A probability current analysis of energy transport in open quantum systems

We introduce a probability current analysis of excitation energy transfer between states of an open quantum system. Expressing the energy transfer through currents of excitation probability between the states in a site representation enables us to gain key insights into the energy transfer dynamics. It allows to, i) identify the pathways of energy transport in large networks of sites and to quantify their relative weights, ii) quantify the respective contributions of unitary dynamics, dephasing, and relaxation/dissipation processes to the energy transfer, and iii) quantify the contribution of coherence to the energy transfer. Our analysis is general and can be applied to a broad range of open quantum system descriptions (with coupling to non-Markovian environments) in a straightforward manner

Compact Representation of Photosynthesis Dynamics by Rule-based Models (Full Version)

Traditional mathematical models of photosynthesis are based on mass action kinetics of light reactions. This approach requires the modeller to enumerate all the possible state combinations of the modelled chemical species. This leads to combinatorial explosion in the number of reactions although the structure of the model could be expressed more compactly. We explore the use of rule-based modelling, in particular, a simplified variant of Kappa, to compactly capture and automatically reduce existing mathematical models of photosynthesis. Finally, the reduction procedure is implemented in BioNetGen language and demonstrated on several ODE models of photosynthesis processes. This is an extended version of the paper published in proceedings of 5th International Workshop on Static Analysis and Systems Biology (SASB) 2014.Comment: SASB 2014 full pape

Effect of foliar application of α-tocopherol and pyridoxine on vegetative growth, flowering, and some biochemical constituents of Calendula officinalis L. plants

A field experiment was conducted during 2010 at the Experimental Farm of Fajr, SB University of Kerman, Iran. The aim was to study the effects of foliar spray of α-tocopherol (0, 50, 100 part per million (ppm)) and pyridoxine (0, 50, 100 ppm) on vegetative growth, flowering parameters, and some chemical constituents of Calendula officinalis L. plants. Most parameters were significantly affected by application of two vitamins which were used in this study. The obtained results could be summarized as follows; pyridoxine at 100 ppm recorded the best value of leaf area, stem height, chlorophyll b, reducing sugars and hyperoside content; no significant difference was found between plants treated with vitamins in terms of chlorophyll a, root length, fresh weight and dry weight of root; the treatment with α-tocopherol at 100 ppm resulted in the highest yield of seed, fresh and dry aerial parts, as compared to control plants; maximum values of carotenoid were obtained by the application of pyridoxine at 50 ppm; and application of both vitamins led to the reduction of flower diameter.Keyswords: Calendula officinalis L., α-tocopherol, pyridoxin

Photoheterotrophic growth of Physcomitrella patens

© Springer-Verlag Berlin Heidelberg 2013. Physcomitrella patens is a model bryophyte representing an early land plant in the green plant lineage. This organism possesses many advantages as a model organism. Its genome has been sequenced, its predominant life cycle stage is the haploid gametophyte, it is readily transformable and it can integrate transformed DNA into its genome by homologous recombination. One limitation for the use of P. patens in photosynthesis research is its reported inability to grow photoheterotrophically, in the presence of sucrose and the Photosystem II inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, which prevents linear photosynthetic electron transport. In this communication we describe the facile isolation of a P. patens strain which can grow photoheterotrophically. Additionally, we have examined a number of photosynthetic parameters for this strain grown under photoautotrophic, mixotrophic (in the presence of sucrose) and photoheterotrophic conditions, as well as the 3-(3,4-dichlorophenyl)-1,1-dimethylurea-inhibited state. The ability to grow P. patens photoheterotrophically should significantly facilitate its use in photosynthetic studies

