Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

Optimally distributed actuator placement and control for a slewing single-link flexible manipulator

A method is proposed for determining the optimal placement and controller design for multiple distributed actuators to reduce the vibrations of flexible structures. In particular, application of piezoceramic patches to a horizontally-slewing single-link flexible manipulator modeled using the assumed modes method is investigated. The optimization method uses simulated annealing and allows placement of any number of distributed actuators of unequal length, although piezoceramics of fixed equal lengths are used in the example. It also designs an linear-quadratic-regulator controller as part of the optimization procedure. The measures of performance used in the investigation to determine optimality are the total mass of the system and the time integral of the absolute value of the hub and tip position error. This study also varies the relative weightings for each of these performance measures to observe the effects on the controller designs and piezoceramic patch positions in the optimized solutions.

Role of Diadegma semiclausum (Hymenoptera: Ichneumonidae) in controlling Plutella xylostella (Lepidoptera: Plutellidae): Cage exclusion experiments and direct observation

We evaluated the role of the larval parasitoid, Diadegma semiclausum Hellen (Hymenoptera: Ichneumonidae), in controlling Plutella xylostella (L.) (Lepidoptera: Plutellidae) by cage exclusion experiments and direct field observation during the winter season in southern Queensland, Australia. The cage exclusion experiment involved uncaged, open cage and closed cage treatments. A higher percentage (54-83%) of P. xylostella larvae on sentinel plants were lost in the uncaged treatment than the closed (4-9%) or open cage treatments (11-29%). Of the larvae that remained in the uncaged treatment, 72-94% were parasitized by D. semiclausum , much higher than that in the open cage treatment (8-37% in first trial, and 38-63% in second trial). Direct observations showed a significant aggregation response of the field D. semiclausum populations to high host density plants in an experimental plot and to high host density plots that were artificially set-up near to the parasitoid source fields. The degree of aggregation varied in response to habitat quality of the parasitoid source field and scales of the manipulated host patches. As a result, density-dependence in the pattern of parasitism may depend on the relative degree of aggregation of the parasitoid population at a particular scale. A high degree of aggregation seems to be necessary to generate density-dependent parasitism by D. semiclausum . Integration of the cage exclusion experiment and direct observation demonstrated the active and dominant role of this parasitoid in controlling P. xylostella in the winter season. A biologically based IPM strategy, which incorporates the use of D. semiclausum with Bt, is suggested for the management of P. xylostella in seasons or regions with a mild temperature.

Learning of foraging skills by fish

This chapter outlines the relationships between a number of key factors that influence learning and memory, and illustrates them by reference to studies on the foraging behaviour of fish. Learning can lead to significant improvements in foraging performance in only a few exposures, and at least some fish species are capable of adjusting their foraging strategy as patterns of patch profitability change. There is also evidence that the memory window for prey varies between fish species, and that this may be a function of environmental predictability. Convergence between behavioural ecology and comparative psychology offers promise in terms of developing more mechanistically realistic foraging models and explaining apparently 'suboptimal' patterns of behaviour. Foraging decisions involve the interplay between several distinct systems of learning and memory, including those that relate to habitat, food patches, prey types, conspecifics and predators. Fish biologists, therefore, face an interesting challenge in developing integrated accounts of fish foraging that explain how cognitive sophistication can help individual animals to deal with the complexity of the ecological context.

Chic chicks: the evolution of chick ornamentation in rails

Competition over access to food has led to the evolution of a variety of exaggerated visual and vocal displays in altricial nestling birds. Precocial chicks that are fed by their parents also vary widely in appearance ranging from those with inconspicuous coloration to those with brightly colored bills, fleshy parts, and plumes. These ornaments are lost by the end of the period of parental dependence, suggesting they function in competition over parental care. We use a comparative approach to evaluate which ecological or life-history variables may have favored the evolution of conspicuous ornamentation in precocial chicks. We compiled data on chick morphology, ecology, and social organization of species in the Family Rallidae, a group with highly variable downy chicks. Chick ornamentation in the form of brightly colored bills, fleshy patches, or plumes is observed in 36 of 97 species for which downy chicks are described. Phylogenetic reconstructions suggest that nonornamentation is the ancestral state. Chick ornamentation has evolved multiple times within the Rallidae and is significantly associated with large clutch sizes and polygamous mating systems. Chick ornamentation was also weakly associated with adult ornamentation and adult dimorphism. We argue that these results support the hypothesis that lineages with higher levels of sibling competition are more likely to evolve ornamented chicks.

