Additional file 1. Additional line graphs, spider graphs, PCA biplots and table of PCA loadings f... more Additional file 1. Additional line graphs, spider graphs, PCA biplots and table of PCA loadings for all tested concentrations and time points, visual effects on representative samples, flowchart of experimental design and scheme of data organization and inputs used for analyses.
Computational and Structural Biotechnology Journal, 2021
The photoautotrophic, unicellular N2-fixer, Cyanothece, is a model organism that has been widely ... more The photoautotrophic, unicellular N2-fixer, Cyanothece, is a model organism that has been widely used to study photosynthesis regulation, the structure of photosystems, and the temporal segregation of carbon (C) and nitrogen (N) fixation in light and dark phases of the diel cycle. Here, we present a simple quantitative model and experimental data that together, suggest external dissolved inorganic carbon (DIC) concentration as a major limiting factor for Cyanothece growth, due to its high C-storage requirement. Using experimental data from a parallel laboratory study as a basis, we show that after the onset of the light period, DIC was rapidly consumed by photosynthesis, leading to a sharp drop in the rate of photosynthesis and C accumulation. In N2-fixing cultures, high rates of photosynthesis in the morning enabled rapid conversion of DIC to intracellular C storage, hastening DIC consumption to levels that limited further uptake. The N2-fixing condition allows only a small fraction of fixed C for cellular growth since a large fraction was reserved in storage to fuel night-time N2 fixation. Our model provides a framework for resolving DIC limitation in aquatic ecosystem simulations, where DIC as a growth-limiting factor has rarely been considered, and importantly emphasizes the effect of intracellular C allocation on growth rate that varies depending on the growth environment.
Comprehensive Modelling Platform is a general framework for public sharing, annotation, and visua... more Comprehensive Modelling Platform is a general framework for public sharing, annotation, and visualisation of domain-specific biological models. For a selected system (e.g. an organism, particular process), the framework is instantiated as a web-based application which allows capturing several aspects of biological models represented as biochemical reaction networks or ordinary differential equations.
The workshop "Cyanobacterium in silico 2015" of the international CyanoNetwork is the c... more The workshop "Cyanobacterium in silico 2015" of the international CyanoNetwork is the closing event of the local CyanoTeam project which has been running in Brno since 2012. The workshop serves two purposes: - to share the results of the CyanoTeam project with leading experts in the field. - to present current and stimulate future collaborations within CyanoNetwork. Invited researchers from related fields will present their research interests.
Biochemical Space (BCS) is a novel framework for practical description of complex biological proc... more Biochemical Space (BCS) is a novel framework for practical description of complex biological processes. It is developed as a part of Comprehensive Modelling Platform (CMP) -- a web-based platform for modelling and analysis of biological processes. In the context of CMP, Biochemical Space glues together complicated quantitative models with an easy-to-understand but yet formal and compact qualitative description. BCS allows to specify formal and well-annotated reaction networks of chemical entities and elemental reactions onto which the mathematical models are projected. BCS is supported by a Biochemical Space Language (BCSL) that combines state-of-the-art rule-based techniques with meta-data formats developed in well-known annotation databases.
Cyanobacteria have gained increased attention as ideal candidates for biotechnological applicatio... more Cyanobacteria have gained increased attention as ideal candidates for biotechnological applications due to their capacity to produce valuable molecules ranging from therapeutic proteins to biofuels. Their natural phenotypic plasticity in highly dynamic environments allows easy deployment of new biotechnologies as well as open possibility for genetic engineering. Here, we present new approach to fast and reliable characterization of cyanobacteria growth in a flat panel photobioreactor examined for changing light, temperature, inorganic carbon and other nutrients availability. The utilization of semi-continuous automatic cultivation with real-time culture growth monitoring provides strong experimental base for both characterization and optimization of cyanobacteria cultures in photobioreactors. At first, we characterized autotrophic growth of Synechocystis sp. PCC 6803 strain denoted as GT-L1,2. This strain is capable of efficient growth under wide range of environmental conditions wi...
The aim of our study is to find optimal conditions for cultivation of photoautotrophic (PA) plant... more The aim of our study is to find optimal conditions for cultivation of photoautotrophic (PA) plant cell cultures in photobioreactors (PBRs) originally designed for microalgae. Plant suspension cultures represent reduced model of a complex system of higher plants. They are used in biotechnology for production of secondary metabolites. They consist of single cells forming uniform population directly accessible to exogenous stimuli, which makes them ideal for experimental use. However, they need CO2 as a carbon source for their growth that makes the cultivation of PA cultures somewhat complicated. PBRs provide variable settings of light composition and intensity, temperature, and additional stirring; online monitoring of cultivation parameters; sterile cultivation conditions; CO2 enriched atmosphere. In addition, PBR enable upscale of culture’s working volume (from regular 70 mL up to 400 mL) providing A) enough homogenous material for consequent experiments, B) intermediate step in adv...
Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communitie... more Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the r...
