Spatial and temporal factors associated with nest survival of Gray Flycatchers in managed ponderosa pine forests

Gray Flycatchers (Empidonax wrightii) breed in a variety of habitats in the arid and semi‐arid regions of the western United States, but little is known about their breeding biology, especially in the northern portion of their range where they nest in ponderosa pine (Pinus ponderosa) forests. From May to July 2014 and 2015, we conducted surveys for singing male Gray Flycatchers along the eastern slope of the Cascade Range in Washington, U.S.A, monitored flycatcher nests, and quantified nest‐site vegetation. We used a logistic‐exposure model fit within a Bayesian framework to model the daily survival probability of flycatcher nests. During the 2 yr of our study, we monitored 141 nests, with 93% in ponderosa pines. Mean clutch size was 3.6 eggs and the mean number of young fledged per nest was 3.2. Predation accounted for 90% of failed nests. We found a positive association between daily nest survival and both nest height and distance of nest substrates from the nearest tree. Flycatchers that locate their nests higher above the ground and further from adjacent trees may be choosing the safest alternative because higher nests may be less exposed to terrestrial predators and nests in trees that are farther from other trees may be less exposed to arboreal predators such as jays (Corvidae) that may forage in patches with connected canopies. Nests in trees farther from other trees may also allow earlier detection of approaching predators and thus aid in nest defense.     

Uncertainty associated with river health assessment in a varying environment: The case of a predictive fish-based index in France

Sensitive biological measures of river ecosystem quality are needed to assess, maintain or restore ecological conditions of water bodies. Since our understanding of these complex systems is imperfect, decision-making requires recognizing uncertainty. In this study, a new predictive multi-metric index based on fish functional traits was developed to assess French rivers. Information on fish assemblage structure, local environment and human-induced disturbances of 1654 French river sites was compiled. A Bayesian framework was used to predict theoretical metric values in absence of human pressure and to estimate the uncertainty associated with these predictions. The uncertainty associated with the index score gives the confidence associated with the evaluation of site ecological conditions.Among the 228 potential metrics tested, only 11 were retained for the index computation. The final index is independent from natural variability and sensitive to human-induced disturbances. In particular, it is affected by the accumulation of different degradations and specific degradations including hydrological perturbations. Predictive uncertainty is globally lower for IPR+ than for underlying metrics.This new methodology seems appropriate to develop bio-indication tools accounting for uncertainty related to reference condition definition and could be extended to other biological groups and areas. Our results support the use of multi-metric indexes to assess rivers and strengthen the idea that examination of uncertainty could contribute greatly to the improvement of the assessment power of bio-indicators.     

Characterization of the passive mechanical properties of spine muscles across species

Passive mechanical properties differ between muscle groups within a species. Altered functional demands can also shift the passive force-length relationship. The extent that passive mechanical properties differ within a muscle group (e.g. spine extensors) or between homologous muscles of different species is unknown. It was hypothesized that multifidus, believed to specialize in spine stabilization, would generate greater passive tensile stresses under isometric conditions than erector spinae, which have more generalized functions of moving and stabilizing the spine; observing greater multifidus moduli in different species would strengthen this hypothesis. Permeabilized fibre bundles (n = 337) from the multifidus and erector spinae of mice, rats, and rabbits were mechanically tested. A novel logistic function was fit to the experimental data to fully characterize passive stress and modulus. Species had the greatest effect on passive muscle parameters with mice having the largest moduli at all lengths. Rats generated less passive stress than rabbits due to a shift of the passive force-length relationship towards longer muscle lengths. Rat multifidus generated slightly greater stresses than erector spinae, but no differences were observed between mouse muscles. The secondary objective was to determine the parameters required to simulate the passive force-length relationship. Experimental data were compared to the passive muscle model in OpenSim. The default OpenSim model, optimized for hindlimb muscles, did not fit any of the spine muscles tested; however, the model could accurately simulate experimental data after adjusting the input parameters. The optimal parameters for modelling the passive force-length relationships of spine muscles in OpenSim are presented.     

The relationship between species richness and standing crop in wetlands: the importance of scale

One of the few important empirical generalizations regarding herbaceous plant systems has been the demonstration that species richness is related to standing crop with maximum richness occurring at moderate levels of standing crop. This relationship is normally demonstrated by comparing among vegetation types (i.e., vegetation with different dominants). We undertook this study to test whether the species richness-standing crop relationship was evident at a finer-grained level of organization, the within vegetation type level. Fifteen wetland sites were sampled in eastern Canada and species richness and standing crop determined in each of 224 0.25 m² quadrats. Each site was relatively homogeneous in terms of the dominant species present and were therefore categorized as single vegetation types. However, as a group, the sites comprised a wide range of vegetation types.A second order polynomial regression indicated a significant bitonic relationship between species richness and standing crop at the among-vegetation types scale, that is, when all 15 sites were combined. At the within-vegetation type level, however, no significant relationships were observed (p>0.05). The results indicate that the model of species richness proposed by Grime has predictive power at a coarse-grained level of organization, among vegetation types, but does not survive the transition to a finer-grained level of organization, the within vegetation type level. Therefore, the higher level processes which structure species richness patterns among vegetation types are not the same processes which determine richness patterns within a vegetation type.     

