Dusan Lazar | Palacky University, Olomouc (original) (raw)

Papers by Dusan Lazar

Photosynthesis Research, 2020

In this work, we reconstructed the absorption spectrum of different Synechocystis sp. PCC 6803 op... more In this work, we reconstructed the absorption spectrum of different Synechocystis sp. PCC 6803 optical strains by summing the computed signature of all pigments present in this organism. To do so, modifications to in vitro pigment spectra were first required: namely wavelength shift, curve smoothing, and the package effect calculation derived from high pigment densities were applied. As a result, we outlined a plausible shape for the in vivo absorption spectrum of each chromophore. These are flatter and slightly broader in physiological conditions yet the mean weight-specific absorption coefficient remains identical to the in vitro conditions. Moreover, we give an estimate of all pigment concentrations without applying spectrophotometric correlations, which are often prone to error. The computed cell spectrum reproduces in an accurate manner the experimental spectrum for all the studied wavelengths in the wild-type, Olive, and PAL strain. The gathered pigment concentrations are in agreement with reported values in literature. Moreover, different illumination setups were evaluated to calculate the mean absorption cross-section of each chromophore. Finally, a qualitative estimate of light-limited cellular growth at each wavelength is given. This investigation describes a novel way to approach the cell absorption spectrum and shows all its inherent potential for photosynthesis research.

Foundations of photosynthesis research have been established mainly by studying the response of p... more Foundations of photosynthesis research have been established mainly by studying the response of plants to changing light, typically to sudden exposure to a constant light intensity after a dark acclimation or light flashes. This approach remains valid and powerful, but can be limited by requiring dark acclimation before time-domain measurements and often assumes that rate constants determining the photosynthetic response do not change between the dark- and light-acclimation.We present experimental data and mathematical models demonstrating that these limits can be overcome by measuring plant responses to sinusoidally modulated light of varying frequency. By its nature, such frequency-domain characterization is performed in light-acclimated plants with no need for prior dark acclimation. Amplitudes, phase shifts, and upper harmonic modulation extracted from the data for a wide range of frequencies can target different kinetic domains and regulatory feedbacks. The occurrence of upper ...

Biomedical Papers, 2019

Background and Aims. The prognosis of patients with heart failure (HF) is still generally unfavor... more Background and Aims. The prognosis of patients with heart failure (HF) is still generally unfavorable. HF with reduced ejection fraction (HFrEF) patients reach target medication doses in very low percentages in daily clinical practice. HF disease management programs (DMP), including nurse and telemedicine support that facilitate achieving target medication doses, may improve the unfavorable prognosis. Methods. We retrospectively analyzed the data of 738 patients with HFrEF who were followed in a single HF center during the years 1975-2011, for 6.4 (median) years. DMP, nurse and telemedicine support is established at this center. Results. The group achieved left ventricle (LV) recovery after the HF treatment. The median LV ejection fraction improved from 25.0% at baseline to 50.0% at the time of the latest data collection. The proportion of NYHA II, III and IV classes decreased from 27.6%, 30.2% and 29.7% to 26.6%, 7.2% and 0.1%, respectively while the proportion of NYHA class I increased from 12.5% to 66.1%. Median NT-proBNP decreased from 975.0 to 324.0 pg/mL. The survival of the patient group was favorable; 79.7% survived 18.1 years after diagnosis of HF. A high percentage of the patients received recommended target or higher than target doses of angiotensin-converting enzyme inhibitors (82.0%) and beta-blockers (78.1%). Conclusion. The established pharmacotherapy resulted from an effective DMP and this contributed to the favorable prognosis.