Additional file 1. Additional line graphs, spider graphs, PCA biplots and table of PCA loadings f... more Additional file 1. Additional line graphs, spider graphs, PCA biplots and table of PCA loadings for all tested concentrations and time points, visual effects on representative samples, flowchart of experimental design and scheme of data organization and inputs used for analyses.
Computational and Structural Biotechnology Journal, 2021
The photoautotrophic, unicellular N2-fixer, Cyanothece, is a model organism that has been widely ... more The photoautotrophic, unicellular N2-fixer, Cyanothece, is a model organism that has been widely used to study photosynthesis regulation, the structure of photosystems, and the temporal segregation of carbon (C) and nitrogen (N) fixation in light and dark phases of the diel cycle. Here, we present a simple quantitative model and experimental data that together, suggest external dissolved inorganic carbon (DIC) concentration as a major limiting factor for Cyanothece growth, due to its high C-storage requirement. Using experimental data from a parallel laboratory study as a basis, we show that after the onset of the light period, DIC was rapidly consumed by photosynthesis, leading to a sharp drop in the rate of photosynthesis and C accumulation. In N2-fixing cultures, high rates of photosynthesis in the morning enabled rapid conversion of DIC to intracellular C storage, hastening DIC consumption to levels that limited further uptake. The N2-fixing condition allows only a small fraction of fixed C for cellular growth since a large fraction was reserved in storage to fuel night-time N2 fixation. Our model provides a framework for resolving DIC limitation in aquatic ecosystem simulations, where DIC as a growth-limiting factor has rarely been considered, and importantly emphasizes the effect of intracellular C allocation on growth rate that varies depending on the growth environment.
Comprehensive Modelling Platform is a general framework for public sharing, annotation, and visua... more Comprehensive Modelling Platform is a general framework for public sharing, annotation, and visualisation of domain-specific biological models. For a selected system (e.g. an organism, particular process), the framework is instantiated as a web-based application which allows capturing several aspects of biological models represented as biochemical reaction networks or ordinary differential equations.
The workshop "Cyanobacterium in silico 2015" of the international CyanoNetwork is the c... more The workshop "Cyanobacterium in silico 2015" of the international CyanoNetwork is the closing event of the local CyanoTeam project which has been running in Brno since 2012. The workshop serves two purposes: - to share the results of the CyanoTeam project with leading experts in the field. - to present current and stimulate future collaborations within CyanoNetwork. Invited researchers from related fields will present their research interests.
Biochemical Space (BCS) is a novel framework for practical description of complex biological proc... more Biochemical Space (BCS) is a novel framework for practical description of complex biological processes. It is developed as a part of Comprehensive Modelling Platform (CMP) -- a web-based platform for modelling and analysis of biological processes. In the context of CMP, Biochemical Space glues together complicated quantitative models with an easy-to-understand but yet formal and compact qualitative description. BCS allows to specify formal and well-annotated reaction networks of chemical entities and elemental reactions onto which the mathematical models are projected. BCS is supported by a Biochemical Space Language (BCSL) that combines state-of-the-art rule-based techniques with meta-data formats developed in well-known annotation databases.
Cyanobacteria have gained increased attention as ideal candidates for biotechnological applicatio... more Cyanobacteria have gained increased attention as ideal candidates for biotechnological applications due to their capacity to produce valuable molecules ranging from therapeutic proteins to biofuels. Their natural phenotypic plasticity in highly dynamic environments allows easy deployment of new biotechnologies as well as open possibility for genetic engineering. Here, we present new approach to fast and reliable characterization of cyanobacteria growth in a flat panel photobioreactor examined for changing light, temperature, inorganic carbon and other nutrients availability. The utilization of semi-continuous automatic cultivation with real-time culture growth monitoring provides strong experimental base for both characterization and optimization of cyanobacteria cultures in photobioreactors. At first, we characterized autotrophic growth of Synechocystis sp. PCC 6803 strain denoted as GT-L1,2. This strain is capable of efficient growth under wide range of environmental conditions wi...
The aim of our study is to find optimal conditions for cultivation of photoautotrophic (PA) plant... more The aim of our study is to find optimal conditions for cultivation of photoautotrophic (PA) plant cell cultures in photobioreactors (PBRs) originally designed for microalgae. Plant suspension cultures represent reduced model of a complex system of higher plants. They are used in biotechnology for production of secondary metabolites. They consist of single cells forming uniform population directly accessible to exogenous stimuli, which makes them ideal for experimental use. However, they need CO2 as a carbon source for their growth that makes the cultivation of PA cultures somewhat complicated. PBRs provide variable settings of light composition and intensity, temperature, and additional stirring; online monitoring of cultivation parameters; sterile cultivation conditions; CO2 enriched atmosphere. In addition, PBR enable upscale of culture’s working volume (from regular 70 mL up to 400 mL) providing A) enough homogenous material for consequent experiments, B) intermediate step in adv...
Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communitie... more Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the r...
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Papers by Jan Červený