Quantitative analysis of aspartate receptor signaling complex reveals that the homogeneous two-state model is inadequate: development of a heterogeneous two-state model

The two-state model of receptor activation, in which a receptor population exists in equilibrium between a single on-state and a single off-state, has long been considered a viable model for the signaling behavior of bacterial chemoreceptors. Here, we show that this simple, homogeneous two-state model is adequate for a pure receptor population with just one adaptation state, but fails to account quantitatively for the observed linear relationship between the apparent attractant affinity (K(1/2)) and kinase activity (V(obs)(apo)) as the adaptation state is varied. Further analysis reveals that the available data are instead consistent with a heterogeneous two-state model in which covalent modification of receptor adaptation sites changes the microscopic properties of the on-state or off-state. In such a system, each receptor molecule retains a single on-state and off-state, but covalent adaptation generates a heterogeneous population of receptors exhibiting a range of different on-states or off-states with different microscopic parameters and conformations. It follows that covalent adaptation transforms the receptor from a simple, two-state toggle switch into a variable switch. In order to identify the microscopic parameters most sensitive to covalent adaptation, six modified, two-state models were examined in which covalent adaptation alters a different microscopic parameter. The analysis suggests that covalent adaptation primarily alters the ligand-binding affinity of the receptor off-state (K(D1)). By contrast, models in which covalent adaptation alters the ligand-binding affinity of the receptor on-state, the maximal kinase stimulation of the on-state or off-state, cooperative interactions between receptors, or the assembly of the receptor-kinase signaling complex are inconsistent with the available evidence. Overall, the findings support a heterogeneous two-state model in which modification of the receptor adaptation sites generates a population of receptors with heterogeneous off-states differing in their attractant affinities.In the process of testing the effects of covalent adaptation on the assembly of the receptor-kinase signaling complex, a new method for estimating the stoichiometric ratio of receptor and CheA in the ternary signaling complex was devised. This method suggests that the ratio of receptor dimers to CheA dimers in the assembled complex is 6:1 or less.     

Increased sugar concentration in response to a wide range of pollinator sounds can be adaptive for the plant: answer to Raguso et al

In Veits et al., we showed that flowers respond to a range of pollinator sounds by increased nectar sugar concentration. Here we clarify that (1) our argument is relevant to most pollinators, and not limited to bees (2) specifically, bees do access Oenothera Drumondii nectar in this area.     

Mathematical model of a three-stage innate immune response to a pneumococcal lung infection

Pneumococcal pneumonia is a leading cause of death and a major source of human morbidity. The initial immune response plays a central role in determining the course and outcome of pneumococcal disease. We combine bacterial titer measurements from mice infected with Streptococcus pneumoniae with mathematical modeling to investigate the coordination of immune responses and the effects of initial inoculum on outcome. To evaluate the contributions of individual components, we systematically build a mathematical model from three subsystems that describe the succession of defensive cells in the lung: resident alveolar macrophages, neutrophils and monocyte-derived macrophages. The alveolar macrophage response, which can be modeled by a single differential equation, can by itself rapidly clear small initial numbers of pneumococci. Extending the model to include the neutrophil response required additional equations for recruitment cytokines and host cell status and damage. With these dynamics, two outcomes can be predicted: bacterial clearance or sustained bacterial growth. Finally, a model including monocyte-derived macrophage recruitment by neutrophils suggests that sustained bacterial growth is possible even in their presence. Our model quantifies the contributions of cytotoxicity and immune-mediated damage in pneumococcal pathogenesis.     

A model for Ca2+ oscillations stimulated by the type 5 metabotropic glutamate receptor: an unusual mechanism based on repetitive, reversible phosphorylation of the receptor

