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Biochemical Model (biochemical + model)
Selected AbstractsOptimal observability of sustained stochastic competitive inhibition oscillations at organellar volumesFEBS JOURNAL, Issue 1 2006Kevin L. Davis When molecules are present in small numbers, such as is frequently the case in cells, the usual assumptions leading to differential rate equations are invalid and it is necessary to use a stochastic description which takes into account the randomness of reactive encounters in solution. We display a very simple biochemical model, ordinary competitive inhibition with substrate inflow, which is only capable of damped oscillations in the deterministic mass-action rate equation limit, but which displays sustained oscillations in stochastic simulations. We define an observability parameter, which is essentially just the ratio of the amplitude of the oscillations to the mean value of the concentration. A maximum in the observability is seen as the volume is varied, a phenomenon we name system-size observability resonance by analogy with other types of stochastic resonance. For the parameters of this study, the maximum in the observability occurs at volumes similar to those of bacterial cells or of eukaryotic organelles. [source] Duchenne's muscular dystrophy: animal models used to investigate pathogenesis and develop therapeutic strategiesINTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY, Issue 4 2003C.A. Collins Summary., Duchenne's muscular dystrophy (DMD) is a lethal childhood disease caused by mutations of the dystrophin gene, the protein product of which, dystrophin, has a vital role in maintaining muscle structure and function. Homologues of DMD have been identified in several animals including dogs, cats, mice, fish and invertebrates. The most notable of these are the extensively studied mdx mouse, a genetic and biochemical model of the human disease, and the muscular dystrophic Golden Retriever dog, which is the nearest pathological counterpart of DMD. These models have been used to explore potential therapeutic approaches along a number of avenues including gene replacement and cell transplantation strategies. High-throughput screening of pharmacological and genetic therapies could potentially be carried out in recently available smaller models such as zebrafish and Caenorhabditis elegans. It is possible that a successful treatment will eventually be identified through the integration of studies in multiple species differentially suited to addressing particular questions. [source] Biochemical aspects in two minimally processed lettuces upon storageINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 2 2007Silvia Tavarini Summary The browning process was studied in two cultivars of minimally processed lettuce (Lactuca sativa var. capitata cv. Verpia and Lactuca sativa var. acephala cv. Lollo Rossa). The analyses were carried out upon storage at 4 °C in the dark. The first interesting result was the resistance to browning of excised leaves of Lollo Rossa, that did not present the typical symptoms of browning. Another important characteristic of Lollo Rossa lettuce was the higher antioxidant ability before storage. The results of biochemical characteristics obtained in this experiment did not show clear evidence supporting the biochemical model of tissue browning involving the sequential synthesis of phenolics and quinones that are regulated, respectively, by phenyl alanine ammonia-lyase, polyphenol oxidase and/or peroxidase. [source] Temperature acclimation in a biochemical model of photosynthesis: a reanalysis of data from 36 speciesPLANT CELL & ENVIRONMENT, Issue 9 2007JENS KATTGE ABSTRACT The Farquhar et al. model of C3 photosynthesis is frequently used to study the effect of global changes on the biosphere. Its two main parameters representing photosynthetic capacity, Vcmax and Jmax, have been observed to acclimate to plant growth temperature for single species, but a general formulation has never been derived. Here, we present a reanalysis of data from 36 plant species to quantify the temperature dependence of Vcmax and Jmax with a focus on plant growth temperature, i.e. the plants' average ambient temperature during the preceding month. The temperature dependence of Vcmax and Jmax within each data set was described very well by a modified Arrhenius function that accounts for a decrease of Vcmax and Jmax at high temperatures. Three parameters were optimized: base rate, activation energy and entropy term. An effect of plant growth temperature on base rate and activation energy could not be observed, but it significantly affected the entropy term. This caused the optimum temperature of Vcmax and Jmax to increase by 0.44 °C and 0.33 °C per 1 °C increase of growth temperature. While the base rate of Vcmax and Jmax seemed not to be affected, the ratio Jmax : Vcmax at 25 °C significantly decreased with increasing growth temperature. This moderate temperature acclimation is sufficient to double-modelled photosynthesis at 40 °C, if plants are grown at 25 °C instead of 17 °C. [source] Extension of a biochemical model for the generalized stoichiometry of electron transport limited C3 photosynthesisPLANT CELL & ENVIRONMENT, Issue 10 2004X. YIN ABSTRACT The widely used steady-state model of Farquhar et al. (Planta 149: 78,90, 1980) for C3 photosynthesis was developed on the basis of linear whole-chain (non-cyclic) electron transport. In this model, calculation of the RuBP-regeneration limited CO2 -assimilation rate depends on whether it is insufficient ATP or NADPH that causes electron transport limitation. A new, generalized equation that allows co-limitation of NADPH and ATP on electron transport is presented herein. The model is based on the assumption that other thylakoid pathways (the Q-cycle, cyclic photophosphorylation, and pseudocyclic electron transport) interplay with the linear chain to co-contribute to a balanced production of NADPH and ATP as required by stromal metabolism. The original model assuming linear electron transport limited either by NADPH or by ATP, predicts quantum yields for CO2 uptake that represent the highest and the lowest values, respectively, of the range given by the new equation. The applicability of the new equation is illustrated for a number of C3 crop species, by curve fitting to gas exchange data in the