviour of different organisms. In this work, a GSM model of X. fastidiosa subsp. pauca De Donno is present...
Towards a multivariate analysis of genome-scale metabolic models derived from t...
Oliveira, Alexandre Rafael Machado; Cunha, Emanuel Rodrigues; Cruz, Fernando João Pereira da; Ribeiro, João Manuel Capela AraújoGenome-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 pre...
merlin, an improved framework for the reconstruction of high-quality genome-sca...
Capela, João; Lagoa, Davide Rafael Santos; Rodrigues, Rúben André Costa; Cunha, Emanuel Rodrigues; Cruz, Fernando; Barbosa, Ana; Bastos, J.; Lima, DiogoGenome-scale metabolic models have been recognised as useful tools for better understanding living organisms metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned versi...