The relationship between the Rubisco reaction mechanism and models of photosynthesis*

Abstract. A new model of photosynthesis published recently in this journal (H. Farazdaghi & G. E. Edwards, Plant, Cell and Environment (1988) 11 , 789–798; 799–809) clams to have a more complete mechanistic basis than currently used models based on the paper of G. D. Farquhar, S. von Caemmerer & J. A. Berry (Planta (1980) 149 , 78–90). In this paper, we examine the validity of the new kinetic expression for the rate of CO₂ fixation by Rubisco, and the derivation of an equation for photosynthetic CO₂ assimilation as a function of light intensity and CO₂ concentration presented in the new model. In addition, we compare measured response curve of photosynthesis to CO₂ and light with simulated curves using alternative models. We conclude that the new model is mechanistically misleading and, empirically, overestimates the extent to which light and CO₂ co-limit the rate of photosynthesis under most physiological conditions.     

Chlorophyll-fluorescence measurements in bryophytes: evidence for three main types of light-curve response

Diffusion theory predicts that, except in the lower part of the daylight range, carbon dioxide supply will always be limiting for photosynthesis in a unistratose leaf. We have used chlorophyll fluorometry to survey the photosynthetic responses of numerous bryophytes to a range of light intensities employing the ‘light curve’ approach. Initially, as light intensity is increased in a stepwise manner, electron transport rate (ETR) in bryophytes follows a saturation curve closely fitted by a negative exponential function, y?=?A(1?–?e^–kx ), where y?=?ETR, x?=?light intensity (or photosynthetic photon flux density), A is the asymptote (ETR at infinitely high light intensity), k is a rate constant and e is the base of natural logarithms. The initial slope of the response curve, Ak, approximates maximum quantum efficiency (F_v/F_m) which is measured on dark-adapted plant material. However, at higher intensities ETR frequently veers away from the saturation curve owing to the onset of either photoinhibition or the dissipation of the excitation energy by a photoprotective mechanism, probably involving reduction of O₂. In the latter case, the measurement of ETR significantly overestimates the rate of photosynthetic carbon fixation. We describe a simple approach that enables these instances of photoprotection and photoinhibition to be identified and discuss the wider significance of the results to the ecology of individual species.     

Quantitative Exposure-Response Assessment Approaches to Evaluate Acute Inhalation Toxicity of Phosgene

Phosgene has been a long-term subject of toxicological research due to its widespread use, high toxicity, and status as a model of chemically induced lung injury. To take advantage of the abundant data set for the acute inhalation toxicity of phosgene, methods for exposure-response analysis that use more data than the traditional no-observed-adverse-effect level approach were used to perform an exposure-response assessment for phosgene. Categorical regression is particularly useful for acute exposures due to the ability to combine studies of various exposure durations, and thus provide estimates of effect severity for a range of both exposure concentrations and durations. Results from the categorical regression approach were compared to those from parametric curve fitting models (i.e., benchmark concentration models) that make use of information from an entire dose-response, but only for one exposure duration. While categorical regression analysis provided results that were comparable to benchmark concentration results, categorical regression provides an improvement over that technique by accounting for the effects of both exposure concentration and duration on response. The other major advantage afforded by categorical regression is the ability to combine studies, allowing the quantitative use of a larger data set, which increases confidence in the final result.     

Investigation of Driving Forces for Charge Extraction in Organic Solar Cells: Transient Photocurrent Measurements on Solar Cells Showing S‐Shaped Current–Voltage Characteristics

The role of drift and diffusion as driving forces for charge carrier extraction in flat heterojunction organic solar cells is examined at the example of devices showing intentional S‐shaped current–voltage (J‐V) characteristics. Since these kinks are related to energy barriers causing a redistribution of the electric field and charge carrier density gradients, they are suitable for studying the limits of charge extraction. The dynamics of this redistribution process are experimentally monitored via transient photocurrents, where the current response on square pulses of light is measured in the μs to ms regime. In combination with drift‐diffusion simulation data, we demonstrate a pile‐up of charge carriers at extraction barriers and a high contribution of diffusion to photocurrent in the case of injection barriers. Both types of barrier lead to S‐kinks in the J‐V curve and can be distinguished from each other and from other reasons for S‐kinks (e.g. imbalanced mobilities) by applying the presented approach. Furthermore, it is also helpful to investigate the driving forces for charge extraction in devices without S‐shaped J‐V curve close to open circuit to evaluate whether their electrodes are optimized.     

