Receptor-agonist interactions in service-theoretic perspective, effects of molecular timing on the shape of dose-response curves

Service-theoretic concepts and methods, widely used in other fields (e.g., telecommunication and operations research), are useful also in a biochemical setting because the treatment of biocatalysts (enzymes, receptors) as servers and their ligands as customers, based on the established formal methods of service or queuing theory, may lead to insights and results unobtainable by conventional, mass-action-law-based theories. In this article, we apply the service-theoretic approach to receptor-agonist systems and show how by changing the stochastic time pattern of "operationally relevant" point events (e.g., instants of agonist arrival, instants of post-climax agonist departure) a great variety of dose-response curves may be generated, even in very simple reaction schemes, which, according to mass action kinetics, invariably lead to hyperbolic r(A) curves (r and A stand for response and agonist concentration, respectively). The molecular timing inherent to a hyperbolic response system is not optimal: for instance, at the agonist concentration A(50), half of the agonist molecules are rejected ("lost") because of unfortunate timing of the arrival events. The fraction of lost arrivers can be diminished considerably if the arrivals are better timed: "sub-Poisson" arrivals improve the timing and, thus, convert hyperbolic r(A) curves into "lifted" nonhyperbolic ones. Conversely, "super-Poisson" arrivals make the non-optimal timing in hyperbolic response systems even worse and, thus, convert hyperbolic r(A) curves into "depressed" nonhyperbolic ones. Furthermore, under special timing conditions, nonhyperbolic r(A) curves can be generated, which are partly lifted, partly depressed relative to the reference hyperbola, and which resemble in shape well-known nonhyperbolic forms of enzyme and receptor kinetics (negatively cooperative, positively cooperative, and sigmoidal kinetics). In addition unusual (undulatory and sawtooth-like) r(A) curves can be generated solely by changing the temporal pattern of arrival and service completion instants. Virtually any shape of dose-response curves may be obtained by allowing for probability distributions whose characteristic shape varies with their mean; we call such distributions "variomorphic" and apply them to the arrival process of agonist molecules.     

Hierarchical Classification I: Single-Linkage Method

This is the first part of a survey of hierarchical clustering algorithms using joining methods: the Single-Linkage algorithm. Complete-Linkage and general algorithms defined by d(A_i, B) = = α,d(A_i, A_r)±α_sd(A_i, A_s)±βd(A_r, A_s) will be discussed in two subsequent papers.     

Kinetics of batch-wise enzymatic cycling system for mass production of chiral compound

Kinetics of batch-wise enzymatic cycling system (oxidoreductase-catalyzed reaction system involving enzyme-coupled cofactor regeneration) has been studied covering a broad range of the conserved total cofactor concentration, [C]₀ (=NAD(P)⁺?+?NAD(P)H), based on reasonable several assumptions. It is composed of two elementary reactions, i.e. product synthesis reaction and cofactor regeneration reaction, both of which have been expressed by Michaelis–Menten type rate equations. A novel dimensionless variable, r, has been introduced, which is defined as the concentration of one of the two cofactor components, [X] (NADH⁺ or NADPH⁺), divided by [C]₀, i.e. r .e[X]/[C]₀. The following results have been obtained. (1) The fundamental equation of the batch-wise enzymatic cycling system has been transformed to a differential equation whose formula is: dr/dT?=?N(r)/D(r) (N(r) and D(r) are quadratic equations of r having different coefficients). (2) It has been elucidated that the batch-wise enzymatic cycling system has two phases, an early short transient phase followed by a long phase in quasi-steady state (QSS). (3) In the enzymatic cycling system, r converges to a definite level regardless of any initial value of r. (4) In QSS, the definite level of r nearly equals the singular solution, r_singular, of the differential equation. (5) The actual rate of the targeted product (chiral compound) formation can be calculated by Michaelis–Menten equation in which the cofactor concentration is [C]₀×r_singular instead of [C]₀. r_singular has been proposed to name “redistribution factor”. (6) It is recommended that the “unit” of the cofactor regeneration enzyme be 2–3 times more used than the “unit” of the synthesis enzyme and that [C]₀ be 15–25 times more than the K_m value. Four special cases relating to the batch-wise enzymatic cycling system have been discussed.     

