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IsoDesign: substrate design for isotopic labelling experiments
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Edité par CCSD -
International audience. In systems biology, studying the functioning of the intricate network of biochemical reactions governing cellular metabolism is crucial for elucidating the behaviour of living organisms. Metabolic Flux Analysis (MFA) addresses this need by quantifying fluxes though metabolic pathways, enabling researchers to investigate regulatory mechanisms, identify metabolic bottlenecks, and optimize cellular processes for various applications, ranging from biotechnology to healthcare.13C-MFA enables the quantification of the rates of biochemical reactions within metabolic networks and uses constraint-based mathematical modelling to calculate metabolic fluxes. In 13C-MFA, the studied microorganism is cultivated in media containing 13C-labelled substrates in isotope labelling experiments (ILE). Mass spectrometry and nuclear magnetic resonance techniques are then employed to measure incorporation of tracer atoms into metabolites within the studied metabolic network. This experimental data is used to calculate fluxes. The precision of these calculated fluxes depends on the quality and on the nature of experimental data and the selection of the most optimal labelled substrates to resolve fluxes across different network topologies. However, choosing the right 13C-labeled forms of the substrates is a time-consuming and labour-intensive task, as multiple configurations must be tested, and the large solution space makes analysing the different combinations challenging. To accelerate the design of optimal 13C tracers, we present IsoDesign, an open-source python software that streamlines 13C tracer design for 13C-MFA. With its intuitive graphical user interface and by leveraging the influx_si software for flux calculation, IsoDesign provides the necessary tools for efficient design of ILEs, enhancing the precision and reducing the cost of 13C-MFA experiments. We showcase the tool using a study of acetate and glucose metabolism regulation in E. coli, showing that IsoDesign significantly facilitates the design of 13C-MFA studies.
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