Principles and practice of foliar analysis as a basis for crop-logging in pine plantations

Summary Principles underlying the use of foliar analysis to diagnose nutrient deficiencies in forest crops are outlined, and the application of foliar diagnosis in crop-logging is discussed. The identification of limiting nutrients and the determination of critical foliar concentrations of deficient elements are prerequisites to the successful introduction of crop-logging as a management tool. The method proposed involves determining the shape of the response curve by graphical methods, and developing an equation to describe the selected model by means of regression analysis. The optimum nutrient concentration is calculated as the point of zero change in slope of the curve,i.e. where dy/dx=0, and the critical level is taken as the concentration at which a ten percent reduction in yield occurs.     

Errors-in-variables in joint population pharmacokinetic/pharmacodynamic modeling

Pharmacokinetic (PK) models describe the relationship between the administered dose and the concentration of drug (and/or metabolite) in the blood as a function of time. Pharmacodynamic (PD) models describe the relationship between the concentration in the blood (or the dose) and the biologic response. Population PK/PD studies aim to determine the sources of variability in the observed concentrations/responses across groups of individuals. In this article, we consider the joint modeling of PK/PD data. The natural approach is to specify a joint model in which the concentration and response data are simultaneously modeled. Unfortunately, this approach may not be optimal if, due to sparsity of concentration data, an overly simple PK model is specified. As an alternative, we propose an errors-in-variables approach in which the observed-concentration data are assumed to be measured with error without reference to a specific PK model. We give an example of an analysis of PK/PD data obtained following administration of an anticoagulant drug. The study was originally carried out in order to make dosage recommendations. The prior for the distribution of the true concentrations, which may incorporate an individual's covariate information, is derived as a predictive distribution from an earlier study. The errors-in-variables approach is compared with the joint modeling approach and more naive methods in which the observed concentrations, or the separately modeled concentrations, are substituted into the response model. Throughout, a Bayesian approach is taken with implementation via Markov chain Monte Carlo methods.     

Estimation of Linkage and Association from Allele Transmission Data

The TDT provides a hypothesis test for the presence of linkage or association (linkage disequilibrium). However, since the TDT is a single test statistic, it cannot be used to separate association and linkage. The importance of this difficulty, following a significant TDT result, has been recently emphasized by Whittaker , Denham and Morris (2000), who alert the community to the possibility that a significant TDT may result from loose linkage and strong association, or from tight linkage and weak association. To attack this problem we start with the parametric model for family‐based allele transmission data of Sham and Curtis (1995) (or Sham (1998)) and find that the parameters in the model are not always identifiable. So we introduce a reparameterization that resolves the identifiability issues and leads to a valid likelihood ratio (LR) test for linkage. Since the linkage and association parameters are both of interest, we next introduce and apply an integrated likelihood (IL) approach to provide separate point estimates and confidence intervals for these parameters. The estimates are shown to have generally small bias and mean square error, while the confidence intervals have good average length and coverage probabilities. We compare the power of the IL approach for testing linkage and, separately association, with the TDT and LR.     

Prioritizing covariates in the planning of future studies in the meta‐analytic framework

Science can be seen as a sequential process where each new study augments evidence to the existing knowledge. To have the best prospects to make an impact in this process, a new study should be designed optimally taking into account the previous studies and other prior information. We propose a formal approach for the covariate prioritization, that is the decision about the covariates to be measured in a new study. The decision criteria can be based on conditional power, change of the p‐value, change in lower confidence limit, Kullback–Leibler divergence, Bayes factors, Bayesian false discovery rate or difference between prior and posterior expectation. The criteria can be also used for decisions on the sample size. As an illustration, we consider covariate prioritization based on genome‐wide association studies for C‐reactive protein levels and make suggestions on the genes to be studied further.     