literature. In comparison with the original model, the new model enables analysis of photosynthetic regulation via the electron transport pathways in response to environmental stresses. [source] Would transformation of C3 crop plants with foreign Rubisco increase productivity?PLANT CELL & ENVIRONMENT, Issue 2 2004A computational analysis extrapolating from kinetic properties to canopy photosynthesis ABSTRACT Genetic modification of Rubisco to increase the specificity for CO2 relative to O2 (,) would decrease photorespiration and in principle should increase crop productivity. When the kinetic properties of Rubisco from different photosynthetic organisms are compared, it appears that forms with high , have low maximum catalytic rates of carboxylation per active site (kcc). If it is assumed that an inverse relationship between kcc and , exists, as implied from measurements, and that an increased concentration of Rubisco per unit leaf area is not possible, will increasing , result in increased leaf and canopy photosynthesis? A steady-state biochemical model for leaf photosynthesis was coupled to a canopy biophysical microclimate model and used to explore this question. C3 photosynthetic CO2 uptake rate (A) is either limited by the maximum rate of Rubisco activity (Vcmax) or by the rate of regeneration of ribulose-1,5-bisphosphate, in turn determined by the rate of whole chain electron transport (J). Thus, if J is limiting, an increase in , will increase net CO2 uptake because more products of the electron transport chain will be partitioned away from photorespiration into photosynthesis. The effect of an increase in , on Rubisco-limited photosynthesis depends on both kcc and the concentration of CO2 ([CO2]). Assuming a strict inverse relationship between kcc and ,, the simulations showed that a decrease, not an increase, in , increases Rubisco-limited photosynthesis at the current atmospheric [CO2], but the increase is observed only in high light. In crop canopies, significant amounts of both light-limited and light-saturated photosynthesis contribute to total crop carbon gain. For canopies, the present average , found in C3 terrestrial plants is supra-optimal for the present atmospheric [CO2] of 370 µmol mol,1, but would be optimal for a CO2 concentration of around 200 µmol mol,1, a value close to the average of the last 400 000 years. Replacing the average Rubisco of terrestrial C3 plants with one having a lower and optimal , would increase canopy carbon gain by 3%. Because there are significant deviations from the strict inverse relationship between kcc and ,, the canopy model was also used to compare the rates of canopy photosynthesis for several Rubiscos with well-defined kinetic constants. These simulations suggest that very substantial increases (> 25%) in crop carbon gain could result if specific Rubiscos having either a higher , or higher kcc were successfully expressed in C3 plants. [source] Parameterization of the CO2 and H2O gas exchange of several temperate deciduous broad-leaved trees at the leaf scale considering seasonal changesPLANT CELL & ENVIRONMENT, Issue 2 2003Y. KOSUGI ABSTRACT A combined model to simulate CO2 and H2O gas exchange at the leaf scale was parameterized using data obtained from in situ leaf-scale observations of diurnal and seasonal changes in the CO2 and H2O gas exchange of four temperate deciduous broad-leaved trees using a porometric method. The model consists of a Ball et al. type stomatal conductance submodel [Ball, Woodrow & Berry, pp. 221,224 in Progress in Photosynthesis Research (ed. I. Biggins), Martinus-Nijhoff Publishers, Dordrecht, The Netherlands, 1987] and a Farquhar et al. type biochemical submodel of photosynthesis (Farquhar, von Caemmerer & Berry, Planta 149, 78,90, 1980). In these submodels, several parameters were optimized for each tree species as representative of the quantitative characteristics related to gas exchange. The results show that the seasonal physiological changes of Vcmax25 in the biochemical model of photosynthesis should be used to estimate the long-term CO2 gas exchange. For Rd25 in the biochemical model of photosynthesis and m in the Ball et al. type stomatal conductance model, the difference should be counted during the leaf expansion period. [source] Changes in leaf photosynthetic parameters with leaf position and nitrogen content within a rose plant canopy (Rosa hybrida)PLANT CELL & ENVIRONMENT, Issue 4 2000M. M. Gonzalez-Real ABSTRACT This paper deals with changes in leaf photosynthetic capacity with depth in a rose (Rosa hybrida cv. Sonia) plant canopy. Measurements of leaf net CO2 assimilation (Al) and total nitrogen content (Nl) were performed in autumn under greenhouse conditions on mature leaves located at different layers within the plant canopy, including the flower stems and the main shoots. These leaves were subjected (i) to contrasting levels of CO2 partial pressure (pa) at saturating photosynthetic photon flux density (I about 1000 ,mol m,2 s,1) and (ii) to saturating CO2 partial pressure (pa about 100 Pa) and varying I, while conditions of temperature were those prevailing in the greenhouse (20,38 °C). A biochemical model of leaf photosynthesis relating Al to intercellular CO2 partial pressure (pi) was parameterized for each layer of leaves, supplying corresponding values of the photosynthetic Rubisco capacity (Vlm) and the maximum rate of electron transport (Jm). The results indicated that rose leaves growing at the top of the canopy had higher values of Jm and Vlm, which resulted from a higher allocation of nitrogen to the uppermost leaves. Mean values of total leaf nitrogen, Nl, decreased about 35% from the uppermost leaves of flower stem to leaves growing at the bottom of the plant. The derived values of non-photosynthetic nitrogen, Nb, varied from 76 mmolN m,2leaf (layer 1) to 60 mmolN m,2leaf (layer 4), representing a large fraction of Nl (50 and 60% in layer 1 and 4, respectively). Comparison of leaf photosynthetic nitrogen (Np=Nl,Nb) and I profiles supports the hypothesis that rose leaves acclimate to the time-integrated absorbed I. The relationships between I and Np, obtained during autumn, spring and summer, indicate that rose leaves seem also to acclimate their photosynthetic capacity seasonally, by allocating more photosynthetic nitrogen to leaves in autumn and spring than in summer. [source] | ||||||||||