Segečová, A, Pérez-Bueno, ML, Barón, M, Červený, J & Roitsch, TG 2019, 'Noninvasive determination of toxic stress biomarkers by high-throughput screening of photoautotrophic cell suspension cultures with multicolor fluorescence imaging.', Plant methods, vol. 15, no. 1.View/Download from: UTS OPUS or Publisher's site
Background:With increasing pollution, herbicide application and interest in plant phenotyping, sensors capturing early responses to toxic stress are demanded for screening susceptible or resistant plant varieties. Standard toxicity tests on plants are laborious, demanding in terms of space and material, and the measurement of growth-inhibition based endpoints takes relatively long time. The aim of this work was to explore the potential of photoautotrophic cell suspension cultures for high-throughput early toxicity screening based on imaging techniques. The investigation of the universal potential of fluorescence imaging methods involved testing of three toxicants with different modes of action (DCMU, glyphosate and chromium). Results:The increased pace of testing was achieved by using non-destructive imaging methods-multicolor fluorescence (MCF) and chlorophyll fluorescence (ChlF). These methods detected the negative effects of the toxicants earlier than it was reflected in plant growth inhibition (decrease in leaf area and final dry weight). Moreover, more subtle and transient effects not resulting in growth inhibition could be detected by fluorescence. The pace and sensitivity of stress detection was further enhanced by using photoautotrophic cell suspension cultures. These reacted sooner, more pronouncedly and to lower concentrations of the tested toxicants than the plants. Toxicant-specific stress signatures were observed as a combination of MCF and ChlF parameters and timing of the response. Principal component analysis was found to be useful for reduction of the collected multidimensional data sets to a few informative parameters allowing comparison of the toxicant signatures. Conclusions:Photoautotrophic cell suspension cultures have proved to be useful for rapid high-throughput screening of toxic stress and display a potential for employment as an alternative to tests on whole plants. The MCF and ChlF methods are capable of distinguishing early stress sig...
Sukačová, K, Búzová, D, Trávníček, P, Červený, J, Vítězová, M & Vítěz, T 2019, 'Optimization of microalgal growth and cultivation parameters for increasing bioenergy potential: Case study using the oleaginous microalga Chlorella pyrenoidosa Chick (IPPAS C2)', Algal Research, vol. 40.View/Download from: UTS OPUS or Publisher's site
© 2019 The aim of the presented research was application of optimized cultivation conditions for lipid production using the oleaginous microalga Chlorella pyrenoidosa Chick (IPPAS C2), followed by an assessment of the bioenergy potential of lipid-rich biomass and biomethane production. The optimization of cultivation parameters led to an increase in lipid production. The average and maximum lipid production for C. pyrenoidosa was 101 ± 22 mg.L −1 .D −1 and 126 mg.L −1 .D −1 , respectively. The average calorific value of the lipid rich-biomass was 27.56 ± 0.93 MJ.kg −1 . However, the recorded biomethane yield of 0.16 ± 0.006 m 3 .kg −1 VS, caused probably by low digestibility of C. pyrenoidosa and by short hydraulic retention time during anaerobic digestion, was interpreted as low. However, the high lipid content along with high calorific value indicated an increased bioenergy potential of microalgal biomass cultivated under the optimized cultivation parameters.
Zavřel, T, Faizi, M, Loureiro, C, Poschmann, G, Stühler, K, Sinetova, M, Zorina, A, Steuer, R & Červený, J 2019, 'Quantitative insights into the cyanobacterial cell economy.', eLife, vol. 8.View/Download from: UTS OPUS or Publisher's site
Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.
Segecova, A, Cerveny, J & Roitsch, T 2018, 'Advancement of the cultivation and upscaling of photoautotrophic suspension cultures using Chenopodium rubrum as a case study', PLANT CELL TISSUE AND ORGAN CULTURE, vol. 135, no. 1, pp. 37-51.View/Download from: UTS OPUS or Publisher's site
Faizi, M, Zavrel, T, Loureiro, C, Cerveny, J & Steuer, R 2018, 'A model of optimal protein allocation during phototrophic growth', BIOSYSTEMS, vol. 166, pp. 26-36.View/Download from: UTS OPUS or Publisher's site
Zavrel, T, Chmelik, D, Sinetova, MA & Cerveny, J 2018, 'Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium Synechocystis', JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, no. 139.View/Download from: Publisher's site
Zavřel, T, Faizi, M, Loureiro, C, Poschmann, G, Stühler, K, Sinetova, M, Zorina, A, Steuer, R & Červený, J 2018, 'Quantitative insights into the cyanobacterial cell economy'.View/Download from: Publisher's site
Abstract Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological adaptations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial adaptations to different growth rates have implications to understand and optimize photosynthetic productivity.