Phytoplankton sterol contents vary with temperature,phosphorus and silicate supply: a study on three freshwater species

The understanding of environmentally induced changes in the biochemical composition of phytoplankton species is of great importance in both physiological studies and ecological food web research. In extensive laboratory experiments we tested the influence of two different temperatures (10°C and 25°C) and a phosphorus supply gradient on the sterol concentrations of the three freshwater phytoplankton species Scenedesmus quadricauda, Cryptomonas ovata and Cyclotella meneghiniana. The diatom C. meneghiniana was additionally exposed to a silicate gradient. In two separate experiments we analysed (1) possible interactive effects of temperature and phosphorus supply and (2) the effect of four phosphorus levels and three silicate levels on algal sterol concentrations. We observed that sterol concentrations were higher at 25°C than at 10°C in S. quadricauda and C. meneghiniana, but were not affected by temperature in C. ovata. Interactive effects of temperature and phosphorus supply on sterol concentrations were found in C. meneghiniana. This presumably was due to the bioconversion of one sterol (24-methylenecholesterol) into another (22-dihydrobrassicasterol). Increasing phosphorus supply resulted in species-specific effects on sterol concentrations, viz. an optimum curve response in S. quadricauda, a saturation curve response in C. meneghiniana and no change in sterol concentration in C. ovata. Effects of silicate supply on the sterols of C. meneghiniana equalled the effects of phosphorus supply. Albeit we did not observe a general trend in the three phytoplankton species tested, we conclude that sterol concentrations of phytoplankton are strongly affected by temperature and nutrient supply. Interactive effects point out the importance of taking into account more than just one environmental factor when assessing the effects of environmentally induced changes on phytoplankton sterol concentrations.     

INORGANIC NITROGEN AND PHOSPHORUS UPTAKE KINETICS IN PALMARIA PALMATA (RHODOPHYTA)1

The N and P uptake responses were studied in a northern Spanish population of the edible red seaweed Palmaria palmata (Linnaeus) Kuntze. The fronds were incubated at different concentrations, and the nutrient depletion in the medium was measured at successive times to calculate uptake rates. Palmaria palmata uptake response was biphasic and nonsaturable for inorganic P. This would allow the species to exploit transient pulses of high P concentration in natural and fertilized conditions. Such a response is a common feature of algae avoiding nutrient deficiency. At average concentrations measured in the ocean, the response was nonsaturable for inorganic N sources, except for ammonium in autumn and winter when it is not the major N source. In contrast to the general rule of ammonium being taken at a higher rate than nitrate, we found similar affinity for both nutrients corresponding to the minor role of ammonium as N source for field populations over the year.     

Genotoxic effects of the pesticides Rubigan, Omite and Rovral in root-meristem cells of Crepis capillaris L.

Three pesticides have been studied for their genotoxicity by the use of assays in the plant Crepis capillaris, aimed at measuring chromosomal aberrations, micronuclei and sister chromosome exchange (SCE). The fungicides Rubigan 12 EC (fenarimol) and Rovral 25 Flo (iprodione) and the insecticide Omite 57 E (propargite) are all widely used nowadays. The aim of our study was to evaluate the genotoxic effects of these pesticides at concentrations corresponding to those applied in agricultural practice. In preliminary experiments we found that these concentrations do not influence cell proliferation and do not inhibit the growth of root meristems. In all experiments formulated commercial products were used. From the results we conclude that the three pesticides did not induce chromosomal aberrations as estimated by metaphase and anaphase analyses. They were also not capable to induce SCE. Rubigan did not induce micronucleus formation even at the highest concentration tested, but Omite and Rovral markedly increased micronucleus formation. The MN response depended on the sampling time and the concentration used, which showed a significant dose–response correlation (r = 0.978, P < 0.01 and r = 0.941, P < 0.01, respectively). A greater increase in micronucleus frequency was observed after Rovral treatment, where the highest concentration gave a response 8–10-fold above the negative control. Both pesticides induced high frequencies of lagging chromosomes, even after exposure to the lower test concentrations. The presence of lagging chromosomes is an indication of anti-microtubule activity of the pesticides tested. This effect was more strongly expressed after exposure to the two higher concentrations of Omite and Rovral. In this case a complete destruction of the mitotic spindle was observed, resulting in C-mitoses as well as in numerical aberrations—polyploidy and aneuploidy. The present findings suggest that Omite and Rovral at concentrations comparable to those used in practice can be regarded as potential aneugens.     