Activation of synaptic receptors and its allosteric regulation

This review considers activation of synaptic receptors (SR) as a process of transduction of the energy of interaction between an agonist (A) and an agonist-recognizing module (R) toward an ion-conducting module (channel,Ch) orG protein within respective complexes (ARCh orARG). The agonist provides functional and, in the case of metabotropic SR, spatial association of protein components in these complexes. Conformational transformations of the latter, which are sufficient for dissociation ofG protein into subunits or opening of an ion-conducting channel, sometimes need additional energy expenditure. The source for this energy can be interaction with one more ligand: guanosine-5′-triphosphate (in the case of metabotropic SR) or glycine (in case of NMDA receptors), which act as co-agonists. The activation of SR is regulated by their allosteric modulators, which affect either the kinetics of interaction between the agonist and receptor by changing the rate of dissociation with the agonist or the kinetics of conformational transitions of the components into the activated or desensitized state.     

Thermodynamical and structural information on photosynthetic systems obtained from electroluminescence kinetics

The relationship between the thermodynamical and structural properties of photosynthetic reaction centers and kinetics and polarization of electric field-induced luminescence was studied. A general model is presented to describe the influence of an electric field on the individual electron transfer rate constants. Comparison of simulations with this model and experimental curves of Photosystem I electroluminescence showed that (a) at least three electrogenic electron transfer steps occur: P-700 to A₀(~30%), A₀ to A₁ (~50%), and A₁ to F_A(~20%), (b) the midpoint potential of A₁/A-₁ is ~ - 0.81 V, and (c) the emission moments of the pigments make on average an angle of 67° with the membrane normal. It is concluded that the analysis of electro-luminescence kinetics may be a powerful technique to obtain information on primary processes using relatively intact systems.     

Characterisation of the Binding of [3H]WAY-100635, a Novel 5-Hydroxytryptamine1A Receptor Antagonist, to Rat Brain

Abstract: The specific binding of [³H]WAY-100635 {N-[2-[4-(2-[O-methyl-³H]methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexane carboxamide trihydrochloride} to rat hippocampal membrane preparations was time, temperature, and tissue concentration dependent. The rates of [³H]WAY-100635 association (k₊₁ = 0.069 ± 0.015 nM^?1 min^?1) and dissociation (k_?1 = 0.023 ± 0.001 min^?1) followed monoexponential kinetics. Saturation binding isotherms of [³H]WAY-100635 exhibited a single class of recognition site with an affinity of 0.37 ± 0.051 nM and a maximal binding capacity (B_max) of 312 ± 12 fmol/mg of protein. The maximal number of binding sites labelled by [³H]WAY-100635 was ～36% higher compared with that of 8-hydroxy-2-(di-n-[³H]-propylamino)tetralin ([³H]8-OH-DPAT). The binding affinity of [³H]WAY-100635 was significantly lowered by the divalent cations CaCl₂ (2.5-fold; p < 0.02) and MnCl₂ (3.6-fold; p < 0.05), with no effect on B_max. Guanyl nucleotides failed to influence the K_D and B_max parameters of [³H]WAY-100635 binding to 5-HT_1A receptors. The pharmacological binding profile of [³H]WAY-100635 was closely correlated with that of [³H]8-OH-DPAT, which is consistent with the labelling of 5-hydroxytryptamine_1A (5-HT_1A) sites in rat hippocampus. [³H]WAY-100635 competition curves with 5-HT_1A agonists and partial agonists were best resolved into high- and low-affinity binding components, whereas antagonists were best described by a one-site binding model. In the presence of 50 µM guanosine 5′-O-(3-thiotriphosphate) (GTPγS), competition curves for the antagonists remained unaltered, whereas the agonist and partial agonist curves were shifted to the right, reflecting an influence of G protein coupling on agonist versus antagonist binding to the 5-HT_1A receptor. However, a residual (16 ± 2%) high-affinity agonist binding component was still apparent in the presence of GTPγS, indicating the existence of GTP-insensitive sites.     