Energy allocation in the cladoceran Daphnia magna Straus,under starvation and refeeding

Summary Models incorporating the energetics of individual daphnids (Cladocera) have been developed to predict the effect of environmental variables, particularly food availability, on population dynamics. One of them, that of Kooijman (1986), assumes that all assimilated energy enters a storage compartment prior to use in production and metabolism, and that under starvation the stores are used to support maintenance, reproduction and somatic growth, in that order of priority. This predicts that, under starvation, reproduction and growth will continue for a time, and that after they cease death will be immediate. Another model, that of McCauley et al. (1990), assumes that assimilated energy is used directly for maintenance and production, and that stores are accumulated to support maintenance metabolism under starvation. This predicts that growth and reproduction should cease immediately upon starvation and that death will not be immediate. We have carried out laboratory experiments, manipulating starvation time, on Daphnia magna to distinguish between these two models. The results support features of both models in that reproduction, but not growth, ceases upon starvation. We therefore developed a third model in which both maintenance and growth are supported from stores under starvation, with maintenance taking priority over growth under these conditions.     

Diversity in the immune system: “Preconceived ideas” or ideas preconceived?

Two concepts of the evolution and regulation of expression of the combining site repertoire of the immune system, are compared. One view is based on the Associative Recognition Theory as formulated by the author and the other is based on the Idiotype Network Idea as conceived by Jerne. The two concepts are analyzed from the point of view of their logic, internal consistency and factual support.     

The role of expert systems in vegetation science

An area of artificial intelligence known as experts systems (or knowledge-based systems) is being applied in many areas of science, technology and commerce. It is likely that the techniques will have an impact on vegetation science and ecology in general. This paper discusses some of those impacts and concludes that the main effects will be in areas of applied ecology especially where ecological expertise is needed either quickly (e.g. disaster management) or across a wide range of ecological disciplines (e.g. land management decisions). Expert systems will provide ecologists with valuable tools for managing data and interacting with other fields of expertise. The impact of expert systems on ecological theory will depend on the degree to which deep knowledge (i.e. knowledge based on first principles rather than on more empirical rules) is used in formulating knowledge bases.     

Sequence homology and structure predictions of the creatine kinase isoenzymes

Comparisons of the protein sequences and gene structures of the known creatine kinase isoenzymes and other guanidino kinases revealed high homology and were used to determine the evolutionary relationships of the various guamidino kinases. A CK framework is defined, consisting of the most conserved sequence blocks, and diagnostic boxes are identified which are characteristic for anyone creatine kinase isoenzyme (e.g. for vertebrate B-CK) and which may serve to distinguish this isoenzyme from all others (e.g. from M-CKs and Mi-CKs). Comparison of the guanidino kinases by near-UV and far-UV circular dichroism further indicates pronounced conservation of secondary structure as well as of aromatic amino acids that are involved in catalysis.Abbreviations GuaK guanidino kinase - CK creatine kinase - B-and M-CK brain and muscle cytosolic CK isoenzyme - Mi-CK mitochondrial CK isoenzyme - ArgK arginine kinase - Cr creatine - PCr phosphorylcreatine - PArg phosphorylarginine     

Molecular Diversity and Evolution of bla TEM Genes Encoding β-Lactamases Resistant to Clavulanic Acid in Clinical E. coli

The molecular diversity of inhibitor-resistant TEM (IRT) enzymes was explored using a strategy which involved DNA amplification by polymerase chain reaction (PCR), analysis of restriction fragment length polymorphism (RFLP), and direct nucleotide sequencing. The study of plasmid-borne genes from 27 strains, resistant to amoxicillin and β-lactamase-inhibitor combinations, identified mutations resulting in amino acid change at positions 69, 244, 275, and 276 known to be associated with the IRT phenotype and a mutation at nucleotide position 162 in the promoter region. These mutations were found to lie on two different gene sequences, described here as ``TEM-1B like' and ``TEM-2 like' restriction linkage groups. Further analysis, of nucleotide sequences of promoter and coding regions of the β-lactamases, confirmed that a given mutation causing IRT phenotype could be associated with two different gene sequence frameworks and two different causal mutations could lie on identical gene sequence framework. These data argue in favor of convergent phenotypic evolution of IRT enzymes under the selective pressure imposed by the intensive clinical use of β-lactam–β-lactamase inhibitor combinations. Received: 18 March 1996 / Accepted: 15 July 1996     

Hückel framework study on the superconducting vibronic interaction in (AB) N chains

Superconducting vibronic interaction in the vibronic superconductivity motif has been studied in the Hückel framework for (AB) _N chain systems. Within the on-site and nearest-neighbor approximation a new vibronic constant, /L, has been introduced, of which the importance has been discussed. The effect of the vibronic operator, , has also been studied. It is also concluded that the size-dependence of the superconducting vibronic interaction also exists in the (AB) _N chain systems.On leave from the Changchun Institute of Applied Chemistry, Academia Sinica, Changchun, P. R. China, as an STA fellowship awardee hosted by the Institute of Physical and Chemical Research of Japan.