A simple method for calculating the productivity of polyphenol separations by polymer-based chromatography

A simple method for calculating the productivity of chromatography processes was proposed based on the iso-resolution curve concept. The model separation system was polyphenol separations by polystyrene divinylbenzene resins with the ethanol–water mixture mobile phase. The distribution coefficient K was determined as a function of ethanol concentration I by linear gradient elution experiments. The HETP-mobile phase velocity u curves were determined as a function of I. Using K and HETP, the iso-resolution curve was calculated, from which the productivity was determined as a function of I. It was found that there is an optimum I, where the highest productivity with the minimum amount of mobile phase consumption is obtained.     

An equilibrium folding intermediate detected in the thermal unfolding transition of ribonuclease S by circular dichroism

The thermal-denaturation transition of ribonuclease S (RNAase S) is measured by circular dichroism at 225 nm. Only conformational transitions involving the S-peptide–S-protein complex are detected at this wavelength. Different pathways of thermal unfolding at high and low concentrations are apparent: at low concentrations the temperature of half-completion of denaturation (T_m) varies with concentration. Above a total enzyme concentration of 50 μM, T_m remains constant. The observed data can be explained on the basis of a model where the association–dissociation step occurs between S-peptide and thermally (at least partly) unfolded S-protein. The complex as a whole undergoes a major folding–unfolding transition in the course of which the S-peptide μ-helix appears to be formed. The unfolded complex is well populated in the unfolding transition region for enzyme concentrations of 100 μM or more. The model succeeds in deducing thermodynamic parameters from the thermal denaturation curves in various different ways. The values thus obtained are fully self-consistent and, moreover, consistent with the values for the apparent association constant and apparent association enthalpy as measured in enzyme-dilution experiments and by batch calorimetry.     

Transient and steady state phase response curves of limit cycle oscillators

The experiment of phase shifts resulting from discrete perturbations of stable biological rhythms has been carried out to study entrainment behavior of oscillators. There are two kinds of phase response curves, which are measured in experiments, according to as one measures the phase shifts immediately or long after the perturbation. The former is the first transient phase response curve and the latter is the steady state phase response curve. We redefine both curves within the framework of dynamical system theory and homotopy theory. Several topological properties of both curves are clarified. Consequently, it is shown that we must compare the shapes of both two phase response curves to investigate the inner structures of biological oscillators. Moreover, we prove that a single limit cycle oscillator involving only two variables cannot simulate transient resetting behavior reported by Pittendrigh and Minis (1964). In other words, the circadian oscillator of Drosophila pseudoobscura does not consist of a single oscillator of two variables. Finally we show that a model which consists of two limit cycle oscillators is able to simulate qualitatively the phase response curves of Drosophila.     

Conditions with high intracellular glucose inhibit sensing through glucose sensor Snf3 in Saccharomyces cerevisiae

Gene expression in micro‐organisms is regulated according to extracellular conditions and nutrient concentrations. In Saccharomyces cerevisiae, non‐transporting sensors with high sequence similarity to transporters, that is, transporter‐like sensors, have been identified for sugars as well as for amino acids. An alternating‐access model of the function of transporter‐like sensors has been previously suggested based on amino acid sensing, where intracellular ligand inhibits binding of extracellular ligand. Here we studied the effect of intracellular glucose on sensing of extracellular glucose through the transporter‐like sensor Snf3 in yeast. Sensing through Snf3 was determined by measuring degradation of Mth1 protein. High intracellular glucose concentrations were achieved by using yeast strains lacking monohexose transporters which were grown on maltose. The apparent affinity of extracellular glucose to Snf3 was measured for cells grown in non‐fermentative medium or on maltose. The apparent affinity for glucose was lowest when the intracellular glucose concentration was high. The results conform to an alternating‐access model for transporter‐like sensors. J. Cell. Biochem. 110: 920–925, 2010. © 2010 Wiley‐Liss, Inc.     

The application of robust calibration to radioimmunoassay.

