Department of Adaptive Biotechnologies

Ing. Jan Červený, Ph.D. – head
Scientists:
RNDr. Diana Búzová, Ph.D.
Bc. Terezie Danišová
Mgr. Lucie Kajan Grodecká, Ph.D.
Mgr. Petra Literáková
MFA David Šohaj Minařík
prof. Dr. Thomas Roitsch
Mgr. Roman Sándor, Ph.D.
Mgr. et Mgr. Anna Segečová, Ph.D.
Dr. Sopan Wagh
Mgr. Tomáš Zavřel, Ph.D.

Ph.D. students:
Mgr. Tomáš Zlámal

Others:
Iveta Jedličková

Motto:

“Our goal is to develop innovative biotechnological solutions using microalgae as effective cell factories that could be naturally incorporated into the daily activities of modern society and contribute to the sustainable development and prosperity of humankind without endangering the Earth’s resources.”

The work of the department combines advanced experimental techniques with systems biology approaches to investigate photosynthetic microorganisms and their interaction with the environment. The department’s activities aim to search for microorganisms (preferably the ones amenable to genetic transformation) that are provided with metabolic pathways leading to production or even secretion of energetically rich substances or substances with attractive bioactivity. The research line is focusing on investigation of stress and adaptive regulatory mechanisms as well as other physiological and biochemical properties of the identified microorganisms under conditions simulating a wide range of natural and industrial environments. For detailed description of the mechanisms and properties and also for optimization of value-added substance production capacity, we have developed an intelligent system for evolutionary optimization of biosystems that enables efficient characterization, phenotypization, genetic evolution (breeding) and optimization of photosynthetic microorganisms in simulated (aquatic) photobioreactor environment and facilitates research on microorganisms with respect to their potential for biotechnological applications. Linking the system with artificial intelligence-based approaches allows for advanced optimization of the developed biotechnological procedures, which are subsequently tested at pilot-scale using standardized and prototype photobioreactors.

In order to expand our understanding of dynamic behavior of complex biological systems (represented in this case by photosynthetic microorganisms), we have been developing a web-based platform for photosynthetic process modeling (www.e-photosynthesis.org and www.e-cyanobacterium.org) in collaboration with the Systems Biology Laboratory, Masaryk University in Brno, led by Dr. David Šafránek. The platform provides easy and intuitive navigation through the structure of photosynthetic systems, storage and presentation of wet-lab experiments and unified representation of related biological networks. The platform serves both as an educational and a research-oriented tool.

The above-mentioned research activities include establishment of a constantly expanding collection of fully characterized photosynthetic microorganisms for biotechnological applications, suitable for both basic and applied research.

Keywords:

bioproduction, bioprospecting, biotechnology, plant cell cultures, evolutionary algorithms, phenotypization, fluorescence, photobioreactors, photosynthetic microorganisms, optimization, microalgae, cyanobacteria, systems biology, breeding, toxicology, cell sorting, artificial intelligence, high-throughput analysis

The department’s main activities are:

Identification of strains suitable for production of selected value-added substances
Application of advanced experimental techniques along with systems biology approaches to investigate photosynthetic microorganisms and their interactions with the environment
Application of methods based on artificial intelligence and control theory for smart optimization and advanced automation to the developed biotechnological procedures
Detailed characterization of investigated biological systems under a wide range of culturing conditions including natural conditions, predictive scenarios and conditions related to global change and industrial processes
Studies of adaptive mechanism response to both optimal and extreme conditions
Optimization of production conditions with respect to limitations of real large scale/industrial cultivation settings
Application of controlled selective/evolutionary pressure (breeding) on different types of photosynthetic microorganisms aiming to raise their production capacity as well as their adaptivity to shifting environmental conditions
Sorting of mixed populations and selection of subpopulations with “on demand” properties
High-throughput fluorescence microscopy analysis of photosynthetic cultures at the single cell level
Establishment and maintenance of a collection of biotechnologically promising strains
Modeling of photosynthetic processes
Development and design of technological solutions for microalgal biotechnology
Development of a reference experimental platform for cross-laboratory validation experiments
Development of methods for characterization, phenotypization and intelligent optimization of production and adaptive properties of investigated strains
Development of methods and protocols customized for fluorescence marking of light-sensitive microorganisms
Development of methods for quantitative analysis of morphological properties of cells and their physiological parameters such as cell viability, DNA topology and characterization of lipid droplet formation
Development and optimization of high-throughput fluorescence methods for ecotoxicological studies of photosynthetic organisms
Development of a computational platform for simulation of predictive experiments (in silico)