An analysis of the influence of age and school-attendance status on the spread of variola minor.

Definitions are proposed for the independent and joint contributions that the chemical groups A and B make to the free energy of association of the ligand A?B with a receptor. The definitions are independent of the choice of the standard state and are consistent with the basic thermodynamic cycle relating the association of the ligands A?B, A?Y and X?B to the receptor Rappaport 1976. The basic idea is the use of the excess free energy of association of the ligand A?Y over the free energy of association of the reference ligand X?Y as the measure of the “independent” contribution of the group A to the binding. This definition allows the free energy of association of the ligand A?B to be written as the sum of the independent contributions of the groups A and B, their joint contribution, and an invariant free energy of association of the reference ligand with any receptor. With the appropriate definition of the receptor-reference ligand complex, water can be chosen as the reference ligand. Using ΔG(A?OH)?AG(HOH), ΔG(H?B?H)?ΔG(HOH) and ΔG(HO?C)?ΔG(HOH) as the definitions of the “independent” contributions of the chemical groups A, B and C to the binding of the ligand A?B?C, the joint contribution of the groups A and C to the binding is ΔG(A?B?C) ? ΔG(A?B?H) ? ΔG(H-B-C) + ΔG(H?B?H).     

Response of Brassica oleracea to temporal variation in attack by two herbivores affects preference and performance of a third herbivore

1. Plants are frequently under attack by multiple insect herbivores, which may interact indirectly through herbivore‐induced changes in the plant's phenotype. The identity, order, and timing of herbivore arrivals may influence the outcome of interactions between two herbivores. How these aspects affect, in turn, subsequently arriving herbivores that feed on double herbivore‐induced plants has not been widely investigated. 2. This study tested whether the order and timing of arrival of two inducing herbivores from different feeding guilds affected the preference and performance of a subsequently arriving third herbivore, caterpillars of Mamestra brassicae L. (Lepidoptera: Noctuidae). Aphids [Brevicoryne brassicae L. (Hemiptera: Aphididae)] and caterpillars [Plutella xylostella L. (Lepidoptera: Yponomeutidae)] were introduced onto wild Brassica oleracea L. (Brassicaceae) plants in different sequences and with different arrival times. The effects of these plant treatments on M. brassicae caterpillars were assessed in pairwise preference tests and no‐choice performance tests. 3. The caterpillars of M. brassicae preferred to feed from undamaged plants rather than double herbivore‐induced plants. Compared with undamaged plants, they preferred plant material on which aphids had arrived first followed by caterpillars, whereas they avoided plant material with the reverse order of herbivore arrival. Performance of the caterpillars increased with increasing arrival time between herbivore infestations in double herbivore‐induced plants. Although M. brassicae grew faster on plants induced by aphids than on those induced by caterpillars alone, its performance was not affected by the order of previous herbivore arrival. 4. These results imply that the timing of colonisation by multiple herbivores determines the outcome of plant‐mediated herbivore–herbivore interactions.     

Maternal feeding strategies, child eating behaviors, and child BMI in low-income African-American preschoolers

Objective: To test the hypothesis that low‐income African‐American preschool children would have a higher BMI if their mothers reported greater “restriction” and “control” in feeding and if mothers reported that children showed greater “food responsiveness” and “desire to drink.” In addition, to test whether higher maternal “pressure to eat” would be associated with lower child BMI. Research Methods and Procedures: A questionnaire was completed by 296 low‐income African‐American mothers of preschool children. It assessed three constructs on maternal feeding strategies (“restriction,” “pressure to eat,” and “control”) and two on child eating behaviors (“food responsiveness” and “desire to drink”). Children's BMI was measured, and mothers’ BMI was self‐reported. Results: The mean (standard deviation) BMI z‐score of the children was 0.34 (1.5), and 44% of the mothers were obese (BMI ≥30 kg/m²). Only maternal “pressure to eat” had a significant overall association with child BMI z‐score (r = ?0.16, p < 0.01). Both maternal “restriction” and “control” were positively associated with children's BMI z‐score in the case of obese mothers (r = 0.20, p = 0.03 and r = 0.24, p = 0.007, respectively), but this was not so in the case of non‐obese mothers (r = ?0.16, p = 0.05 and r = ?0.07, p = 0.39, respectively). Discussion: Among low‐income African Americans, the positive association between maternal restriction and control in feeding and their preschoolers’ BMI was limited to obese mothers. Relations between parent feeding strategies and child weight status in this population may differ on the basis of maternal weight status.     

