Inhibition by light of CO2 evolution from dark respiration: Comparison of two gas exchange methods

Two approaches to determine the fraction (μ) of mitochondrial respiration sustained during illumination by measuring CO₂ gas exchange are compared. In single leaves, the respiration rate in the light (`day respiration' rate R<sub>d</sub>) is determined as the ordinate of the intersection point of A–c<sub>i</sub> curves at various photon flux densities and compared with the CO<sub>2</sub> evolution rate in darkness (`night respiration' rate R_n). Alternatively, using leaves with varying values of CO₂ compensation concentration (Γ), intracellular resistance (r_i) and R_n, an average number for μ can be derived from the linear regression between Γ and the product r_iċR_n. Both methods also result in a number c* for that intercellular CO₂ concentration at which net CO₂ uptake rate is equal to –R_d. c* is an approximate value of the photocompensation point Γ* (Γ in the absence of mitochondrial respiration), which is related to the CO₂/O₂ specificity factor of Rubisco S_c/o. The presuppositions and limitations for application of both approaches are discussed. In leaves of Nicotiana tabacum, at 22 °C, single leaf measurements resulted in mean values of μ = 0.71 and c_* = 34 μmol mol⁻¹. At the photosynthetically active photon flux density of 960 μmol quanta m⁻² s⁻¹, nearly the same numbers were derived from the linear relationship between Γ and r_iċR_n. c* and R_d determined by single leaf measurements varied between 31 and 41 μmol mol⁻¹ and between 0.37 and 1.22 μmol m⁻² s⁻¹, respectively. A highly significant negative correlation between c* and R_d was found. From the regression equation we obtained estimates for Γ* (39 μmol mol⁻¹), S_c/o (96.5 mol mol⁻¹) and the mesophyll CO₂ transfer resistance (7.0 mol⁻¹ m² s). This revised version was published online in June 2006 with corrections to the Cover Date.     

Kinetic model of ethopropazine interaction with horse serum butyrylcholinesterase and its docking into the active site.

The action of a potent tricyclic cholinesterase inhibitor ethopropazine on the hydrolysis of acetylthiocholine and butyrylthiocholine by purified horse serum butyrylcholinesterase (EC 3.1.1.8) was investigated at 25 and 37 degrees C. The enzyme activities were measured on a stopped-flow apparatus and the analysis of experimental data was done by applying a six-parameter model for substrate hydrolysis. The model, which was introduced to explain the kinetics of Drosophila melanogaster acetylcholinesterase [Stojan et al. (1998) FEBS Lett. 440, 85-88], is defined with two dissociation constants and four rate constants and can describe both cooperative phenomena, apparent activation at low substrate concentrations and substrate inhibition by excess of substrate. For the analysis of the data in the presence of ethopropazine at two temperatures, we have enlarged the reaction scheme to allow primarily its competition with the substrate at the peripheral site, but the competition at the acylation site was not excluded. The proposed reaction scheme revealed, upon analysis, competitive effects of ethopropazine at both sites; at 25 degrees C, three enzyme-inhibitor dissociation constants could be evaluated; at 37 degrees C, only two constants could be evaluated. Although the model considers both cooperative phenomena, it appears that decreased enzyme sensitivity at higher temperature, predominantly for the ligands at the peripheral binding site, makes the determination of some expected enzyme substrate and/or inhibitor complexes technically impossible. The same reason might also account for one of the paradoxes in cholinesterases: activities at 25 degrees C at low substrate concentrations are higher than at 37 degrees C. Positioning of ethopropazine in the active-site gorge by molecular dynamics simulations shows that A328, W82, D70, and Y332 amino acid residues stabilize binding of the inhibitor.     

Distribution-free ROC analysis using binary regression techniques

Receiver operating characteristic (ROC) regression methodology is used to identify factors that affect the accuracy of medical diagnostic tests. In this paper, we consider a ROC model for which the ROC curve is a parametric function of covariates but distributions of the diagnostic test results are not specified. Covariates can be either common to all subjects or specific to those with disease. We propose a new estimation procedure based on binary indicators defined by the test result for a diseased subject exceeding various specified quantiles of the distribution of test results from non-diseased subjects with the same covariate values. This procedure is conceptually and computationally simplified relative to existing procedures. Simulation study results indicate that the approach has fairly high statistical efficiency. The new ROC regression methodology is used to evaluate childhood measurements of body mass index as a predictive marker of adult obesity.     

