Browsing by Author "Lopes, Marta B."
Now showing 1 - 7 of 7
Results Per Page
Sort Options
- A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responsesPublication . Rosa, Filipa; Sales, Kevin C.; Cunha, Bernardo R.; Couto, Andreia; Lopes, Marta B.; Calado, CecíliaReporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the heterologous gene or even in the general cellular metabolism. Fourier transform mid-infrared (FT-MIR) spectroscopy was evaluated to simultaneously analyze in a rapid (minutes) and high-throughput mode (using 96-wells microplates), the transfection efficiency, and the effect of the transfection process on the host cell biochemical composition and metabolism. Semi-adherent HEK and adherent AGS cell lines, transfected with the plasmid pVAX-GFP using Lipofectamine, were used as model systems. Good partial least squares (PLS) models were built to estimate the transfection efficiency, either considering each cell line independently (R 2 ≥ 0.92; RMSECV ≤ 2 %) or simultaneously considering both cell lines (R 2 = 0.90; RMSECV = 2 %). Additionally, the effect of the transfection process on the HEK cell biochemical and metabolic features could be evaluated directly from the FT-IR spectra. Due to the high sensitivity of the technique, it was also possible to discriminate the effect of the transfection process from the transfection reagent on KEK cells, e.g., by the analysis of spectral biomarkers and biochemical and metabolic features. The present results are far beyond what any reporter gene assay or other specific probe can offer for these purposes.
- In situ near infrared spectroscopy monitoring of cyprosin production by recombinant Saccharomyces cerevisiae strainsPublication . Sampaio, Pedro; Sales, Kevin C.; Rosa, Filipa O.; Lopes, Marta B.; Calado, CecíliaNear infrared (NIR) spectroscopy was used to in situ monitoring the cultivation of two recombinant Saccharomyces cerevisiae strains producing heterologous cyprosin B. NIR spectroscopy is a fast and non-destructive technique, that by being based on overtones and combinations of molecular vibrations requires chemometrics tools, such as partial least squares (PLS) regression models, to extract quantitative information concerning the variables of interest from the spectral data. In the present work, good PLS calibration models based on specific regions of the NIR spectral data were built for estimating the critical variables of the cyprosin production process: biomass concentration, cyprosin activity, cyprosin specific activity, the carbon sources glucose and galactose concentration and the by-products acetic acid and ethanol concentration. The PLS models developed are valid for both recombinant S. cerevisiae strains, presenting distinct cyprosin production capacities, and therefore can be used, not only for the real-time control of both processes, but also in optimization protocols. The PLS model for biomass yielded a R2 = 0.98 and a RMSEP = 0.46 g dcw l−1, representing an error of 4% for a calibration range between 0.44 and 13.75 g dcw l−1. A R2 = 0.94 and a RMSEP = 167 U ml−1 were obtained for the cyprosin activity, corresponding to an error of 6.7% of the experimental data range (0–2509 U ml−1), whereas a R2 = 0.93 and RMSEP = 672 U mg−1 were obtained for the cyprosin specific activity, corresponding to an error of 7% of the experimental data range (0–11,690 U mg−1). For the carbon sources glucose and galactose, a R2 = 0.96 and a RMSECV of 1.26 and 0.55 g l−1, respectively, were obtained, showing high predictive capabilities within the range of 0–20 g l−1. For the metabolites resulting from the cell growth, the PLS model for acetate was characterized by a R2 = 0.92 and a RMSEP = 0.06 g l−1, which corresponds to a 6.1% error within the range of 0.41–1.23 g l−1; for the ethanol, a high accuracy PLS model with a R2 = 0.97 and a RMSEP = 1.08 g l−1 was obtained, representing an error of 9% within the range of 0.18–21.76 g l−1. The present study shows that it is possible the in situ monitoring and prediction of the critical variables of the recombinant cyprosin B production process by NIR spectroscopy, which can be applied in process control in real-time and in optimization protocols. From the above, NIR spectroscopy appears as a valuable analytical tool for online monitoring of cultivation processes, in a fast, accurate and reproducible operation mode.
- In situ NIR spectroscopy monitoring of plasmid production processes effect of producing strain, medium composition and the cultivation strategyPublication . Lopes, Marta B.; Gonçalves, Geisa A. L.; Felício-Silva, Daniel; Prather, Kristala L. J.; Monteiro, Gabriel; Prazeres, Duarte M. F.; Calado, CecíliaBACKGROUNDWhile the pharmaceutical industry keeps an eye on plasmid DNA production for new generation gene therapies, real-time monitoring techniques for plasmid bioproduction are as yet unavailable. This work shows the possibility of in situ monitoring of plasmid production in Escherichia coli cultures using a near infrared (NIR) fiber optic probe. RESULTSPartial least squares (PLS) regression models based on the NIR spectra were developed for predicting bioprocess critical variables such as the concentrations of biomass, plasmid, carbon sources (glucose and glycerol) and acetate. In order to achieve robust models able to predict the performance of plasmid production processes, independently of the composition of the cultivation medium, cultivation strategy (batch versus fed-batch) and E. coli strain used, three strategies were adopted, using: (i) E. coliDH5 cultures conducted under different media compositions and culture strategies (batch and fed-batch); (ii) engineered E. coli strains, MG1655endArecApgi and MG1655endArecA, grown on the same medium and culture strategy; (iii) diverse E. coli strains, over batch and fed-batch cultivations and using different media compositions. PLS models showed high accuracy for predicting all variables in the three groups of cultures. CONCLUSIONNIR spectroscopy combined with PLS modeling provides a fast, inexpensive and contamination-free technique to accurately monitoring plasmid bioprocesses in real time, independently of the medium composition, cultivation strategy and the E. coli strain used.