Photosynthetica, 2018

Chlorophyll (Chl) a fluorescence induction (transient), measured by exposing dark-adapted samples... more Chlorophyll (Chl) a fluorescence induction (transient), measured by exposing dark-adapted samples to high light, shows a polyphasic rise, which has been the subject of extensive research over several decades. Several Chl fluorescence parameters based on this transient have been defined, the most widely used being the F V [= (F M-F 0)]/F M ratio as a proxy for the maximum quantum yield of PSII photochemistry. However, considerable additional information may be derived from analysis of the shape of the fluorescence transient. In fact, several performance indices (PIs) have been defined, which are suggested to provide information on the structure and function of PSII, as well as on the efficiencies of specific electron transport reactions in the thylakoid membrane. Further, these PIs have been proposed to quantify plant tolerance to stress, such as by high light, drought, high (or low) temperature, or N-deficiency. This is an interesting idea, since the speed of the Chl a fluorescence transient measurement (<1 s) is very suitable for high-throughput phenotyping. In this review, we describe how PIs have been used in the assessment of photosynthetic tolerance to various abiotic stress factors. We synthesize these findings and draw conclusions on the suitability of several PIs in assessing stress responses. Finally, we highlight an alternative method to extract information from fluorescence transients, the Integrated Biomarker Response. This method has been developed to define multi-parametric indices in other scientific fields (e.g., ecology), and may be used to combine Chl a fluorescence data with other proxies characterizing CO 2 assimilation, or even growth or grain yield, allowing a more holistic assessment of plant performance.

Biochimica et biophysica acta, Mar 24, 2016

Remote Sensing of Environment, 2016

There are many studies showing the active optical reaction of a green leaf to the changing surrou... more There are many studies showing the active optical reaction of a green leaf to the changing surroundings based on chloroplast movement and their rearrangement in plant cells. These studies concentrated mostly on the effect of one feature (leaf type, leaf side or light type) on the leaf optical spectra. We have measured the diffuse reflectance and transmittance spectra of tobacco green leaves in combination of 4 variants: in normal and water infiltrated leaves, in collimated or diffuse incident light, on both the adaxial and abaxial leaf sides, and for the face or side chloroplast arrangement. A Simple Explicitly Non-Linear Empirical model for Leaf Optical Properties (SENLELOP model) is used to theoretically describe, simulate and fit the deviations from the Lambert-Beer's law causing nonlinearity in the measured spectral changes. It is shown that the incident diffuse light is captured by the leaf more effectively than the collimated light. The light incident from the adaxial leaf side is more effectively absorbed than the same light incident from the abaxial leaf side. The air in intercellular spaces of natural leaf increases about twice the beam path and strongly deepens the non-linearity of the absorption process when compared with water infiltrated leaf. The chloroplast arrangement in the palisade cells is reflected in most of the studied differences. The leaf absorbance changed in our case of tobacco leaves up to 30% when the chloroplasts moved from the face to the side position. This change depends strongly on the wavelength and quite slightly on the character of incident light. Further analysis predicts that in practice the effect of chloroplast rearrangement on the reflectance spectra is in dependence on the wavelength of the light about 2-5% in our case of fully developed green leaves but can be higher in some cases. Thus it can affect values of some of the indices used in the remote sensing.

Photosynthesis in silico, 2009

ABSTRACT In this chapter we describe modeling efforts of fluorescence rise (FLR) transients over ... more ABSTRACT In this chapter we describe modeling efforts of fluorescence rise (FLR) transients over the last 20 years. During this period the complexity of the models has increased significantly. Nowadays, the more complex models consist of a combination of the Kok model for the reactions on the donor side of photosystem II (PS II), the reversible radical pair model for the primary PS II photochemistry, the two-electron gate model for electron transport on the acceptor side of PS II, reactions related to reduction and oxidation of plastoquinone (PQ) and, in some cases, of cytochrome b6f, plastocyanin and photosystem I. In some models additional processes are considered like electric field effects and dark reactions of photosynthesis occurring in the stroma and cytosol. The chapter begins with an introduction of topics important for the construction of a model: relevant fluorescence theories, measuring techniques, the physiology behind the FLR, the role of the integrity of the sample, enzyme kinetics and rate constants. Subsequently several published models are discussed. A major problem for many FLR models is that the fluorescence rises much faster (often by a factor 10) than experimentally observed. Possible reasons for this mismatch are discussed in the context of different models. The large majority of models is based on the postulate that the redox state of QA is the major determinant of the variable fluorescence yield. In several models P680+ and quenching by the PQ pool are added, but this is still insufficient to correctly model the slowest rise phase. The question is raised whether additional assumptions are needed to correctly simulate the O—J—I—P transient. At the end of the chapter the fluorescence decrease following the initial rise is discussed. Only a few models include this part of the fluorescence transient. A flaw of these models is that they ignore the experimentally observed transient block at the acceptor side of photosystem I, limiting both electron flow and proton transport during the FLR. As a consequence, activation of photosynthesis occurs in models with considerably faster kinetics than observed experimentally.