The minute concentrations of many biochemically and clinically important substances are currently estimated by radioimmunoassay (RIA). Traditionally, the most popular approaches to the statistical analysis of RIA data have been to linearize the data through transformation and fit the calibration curve using least squares or to directly fit a nonlinear calibration curve using least squares. Estimates of the hormone concentration in patients are then obtained using this curve. Unfortunately, the transformation is frequently unsuccessful in linearizing the data. Furthermore, the least squares fit can lead to erroneous results in both approaches since the many sources of error which exist in the RIA process often result in outlier observations. In this paper, an approach to the analysis of RIA data which incorporates robust estimation methods is described. An algorithm is presented for obtaining the M-estimates of nonlinear calibration curves. The curves to be fitted are modified hyperbolae based on 12 to 16 observations. A procedure, based on the application of the Bonferroni Inequality, is presented for obtaining tolerance-like interval estimates of the concentration of the hormone of interest in the patients. Results of simulations are cited to support the method of construction of confidence bands for the fitted calibration curve. Data obtained from the Veteran's Hospital, Buffalo, New York are used to illustrate the application of the algorithm which is presented.     

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel‐contaminated soil

Ecotoxicology is primarily concerned with predicting the effects of toxic substances on the biological components of the ecosystem. In remote, high latitude environments such as Antarctica, where field work is logistically difficult and expensive, and where access to adequate numbers of soil invertebrates is limited and response times of biota are slow, appropriate modeling tools using microbial community responses can be valuable as an alternative to traditional single‐species toxicity tests. In this study, we apply a Bayesian nonparametric model to a soil microbial data set acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. We model community change in terms of OTUs (operational taxonomic units) in response to a range of total petroleum hydrocarbon (TPH) concentrations. The Shannon diversity of the microbial community, clustering of OTUs into groups with similar behavior with respect to TPH, and effective concentration values at level x, which represent the TPH concentration that causes x% change in the community, are presented. This model is broadly applicable to other complex data sets with similar data structure and inferential requirements on the response of communities to environmental parameters and stressors.     

A Bayesian Approach to Dose–Response Assessment and Synergy and Its Application to In Vitro Dose–Response Studies

Summary In this article, we propose a Bayesian approach to dose–response assessment and the assessment of synergy between two combined agents. We consider the case of an in vitro ovarian cancer research study aimed at investigating the antiproliferative activities of four agents, alone and paired, in two human ovarian cancer cell lines. In this article, independent dose–response experiments were repeated three times. Each experiment included replicates at investigated dose levels including control (no drug). We have developed a Bayesian hierarchical nonlinear regression model that accounts for variability between experiments, variability within experiments (i.e., replicates), and variability in the observed responses of the controls. We use Markov chain Monte Carlo to fit the model to the data and carry out posterior inference on quantities of interest (e.g., median inhibitory concentration IC ₅₀ ). In addition, we have developed a method, based on Loewe additivity, that allows one to assess the presence of synergy with honest accounting of uncertainty. Extensive simulation studies show that our proposed approach is more reliable in declaring synergy compared to current standard analyses such as the median‐effect principle/combination index method ( Chou and Talalay, 1984 , Advances in Enzyme Regulation 22, 27–55), which ignore important sources of variability and uncertainty.     

Kinetics of glucose stimulatory effect on silica deposition and growth of natural populations of Fragilaria crotonensis

Diatoms are known to exploit organic substrates for growth; however, convincing evidence that they can utilize dissolved organic carbon under natural conditions is not available. In 2008–2009, we performed in situ experiments examining the effect of glucose addition on silica deposition kinetics and growth rates of Fragilaria crotonensis in the eutrophic ?ímov Reservoir (Czech Republic). Silica deposition kinetics was measured at 4‐h intervals over a 24‐h incubation with PDMPO [2‐(4‐pyridyl)‐5{[4‐dimethylaminoethyl‐aminocarbamyl)‐methoxy] phenyl}oxazole] fluorescence probe. A significant stimulatory effect of glucose supplemented at the concentration of 10^?4 M on Fragilaria silification was observed at 20 and 24 h. Fragilaria growth rates almost doubled upon glucose enrichment compared with the untreated control at 24 h. In addition, we conducted a dose‐response experiment testing the glucose additions from 10^?8 to 10^?3 M in a 24‐h incubation. Glucose stimulated both Fragilaria silification and growth at concentrations >10^–7 M, which might occasionally occur in a reservoir as a result of accidental contamination of water by organic pollution.