Why do eastern curlews Numenius madagascariensis feed on prey that lowers intake rate before migration?

Eastern curlews Numenius madagascariensis spending the nonbreeding season in eastern Australia foraged on three intertidal decapods: soldier crab Mictyris longicarpus, sentinel crab Macrophthalmus crassipes and ghost-shrimp Trypaea australiensis. Due to their ecology, these crustaceans were spatially segregated (=distributed in 'patches') and the curlews intermittently consumed more than one prey type. It was predicted that if the curlews behaved as intake rate maximizers, the time spent foraging on a particular prey (patch) would reflect relative availabilities of the prey types and thus prey-specific intake rates would be equal. During the mid-nonbreeding period (November-December), Mictyris and Macrophthalmus were primarily consumed and prey-specific intake rates were statistically indistinguishable (8.8 versus 10.1 kJ x min(-1)). Prior to migration (February), Mictyris and Trypaea were hunted and the respective intake rates were significantly different (8.9 versus 2.3 kJ x min(-1)). Time allocation to Trypaea-hunting was independent of the availability of Mictyris. Thus, consumption of Trypaea depressed the overall intake rate. Six hypotheses for consuming Trypaea before migration were examined. Five hypotheses: the possible error by the predator, prey specialization, observer overestimation of time spent hunting Trypaea, supplementary prey and the choice of higher quality prey due to a digestive bottleneck, were deemed unsatisfactory. The explanation for consumption of a low intake-rate but high quality prey (Trypaea) deemed plausible was diet optimisation by the Curlews in response to the pre-migratory modulation (decrease in size/processing capacity) of their digestive system. With a seasonal decrease in the average intake rate, the estimated intake per low tide increased from 1233 to 1508 kJ between the mid-nonbreeding and pre-migratory periods by increasing the overall time spent on the sandflats and the proportion of time spent foraging.

Modal characteristics of a flexible beam with multiple distributed actuators

A flexible structure with surface-bonded piezoceramic patches is modelled using Timoshenko beam theory. Exact mode shapes and natural frequencies associated with the flexural motion are computed for various piezoceramic distributed actuator arrangements. The effects of patch placement and of shear on the modal characteristics are demonstrated using a cantilevered beam as an example. Perfect bonding of the piezoceramic to the beam substructure is assumed, and for the purposes of this paper only passive piezoceramic properties are considered. The modelling technique and results obtained in a closed form are intended to assist investigations into the modelling and control of active structures with surface-bonded piezoceramic actuators. (C) 2003 Elsevier Science Ltd. All rights reserved.

The Randomized Nitric Oxide Tocolysis Trial (RNOTT) for the treatment of preterm labor

Objective: This study was undertaken to assess the effectiveness of glyceryl trinitrate (GTN) patches in comparison with beta2 sympathornimetics (beta2) for the treatment of preterm labor. Study design: A multicenter, multinational, randomized controlled trial was conducted in tertiary referral teaching hospitals. Women in threatened preterm labor with positive fetal fibronectin or ruptured membranes between 24 and 35 weeks' gestation were recruited and randomly assigned to either beta2 or GTN with rescue beta2 tocolysis if moderate-to-strong contractions persisted at 2 hours. Obstetric and neonatal outcomes were assessed. Results: Two hundred thity-eight women were recruited and randomly assigned, 117 to beta2 and 121 to GTN. On a strict intention-to-treat basis, there was no significant difference in the time to delivery using Kaplan-Meier curves (P = .451). At 2 hours, 27% of women receiving beta2 had moderate or stronger contractions compared with 53% in the GTN group (P < .001). This led to 35% of women in the GTN group receiving rescue treatment. If delivery or requirement for beta2 rescue are regarded as treatment failure, then a significant difference was observed between the 2 arms (P = .0032). There were no significant differences in neonatal outcomes. Conclusion: GTN is a less efficacious tocolytic compared with beta2 sympathomimetics. (C) 2004 Elsevier Inc. All rights reserved.