DIFFERENTIATION OF ULVA MUTABILIS (CHLOROPHYTA) GAMETANGIA AND GAMETE RELEASE ARE CONTROLLED BY EXTRACELLULAR INHIBITORS1

Blade cells of Ulva mutabilis Føyn (Chlorophyta) excrete regulatory factors into their cell walls and into the environment. These factors are essential for the maintenance of the vegetative state. “Sporulation inhibitor-1a” (SI-1a) is a glycoprotein that was isolated from the culture medium of axenic Ulva growing as an undifferentiated callus. This protein was unusually stable to denaturing treatments and showed an extremely high apparent molecular mass (M_r) of 1–4 × 10⁷ daltons estimated by size exclusion chromatography. The glycosylation was not essential for activity. SI-1a suppressed gametogenesis completely at concentrations lower than 10^?14 M. When Ulva developed normally in the presence of their symbiotic bacteria, smaller forms of SI-1 accumulated in the medium (10⁴–10⁶ daltons). Sporulation inhibitors of the same size spectrum and with similar properties were also extracted from crude cell walls of nonaxenic Ulva. A class of different nonprotein sporulation inhibitors (SI-2) of very low M_r and yet unknown structure was isolated from the inner space between the two blade cell layers. Excretion of all SI-1 forms decreased with maturation of the thallus, whereas the overall concentration of SI-2 in the thallus stayed constant throughout the life cycle. The SI-2 affected different Ulva species whereas SI-1 was species-specific. Gametogenesis was induced upon removal of both Sporulation inhibitors from small single-layered fragments of mature blades. After a “determination phase” of 23–46 h, dependent on the time of induction within the cell cycle, the cells became irreversibly committed to differentiation and were no longer susceptible to SI-1 or SI-2. Subsequently, during a 28-h “differentiation phase,” 16 progametes were formed by synchronous genome doublings and cell divisions and differentiated into mature gametes. These became motile and were released from the gametangia when the concentration of a “swarming inhibitor” of low M_r, excreted mainly during the “determination phase,” declined below a threshold concentration. The biochemical properties of these regulatory factors and their effects on gametogenesis and gamete release are described.     

Statistical Description of Food Microstructure. Extraction of Some Correlation Functions From 2D Images

Two algorithms able to compute lineal-path distribution function L(z) and two-point correlation function, S ₂ (r ₁ ,r ₂ ) from 2D digital images of foods were developed and validated. Particularly, “Altamura” and “White” breads as well as “Napoli” sausages were studied. Lineal-path function was modeled by considering the foods as two-phase random systems composed from polydisperse overlapping disks. Instead, two-point correlation function was modeled by using a Debye’s equation. In all cases a good agreement between experimental and theoretical trend was obtained stating the high accuracy of the algorithms in the extraction of correlation functions as well as the possibility to model breads and sausages as two-phase random systems. Also, important morphological properties such as pores distribution, pore size homogeneity and their spatial distribution, were obtained. For instance, although the estimated radius of the pores was lower for “Altamura” bread rather that for “White”, its slowest decay of L(z) highlighted that the pores showed a high dimensional inhomogeneity.     