Plant Methods, 2015

Current methods of in-house plant phenotyping are providing a powerful new tool for plant biology... more Current methods of in-house plant phenotyping are providing a powerful new tool for plant biology studies. The self-constructed and commercial platforms established in the last few years, employ non-destructive methods and measurements on a large and high-throughput scale. The platforms offer to certain extent, automated measurements, using either simple single sensor analysis, or advanced integrative simultaneous analysis by multiple sensors. However, due to the complexity of the approaches used, it is not always clear what such forms of plant phenotyping can offer the potential end-user, i.e. plant biologist. This review focuses on imaging methods used in the phenotyping of plant shoots including a brief survey of the sensors used. To open up this topic to a broader audience, we provide here a simple introduction to the principles of automated non-destructive analysis, namely RGB, chlorophyll fluorescence, thermal and hyperspectral imaging. We further on present an overview on how and to which extent, the automated integrative in-house phenotyping platforms have been used recently to study the responses of plants to various changing environments.

Plant Methods, 2015

Background: Recently emerging approaches to high-throughput plant phenotyping have discovered the... more Background: Recently emerging approaches to high-throughput plant phenotyping have discovered their importance as tools in unravelling the complex questions of plant growth, development and response to the environment, both in basic and applied science. High-throughput methods have been also used to study plant responses to various types of biotic and abiotic stresses (drought, heat, salinity, nutrient-starving, UV light) but only rarely to cold tolerance. Results: We present here an experimental procedure of integrative high-throughput in-house phenotyping of plant shoots employing automated simultaneous analyses of shoot biomass and photosystem II efficiency to study the cold tolerance of pea (Pisum sativum L.). For this purpose, we developed new software for automatic RGB image analysis, evaluated various parameters of chlorophyll fluorescence obtained from kinetic chlorophyll fluorescence imaging, and performed an experiment in which the growth and photosynthetic activity of two different pea cultivars were followed during cold acclimation. The data obtained from the automated RGB imaging were validated through correlation of pixel based shoot area with measurement of the shoot fresh weight. Further, data obtained from automated chlorophyll fluorescence imaging analysis were compared with chlorophyll fluorescence parameters measured by a non-imaging chlorophyll fluorometer. In both cases, high correlation was obtained, confirming the reliability of the procedure described. Conclusions: This study of the response of two pea cultivars to cold stress confirmed that our procedure may have important application, not only for selection of cold-sensitive/tolerant varieties of pea, but also for studies of plant cold-response strategies in general. The approach, provides a very broad tool for the morphological and physiological selection of parameters which correspond to shoot growth and the efficiency of photosystem II, and is thus applicable in studies of various plant species and crops.

Biosystems, 2011

E-photosynthesis framework is a web-based platform for modeling and analysis of photosynthetic pr... more E-photosynthesis framework is a web-based platform for modeling and analysis of photosynthetic processes. Compared to its earlier version, the present platform employs advanced software methods and technologies to support an effective implementation of vastly diverse kinetic models of photosynthesis. We report on the first phase implementation of the tool new version and demonstrate the functionalities of model visualization, presentation of model components, rate constants, initial conditions and of model annotation. The demonstration also includes export of a model to the Systems Biology Markup Language format and remote numerical simulation of the model.