Zavřel, T, Szabó, M, Tamburic, B, Evenhuis, C, Kuzhiumparambil, U, Literáková, P, Larkum, AWD, Raven, JA, Červený, J & Ralph, PJ 2018, 'Effect of carbon limitation on photosynthetic electron transport in Nannochloropsis oculata.', Journal of photochemistry and photobiology. B, Biology, vol. 181, pp. 31-43.View/Download from: UTS OPUS or Publisher's site
This study describes the impacts of inorganic carbon limitation on the photosynthetic efficiency and operation of photosynthetic electron transport pathways in the biofuel-candidate microalga Nannochloropsis oculata. Using a combination of highly-controlled cultivation setup (photobioreactor), variable chlorophyll a fluorescence and transient spectroscopy methods (electrochromic shift (ECS) and P700 redox kinetics), we showed that net photosynthesis and effective quantum yield of Photosystem II (PSII) decreased in N. oculata under carbon limitation. This was accompanied by a transient increase in total proton motive force and energy-dependent non-photochemical quenching as well as slightly elevated respiration. On the other hand, under carbon limitation the rapid increase in proton motive force (PMF, estimated from the total ECS signal) was also accompanied by reduced conductivity of ATP synthase to protons (estimated from the rate of ECS decay in dark after actinic illumination). This indicates that the slow operation of ATP synthase results in the transient build-up of PMF, which leads to the activation of fast energy dissipation mechanisms such as energy-dependent non-photochemical quenching. N. oculata also increased content of lipids under carbon limitation, which compensated for reduced NAPDH consumption during decreased CO2 fixation. The integrated knowledge of the underlying energetic regulation of photosynthetic processes attained with a combination of biophysical methods may be used to identify photo-physiological signatures of the onset of carbon limitation in microalgal cultivation systems, as well as to potentially identify microalgal strains that can better acclimate to carbon limitation.
Abstract Photoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function, typically reduces the proteome available for other cellular functions. Here, we develop a minimal semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation. The model is parametrized using literature data and experimentally obtained growth curves. Of particular interest are the resulting cyanobacterial growth laws as fundamental characteristics of cellular growth. We show that the model gives rise to similar growth laws as observed for heterotrophic organisms, with several important differences due to the distinction between light energy and carbon uptake. We discuss recent experimental data supporting the model results and show that minimal growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.
Sukačová, K & Červený, J 2017, 'Can algal biotechnology bring effective solution for closing the phosphorus cycle? Use of algae for nutrient removal - Review of past trends and future perspectives in the context of nutrient recovery', European Journal of Environmental Sciences, vol. 7, no. 1, pp. 63-72.View/Download from: Publisher's site
© 2017 The Author. Eutrophication of water by nutrient pollution is a global environmental issue. Biological methods for removing nutrients are environmentally friendly and sustainable. Therefore, this article summarizes main trends in the use of algae for removing nutrients from wastewater using both suspended and attached algal-based systems. A wide variety of algal species and experimental approaches has been tested to date. Researchers report that algae are able to effectively remove a variety of pollutants and nutrients. This review also discusses the potential of algal-based technology for nutrient, especially phosphorus, recovery. Despite the fact that effective nutrient removal has been demonstrated, there are still many challenges to be overcome in the development of succesfull technologies.