- Kinetic modeling of plasmid bioproduction in Escherichia coli DH5α cultures over different carbon-source compositionsPublication . Lopes, Marta B.; Martins, Gabriel; Calado, CecíliaThe need for the development of economic high plasmid production in Escherichia coli cultures is emerging, as a result of the latest advances in DNA vaccination and gene therapy. In order to contribute to achieve that, a model describing the kinetics involved in the bioproduction of plasmid by recombinant E. coli DH5α is presented, as an attempt to understand the complex and non-linear metabolic relationships and the plasmid production occurring in dynamic batch culture environments, run under different media compositions of glucose and glycerol, that result in distinct maximum biomass growths (between 8.2 and 12.8 g DCW/L) and specific plasmid productions (between 1.1 and 7.4 mg/g DCW). The model based on mass balance equations for biomass, glucose, glycerol, acetate and plasmid accurately described different culture behaviors, using either glucose or glycerol as carbon source, or mixtures of both. From the 17 parameters obtained after model simplification, the following 10 parameters were found to be independent of the carbon source composition: the substrate affinity constants, the inhibitory constants of biomass growth on glycerol by glucose, of biomass growth on acetate by glycerol and the global biomass growth by acetate, and the yields of biomass on acetate, acetate on glucose and glycerol, and plasmid on glucose. The parameters that depend on the culture composition, and that might explain the differences found between cultures, were: maximum specific growth rates on glucose, glycerol and acetate; biomass yield on glucose and glycerol; and plasmid yield on glycerol and acetate. Moreover, a crucial role of acetate in the plasmid production was revealed by the model, with most of plasmid production being associated to the acetate consumption. The model provides meaningful insight on the E. coli dynamic cell behavior concerning the plasmid bioproduction, which might lead to important guidelines for culture optimization and process scale-up and control.
- Modelling, monitoring and control of plasmid bioproduction in Escherichia coli culturesPublication . Lopes, Marta B.; Scholtz, Teresa; Silva, Daniel; Santos, Inês; Silva, Tito; Sampaio, Pedro; Couto, Andreia; Lopes, Vitor V.; Calado, CecíliaAn integrated approach for modelling, monitoring and control the plasmid bioproduction in Escherichia coli cultures is presented. In a first stage, by the implementation of a kinetic model for E. coli cultures, a better bioprocess understanding was reached, concerning the availability of nutrients and products along the bioprocess, and their effects on the plasmid production. Results presented may provide significant help for future modelling and monitoring implementation. In a second stage, FTIR spectroscopy coupled with chemometrics, namely PLS regression, shows its potential as a high-throughput technique for simultaneously estimating the key variables involved in the plasmid production process by E. coli cultures run under distinct conditions. Finally, owing to online monitoring and process control, an NIR fibre optic probe and chemometrics provided promising results concerning the control of biomass and carbon sources in E. coli cultures.
- Monitoring the ex-vivo expansion of human mesenchymal stem/stromal cells in xeno-free microcarrier-based reactor systems by MIR spectroscopyPublication . Rosa, Filipa; Sales, Kevin C.; Carmelo, Joana G.; Fernandes-Platzgummer, Ana; Silva, Cláudia L. da; Lopes, Marta B.; Calado, CecíliaHuman mesenchymal stem/stromal cells (MSCs) have received considerable attention in the field of cell-based therapies due to their high differentiation potential and ability to modulate immune responses. However, since these cells can only be isolated in very low quantities, successful realization of these therapies requires MSCs ex-vivo expansion to achieve relevant cell doses. The metabolic activity is one of the parameters often monitored during MSCs cultivation by using expensive multi-analytical methods, some of them time-consuming. The present work evaluates the use of mid-infrared (MIR) spectroscopy, through rapid and economic high-throughput analyses associated to multivariate data analysis, to monitor three different MSCs cultivation runs conducted in spinner flasks, under xeno-free culture conditions, which differ in the type of microcarriers used and the culture feeding strategy applied. After evaluating diverse spectral preprocessing techniques, the optimized partial least square (PLS) regression models based on the MIR spectra to estimate the glucose, lactate and ammonia concentrations yielded high coefficients of determination (R2 ≥ 0.98, ≥0.98, and ≥0.94, respectively) and low prediction errors (RMSECV ≤ 4.7%, ≤4.4% and ≤5.7%, respectively). Besides PLS models valid for specific expansion protocols, a robust model simultaneously valid for the three processes was also built for predicting glucose, lactate and ammonia, yielding a R2 of 0.95, 0.97 and 0.86, and a RMSECV of 0.33, 0.57, and 0.09 mM, respectively. Therefore, MIR spectroscopy combined with multivariate data analysis represents a promising tool for both optimization and control of MSCs expansion processes.
- Real-time plasmid monitoring of batch and fed-batch Escherichia coli cultures by NIR spectroscopyPublication . Lopes, Marta B.; Sales, Kevin C.; Lopes, Vítor V.; Calado, CecíliaThe development of in-situ monitoring techniques enabling the real-time acquisition of information concerning the key variables over different Escherichia coli cultivation conditions and strategies is a crucial step towards the optimization of a plasmid bioproduction process. This work shows the use of a Near-InfraRed (NIR) fiber optic probe immersed in the culture broth for the real-time acquisition of NIR spectra along different E. coli cultures conducted with mixtures of the carbon sources glucose and glycerol, and performed in both batch and fed-batch modes. Accurate partial least squares models based on the acquired spectral data over such different cultivation conditions were built, yielding a R 2 = 0.97 for biomass and plasmid productions and a RMSEP of 0.34 and 7.52, respectively; a R 2 of 0.93 and a RMSEP of 0.46 and 0.33 was obtained for glucose and glycerol, respectively; the acetate model produced a R 2 of 0.96 and a RMSEP of 0.32.