Application of a photosystem II model for analysis of fluorescence induction curves in the 100 ns to 10 s time domain after excitation with a saturating light pulse

A mathematical model of photosystem II (PSII) events was used to analyze chlorophyll fluorescence transients in the time domain from 100 ns to 10 s after excitation with a saturating 10-ns flash, applied as a part of specialized illumination protocol, using preparations of a thermophilic strain of the unicellular green alga, Chlorella pyrenoidosa Chick (using both intact and diuron-treated cells). Analysis of simulation results has proven that particular attention should be given to flash-induced recombination processes, including nonradiative recombination in PSII, while subsequent charge transfer along the electron transport chain of thylakoid membrane can be adequately described by a single reaction of quinone reoxidation. The PSII model was extended by taking inhibition by diuron of the electron transport in the acceptor side of PSII into account, which allowed simulation of fluorescence induction curves observed in the presence of this inhibitor. The model parameters were determined (stromal pH, rate constants of nonradiative recombination, and the initial reduction state of the quinone pool) which provided adequate simulation of experimentally observed ratios of the maximal and initial fluorescence levels (F _m/F ₀).     

Conditional and Unconditional Simulation of Healthy Patients' Visual Fields

This paper describes a simulation problem, motivated by the study of glaucoma, a very serious and widespread ocular illness. To ascertain whether a patient suffers from glaucoma, a perimetric test is done, but the evolution of the disease is very slow, and large longitudinal sets of tests taken on the same patient are needed to study its evolution, to analyze the efficiency of existing methods to detect the progression of glaucoma and to develop new ones. Simulation can be a very useful procedure to get appropriate data sets to work with. Our aim in this work is to simulate several VFs in a healthy patient to reflect his evolution in time. We use a spatio‐temporal model to simulate from, taking into account the correlation existing between the observed (or simulated) values in space and time. Two different simulation procedures (unconditional and conditional) are studied, and applied to obtain the simulations we are interested in. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Decreasing functional responses as a result of adaptive consumer behavior

Summary Several different mechanisms that may produce decreasing functional responses are investigated using models that assume that an optimally foraging consumer is exploiting one or two resources. Decreasing functional responses are associated with situations in which there are costs to resource consumption. If the process of resource acquisition has costs, decreasing functional responses may occur when there is a single homogeneous resource. If the cost is solely a function of the amount of resource ingested, decreasing functional responses on a single resource do not occur. Both types of cost can produce decreasing functional responses when there are two resource types and a trade-off relationship between consumption of one and consumption of the other. Decreasing functional responses seem to be most likely to occur on a food that yields high benefits and costs per unit of foraging time or effort when there is an alternative resource which yields low benefits and costs. Given this type of foraging choice, the functional response is most likely to decrease when the benefits of ingestion increase at a decreasing rate, and the costs of ingestion increase at an increasing rate with amount ingested. An important and unique consequence of decreasing functional responses is the possibility of population cycles in differential equation models of consumer-resource systems with non-reproducing resources; this is illustrated with a simple comsumer-resource model.     

On the classification of regular systems of inbreeding

Regular systems of inbreeding are defined as those with discrete, nonoverlapping generations and with the same number of individuals and mating pattern in every generation. Given the number of individuals in a generation, there are many possible regular mating systems. A notion of when two such mating systems are equivalent is introduced, and several necessary conditions are given for such an equivalence. The use of these conditions is illustrated for N = 2, 3, 4 and 5 individuals, and a complete enumeration has been found for these cases: the numbers of inequivalent mating systems are 1, 5, 57 and 858, respectively. The maximal eigenvalue of the matrix q that specifies the recursion relations satisfied by the probabilities of identity have also been found for these cases. For N = 3 and 4 (and 2 trivially), circular mating gives the slowest rate of approach to genetic uniformity of those systems that do evolve to uniformity, but for N = 5 there are two other mating systems that have a slower rate of convergence, and for N = 6 partial results show that there are many such examples.Deceased     