Zavrel, T, Ocenasova, P & Cerveny, J 2017, 'Phenotypic characterization of Synechocystis sp PCC 6803 substrains reveals differences in sensitivity to abiotic stress', PLOS ONE, vol. 12, no. 12.View/Download from: UTS OPUS or Publisher's site
Zavrel, T, Knoop, H, Steuer, R, Jones, PR, Cerveny, J & Trtilek, M 2016, 'A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry', BIORESOURCE TECHNOLOGY, vol. 202, pp. 142-151.View/Download from: Publisher's site
Červený, J, Sinetova, MA, Zavřel, T & Los, DA 2015, 'Mechanisms of high temperature resistance of Synechocystis sp. PCC 6803: An Impact of histidine kinase 34', Life, vol. 5, no. 1, pp. 676-699.View/Download from: Publisher's site
© 2015 by the authors; licensee MDPI, Basel, Switzerland. Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying responses and acclimation to different abiotic stresses. Changes in transcriptome, proteome, lipidome, and photosynthesis in response to short term heat stress are well studied in this organism, and histidine kinase 34 (Hik34) is shown to play an important role in mediating such response. Corresponding data on long term responses, however, are fragmentary and vary depending on parameters of experiments and methods of data collection, and thus are hard to compare. In order to elucidate how the early stress responses help cells to sustain long-term heat stress, as well as the role of Hik34 in prolonged acclimation, we examined the resistance to long-term heat stress of wild-type and ΔHik34 mutant of Synechocystis. In this work, we were able to precisely control the long term experimental conditions by cultivating Synechocystis in automated photobioreactors, measuring selected physiological parameters within a time range of minutes. In addition, morphological and ultrastructural changes in cells were analyzed and western blotting of individual proteins was used to study the heat stress-affected protein expression. We have shown that the majority of wild type cell population was able to recover after 24 h of cultivation at 44 °C. In contrast, while ΔHik34 mutant cells were resistant to heat stress within its first hours, they could not recover after 24 h long high temperature treatment. We demonstrated that the early induction of HspA expression and maintenance of high amount of other HSPs throughout the heat incubation is critical for successful adaptation to long-term stress. In addition, it appears that histidine kinase Hik34 is an essential component for the long term high temperature resistance.
Zavrel, T, Sinetova, MA, Buzova, D, Literakova, P & Cerveny, J 2015, 'Characterization of a model cyanobacterium Synechocystis sp PCC 6803 autotrophic growth in a flat-panel photobioreactor', ENGINEERING IN LIFE SCIENCES, vol. 15, no. 1, pp. 122-132.View/Download from: Publisher's site
Cerveny, J, Sinetova, MA, Valledor, L, Sherman, LA & Nedbal, L 2013, 'Ultradian metabolic rhythm in the diazotrophic cyanobacterium Cyanothece sp ATCC 51142', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 110, no. 32, pp. 13210-13215.View/Download from: Publisher's site
Sinetova, MA, Cerveny, J, Zavrel, T & Nedbal, L 2012, 'On the dynamics and constraints of batch culture growth of the cyanobacterium Cyanothece sp ATCC 51142', JOURNAL OF BIOTECHNOLOGY, vol. 162, no. 1, pp. 148-155.View/Download from: Publisher's site
Safranek, D, Cerveny, J, Klement, M, Pospisilova, J, Brim, L, Lazar, D & Nedbal, L 2011, 'E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes', BIOSYSTEMS, vol. 103, no. 2, pp. 115-124.View/Download from: Publisher's site
Korecko, J, Jirka, V, Sourek, B & Cerveny, J 2010, 'Module greenhouse with high efficiency of transformation of solar energy, utilizing active and passive glass optical rasters', SOLAR ENERGY, vol. 84, no. 10, pp. 1794-1808.View/Download from: Publisher's site
Nedbal, L, Cerveny, J, Keren, N & Kaplan, A 2010, 'Experimental validation of a nonequilibrium model of CO2 fluxes between gas, liquid medium, and algae in a flat-panel photobioreactor', JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, vol. 37, no. 12, pp. 1319-1326.View/Download from: Publisher's site
Cerveny, J & Nedbal, L 2009, 'Metabolic Rhythms of the Cyanobacterium Cyanothece sp ATCC 51142 Correlate with Modeled Dynamics of Circadian Clock', JOURNAL OF BIOLOGICAL RHYTHMS, vol. 24, no. 4, pp. 295-303.View/Download from: Publisher's site
Cerveny, J, Setlik, I, Trtilek, M & Nedbal, L 2009, 'Photobioreactor for cultivation and real-time, in-situ measurement of O-2 and CO2 exchange rates, growth dynamics, and of chlorophyll fluorescence emission of photoautotrophic microorganisms', ENGINEERING IN LIFE SCIENCES, vol. 9, no. 3, pp. 247-253.View/Download from: Publisher's site