Lumbricus terrestris hemoglobin: A comparison of small-angle X-ray scattering and cryoelectron microscopy data

The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of cylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm⁻¹ and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h > 1 nm⁻¹) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex. © John Wiley & Sons, Inc. Biopoly 45: 289–298, 1998     

Morphology of Hair Pigmentation in Wild Red Foxes, Silver Foxes, and Their Hybrids

The effects of dominant allele A ^r of locus Agoution the morphology of hair pigmentation were described in foxes. The A ^r allele was shown to determine the type of melanin and its content in hair with no effect on the morphology of pigment granules and their distribution throughout a hair. Using the method of electron spin resonance (ESR), the types of melanin (eumelanin and pheomelanin) and their content in the hair of red (A ^r A ^r EE) and silver (aaEE) foxes and their hybrids (A ^r aEE) were determined. In silver foxes, only one type of melanin (eumelanin) was found. In red foxes and their hybrids (which are phenotypically similar but darker than red foxes), both types of melanin (eu- and pheomelanin) were found. The highest melanin content was detected in the coat of silver foxes. In the hybrids, the total melanin content was lower than in silver foxes, but significantly higher than in red foxes. In red foxes, the contribution of pheomelanin to the total hair melanin content was twice as large as in the hybrids.     

Dependence of chlorophyll P700 redox transients during the induction period on the transmembrane distribution of protons in chloroplasts of pea leaves

Differential absorbance measurements and fluorometry were applied to examine the impact of dicyclohexylcarbodiimide (DCCD, an inhibitor of H⁺ conductance in thylakoid membranes) and nigericin (a K⁺/H⁺ antiporter) on photoinduced redox state transients of chlorophyll P700 and the induction curves of chlorophyll fluorescence in pea (Pisum sativum L., cv. Premium) leaves. The treatment of leaves with DCCD strongly modified the kinetics of P700⁺ absorbance changes (ΔA ₈₁₀) by promoting rapid photooxidation of P700. These characteristic changes in ΔA ₈₁₀ induction kinetics and P700⁺ accumulation did not appear when the leaves were treated with DCCD in the presence of nigericin. In addition to opposite modifications of ΔA ₈₁₀ kinetics evoked by permeability-modifying agents, the fluorescence induction curves differed conspicuously depending on leaf incubation in DCCD solutions with or without nigericin. The observed modifications of fluorescence induction curves and ΔA ₈₁₀ indicate that DCCD suppresses electron transport from photosystem II (PSII) to P700, whereas this inhibition is removed by nigericin. The results suggest that slowing down of the electron transport rate in the presence of DCCD was caused by elevation of ΔpH in thylakoids. The prevention of pH gradient formation in the presence of protonophore lowered also the steady-state P700⁺ level in far-red irradiated leaves and accelerated the subsequent dark reduction of P700. These findings indicate that PSI-driven cyclic electron flow is accelerated after the removal of the pH gradient.     

Heritability and evolvability of fitness and nonfitness traits: Lessons from livestock

Data from natural populations have suggested a disconnection between trait heritability (variance standardized additive genetic variance, V_A) and evolvability (mean standardized V_A) and emphasized the importance of environmental variation as a determinant of trait heritability but not evolvability. However, these inferences are based on heterogeneous and often small datasets across species from different environments. We surveyed the relationship between evolvability and heritability in >100 traits in farmed cattle, taking advantage of large sample sizes and consistent genetic approaches. Heritability and evolvability estimates were positively correlated (r = 0.37/0.54 on untransformed/log scales) reflecting a substantial impact of V_A on both measures. Furthermore, heritabilities and residual variances were uncorrelated. The differences between this and previously described patterns may reflect lower environmental variation experienced in farmed systems, but also low and heterogeneous quality of data from natural populations. Similar to studies on wild populations, heritabilities for life‐history and behavioral traits were lower than for other traits. Traits having extremely low heritabilities and evolvabilities (17% of the studied traits) were almost exclusively life‐history or behavioral traits, suggesting that evolutionary constraints stemming from lack of genetic variability are likely to be most common for classical “fitness” (cf. life‐history) rather than for “nonfitness” (cf. morphological) traits.     