Simulations of voltage clamping poorly space-clamped voltage-dependent conductances in a uniform cylindrical neurite

Significant error is made by using a point voltage clamp to measure active ionic current properties in poorly space-clamped cells. This can even occur when there are no obvious signs of poor spatial control. We evaluated this error for experiments that employ an isochronal I(V) approach to analyzing clamp currents. Simulated voltage clamp experiments were run on a model neuron having a uniform distribution of a single voltage-gated inactivating ionic current channel along an elongate, but electrotonically compact, process. Isochronal Boltzmann I(V) and kinetic parameter values obtained by fitting the Hodgkin-Huxley equations to the clamp currents were compared with the values originally set in the model. Good fits were obtained for both inward and outward currents for moderate channel densities. Most parameter errors increased with conductance density. The activation rate parameters were more sensitive to poor space clamp than the I(V) parameters. Large errors can occur despite normal-looking clamp curves.     

Effects of Thallus Temperature and Hydration on Photosynthetic Parameters of Cetraria Islandica from Contrasting Habitats

Two methods of induced in vivo chlorophyll (Chl) fluorescence were used to investigate the effects of varying thallus temperature and hydration on the performance of photosynthetic apparatus of a foliar lichen Cetraria islandica: slow Chl fluorescence induction kinetic with the analysis of quenching mechanisms, and rapid irradiance response curves of photosynthesis derived from quantum yield of photochemical reactions of photosystem 2 (₂) recorded at increasing irradiances. We compared responses of photosynthetic apparatus in populations of C. islandica growing in lower altitude (LAP: 1 350 m a.s.l.) and in higher altitude (HAP: 2 000 m a.s.l.). At each altitude, the samples were collected both in fully irradiated sites (HI) and in shade (LI). Temperature optimum of photosynthetic processes was the same for LAP and HAP thalli of LI populations (18 °C), while it was significantly lower for HI HAP (14 °C). Gradual dehydration of fully hydrated thalli led to initial increase (up to 20 % of water saturation deficit, WSD) in F_V/F_M and ₂, no change at 20–50 % WSD, and a dramatic decrease of the parameters within 50–80 % of WSD. LI HAP of C. islandica was the best adapted population to low temperature having higher rates of photochemical processes of photosynthesis than HI HAP within temperature range of –5 to +5 °C. The differences between populations were apparent also in Chl content and thallus morphology.     

Equivalence of regression curves sharing common parameters

In clinical trials, the comparison of two different populations is a common problem. Nonlinear (parametric) regression models are commonly used to describe the relationship between covariates, such as concentration or dose, and a response variable in the two groups. In some situations, it is reasonable to assume some model parameters to be the same, for instance, the placebo effect or the maximum treatment effect. In this paper, we develop a (parametric) bootstrap test to establish the similarity of two regression curves sharing some common parameters. We show by theoretical arguments and by means of a simulation study that the new test controls its significance level and achieves a reasonable power. Moreover, it is demonstrated that under the assumption of common parameters, a considerably more powerful test can be constructed compared with the test that does not use this assumption. Finally, we illustrate the potential applications of the new methodology by a clinical trial example.     

Matching in studies of classification accuracy: implications for analysis, efficiency, and assessment of incremental value

Summary.   In case–control studies evaluating the classification accuracy of a marker, controls are often matched to cases with respect to factors associated with the marker and disease status. In contrast with matching in epidemiologic etiology studies, matching in the classification setting has not been rigorously studied. In this article, we consider the implications of matching in terms of the choice of statistical analysis, efficiency, and assessment of the incremental value of the marker over the matching covariates. We find that adjustment for the matching covariates is essential, as unadjusted summaries of classification accuracy can be biased. In many settings, matching is the most efficient covariate-dependent sampling scheme, and we provide an expression for the optimal matching ratio. However, we also show that matching greatly complicates estimation of the incremental value of the marker. We recommend that matching be carefully considered in the context of these findings.     

