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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.
BACKGROUND: With limited agricultural land and increasing human population, it is essential to enhance overall photosynthesis and thus productivity. Oxygenic photosynthesis begins with light absorption, followed by excitation energy transfer to the reaction centres, primary photochemistry, electron and proton transport, NADPH and ATP synthesis, and then CO2 fixation (Calvin-Benson cycle, as well as Hatch-Slack cycle). Here we cover some of the discoveries related to this process, such as the existence of two light reactions and two photosystems connected by an electron transport 'chain' (the Z-scheme), chemiosmotic hypothesis for ATP synthesis, water oxidation clock for oxygen evolution, steps for carbon fixation, and finally the diverse mechanisms of regulatory processes, such as 'state transitions' and 'non-photochemical quenching' of the excited state of chlorophyll a. SCOPE: In this review, we emphasize that mathematical modelling is a highly valuable tool in understanding and making predictions regarding photosynthesis. Different mathematical models have been used to examine current theories on diverse photosynthetic processes; these have been validated through simulation(s) of available experimental data, such as chlorophyll a fluorescence induction, measured with fluorometers using continuous (or modulated) exciting light, and absorbance changes at 820 nm (ΔA820) related to redox changes in P700, the reaction centre of photosystem I. CONCLUSIONS: We highlight here the important role of modelling in deciphering and untangling complex photosynthesis processes taking place simultaneously, as well as in predicting possible ways to obtain higher biomass and productivity in plants, algae and cyanobacteria.
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- biomasa MeSH
- chlorofyl a * MeSH
- chlorofyl MeSH
- fotosyntéza * MeSH
- fotosystém II - proteinový komplex MeSH
- kyslík MeSH
- lidé MeSH
- světlo MeSH
- transport elektronů MeSH
- voda MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
Understanding the net photosynthesis of plant canopies requires quantifying photosynthesis in challenging environments, principally due to the variable light intensities and qualities generated by sunlight interactions with clouds and surrounding foliage. The dynamics of sunflecks and rates of change in light intensity at the beginning and end of sustained light (SL) events makes photosynthetic measurements difficult, especially when dealing with less accessible parts of plant foliage. High time resolved photosynthetic monitoring from pulse amplitude modulated (PAM) fluorometers has limited applicability due to the invasive nature of frequently applied saturating flashes. An alternative approach used here provides remote (<5 m), high time resolution (10 s), PAM equivalent but minimally invasive measurements of photosynthetic parameters. We assessed the efficacy of the QA flash protocol from the Light-Induced Fluorescence Transient (LIFT) technique for monitoring photosynthesis in mature outer canopy leaves of potted Persea americana Mill. cv. Haas (Avocado) trees in a semi-controlled environment and outdoors. Initially we established that LIFT measurements were leaf angle independent between ±40° from perpendicular and moreover, that estimates of 685 nm reflectance (R685) from leaves of similar chlorophyll content provide a species dependent, but reasonable proxy for incident light intensity. Photosynthetic responses during brief light events (≤10 min), and the initial stages of SL events, showed similar declines in the quantum yield of photosystem II (ΦII) with large transient increases in 'constitutive loss processes' (ΦNO) prior to dissipation of excitation by non-photochemical quenching (ΦNPQ). Our results demonstrate the capacity of LIFT to monitor photosynthesis at a distance during highly dynamic light conditions that potentially may improve models of canopy photosynthesis and estimates of plant productivity. For example, generalized additive modelling performed on the 85 dynamic light events monitored identified negative relationships between light event length and ∆ΦII and ∆electron transport rate using either ∆photosynthetically active radiation or ∆R685 as indicators of leaf irradiance.
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- chlorofyl MeSH
- fluorescence MeSH
- fotosyntéza fyziologie MeSH
- listy rostlin fyziologie MeSH
- Persea fyziologie MeSH
- stromy fyziologie MeSH
- světlo MeSH
- technologie dálkového snímání přístrojové vybavení metody MeSH
- teoretické modely MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
It has been suggested that atmospheric CO2 concentration and frequency of cloud cover will increase in future. It remains unclear, however, how elevated CO2 influences photosynthesis under complex clear versus cloudy sky conditions. Accordingly, diurnal changes in photosynthetic responses among beech trees grown at ambient (AC) and doubled (EC) CO2 concentrations were studied under contrasting sky conditions. EC stimulated the daily sum of fixed CO2 and light use efficiency under clear sky. Meanwhile, both these parameters were reduced under cloudy sky as compared with AC treatment. Reduction in photosynthesis rate under cloudy sky was particularly associated with EC-stimulated, xanthophyll-dependent thermal dissipation of absorbed light energy. Under clear sky, a pronounced afternoon depression of CO2 assimilation rate was found in sun-adapted leaves under EC compared with AC conditions. This was caused in particular by stomata closure mediated by vapour pressure deficit.
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- biologické modely MeSH
- buk (rod) fyziologie MeSH
- fotosyntéza fyziologie MeSH
- látky znečišťující vzduch metabolismus MeSH
- listy rostlin fyziologie MeSH
- oxid uhličitý metabolismus MeSH
- počasí * MeSH
- světlo MeSH
- xanthofyly metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA-like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae.
