Welcome & What can we offer
In Department of Adaptive Biotechnologies (DoAB), affiliated to the Centrum for System Biology (C4Sys), we combine advanced experimental methods and systems biology approaches to research photosynthetic microorganisms and their interactions with environment. The aim of Department activities is to search for microorganisms that have metabolic pathways leading to production or even secretion of energy-rich valuable biocompounds and substances that are ideally genetically transformable. This requires proper selection and management of cultivation technology that allows long-term viable culturing. We are developing platforms and methods for characterization and optimization of photosynthetic microorganisms in simulated (aquatic) environment of photobioreactors that allows to explore perspective of selected microorganisms for use in biotechnologies. In particular, we focus on investigation of their primary production and carbon sequestration capacity, investigation of stress and adaptation mechanisms, and other physiological and biochemical properties. Essential part of the platform is fluorescence activated cell sorting that extends the capacity of the platform towards controlled evolution/breeding of various microorganisms. Methods and protocols for fluorescence staining specific for light sensitive photosynthetic microorganisms are designed with respect to staining limitations (extracellular polysaccharides formation, membrane/ cell wall permeability, etc.). The methods and protocols allow routine analyses such as quantification of cell morphological properties, quantification of physiological parameters like cell viability and DNA topology, and identification of lipid droplets formation. All data generated using these methods contain single cell level information from statistically significant sample of thousands cells per sample.
How can you access
General questions
Scientific Secretary: Petra Literáková (literakova.p@czechglobe.cz)
Head: Jan Červený (cerveny.j@czechglobe.cz)
Staff: Diana Búzová, Dominik Chmelík, Iveta Jedličková, Anna Segečová, Kateřina Svobodová, Tomáš Zavřel
Address: Drásov 470, 66424 Drásov, Czech Republic
Web-services on-line
Tidy Up PBR Data
Tool for advanced manipulation with complex data generated by PSI Photobioreactor sofware. The data uploaded to this tool are expected in CSV (or TSV) multi-column format, containing each column description in the first row. Most simple untidy data preparation procedure is to export data from the software in ODS format and then export last Data sheet as CSV file in Excel.
In general this tool can be used on any numeric data table, e.g. for large datasets averaging, etc.
URL: https://gcri-doab.shinyapps.io/TidyUpPBRData/
Scripts for algorithmization of growth characterization
Set of open access scripts developed for automatic characterization of microbial suspensions using standardized PSI Photobioreactor software. The code that enables automatization functionality in PSI Photobioreactor software has been developed as an open source and is available together with other growth characterization algorithms on following web page.
URL: https://gcri-doab.github.io/PBR-Scripts/
Instruments and platforms access
Experimental platform for the characterization and optimization of microalgae
As an essential part of the experimental platform for the characterization and optimization of microalgae, flat-panel photobioreactors are used for strain cultivation and real-time monitoring. As a light source in this type of photobioreactor, light emitting diodes (LEDs) designed in a chessboard configuration either combining white and red LEDs to simulate natural conditions or red and blue LEDs to address biotechnologically relevant light use profiles of the most abundant photosynthetic pigments are used. The photobioreactor capacity allows the measurement of optical density of the suspension by an integrated densitometer and the steady state pigment fluorescence emission yield by a built-in fluorometer. Photosynthesis related gasses, carbon dioxide and dioxygen are measured in their dissolved forms. Temperature is controlled by a Peltier thermoelectric cell which is incorporated in the instrument base and is in direct contact with the cultivation vessel via a thermal bridge. Culture homogenization within the cultivation vessel is secured by a combination of inflow gas bubbling and the rotation of a magnetic stirrer bar in the vertical plane of the vessel. Additional photobioreactor accessories such as a system for the precise preparation of gas mixtures and a system for the dynamic gas mixture concentration analyses are accessible as an integrative part of the platform.
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High-throughput single cell level characterization
In addition to whole population monitoring in photobioreactors, the platform uses the capacity of high-throughput imaging flow cytometry that combines the quantitative power of large sample sizes, common to flow cytometry techniques, with the information content of super-speed planar microscopy. This enables the statistical analyses of entire populations with the capability to focus at the single cell level. These approaches not only allow the analysis of individual cells in all populations, but allow the documentation of various cellular features and the analysis of gene expression.
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Membrane Inlet Mass Spectrometer (MIMS) Gas Analyzer
Application of membrane inlet mass spectrometry (MIMS) for analysis of gases in both aquatic and gaseous environments allows the parallel quantification of a multitude of gases on a time scale of a few seconds. Whereas in environmental research MIMS is also very successfully applied in soil sciences or in studies on microbial turnover processes. The utilization of MIMS in combination with capacity of experimental platform for characterization and optimization provides an elegant solution for fast and precise real-time measurement of volatile products accumulation and dynamics during whole culturing process.
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Other C4Sys Open Access Infrastructure available on request:
- High volume centrifuge (Cell Biology Instrument)
- Real-time PCR cycler (Molecular Biology Instruments)
- Horizontal and vertical electrophoresis gel systems (Molecular Biology Instruments)
- Gel and blot imaging and analysis system (Molecular Biology Instruments)
- Microplate reader (Cell Biology Instrument)
- Lyophilisator/Freeze-Dryer (Cell Biology Instrument)
- Large volume growth chambers (Cell Biology Instrument)
- Microbiological incubators (Cell Biology Instrument)