Nedbal, L, Trtilek, M, Cerveny, J, Komarek, O & Pakrasi, HB 2008, 'A photobioreactor system for precision cultivation of photoautotrophic microorganisms and for high-content analysis of suspension dynamics', BIOTECHNOLOGY AND BIOENGINEERING, vol. 100, no. 5, pp. 902-910.View/Download from: Publisher's site
Nedbal, L, Cerveny, J, Rascher, U & Schmidt, H 2007, 'E-photosynthesis: a comprehensive modeling approach to understand chlorophyll fluorescence transients and other complex dynamic features of photosynthesis in fluctuating light', PHOTOSYNTHESIS RESEARCH, vol. 93, no. 1-3, pp. 223-234.View/Download from: Publisher's site
Schreiber, I, Muzika, F & Červený, J 2019, 'Reaction Networks, Oscillatory Motifs and Parameter Estimation in Biochemical Systems', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 30-41.View/Download from: Publisher's site
© 2019, Springer Nature Switzerland AG. We outline an approach to analysis of dynamics of biosystems formulated as reaction networks. In particular, we discuss stability analysis provided that stoichiometric equations are given for each reaction step together with power law rate expressions. Based on stoichiometry alone, the network at stationary state can be decomposed into elementary subnetworks (elementary modes, extreme currents, fluxes). Assuming power law kinetics, the capacity of the elementary subnetworks for displaying dynamical instabilities, such as bistability and oscillations, is evaluated. These subnetworks are then suitably combined to form the entire network satisfying certain stability constraints implied by experiments. Specifically, we assume that an experimentally measured biosystem represented by a reaction network displays an experimentally observed change from a steady state to oscillations. For the assumed reaction mechanism only a limited set kinetic parameters is known. In contrast, input/output parameters are known from the experiment. The set of unknown kinetic parameters may be estimated by finding a suitable linear combination of elementary modes via linear optimization so that the dynamics displayed by the model fits the experimentally observed behavior. Moreover, reaction network theory is useful in identifying subnetworks that are destabilizing the steady state to yield oscillations. Such subnetworks are called oscillatory motifs and possess a characteristic topology. As an example, we analyze a carbon-nitrogen metabolism of cyanobacteria and examine its oscillatory dynamics.
Benes, N, Brim, L, Pastva, S, Safranek, D, Trojak, M, Cerveny, J & Salagovic, J 2018, 'Fully automated attractor analysis of cyanobacteria models', 2018 22nd International Conference on System Theory, Control and Computing, ICSTCC 2018 - Proceedings, International Conference on System Theory, Control and Computing, IEEE, Romania, pp. 354-359.View/Download from: UTS OPUS or Publisher's site
© 2018 IEEE. Complex dynamics arising in biological systems can be characterised by various kinds of attractors. To that end, the task of determining attractors becomes important in modern systems analysis. Biological systems are typically formalised as highly parametrised continuous-time ODE models. Such models can be abstracted in the form of parametrised graphs. In such abstractions, attractors are observed in the form of terminal strongly connected components (tSCCs). In this paper, we demonstrate a novel method for detecting tSCCs in parametrised graphs on several models of cyanobacteria taken from the domain-specific online platform e-cyanobacterium.org.
Cerveny, J, Schreiber, I & Safranek, D 2018, 'Systems biology approaches for advancing biotechnology of microalgae', BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY, WILEY, pp. 8-8.
Trojak, M, Safranek, D, Hrabec, J, Salagovic, J, Romanovska, F & Cerveny, J 2016, 'E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria', COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY (CMSB 2016), 14th International Conference on Computational Methods in Systems Biology (CMSB), SPRINGER INTERNATIONAL PUBLISHING AG, Univ Cambridge, Comp Lab, Cambridge, ENGLAND, pp. 316-322.View/Download from: Publisher's site
Vlachynska, A, Cerveny, J, Cmiel, V & Turecek, T 2016, 'Automatic Image-Based Method for Quantitative Analysis of Photosynthetic Cell Cultures', Hybrid Artificial Intelligent Systems, 11th International Conference on Hybrid Artificial Intelligence Systems (HAIS), SPRINGER-VERLAG BERLIN, Seville, SPAIN, pp. 402-413.View/Download from: Publisher's site
Fedorko, J, Buzova, D & Cerveny, J 2015, 'Development of methods for breeding high-lipid-content algal strain Chlamydomonas reinhardtii using fluorescence-activated cell sorting', GLOBAL CHANGE: A COMPLEX CHALLENGE, 4th Annual Global Change - A Complex Challenge, GLOBAL CHANGE RESEARCH CENTRE CAS, Brno, CZECH REPUBLIC, pp. 150-153.