Do sex ratio and development differ in sexually size‐dimorphic shiny cowbirds (Molothrus bonariensis) parasitizing smaller and larger hosts?

Two possible patterns of bias in primary sex ratio have been proposed for size‐dimorphic brood parasites that do not evict host chicks: (1) larger males should be laid at greater frequency in hosts larger than the parasite because they compete better (increasing their survival) than females with large host nest‐mates, and (2) more costly males (i.e. the larger sex) should be laid at greater frequency in hosts smaller than the parasite because, in these hosts, parasite nestlings are provisioned at a higher rate and grow faster than in larger hosts. We tested these hypotheses in two hosts of the sexually size‐dimorphic shiny cowbird, Molothrus bonariensis, one smaller (house wren, Troglodytes aedon) and one larger (chalk‐browed mockingbird, Mimus saturninus) than the parasite. We measured: (1) sex ratio at laying; (2) development of sexual differences in body mass during the nestling stage; and (3) chick survival and sex ratio of chicks before fledging. In both hosts, we found sexual differences in body mass of nestlings from 7 days of age onwards, although we did not find a bias in the sex ratio of eggs laid and chicks fledged. The results of the present study do not support the hypothesis that shiny cowbird females benefit from biasing the primary sex ratio depending on the size of the hosts they parasitize. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 442–448.     

Heterogeneous communities with lognormal species abundance distribution: Species-area curves and sustainability

Heterogeneous species abundance models are models in which the dynamics differ between species, described by variation among parameters defining the dynamics. Using a dynamic and heterogeneous species abundance model generating the lognormal species abundance distribution it is first shown that different degrees of heterogeneity may result in equivalent species abundance distributions. An alternative to Preston's canonical lognormal model is defined by assuming that reduction in resources, for example reduction in available area, increases the density regulation of each species. This leads to species-individual curves and species-area curves that are approximately linear in a double logarithmic plot. Preston's canonical parameter gamma varies little along these curves and takes values in the neighborhood of one. Quite remarkably, the curves, which define the sensitivity of the community to area reductions, are independent of the heterogeneity among species for this model. As a consequence, the curves can be estimated from a single sample from the community using the Poisson lognormal distribution. It is shown how to perform sensitivity analysis with respect to over-dispersion in sampling relative to the Poisson distribution as well as sampling intensity, that is, the fraction of the community sampled. The method is exemplified by analyzing three simulated data sets.     

Can the Study of Natural Vegetation Succession Assist in the Control of Soil Erosion on Abandoned Croplands on the Loess Plateau,China?

In the Loess Plateau, China, arable cultivation of slope lands is common and associated with serious soil erosion. Planting trees or grass may control erosion, but planted species may consume more soil water and can threaten long‐term ecosystem sustainability. Natural vegetation succession is an alternative ecological solution to restore degraded land, but there is a time cost, given that the establishment of natural vegetation, adequate to prevent soil erosion, is a longer process than planting. The aims of this study were to identify the environmental factors controlling the type of vegetation established on abandoned cropland and to identify candidate species that might be sown soon after abandonment to accelerate vegetation succession and establishment of natural vegetation to prevent soil erosion. A field survey of thirty‐three 2 × 2–m plots was carried out in July 2003, recording age since abandonment, vegetation cover, and frequency of species together with major environmental and soil variables. Data were analyzed using correspondence analysis, classification tree analysis, and species response curves. Four vegetation types were identified and the data analysis confirmed the importance of time since abandonment, total P, and soil water in controlling the type of vegetation established. Among the dominant species in the three late‐successional vegetation types, the most appropriate candidates for accelerating and directing vegetation succession were King Ranch bluestem (Bothriochloa ischaemum) and Lespedeza davurica (Leguminosae). These species possess combinations of the following characteristics: tolerance of low water and nutrient availability, fibrous root system and strong lateral vegetative spread, and a persistent seed bank.