10 documents found, page 1 of 1
Design and optimization of microbial communities
Santos, Sophia TorresMicrobial communities directly affect surrounding environments and are an important biological process, with potential applications in a variety of fields, such as biotechnology, environmental, and human health. However, the overall understanding of interactions and dynamics in microbial communities remains a challenge. Synergies between computational methods and genome-scale metabolic models have been explored...
Ecological modelling approaches for predicting emergent properties in microbial...
Berg, Naomi Iris van den; Machado, Daniel; Santos, Sophia Torres; Rocha, I.; Chacón, Jeremy; Harcombe, William; Mitri, Sara; Patil, Kiran R.Recent studies have brought forward the critical role of emergent properties in shaping microbial communities and the ecosystems of which they are a part. Emergent properties---patterns or functions that cannot be deduced linearly from the properties of the constituent parts---underlie important ecological characteristics such as resilience, niche expansion and spatial self-organization. While it is clear that ...
Towards metabolic optimization of CHO cells: in silico improvement of culture m...
Hamdi, Anis; Santos, Sophia Torres; Rocha, IsabelThe emergence of omics tools and bioinformatics potentiated the development of new strategies to optimize several expression platforms, in particular mammalian cell lines, being CHO cells one of the most commonly used cell line for the production of recombinant proteins. Foremost, computational modelling combined with CHO cell omics data can help optimizing growth parameters, as well as improving the final prod...
Mapping Salmonella typhimurium pathways using ¹³C metabolic flux analysis
Correia, Daniela Matilde Marques; Sargo, C.; Silva, A.; Santos, Sophia Torres; Giordano, Roberto C.; Ferreira, Eugénio C.; Zangirolami, Teresa C.In the last years, Salmonella has been extensively studied not only due to its importance as a pathogen, but also as a host to produce pharmaceutical compounds. However, the full exploitation of Salmonella as a platform for bioproduct delivery has been hampered by the lack of information about its metabolism. Genome-scale metabolic models can be valuable tools to delineate metabolic engineering strategies as lo...
Inferring optimal minimal medium on genome-scale metabolic models using evoluti...
Santos, Sophia Torres; Correia, Sara; Rocha, IsabelGenome-scale metabolic models (GSMMs) are a valuable tool for the study of metabolic systems biology through biomedical to industrial research and are becoming available for an increasing number of single organisms and more recently also for microbial communities. One of the most promising features for the use of GSMMs is the rational design of microorganisms in isolation or in communities that could turn them ...
A computation tool for the estimation of biomass composition from genomic and t...
Santos, Sophia Torres; Rocha, IsabelGiven the huge potential impact of the growing number of complete genome-scale metabolic network reconstructions of organisms, it is necessary to use bioinformatics tools to simplify and accelerate the course of knowledge in this field. One essential component of genome-scale metabolic model is biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formu...
Towards an improved version of Kluyveromyces lactis genome-scale metabolic model
Dias, Oscar; Santos, Sophia Torres; Ferreira, Eugénio C.; Rocha, I.Kluyveromyces lactis (K. lactis) is a Crabtree-negative yeast, which as the ability to metabolise lactose. Its complete genome sequence is available since 2004 [1], whereas we have published the genome wide metabolic annotation in 2012 [2] and the iOD907 metabolic model in 2014 [3]. For the initial construction of the iOD907 model, the iMM904 [4] baker’s yeast model was used to overcome the lack of specific stu...
Development of computational and experimental methods for biomass composition a...
Santos, Sophia Torres; Rocha, I.The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as ...
Reconstruction and validation of iTR383, a genome-scale metabolic model for Hel...
Resende, Tiago; Correia, Daniela Matilde Marques; Santos, Sophia Torres; Rocha, I.Helicobacter pylori 26695, a highly pathogenic bacterium, is a human gastric epithelia colonizer, correlated with the development of duodenal and gastric ulcers, and gastric cancer worldwide. Its genome has been previously sequenced and annotated, and two genome-scale metabolic models have been developed; however, since their publication, vast amounts of data and new methodologies have been developed. In order ...
Development of computational methods for the determination of biomass compositi...
Santos, Sophia TorresThe use of genome-scale metabolic models is rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation, since this reaction will be used as the objective function in most simulation approaches. In order to obtain a reliable metabolic model, the biomass precursors and their coefficients must be as precise as possible. Ideally, the determination of t...