Eight-legged swimmers: Behavioral responses to floods in two South American spiders

Arthropods inhabiting floodplains have to cope with regular cycles of wet and dry conditions. Allocosa senex and Allocosa marindia are two sympatric and synchronic sand-dwelling wolf spiders that construct burrows along South American coasts and are subject to periodic floods. Our objective was to study tolerance to immersion and describe the behavioral responses to that event in A. senex and A. marindia. We placed each spider in a terrarium with sand as substrate to allow burrow construction. Then, we gradually increased water levels and recorded the behavioral responses for 30 min. None of the individuals died during the artificial flood. More adults of A. senex performed “dives” and “floats” compared to A. marindia. Also, A. senex showed higher occurrences of “floats,” “swims,” and swam for longer than A. marindia. Finally, females of both species swam more frequently than males. Our findings indicate that both Allocosa are able to withstand floods, showing differential tactics according to the life histories of each sex and species.     

The role of optimal control in assessing the most cost-effective implementation of a vaccination programme: HPV as a case study

Consider a population that develops over units of time labelled by zero and the negative integers. It is assumed that at any time r ? 0 there are respectively N(m, a) males of age a and N(f, b) of females of age b, where a = 1, … , A_m and b = 1, … , A_f. At time 0 a sample of n copies of a gene are assumed to be observed, where n ? min_ab(N(m, a), N(f, b)). It is assumed that at any particular time r any possible mating is equally probable and that numbers of gametes contributed to offspring of age 1 and sex u by parents of sex v are exchangeable within age groups and independently distributed among age-groups. Coalescent theory is then derived, with time measured in multiples 2N_eC of the effective population size N_eC, which depends on a measure T of the generation interval. Theory is developed for both autosomal and sex-linked loci in two special cases.     

Usefulness of thermoluminescence in herbicide research

Many herbicides of different chemical structure inhibit photosynthetic electron flow by interrupting the photosyn‐thetic electron flow by interrupting the photosynthetic electron transport chain between the primary acceptor (Q_A) and the secondary acceptor (Q_B) of photosystem 2 (PS2). Thermoluminescence (TL) originates from PS2, and the bands of the glow curve can be related to the charge recombination between positively charged donors and negatively charged acceptors. The glow curve of TL is strongly influenced by addition of PS2 herbicides. The herbicide treatment shifts the peak position and activation energy of the TL band related to Q_A, suggesting that herbicide binding affects the midpoint redox potential not only of Q _B but also that of Q_A. On the basis of the band shift the herbicides of various chemical structures can be classified into different “thermodynamical” groups which relfect the differences in the binding properties of these herbicides. As a new approach TL seems to be a useful technique in studying the mechanism and site of action of herbicides that inhibit electron transport of PS2.     

Nonhyperbolic kinetics of Na,K-ATPase--a new viewpoint]

The kinetics of the 130 kDa monomer obtained by treatment of duck salt gland Na,K-ATPase with C12E8 was compared with that of the membrane-bound enzyme. The shapes of the substrate-velocity curves for the membrane-bound and solubilized forms were quite different: a hyperbolic one for the monomeric Na,K-ATPase and a nonhyperbolic one for the native enzyme. A reaction scheme for ATP hydrolysis based on a comparative analysis of kinetic properties of these two forms is proposed. Experimental evidence in favour of this hypothesis is presented.     

Effects of cyclic spouse separation on conception times

The lengthening of conceptive delays under conditions of natural fertility by cyclic spouse separation is investigated as a problem in renewal processes. Separations are “complete” if they reduce the conditional monthly probability of conception, or fecundability, to zero, and “incomplete” if they merely reduce it, from f to r say. Earlier work respecting cyclic separation by Menken (1979) is extended with formulas for the mean and variance of conceptive delays conditional on T, the ordinal month of the cycle of separation and nonseparation when the woman passes from anovulation into the fecundable state. A simple expression relating fecundabilities f and r and the conditional proportions P_s(T) and P_s-(T) conceiving during separation and nonseparation is obtained.