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- fotosyntéza * MeSH
- fototrofní procesy MeSH
- fylogeneze MeSH
- genom bakteriální MeSH
- molekulární evoluce * MeSH
- multigenová rodina MeSH
- operon MeSH
- plazmidy genetika metabolismus MeSH
- přenos genů horizontální * MeSH
- replikace DNA MeSH
- Rhodobacteraceae klasifikace genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The effect of temperature on stomatal conductance (gs) and corresponding gas exchange parameters was studied in two tree species with contrasting leaf anatomy and ecophysiology-a broadleaf angiosperm, Populus deltoides x nigra (poplar), and a needle-leaf gymnosperm, Pinus taeda (loblolly pine). Experiments were conducted in growth chambers across a leaf temperature range of 19-48°C. Manipulations of temperature were done in well-watered and drought soil conditions and under ambient (400 ppm) and elevated (800 ppm) air CO2 concentrations. Increases in leaf temperature caused stomatal opening at both ambient and elevated [CO2]. The gs increased by 42% in poplar and by 40% in loblolly pine when leaf temperature increased from 30°C to 40°C at a vapour pressure difference of 1 kPa. Stomatal limitation to photosynthesis decreased in elevated temperature in loblolly pine but not in poplar. The ratio of net photosynthesis to gs depended on leaf temperature, especially at high temperatures. Evaporative cooling of transpiring leaves resulted in reductions in leaf temperature up to 9°C in well-watered poplar but only 1°C in drought-stressed poplar and in loblolly pine. As global mean temperatures rise and temperature extremes become more frequent and severe, understanding the effect of temperature on gs, and modelling that relationship, will become increasingly important.
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 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 parameterized 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 coarse-grained growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.
BACKGROUND: Photosynthetic microalgae have been in the spotlight of biotechnological production (biofuels, lipids, etc), however, current barriers in mass cultivation of microalgae are limiting its successful industrialization. Therefore, a mathematical model integrating both the biological and hydrodynamical parts of the cultivation process may improve our understanding of relevant phenomena, leading to further optimization of the microalgae cultivation. RESULTS: We introduce a unified multidisciplinary simulation tool for microalgae culture systems, particularly the photobioreactors. Our approach describes changes of cell growth determined by dynamics of heterogeneous environmental conditions such as irradiation and mixing of the culture. Presented framework consists of (i) a simplified model of microalgae growth in a culture system (the advection-diffusion-reaction system within a phenomenological model of photosynthesis and photoinhibition), (ii) the fluid dynamics (Navier-Stokes equations), and (iii) the irradiance field description (Beer-Lambert law). To validate the method, a simple case study leading to hydrodynamically induced fluctuating light conditions was chosen. The integration of computational fluid dynamics (ANSYS Fluent) revealed the inner property of the system, the flashing light enhancement phenomenon, known from experiments. CONCLUSION: Our physically accurate model of microalgae culture naturally exhibits features of real system, can be applied to any geometry of microalgae mass cultivation and thus is suitable for biotechnological applications.
BACKGROUND: The cost-benefit model for the evolution of botanical carnivory provides a conceptual framework for interpreting a wide range of comparative and experimental studies on carnivorous plants. This model assumes that the modified leaves called traps represent a significant cost for the plant, and this cost is outweighed by the benefits from increased nutrient uptake from prey, in terms of enhancing the rate of photosynthesis per unit leaf mass or area (AN) in the microsites inhabited by carnivorous plants. SCOPE: This review summarizes results from the classical interpretation of the cost-benefit model for evolution of botanical carnivory and highlights the costs and benefits of active trapping mechanisms, including water pumping, electrical signalling and accumulation of jasmonates. Novel alternative sequestration strategies (utilization of leaf litter and faeces) in carnivorous plants are also discussed in the context of the cost-benefit model. CONCLUSIONS: Traps of carnivorous plants have lower AN than leaves, and the leaves have higher AN after feeding. Prey digestion, water pumping and electrical signalling represent a significant carbon cost (as an increased rate of respiration, RD) for carnivorous plants. On the other hand, jasmonate accumulation during the digestive period and reprogramming of gene expression from growth and photosynthesis to prey digestion optimizes enzyme production in comparison with constitutive secretion. This inducibility may have evolved as a cost-saving strategy beneficial for carnivorous plants. The similarities between plant defence mechanisms and botanical carnivory are highlighted.
Cadmium (Cd) is an important environmental pollutant and is poisonous to most organisms. We aimed to unravel the mechanisms of Cd toxicity in the model water plant Ceratophyllum demersum exposed to low (nM) concentrations of Cd as are present in nature. Experiments were conducted under environmentally relevant conditions, including nature-like light and temperature cycles, and a low biomass to water ratio. We measured chlorophyll (Chl) fluorescence kinetics, oxygen exchange, the concentrations of reactive oxygen species and pigments, metal binding to proteins, and the accumulation of starch and metals. The inhibition threshold concentration for most parameters was 20 nM. Below this concentration, hardly any stress symptoms were observed. The first site of inhibition was photosynthetic light reactions (the maximal quantum yield of photosystem II (PSII) reaction centre measured as Fv /Fm , light-acclimated PSII activity ΦPSII , and total Chl). Trimers of the PSII light-harvesting complexes (LHCIIs) decreased more than LHC monomers and detection of Cd in the monomers suggested replacement of magnesium (Mg) by Cd in the Chl molecules. As a consequence of dysfunctional photosynthesis and energy dissipation, reactive oxygen species (superoxide and hydrogen peroxide) appeared. Cadmium had negative effects on macrophytes at much lower concentrations than reported previously, emphasizing the importance of studies applying environmentally relevant conditions. A chain of inhibition events could be established.
- MeSH
- fotosyntéza * MeSH
- fotosystém II - proteinový komplex metabolismus MeSH
- kadmium toxicita MeSH
- Magnoliopsida účinky léků fyziologie účinky záření MeSH
- peroxid vodíku metabolismus MeSH
- reaktivní formy kyslíku metabolismus MeSH
- superoxidy metabolismus MeSH
- světlo MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