In parallel with experimental investigations, the molecular mechanisms responsible for Ca²⁺ oscillations have been much investigated with computational models. In the vast majority of cell-types, these oscillations rely on the biphasic regulation of the inositol 1,4,5-trisphosphate (InsP₃) receptor by cytosolic Ca²⁺. However, when Ca²⁺ oscillations are initiated by agonist stimulation of the type 5 metabotropic glutamate (mGlu5) receptor, oscillatory behaviour is tightly controlled by repetitive cycles of receptor phosphorylation/dephosphorylation leading to the periodic activation/deactivation of the G protein-activated signalling cascade downstream of this G protein-coupled receptor. We present a minimal model for mGlu5 receptor-induced Ca²⁺ oscillations, taking into account receptor phosphorylation by a protein kinase C isoenzyme sensitive to diacylglycerol but not to Ca²⁺. Depending on the density of receptors and the level of stimulation, the model reproduces Ca²⁺ oscillations based on either a ‘dynamic uncoupling’ mechanism or InsP₃ receptor dynamics. When based on the former mechanism, Ca²⁺ oscillation frequency is insensitive to the level of stimulation, while the level of receptor expression is a determinant of oscillation frequency. When investigating the conditions for the occurrence of oscillations, the model predicts that dynamic uncoupling likely relies on a steep relationship between the activity of PKC and the amount of phosphorylated mGlu5 receptor. Finally, we use the model to simulate the adaptation of the signalling pathway during periods of prolonged stimulation associated with receptor desensitization/internalization. The model suggests that the existence of both oscillatory mechanisms could allow for a significant lengthening of the repetitive Ca²⁺ responses under these conditions.     

Binding crevice for TT-232 in a homology model of type 1 somatostatin receptor

Somatostatin receptor type 1 was modelled based on the atomic structure of bovine rhodopsin. Possible ways of binding interaction between somatostatin receptor type 1 and TT-232, a cycloheptapeptide analogue of somatostatin with broad therapeutic potential, were analysed by molecular docking. The twelve TT-232 conformations, obtained by NMR measurements in H(2)O-D(2)O mixture, were similar, disclosing a consensus backbone conformation. Several residues interacting with TT-232, such as Val133, Asp137 (helix 3), Arg197 (helix 4), Phe287, Gln291, Asn294 (helix 6), Ser305, and Tyr313 (helix 7), were found. In accordance, in vitro binding experiments indicated high-affinity binding of TT-232 to (125)I labelled somatostatin sites in brain membranes. The single binding crevice obtained by docking may allow the design and discovery of new peptidomimetics of TT-232 in the future.     

Growth response of lentil and wheat to Glomus clarum NT4 over a range of P levels in a Saskatchewan soil containing indigenous AM fungi

 The growth responses of lentil (Lens esculenta L. cv. Laird) and two wheat cultivars (Triticum aestivum L. cv. Laura and Neepawa) to Glomus clarum NT4 in soil containing indigenous arbuscular mycorrhizal fungi (AMF) and fertilized with phosphorus at different (0, 5, 10, 20 ppm) levels was studied in a growth chamber. Soil was inoculated with a monospecific culture of G. clarum NT4 to provide an inoculant:indigenous AMF ratio of ca. 1 : 100. The shoot and root growth, and AMF colonization levels of NT4-inoculated lentil were significantly (P≤0.05) greater than the appropriate control plants in the unfertilized soil at 48 days after planting (DAP). At 95 DAP, NT4 inoculation had significantly increased the shoot dry weight (P≤0.08) and AMF colonization (P≤0.05) of lentil plants receiving 5 mg P kg^–1 soil, whereas 20 mg P kg^–1 soil reduced the shoot growth of NT4-inoculated plants. The NT4 inoculant had no effect (P≤0.05) on shoot P content, but increased (P≤0.08) the P-use efficiency of lentil plants receiving 5 mg P kg^–1 soil. In contrast to the inoculant's effect on lentil, NT4 generally had no positive effect on any of the parameters assessed for wheat cv. Laura at any P level at 48 or 95 DAP. Similarly, there was no positive effect of NT4 on shoot or root growth, or AMF colonization of wheat cv. Neepawa plants at any P level at 48 DAP. However, NT4 inoculation increased the grain yield of Neepawa by 20% (P≤0.05) when fertilized with 20 mg P kg^–1 soil. This yield increase was associated with a significant (P≤0.05) reduction in root biomass and a significant (P≤0.05) increase in the grain P content of inoculated plants. Thus, NT4 appears to have a preference for the Neepawa cultivar. Our results show that lentil was more dependent on mycorrhizae than wheat and responded to an AMF inoculant even in soil containing high levels of indigenous AMF. It might, therefore, be possible to develop mixed inoculants containing rhizobia and AMF for field production of legumes. Accepted: 22 February 1997     

An automated method to morph finite element whole-body human models with a wide range of stature and body shape for both men and women