The effects of habitat fragmentation due to forestry plantation establishment on the demography and genetic variation of a marsupial carnivore, Antechinus agilis

We conducted a demographic and genetic study to investigate the effects of fragmentation due to the establishment of an exotic softwood plantation on populations of a small marsupial carnivore, the agile antechinus (Antechinus agilis), and the factors influencing the persistence of those populations in the fragmented habitat. The first aspect of the study was a descriptive analysis of patch occupancy and population size, in which we found a patch occupancy rate of 70% among 23 sites in the fragmented habitat compared to 100% among 48 sites with the same habitat characteristics in unfragmented habitat. Mark-recapture analyses yielded most-likely population size estimates of between 3 and 85 among the 16 occupied patches in the fragmented habitat. Hierarchical partitioning and model selection were used to identify geographic and habitat-related characteristics that influence patch occupancy and population size. Patch occupancy was primarily influenced by geographic isolation and habitat quality (vegetation basal area). The variance in population size among occupied sites was influenced primarily by forest type (dominant Eucalyptus species) and, to a lesser extent, by patch area and topographic context (gully sites had larger populations). A comparison of the sex ratios between the samples from the two habitat contexts revealed a significant deficiency of males in the fragmented habitat. We hypothesise that this is due to male-biased dispersal in an environment with increased dispersal-associated mortality. The population size and sex ratio data were incorporated into a simulation study to estimate the proportion of genetic diversity that would have been lost over the known timescale since fragmentation if the patch populations had been totally isolated. The observed difference in genetic diversity (gene diversity and allelic richness at microsatellite and mitochondrial markers) between 16 fragmented and 12 unfragmented sites was extremely low and inconsistent with the isolation of the patch populations. Our results show that although the remnant habitat patches comprise approximately 2% of the study area, they can support non-isolated populations. However, the distribution of agile antechinus populations in the fragmented system is dependent on habitat quality and patch connectivity. (C) 2004 Elsevier Ltd. All rights reserved.

Adsorption of argon on homogeneous graphitized thermal carbon black and heterogeneous carbon surface

In this paper we investigate the effects of surface mediation on the adsorption behavior of argon at different temperatures on homogeneous graphitized thermal carbon black and on heterogeneous nongraphitized carbon black surface. The grand canonical Monte Carlo (GCMC) simulation is used to study the adsorption, and its performance is tested against a number of experimental data on graphitized thermal carbon black (which is known to be highly homogeneous) that are available in the literature. The surface-mediation effect is shown to be essential in the correct description of the adsorption isotherm because without accounting for that effect the GCMC simulation results are always greater than the experimental data in the region where the monolayer is being completed. This is due to the overestimation of the fluid–fluid interaction between particles in the first layer close to the solid surface. It is the surface mediation that reduces this fluid–fluid interaction in the adsorbed layers, and therefore the GCMC simulation results accounting for this surface mediation that are presented in this paper result in a better description of the data. This surface mediation having been determined, the surface excess of argon on heterogeneous carbon surfaces having solid–fluid interaction energies different from the graphite can be readily obtained. Since the real heterogeneous carbon surface is not the same as the homogeneous graphite surface, it can be described by an area distribution in terms of the well depth of the solid–fluid energy. Assuming a patchwise topology of the surface with patches of uniform well depth of solid–fluid interaction, the adsorption on a real carbon surface can be determined as an integral of the local surface excess of each patch with respect to the differential area. When this is matched against the experimental data of a carbon surface, we can derive the area distribution versus energy and hence the geometrical surface area. This new approach will be illustrated with the adsorption of argon on a nongraphitized carbon at 87.3 and 77 K, and it is found that the GCMC surface area is different from the BET surface area by about 7%. Furthermore, the description of the isotherm in the region of BET validity of 0.06 to 0.2 is much better with our method than with the BET equation.