Zavrel, T, Ocenasova, P, Sinetova, M & Cerveny, J 2015, 'Comparative growth characterization of frequently used substrains of the model cyanobacterium Synechocystis sp PCC 6803 under varying culture conditions', GLOBAL CHANGE: A COMPLEX CHALLENGE, 4th Annual Global Change - A Complex Challenge, GLOBAL CHANGE RESEARCH CENTRE CAS, Brno, CZECH REPUBLIC, pp. 154-157.
Klement, M, Děd, T, Šafránek, D, Červený, J, Müller, S & Steuer, R 2014, 'Biochemical space: A framework for systemic annotation of biological models', Electronic Notes in Theoretical Computer Science, pp. 31-44.View/Download from: Publisher's site
In this tool paper, we target the problem of unique annotation of organism-specific computational models presented in a public model database. In particular, we present Biochemical Space, a novel annotation methodology accompanied with a set of software tools that allow to create, manage and maintain the Biochemical Space content. The main idea behind is to create a transparent well-annotated reaction network of chemical entities and elemental reactions onto which the mathematical models are projected. For a given organism, the Biochemical Space represents a unifying platform for understanding of the related biological processes. The contribution of the methodology is three-fold: (i) systemic projection of models to a well-structured biological knowledge, (ii) simplification of annotation procedure, (iii) targetting several problems such as the presence of lumped model variables, combinatorial explosion in chemical modifications of entities, and hierarchical organisation of locations of individual entities. In these aspects the Biochemical Space goes beyond the features of current standards such as SBML. Application of the framework is demonstrated on a set of annotation data compiled for complex cyanobacteria processes. © 2014 Elsevier B.V.
Klement, M, Šafránek, D, Děd, T, Pejznoch, A, Nedbal, L, Steuer, R, Červený, J & Müller, S 2013, 'A comprehensive web-based platform for domain-specific biological models', Electronic Notes in Theoretical Computer Science, pp. 61-67.View/Download from: Publisher's site
A Comprehensive Modeling Platform, that is, a general framework for public sharing, annotation, and visualization of domain-specific biological models, is presented. For a selected organism, the framework is instantiated as a web-based application which allows to capture several aspects of biological models represented as biochemical reaction networks or ordinary differential equations. The key feature of the instantiation for a given organism relies on mapping kinetic models to a precise textual and a schematic graphical representation of the related biological knowledge, thereby supporting the systems biological view of the modeled organism. Besides model repository and annotation, the platform includes basic model analysis features such as simulation and static analysis. © 2013 Elsevier B.V.
Fiser, J, Zitek, P & Cerveny, J 2011, 'RELAY FEEDBACK OSCILLATOR DESIGN FOR MODELING CIRCADIAN RHYTHMS IN CYANOBACTERIA', PROCEEDINGS OF THE ASME INTERNATIONAL MECHANICAL ENGINEERING CONGRESS AND EXPOSITION 2011, VOL 2, ASME International Mechanical Engineering Congress and Exposition (IMECE), AMER SOC MECHANICAL ENGINEERS, Denver, CO, pp. 549-+.
Fiser, J, Zitek, P & Cerveny, J 2008, 'Oscillators for Modeling Biomass Growth Adaptation to Circadian Rhythms', 2008 UKSIM TENTH INTERNATIONAL CONFERENCE ON COMPUTER MODELING AND SIMULATION, UKSim 10th International Conference on Computer Modelling and Simulation (EUROSIM/UKSim), IEEE COMPUTER SOC, Emmanuel Coll, Cambridge, ENGLAND, pp. 175-179.View/Download from: Publisher's site
Nedbal, L, Brezina, V, Cerveny, J & Trtilek, M 2004, 'Photosynthesis in dynamic light: systems biology of unconventional chlorophyll fluorescence transients in Synechocystis sp PCC 6803', PHOTOSYNTHESIS RESEARCH, International Satellite Meeting in honor of Norio Murata on Photosynthesis and the Post-Genomic Era, SPRINGER, Trois Rivieres, CANADA, pp. 99-106.View/Download from: Publisher's site
Masojidek, J, Papacek, S, Sergejevova, M, Jirka, V, Cerveny, J, Kunc, J, Korecko, J, Verbovikova, O, Kopecky, J, Stys, D & Torzillo, G 2002, 'A closed solar photobioreactor for cultivation of microalgae under supra-high irradiance: basic design and performance', JOURNAL OF APPLIED PHYCOLOGY, 9th International Conference on Applied Algology, KLUWER ACADEMIC PUBL, AGUADULCE, SPAIN, pp. 239-248.View/Download from: Publisher's site