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2012

Aureococcus anophagefferens is a picoplanktonic microalga that is very well adapted to growth at ... more Aureococcus anophagefferens is a picoplanktonic microalga that is very well adapted to growth at low nutrient and low light levels, causing devastating blooms ("brown tides") in estuarine waters. To study the factors involved in long-term acclimation to different light intensities, cells were acclimated for a number of generations to growth under low light (20 μmol photons m − 2 s − 1), medium light (60 or 90 μmol photons m − 2 s − 1) and high light (200 μmol photons m − 2 s − 1), and were analyzed for their contents of xanthophyll cycle carotenoids (the D pool), fucoxanthin and its derivatives (the F pool), Chls c 2 and c 3 , and fucoxanthin Chl a/c polypeptides (FCPs). Higher growth light intensities resulted in increased steady state levels of both diadinoxanthin and diatoxanthin. However, it also resulted in the conversion of a significant fraction of fucoxanthin to 19′-butanoyloxyfucoxanthin without a change in the total F pool. The increase in 19′-butanoyloxyfucoxanthin was paralleled by a decrease in the effective antenna size, determined from the slope of the change in F 0 as a function of increasing light intensity. Transfer of acclimated cultures to a higher light intensity showed that the conversion of fucoxanthin to its derivative was a relatively slow process (time-frame of hours). We suggest the replacement of fucoxanthin with the bulkier 19′-butanoyloxyfucoxanthin results in a decrease in the light-harvesting efficiency of the FCP antenna and is part of the long-term acclimative response to growth at higher light intensities.

Bioinformatics, 2008

Motivation: It is a question of whether the supramolecular organization of the protein complex ha... more Motivation: It is a question of whether the supramolecular organization of the protein complex has an impact on its function, or not. In the case of the photosystem II (PSII), water splitting might be influenced by cooperation of the PSIIs. Since PSII is the source of the atmospheric oxygen and because better understanding of the water splitting may contribute to the effective use of water as an alternative energy source, possible cooperation should be analyzed and discussed. Results: We suggest that the dimeric organization of the PSII induces cooperation in the water splitting. We show that the model of monomeric PSII is unable to produce the oxygen after the second short flash (associated with the double turnover of the PSII), in contrast to the experimental data and model of dimeric PSII with considered cooperation. On the basis of this fact and partially from the support from other studies, we concluded that the double turnover of the PSII induced by short flashes might be caused by the cooperation in the water splitting. We further discuss a possibility that the known pathway of the electron transport through the PSII might be incomplete and besides D1-Y161, other cofactor which is able to oxidize the special chlorophyll pair (P680) must be considered in the monomeric PSII to explain the oxygen production after the second short flash. Availability: Commented SBML codes (.XML files) of the monomeric and dimeric PSII models will be available (at the time of publication) in the BioModels database (www.ebi.ac.uk/biomodels).

In photosynthesis, electron transport-coupled proton movement initiates the formation of the ligh... more In photosynthesis, electron transport-coupled proton movement initiates the formation of the light-induced electric potential difference, ΔΨ, across the thylakoid membrane (TM). Ions are transported across the TM to counterbalance the charge of protons accumulated in the lumen. The objective of this work is to construct range of mathematical models for simulation of ΔΨ, using the transition state rate theory (TSRT) for description of movement of ions through the channels. The TSRT considers either single-ion (TSRT-SI) or multi-ion occupancy (TSRT-MI) in the channels. Movement of ions through the channel pore is described by means of energy barriers and binding sites; ions move in and out of vacant sites with rate constants that depend on the barrier heights and well depths, as well as on the interionic repulsion in TSRT-MI model. Three energy motifs are used to describe the TSRT-SI model: two-barrier one-site (2B1S), three-barrier two-site (3B2S), and four-barrier three-site (4B3S). The 3B2S energy motif is used for the TSRT-MI model. The accumulation of cations due to the TM surface negative fixed charges is also taken into account. A model employing the electro-diffusion theory instead of the TSRT is constructed for comparison. The dual wavelength transmittance signal (ΔA515-560 nm) measuring the electrochromic shift (ECS) provides a proxy for experimental light-induced ΔΨ. The simulated ΔΨ traces qualitatively agree with the measured ECS traces. The models can simulate different channel conducting regimes and assess their impact on ΔΨ. The ionic flux coupling in the TSRT-MI model suggests that an increase in the internal or external K + concentration may block the outward or the inward Mg 2+ current, respectively.