Patch dynamics in grazed subtropical native pastures in south-east Queensland

Patch formation is common in grazed grasslands but the mechanisms involved in the formation and maintenance of patches are not clear. To increase our knowledge on this subject we examined possible reasons for patch formation and the influence of management on changes between patch states in three experiments in native pasture communities in the Crows Nest district, south-east Queensland. In these communities, small-scale patches (tall grassland (dominated by large and medium tussock grasses), short swards (dominated by short tussock grasses and sedges), and lawns (dominated by stoloniferous and/or rhizomatous grasses)) are readily apparent. We hypothesized that the formation of short sward and lawn patches in areas of tall grassland was due to combinations of grazing and soil fertility effects. This was tested in Experiment 1 by applying a factorial combination of defoliation, nutrient application and transplants of short tussock and stoloniferous species to a uniform area of tall grassland. Total species density declined during the experiment, was lower with high nutrient applications, but was not affected by defoliation. There were significant changes in abundance of species that provided support for our hypotheses. With light defoliation and low nutrients, the tall grassland remained dominated by large tussock grasses and contained considerable amounts of forbs. With heavy defoliation, the pastures were dominated by medium tussock grasses and there were significant decreases in forbs and increases in sedges (mainly with low nutrients) and stoloniferous grasses (mainly with high nutrients). Total germinable seed densities and those of most species groups were significantly lower in the heavy defoliation than the light defoliation plots. Total soil seed numbers were not affected by nutrient application but there were fewer seeds of the erect forbs and more sedge seeds in plots with high nutrients. The use of resting from grazing and fire to manage transitions between patches was tested. In Experiment 2, changes in species density and abundance were measured for 5 years in the three patch types with and without grazing. Experiment 3 examined the effects of fire, grazing and resting on short sward patches over 4 years. In Experiment 2, total species density was lower in lawn than short sward or tall grassland patches, and there were more species of erect forbs than other plant groups in all patch types. The lawn patches were originally dominated by Cynodon spp. This dominance continued with grazing but in ungrazed patches the abundance of Cynodon spp. declined and that of forbs increased. In the short sward patches, dominance of short tussock grasses continued with grazing but in ungrazed plots their abundance declined while that of large tussock grasses increased. The tall grassland patches remained dominated by large and medium tussock species. In Experiment 3, fire had no effect on species abundance. On the grazed plots the short tussock grasses remained dominant but where the plots were rested from grazing the small tussock grasses declined and the large tussock grasses increased in abundance. The slow and relatively small changes in these experiments over 4 or 5 years showed how stable the composition of these pastures is, and that rapid changes between patch types are unlikely.

Selective modulation of neuronal nicotinic acetylcholine receptor channel subunits by G(o)-protein subunits

protein modulation of neuronal nicotinic acetylcholine receptor ( nAChR) channels in rat intrinsic cardiac ganglia was examined using dialyzed whole-cell and excised membrane patch-recording configurations. Cell dialysis with GTP gamma S increased the agonist affinity of nAChRs, resulting in a potentiation of nicotine-evoked whole-cell currents at low concentrations. ACh- and nicotine-evoked current amplitudes were increased approximately twofold in the presence of GTP gamma S. In inside-out membrane patches, the open probability (NPo) of nAChR-mediated unitary currents was reversibly increased fourfold after bath application of 0.2mM GTP gamma S relative to control but was unchanged in the presence of GDP gamma S. The modulation of nAChR-mediated whole- cell currents was agonist specific; currents evoked by the cholinergic agonists ACh, nicotine, and 1,1-dimethyl-4-phenylpiperazinium iodide, but not cytisine or choline, were potentiated in the presence of GTP gamma S. The direct interaction between G-protein subunits and nAChRs was examined by bath application of either G(o)alpha or G beta gamma subunits to inside-out membrane patches and in glutathione S-transferase pull-down and coimmunoprecipitation experiments. Bath application of 50 nM G beta gamma increased the open probability of ACh- activated single-channel currents fivefold, whereas G(o)alpha( 50 nM) produced no significant increase in NPo. Neuronal nAChR subunits alpha 3-alpha 5 and alpha 2 exhibited a positive interaction with G(o)alpha and G beta gamma, whereas beta 4 and alpha 7 failed to interact with either of the G-protein subunits. These results provide evidence for a direct interaction between nAChR and G-protein subunits, underlying the increased open probability of ACh-activated single-channel currents and potentiation of nAChR-mediated whole-cell currents in parasympathetic neurons of rat intrinsic cardiac ganglia.

