Research at Group BIOSYSTEMS

The BIOSYSTEMS group uses competences in systems biotechnology and bioengineering to foster the development of a knowledge-based bio-economy, leading to new added-value products and processes. BIOSYSTEMS group comprises 18 integrated PhD members, 26 PhD students and 21 other researchers divided into 4 sub-groups, corresponding to specific scientific domains:

Research Labs

1 The Bioinformatics and Systems Biology Bioinformatics and Systems Biology team develops computational tools for metabolic model construction, simulation and optimization, and automatic retrieval of relevant information laying in the literature (text miming). An important topic deals with the development of Evolutionary methods for strain optimization. Other topics relate to database integration, gene expression and metabolomics data analysis and mining. The main applications include the identification of targets for metabolic engineering, aiming at the construction of improved cellular factories for the production of succinic, fumaric or amino acids, and the model-driven physiological characterization of pathogens (such as H. pylori or S. faecalis) and the identification for drug targets for unmet health concerns.

2 The Synthetic Biology The Bioinformatics and Systems Biology two main research lines are being developed: the design of new pathways in E. coli and C. pasteurianum, with new and/or improved functions towards the triggered production of curcumin and butanol, and the engineering of new carriers (viral particles) and molecules (aptamers and peptides) for targeting and treatment of cancer. Ongoing research includes: engineering a novel biosynthetic pathway for the production of curcuminoids in E. coli; development of tools for the genetic manipulation of C. pasteurianum; selection and isolation of new molecules with high affinity to cancer cells; development of a phage-based nanocarrier for cancer treatment and diagnosis.

3 The Monitoring and control of bioprocesses Monitoring and control of bioprocesses includes the design of software sensors for state and parameter estimation; Process Analytical Technology solutions for bioprocess characterization; and the development of image analysis procedures and chemometrics tools. Ongoing research includes: image analysis techniques to characterize the biomass morphology and physiology, and to characterize the main groups of bacteria present in biological wastewater treatment; chemometric techniques, combined with spectroscopy techniques and image analysis tools, for supervision, prediction and control of biological wastewater treatment and biotechnological processes; electronic tongues for goat milk adulterations, gliadins detection in foodstuffs and for monitoring cork contaminants.

4 The Bioprocess development and optimization Bioprocess development and optimization research line the activities are focused in the improvement of bioprocesses based in fungi cultures, by operating conditions optimization and bioreactor type selection. Aerobic cultures of different yeast species have been studied, through cell physiology characterization under stressful conditions in bioreactor environment and by O2 mass transfer phenomena characterization and modeling, with particular interest in complex systems with biphasic liquid culture media. Y. lipolytica has been used as a cell model, and it has been exploited applying the biorefinery concept for the production aroma, enzymes and organic acids, using low-cost renewable substrates.

Research Areas

1 Systems Biology of recombinant microorganisms

2 OptFlux - In Silico Metabolic Engineering Platform Simulation of metabolic networks and optimization of bacterial strains to attain industrial aims.

3 Merlin - In Silico Metabolic Engineering Platform

4 Mathematical and Computational Tools for Large-Scale Microbial Modelling

5 Biomedical Text Mining

6 Synthetic biology sensors

7 Monitoring of activated sludge processes

8 Protozoa in Wastewater Treatment Processes

9 Anaerobic Digestion

10 Other Applications of QIA in Biotechnology

11 Biotechnological application of Yarrowia lipolytica

12 Strategies of oxygen transfer rate improvement to microbial cultures: hyperbaric bioreactors

13 Up-grading of agro-industrial wastes

14 Synthetic biology approaches for engineering new pathways, functions and organisms

15 Bioprocess Modelling

16 Software Sensors

17 Control of Fermentation Processes