Field data analyses have shown that small female, obese, and/or older occupants are at increased risks of death and serious injury in motor-vehicle crashes compared with mid-size young men. The current adult finite element (FE) human models represent occupants in the same three body sizes (large male, mid-size male, and small female) as those for the contemporary adult crash dummies. Further, the time needed to develop an FE human model using the traditional method is measured in months or even years. In the current study, an improved regional mesh morphing method based on landmark-based radial basis function (RBF) interpolation was developed to rapidly morph a mid-size male FE human model into different geometry targets. A total of 100 human models with a wide range of human attributes were generated. A pendulum chest impact condition was applied to each model as an initial assessment of the resulting variability in response. The morphed models demonstrated mesh quality similar to the baseline model. The peak impact forces and chest deflections in the chest pendulum impacts varied substantially with different models, supportive of consideration of population variation in evaluating the occupant injury risks. The method developed in this study will enable future safety design optimizations targeting at various vulnerable populations that cannot be considered with the current models.     

Design and characterization of a system for exposure of cultured cells to extremely low frequency electric and magnetic fields over a wide range of field strengths

A system is described that is capable of producing extremely low frequency (ELF) magnetic fields for relatively short-term exposure of cultured mammalian cells. The system utilizes a ferromagnetic core to contain and direct the magnetic field of a 1,000 turn solenoidal coil and can produce a range of flux densities and induced electric fields much higher than those produced by Helmholtz coils. The system can generate magnetic fields from the microtesla (μT) range up to 0.14 T with induced electric field strengths on the order of 1.0 V/m. The induced electric field can be accurately varied by changing the sample chamber configuration without changing the exposure magnetic field. This gives the system the ability to separate the bioeffects of magnetic and induced electric fields. In the frequency range of 4–100 Hz and magnetic flux density range of 0.005–0.14 T, the maximum total harmonic distortion of the induced electric field is typically less than 1.0%. The temperature of the samples is held constant to within 0.4°C by constant perfusion of warmed culture medium through the sample chamber. © 1993 Wiley-Liss, Inc.     

Clinal adaptation and adaptive plasticity in Artemisia californica: implications for the response of a foundation species to predicted climate change

Local adaptation and plasticity pose significant obstacles to predicting plant responses to future climates. Although local adaptation and plasticity in plant functional traits have been documented for many species, less is known about population‐level variation in plasticity and whether such variation is driven by adaptation to environmental variation. We examined clinal variation in traits and performance – and plastic responses to environmental change – for the shrub Artemisia californica along a 700 km gradient characterized (from south to north) by a fourfold increase in precipitation and a 61% decrease in interannual precipitation variation. Plants cloned from five populations along this gradient were grown for 3 years in treatments approximating the precipitation regimes of the north and south range margins. Most traits varying among populations did so clinally; northern populations (vs. southern) had higher water‐use efficiencies and lower growth rates, C : N ratios and terpene concentrations. Notably, there was variation in plasticity for plant performance that was strongly correlated with source site interannual precipitation variability. The high‐precipitation treatment (vs. low) increased growth and flower production more for plants from southern populations (181% and 279%, respectively) than northern populations (47% and 20%, respectively). Overall, precipitation variability at population source sites predicted 86% and 99% of variation in plasticity in growth and flowering, respectively. These striking, clinal patterns in plant traits and plasticity are indicative of adaptation to both the mean and variability of environmental conditions. Furthermore, our analysis of long‐term coastal climate data in turn indicates an increase in interannual precipitation variation consistent with most global change models and, unexpectedly, this increased variation is especially pronounced at historically stable, northern sites. Our findings demonstrate the critical need to integrate fundamental evolutionary processes into global change models, as contemporary patterns of adaptation to environmental clines will mediate future plant responses to projected climate change.     

SPR and NMR characterization of the molecular interaction between A9 peptide and a model system of HER2 receptor: A fragment approach for selecting peptide structures specific for their target

The binding process of A9 peptide toward HER2‐DIVMP, a synthetic model of the receptor domain IV, was studied by using the surface plasmon resonance (SPR) technique, with the aim of validating it as a fast and reliable screening method for selecting peptide ligands specifically targeting a domain of their target. To investigate the structural basis of A9 binding to the model of HER2‐DIVMP, multiple ligand‐based nuclear magnetic resonance (NMR) methods were applied. The use of saturation transfer difference (STD) and WaterLOGSY NMR experiments identified key residues in the peptide for the receptor binding. Moreover, the bound conformation of the A9 peptide was obtained using transferred nuclear Overhauser effect spectroscopy (trNOESY) experiments. The NMR data revealed an extended binding surface that confirms an in silico model previously reported. These structural findings could provide good starting points for future lead structures optimization specific for the receptor target.