Conjunctival benign reactive lymphoid hyperplasia associated with myopic scleral thinning

Known causes of conjunctival salmon patches include lymphoma, amyloidosis, sarcoidosis, leukaemia and benign reactive lymphoid hyperplasia. The aetiology of benign reactive lymphoid hyperplasia is thought to be a localized reactive change induced by an irritative or antigenic stimulus. The case of benign reactive lymphoid hyperplasia reported herein occurred in a myopic patient with extremely thin sclera. The authors' hypothesis is that choroidal antigens are able to perfuse through thin sclera and act as chronic irritants to the overlying conjunctiva resulting in a lymphoid response and subsequent salmon patch formation.

Modeling the age of tropical moist forest fragments in heavily-cleared lowland landscapes of Colombia

Increasingly, large areas of native tropical forests are being transformed into a mosaic of human dominated land uses with scattered mature remnants and secondary forests. In general, at the end of the land clearing process, the landscape will have two forest components: a stable component of surviving mature forests, and a dynamic component of secondary forests of different ages. As the proportion of mature forests continues to decline, secondary forests play an increasing role in the conservation and restoration of biodiversity. This paper aims to predict and explain spatial and temporal patterns in the age of remnant mature and secondary forests in lowland Colombian landscapes. We analyse the age distributions of forest fragments, using detailed temporal land cover data derived from aerial photographs. Ordinal logistic regression analysis was applied to model the spatial dynamics of mature and secondary forest patches. In particular, the effect of soil fertility, accessibility and auto-correlated neighbourhood terms on forest age and time of isolation of remnant patches was assessed. In heavily transformed landscapes, forests account for approximately 8% of the total landscape area, of which three quarters are comprised of secondary forests. Secondary forest growth adjacent to mature forest patches increases mean patch size and core area, and therefore plays an important ecological role in maintaining landscape structure. The regression models show that forest age is positively associated with the amount of neighbouring forest, and negatively associated with the amount of neighbouring secondary vegetation, so the older the forest is the less secondary vegetation there is adjacent to it. Accessibility and soil fertility also have a negative but variable influence on the age of forest remnants. The probability of future clearing if current conditions hold is higher for regenerated than mature forests. The challenge of biodiversity conservation and restoration in dynamic and spatially heterogeneous landscape mosaics composed of mature and secondary forests is discussed. (c) 2004 Elsevier B.V. All rights reserved.

Genetic diversity and regional identity in the Australian remnant Nothofagus moorei

Nothofagus moorei (F. Muell.) Krasser has a disjunct and narrow distribution in south-eastern Australian cool temperate rainforest. To assess the conservation-genetic priorities for this species, the genetic diversity of 20 populations sampled from the largest remnant patches at northern and southern distributional extremes, the McPherson and Barrington ranges (a total of 146 individuals), was investigated by using inter simple sequence repeats (ISSR). Regeneration in northern regions of N. moorei has been documented to be predominantly by vegetative means, but our results indicate little evidence of clonality outside the multi-stemmed rings of trees. In addition, genetic diversity was considerably higher in the northern (McPherson, h = 0.1613) than in the southern range (Barrington, h = 0.1159), and genetic differentiation was significantly positively correlated with geographic distance in the former region, but not the latter. Total intraspecific variation was moderate, as measured by Shannon's diversity index, I = 0.2719, and Nei's gene diversity, h = 0.1672, and is considered at the high end of spectrum for estimates of narrow endemic species. An analysis of molecular variation indicated that the majority of genetic variation is partitioned among individuals within population (60%; P < 0.001), rather than among populations within regions (10%; P < 0.001). However, a large and significant component of the measured diversity was partitioned between northern and southern regions (29%; P < 0.001). Several hypotheses are outlined to explain these differences and management implications are discussed. However, given the narrow range, poor dispersal mechanism and restriction to cool temperate rainforest, the continued existence of N. moorei is most threatened by environmental instability and habitat loss resulting from global climate change. In this context the northern regions of the species are most at risk and extinction of such populations would lead to a significant loss of genetic variation for the species as a whole.