A model was constructed which includes electron transport (linear and cyclic and Mehler type reac... more A model was constructed which includes electron transport (linear and cyclic and Mehler type reaction) coupled to proton translocation, counter ion movement, ATP synthesis, and Calvin-Benson cycle. The focus is on modeling of the light-induced total electric potential difference (ΔΨ) which in this model originates from the bulk phase electric potential difference (ΔΨ b), the localized electric potential difference (ΔΨ c), as well as the surface electric potential difference (ΔΨ s). The measured dual wavelength transmittance signal (ΔA515– 560 nm, electrochromic shift) was used as a proxy for experimental ΔΨ. The predictions for theoretical ΔΨ vary with assumed contribution of ΔΨ s , which might imply that the measured ΔA515–560 nm trace on a long time scale reflects the interplay of the ΔΨ components. Simulations also show that partitioning of proton motive force (pmf) to ΔΨ b and ΔpH components is sensitive to the stoichiometric ratio of H + /ATP, energy barrier for ATP synthesis, ionic strength, buffer capacity and light intensity. Our model shows that high buffer capacity promotes the establishment of ΔΨ b , while the formation of pH i minimum is not 'dissipated' but 'postponed' until it reaches the same level as that for low buffer capacity. Under physiologically optimal conditions, the output of the model shows that at steady state in light, the ΔpH component is the main contributor to pmf to drive ATP synthesis while a low ΔΨ b persists energizing the membrane. Our model predicts 11 mV as the resting electric potential difference across the thylakoid membrane in dark. We suggest that the model presented in this work can be integrated as a module into a more comprehensive model of oxygenic photosynthesis.

Although the chloroplast movement can be strongly affected by ambient temperature, the informatio... more Although the chloroplast movement can be strongly affected by ambient temperature, the information about chloroplast movement especially related to high temperatures is scarce. For detailed investigation of the effects of heat stress (HS) on tobacco leaves (Nicotiana tabacum L. cv. Samsun), we used two different HS treatments in dark with wide range of elevated temperatures (25–45°C). The leaf segments were either linearly heated in water bath at heating rate of 2°C min-1 from room temperature up to maximal temperature (T m) and then linearly cooled down to 25°C or incubated for 5 min in water bath at the same T m followed by 5 min incubation at 25°C (T-jump). The changes in light-induced chloroplast movement caused by the HS pretreatment were detected after the particular heating regime at 25°C using a method of time-dependent collimated transmittance (CT) and compared with the chlorophyll O–J–I–P fluorescence rise (FLR) measurements. The inhibition of chloroplast movement started at about 40°C while the fluorescence parameters responded generally at higher T m. This difference in sensitivity of CT and FLR was higher for the T-jump than for the linear HS indicating importance of applied heating regime. A possible influence of chloroplast movement on the FLR measurement and a physiological role of the HS-impaired chloroplast movement are discussed.