Functional properties of the oxygen evolving complex of photosystem 2

This Thesis presents the results of a study by electron paramagnetic resonance (EPR) and measurements of oxygen evolution of the Oxygen Evolving Complex of Photosystem 11 (PS-II) in PS-II enriched membranes from spinach.The experimental part of this Thesis is preceded by a general introduction (Chapter 1) and a brief overview and rationale of methods and techniques used (Chapter 2).Chapter 3 describes an EPR study of PS-11 after Ca 2+depletion and subsequent Cl -depletion. The anions Ca 2+and Cl -are essential for oxygen evolution. After Ca 2+depletion in PS-II in the presence the Ca 2+chelator ethylene glycol his (β-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA), the S 2 state exhibits a modified multiline signal which is stable in the dark. It is found that the modification of S 2 is due to binding of EGTA to PS-11 which occurs after removal of Ca 2+. The pH buffer 4-(N-morpholino)ethanesulphonic acid (MES) modified the S 2 state in a similar fashion to EGTA as indicated by the EPR spectrum. EGTA and MES possibly bind with their anionic oxo-groups nearby or at the Mn cluster itself. It is also found that the EGTA binding- affinity is lowered by subsequent Cl -depletion in EGTA-treated/Ca 2+-depleted PS-II After Cl -depletion in the presence of millimolar EGTA concentrations, the S 2 state remains modified by bound EGTA. However, the S 2 state is not detected by EPR due to an additional modification of S 2 induced by Cl -depletion. Addition of Cl -in darkness reversed this Cl --depletion effect and resulted in the reconstitution of the EGTA-modified multiline EPR signal. Also the S 3 state is reversibly modified after Cl -depletion in Ca 2+-depleted PS-II resulting in a narrowing of the S 3 EPR signal. The Cl --dependent EPR properties of the S 2 and S 3 state in Ca 2+-depleted PS-II indicate that the Cl -which is essential for oxygen evolution, remains functionally bound after Ca 2+- depletion. The observed effects of Ca 2+and Cl -depletion in PS-II may he relevant to the proposed role(s) of Ca 2+and Cl -in controlling substrate binding in the charge accumulation cycle.Chapter 4 presents an EPR study of the charge accumulation properties after Cl -depletion in PS-II whereas Ca 2+remains present in PS-II The light-intensity dependence of oxygen evolution is measured to study enzyme kinetics. The results indicate the presence of two Cl --binding sites in PS- II One of the sites is not essential for oxygen evolution and has not been previously reported in the literature. This site is depleted of Cl -by washes of PS-II membranes in Cl --free buffer solutions at pH 6.3. This Cl --depletion treatment results in a small decrease of the quantum yield of water oxidation and an increase of the S 2 g = 4 EPR signal intensity at the expense of the S 2 multiline EPR signal. The second site is essential for oxygen evolution and is equivalent to that studied in previous work on Cl --depleted PS-II. This site is depleted of Cl -by short incubation of diluted Cl --free washed PS-II membrane suspensions at pH 10. After this treatment no S 2 multiline signal can be generated and an intense S 2g = 4 EPR signal is observed corresponding to 40-100 % of the centers. The S 2 g = 4 signal is relatively stable in the dark. This probably indicates a lowered oxidation potential of S 2 . These centers are unable to undergo further charge accumulation. A fraction of the centers, different from that corresponding to the S 2 g = 4 signal, does not exhibit an S 2 EPR signal and is able to advance to the S 3 state, giving rise to a narrow EPR signal around g = 2. The S042-and F -anions, which have previously been used to facilitate Cl --depletion, have specific effects in pH 10/Cl --depleted PS-II and give rise to S 2 EPR properties that previously have been observed after Cl --depletion treatments in the presence of these anions. Addition of F -to pH 10/Cl --depleted PS-II results in reconstitution of oxygen evolution in - 45 % of the centers in which, however, the enzyme turnover is slowed down.Chapter 5 presents an EPR study of I --activated PS-II. The oxygen evolving activity of I --activated PS-II is nearly similar to that after Cl -reconstitution. A fraction of I --activated centers exhibits a characteristic S 2 g = 4 EPR signal. However, a second and significant fraction of active centers exhibits no S 2 EPR signal. The comparison with the effects of other anions described in Chapter 4 and in the literature, points to a correlation between the S 2 EPR properties and the size of the anion that occupies the Cl --site essential for oxygen evolution. The effects of I -on the properties of S 2 presumably reflect subtle structural changes of the Mn cluster since the I --induced modifications of S 2 are eliminated by addition of ethanol, resulting in the reconstitution of the normal S 2 multiline signal. However, no effects of ethanol are observed in pH 10/Cl --depleted and F --treated PS-II, both of which exhibit an intense g = 4 signal in the S 2 state (Chapter 4). This appears to indicate that the effects of ethanol on the S 2 EPR properties are modulated by the anion occupying the Cl -site essential for oxygen evolution. If the observed ethanol effects would originate from ethanol binding to PS-II the results may be relevant for the role of Cl -in the mechanism of water oxidation, and may indicate that Cl -modulates the substrate affinity.In Chapter 6 the microwave power saturation of Tyr D.in untreated PS-II is investigated to reveal information on the magnetic properties of the oxygen evolving complex in the different oxidation states. The S 1 state is not detected by conventional EPR. Nevertheless, by using Tyr D.as a magnetic probe, two magnetically distinct forms of S 1 are detected which are interconverlible. After 30 min. dark-adaptation (0 °C) a rapidly relaxing S 1 Tyr D.is observed which is converted to a slowly relaxing form upon 17 h dark-adaptation (0 °C), in agreement with a pulsed EPR study in the literature. This conversion is accelerated by phenyl-p-benzoquinone (PPBQ) used as an electron acceptor. This effect of PPBQ is presumably is induced by the reduced form of PPBQ (PPBQH 2 ) since it is avoided by addition of relatively low concentrations of PPBQ to samples to which ferricyanide was added to maintain PPBQ in the oxidized form. It is shown that the slowly relaxing S 1 state becomes rapidly relaxing on the first enzyme cycle. The event responsible for this conversion occurs on the S 3 to S 0 transition or on the S 0 to S 1 transition. It has been previously proposed that the rapidly and slowly relaxing forms of S 1 correspond to a paramagnetic and diamagnetic S 1 state, respectively, reflecting structurally different Mn clusters. However, in view of the results from this work, it may be considered that the Mn cluster in S 1 is diamagnetic and that the rapidly relaxing TyrD. in S 1 is due to a nearby paramagnetic species different from the Mn cluster.Chapter 7 presents a microwave power saturation study of Tyr D.in PS-II after Cl -depletion as described in Chapter 4. The spin state of the Mn cluster in Cl --depleted PS-II giving rise to an S 2 g=4 signal, significantly enhances the microwave power saturation of Tyr D.. However, on the basis of a mathematical model for the dipolar interaction between two spin systems, it is considered that the spins contributing to the S 2 g = 4 EPR signal are magnetically decoupled from Tyr D., due the mismatch between the g-values of the two spin systems. These results suggest that the S 2 g = 4 signal originates from an S = 3/2 spin state of the Mn cluster which also gives rise to a contribution of spins at g = 2

