Our team has been working together since 2012. During the years members of our group have collaborated with local Latvian scientific as well as international groups in various scientific projects. We have worked on several different organisms from a computational biology modelling perspective, in order to improve the biotechnological potential of sustainable and green production for high value products, enrich and upgrade bio-degradation technologies, researched and analysed plant bioprocesses, stress tolerance and the potential of secondary by-product reuse and much more
Many microorganisms have a large industrial potential in biotechnology, health, pharmacy, agriculture. We believe that all these industries can benefit from a greener and more sustainable future, considering economically feasible zero waste technologies and applications. Especially, knowing that computational biology has already demonstrated its success and significance for many industries so far and can still offer much benefit to many conventional industry processes which must be evolved for the sake of a sustainable future.
Our team has an extensive and well-established experience in supporting and collaborating on the analysis of biological processes for many different microorganisms by modelling as well as predicting stress tolerance and revealing new high value chemical production applications. We have developed, improved and created several metabolic models for Zymomonas mobilis, Kluyveromyces marxianus, Saccharomyces cerevisiae, Escherichia coli, Rhodotorula glutinis and others.
We have participated in:
- Analysis of biotechnological potential;
- Prediction of biomass precursors impact on growth;
- Optimisation of metabolic flux shifts for different purposes and applications;
- Optimization of diets, growth and environmental impact on organisms;
- Analysis of stress tolerance;
- Analysis of carbon, nitrogen and ion impact on organism’s growth and production yields;
- Optimization of organism’s energetic requirements for different biological processes.
And much more …
Plant and Algae
Plants and algae are most commonly considered photosynthetic eukaryotic organisms which account for more than 80 % of all total earth biomass, are a major food source in the animal kingdom, major oxygen bio producer on earth, controls water, carbon, nitrogen and other major chemical cycles. However, most plants and algae are sensitive to environmental changes and different stresses. Thus, our group have payed specific attention to plant and algae bioprocess modelling.
We have gained experience on plant and algae computational biology modelling, where we focused on multi-compartmentation biological process analysis in stress and the impact of substrate composition change:
- We have developed a Solanum lycopersicum fruit kinetic metabolic model for prediction of ripening stages and highlighted the potential of metabolic profiling control.
- We have developed and analysed high bush blueberry (Vaccinium corymbosum) multi – compartment metabolic model and researched the anthocyanins production potential in later fruit ripening stages.
- We have developed multi-compartmented Arabidopsis thaliana metabolic model and analysed the potential of new synthetic signalling pathway genetic engineering to increase the plant by-products commercial value.
We have developed red algae Galdieria sulphuraria metabolic model to predict the best agricultural residue composition consumption potential for maximizing the quantity of proteins and fatty acids in algae.
Insects for long time have been a rich protein source for humans and animals. However, they have been insufficiently studied for applications in pollution degradation, ecology, waste recycling, human health etc. Our group sees the great potential and need of the insect application.
We have developed the Hermetia illucens larvae metamorphism stage metabolic model to predict the impact of different diets and substrates on resource allocation to other body parts of larvae. This will support the increase of larvae yield in field experiments, as well as the generation of more precise data for cost calculations and help finetune the substrate diet composition.
Computational Biology Software
Computational modelling has become a required step in any industrial application, which facilitates and automates processes, predict results and even recommends new hypothesis, methods and monitor the development processes.
Our group have developed several tools which help the scientific community to analyse biological datasets:
- IMFLer static single-page web application that enables the reading and management of metabolic model layout maps, as well as immediate visualization of results from both FBA and flux variability analysis (FVA).;
- IgemRNA transcriptomics and metabolomics data integration optimisation and analysis tool in Matlab compatible with Cobra Toolbox 3.0;
- SpaceScanner is a COPASI wrapper for the automated management of global stochastic optimization experiments.
- ConvAn is a convergence analyzing tool for optimization of biochemical networks