We studied the temperature dependence of chlorophyll fluorescence intensity in barley leaves unde... more We studied the temperature dependence of chlorophyll fluorescence intensity in barley leaves under weak and actinic light excitation during linear heating from room temperature to 50 • C. The heat-induced fluorescence rise usually appearing at around 40–50 • C under weak light excitation was also found in leaves treated with 3-(3 ,4-dichlorophenyl)-1,1-dimethylurea (DCMU) or hydroxylamine (NH 2 OH). However, simultaneous treatment with both these compounds caused a disappearance of the fluorescence rise. We have suggested that the mechanism of the heat-induced fluorescence rise in DCMU-treated leaves is different than that in untreated or NH 2 OH-treated leaves. In DCMU-treated leaves, the heat-induced fluorescence rise reflects an accumulation of Q A − even under weak light excitation due to the thermal inhibition of the S 2 Q A − recombination as was further documented by a decrease in the intensity of the thermoluminescence Q band. Mathematical model simulating this experimental data also supports our interpretation. In the case of DCMU-untreated leaves, our model simulations suggest that the heat-induced fluorescence rise is caused by both the light-induced reduction of Q A and enhanced back electron transfer from Q B to Q A. The simulations also revealed the importance of other processes occurring during the heat-induced fluorescence rise, which are discussed with respect to experimental data.

The relative height of the so called F pl ('plateau') appearing between the O and P steps in the ... more The relative height of the so called F pl ('plateau') appearing between the O and P steps in the initial chlorophyll a fluorescence rise (FR) under low exciting light, is frequently used for a determination of the relative amount of Q B-non-reducing photosystem II centers ([PSII-Q B-non] rel). On the basis of theoretical approach it has been already suggested that the F pl level can be influenced, among others, by the intensity of exciting light. In this contribution, we present a calculation of [PSII-Q B-non] rel from the FRs measured at different intensities of exciting light (2 Á/115 mmol photons m (2 s (1). We have found that the higher intensity of exciting light, the higher is the estimation of [PSII-Q B-non] rel (8 Á/45%); thus the numerical expression of [PSII-Q B-non] rel using the F pl level in the FR is not plausible. Our experimental results were also successfully simulated by a simple mathematical model. We recommend to use as low intensity of exciting light as possible for an estimation of [PSII-Q B-non] rel from the FR. As Q B-reducing PSII centers contribute to the F pl level even at very low intensities of exciting light, we further recommend to use this method for an approximate estimation of the changes in [PSII-Q B-non] rel , rather than for the numerical estimation of [PSII-Q B-non] rel .

We developed transgenic rice plants (Oryza sativa L. cv. Daeribbyeo) overproducing cytosolic glut... more We developed transgenic rice plants (Oryza sativa L. cv. Daeribbyeo) overproducing cytosolic glutathione reductase (GR) using a GR gene from Brassica campestris and studied their response to photo-oxidative stress in the presence of methyl viologen (MV, 10 and 50 µM concentrations) under room (25 °C) and moderately elevated (35 °C) temperature by analysis of chlorophyll (Chl) a fluorescence parameters (F V /F M , q N , and q P) and of Chl content. Elevated temperature enhanced and accelerated the photo-oxidative damage to photosynthetic apparatus expressed mainly by a fast decrease of q N. Higher temperature supported the protective reaction in transformed rice plants for lower MV concentration (10 µM) and eliminated the enhanced tolerance of photosystem 2 photochemistry to photooxidative stress for higher (50 µM) MV concentration. Different mechanisms and temperature dependence of oxidative and protective reactions explain the results.

Photosynthesis Research, 2020

Biomedical Papers, 2019

Photosynthetica, 2018

Biochimica et biophysica acta, Mar 24, 2016

Remote Sensing of Environment, 2016

Photosynthesis in silico, 2009

Plant Methods, 2015

Biosystems, 2011

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2012

Bioinformatics, 2008

My text for our Ph.D. students of Biophysics mentioning a few words about chlorophyll fluorescenc... more My text for our Ph.D. students of Biophysics mentioning a few words about chlorophyll fluorescence and related phenomena.