Transplastomic tobacco plants expressing a fatty acid desaturase gene exhibit altered fatty acid profiles and improved cold tolerance

The possibility of altering the unsaturation level of fatty acids in plant lipids by genetic transformation has implications for the stress tolerance of higher plants as well as for their nutritional value and industrial utilisation. While the integration and expression of transgenes in the plastome has several potential advantages over nuclear transformation, very few attempts have been made to manipulate fatty acid biosynthesis using plastid transformation. We produced transplastomic tobacco plants that express a Delta9 desaturase gene from either the wild potato species Solanum commersonii or the cyanobacterium Anacystis nidulans, using PEG-mediated DNA uptake by protoplasts. Incorporation of chloroplast antibioticinsensitive point mutations in the transforming DNA was used to select transformants. The presence of the transcript and the Delta9 desaturase protein in transplastomic plants was confirmed by northern and western blot analyses. In comparison with control plants, transplastomic plants showed altered fatty acid profiles and an increase in their unsaturation level both in leaves and seeds. The two transgenes produced comparable results. The results obtained demonstrate the feasibility of using plastid transformation to engineer lipid metabolic pathways in both vegetative and reproductive tissues and suggest an increase of cold tolerance in transplastomic plants showing altered leaf fatty acid profiles. This is the first example of transplastomic plants expressing an agronomically relevant gene produced with the ‘‘binding-type’’ vectors, which do not contain a heterologous marker gene. In fact, the transplastomic plants expressing the S. commersonii gene contain only plant-derived sequences, a clear attraction from a public acceptability perspective