In vitro depolymerization dynamics of brain endogenous microtubules

A subcellular fraction containing fragments of endogenous microtubules stabilized in 50% glycerol was separated by diferential centrifugation of rat brain homogenates. The pellets were suspended in glycerol-deficient media, and microtubule depolymerization was monitored by measuring the decrease of sedimentable tubulin. Concomitantly, the number and size of microtubules in the suspensions were followed via electron microscopy. Depolymerization was accompanied by a proportional decrease in the number of microtubules, whereas the average size did not change significantly. After approximately 20 min, a subpopulation of microtubules became stable and did not suffer further depolymerization. These results indicate that upon dilution some microtubules completely depolymerize, whereas others remain stable in the glycerol-deficient medium. The degree of depolymerization depended on both the volume of the resuspension media and on the final glycerol concentration. The results suggest that the depolymerization of the remaining microtubules is prevented by stabilizing factors released from depolymerizing microtubules. Tubulin dimers are not one of these factors, since depolymerization was not altered by the addition of colchicine or by changing the concentration of free tubulin in the medium.     

Confidence Intervals on Ratios of Variance Components for the Unbalanced Two Factor Nested Model

The model considered in this article is the two-factor nested unbalanced variance component model: for p = 1, 2, …, P; q = 1, 2, …, Q_p; and r = 1, 2, …, R_pq. The random variables Y_pqr are observable. The constant μ is an unknown parameter, and A_p, B_pq and C_pqr are (unobservable) normal and independently distributed random variables with zero means and finite variances σ²_A, σ²_B, and σ²_C, respectively. Approximate confidence intervals on ?_A and ?_B using unweighted means are derived, where The performance of these approximate confidence intervals are evaluated using computer simulation. The simulated results indicate that these proposed confidence intervals perform satisfactorily and can be used in applied problems.     

Effect of Zeitgeber Intensity Reduction on a Simulated Dual-Oscillator Human Circadian System: Classical and Dynamic Analysis

The two-oscillator model of human circadian rhythmicity was analyzed when a zeitgeber relative intensity of 1, 0.5, or 0.1 was introduced into the equations. Fourier analysis was compared with dynamic analysis such as attractor reconstruction or Liapunov exponent calculation. After a 50 or 90% reduction in zeitgeber intensity, the dynamics of the system became equivalent and differed significantly from those of a system with maximal zeitgeber intensity. When 10% aleatory noise was added to the data, the analysis was still applicable, and the results obtained were essentially the same as in the absence of noise. Dynamic analysis could thus provide a distinct classification for periodic data, based on the type of analysis.     

The regulatory status of the fixL- and fixJ-like genes in Bradyrhizobium japonicum may be different from that in Rhizobium meliloti

Summary The cloning, sequencing and mutational analysis of the Bradyrhizobium japonicum symbiotic nitrogen fixation genes fixL and fixJ are reported here. The two genes were adjacent and probably formed an operon, fixLJ. The predicted FixL and FixJ proteins, members of the two-component sensor/regulator family, were homologous over almost their entire lengths to the corresponding Rhizobium meliloti proteins (approx. 50% identity). Downstream of the B. japonicum fixJ gene was found an open reading frame with 138 codons (ORF138) whose product shared 36% homology with the N-terminal part of FixJ. Deletion and insertion mutations within fixL and fixJ led to a loss of approximately 90% wildtype symbiotic nitrogen fixation (Fix) activity, whereas an ORF138 mutant was Fix⁺. In fixL, fixJ and ORF138 mutant backgrounds, the aerobic expression of the fixR-nifA operon was not affected. NifA itself did not regulate the expression of the fixJ gene. Thus, the B. japonicum FixL and FixJ proteins were neither involved in the regulation of aerobic nifA gene expression nor in the anaerobic NifA-dependent autoregulation of the fixRnifA operon; rather they appeared to control symbiotically important genes other than those whose expression was dependent on the NifA protein. The fixL and fixJ mutant strains were unable to grow anaerobically with nitrate as the terminal electron acceptor. Therefore, some of the FixJ-dependent genes in B. japonicum may be concerned with anaerobic respiration.