Characterization of surface binding sites in glycoside hydrolases: A computational study

Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty‐five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut‐off differences in each SBSs with different ligand size, molecular docking were performed. Molecular docking results were used to refine SBSs classification and binding sites cut‐off. Docking results predicted putative ligands positions and displayed dependence of the ligands binding mode to the structural type of SBSs. Physicochemical properties of SBSs were calculated for all docking results with YASARA Structure. The results showed that all SBSs are hydrophilic, while their charges could vary and depended to ligand size and defined cut‐off. Surface binding sites type B had highest average values of solvent accessible surface area. Analysis of interactions showed that hydrophobic interactions occur more than hydrogen bonds, which is related to the presence of aromatic residues and carbohydrates interactions.     

Central Place Foraging in Nonpatchy Habitats

This paper deal with a model of optimal foraging in a habitat with arbitrary food distribution. It takes into account an arbitrary risk cost related to the distance to the animal's nest. Food acquisition and risk cost are accounted for in common units of fitness. The resulting problem is solved in the context of Calculus of Variations. The optimal duration of absence from the nest and the optimal spatial allocation of foraging time are obtained: the optimal strategy leads to separate the habitat into a region to exploit and a region to ignore. The definition of these two distinct regions depends on the relative importance of risk and food availability. With realistic risk costs, the resulting strategy indicates a highly selective behaviour when far from the nest, as observed in field studies. The model is also extended to take account of the need of returning to the nest to guard it or to feed the young.     

The cost of mutualism in a fly-fungus interaction

The movement ability of individuals has become increasingly important to a variety of ecological questions. In this study, I investigate how plant structure and changes in body size through development affect the movement ability of a predaceous stinkbug, Podisus maculiventris, on three species of goldenrod (Solidago spp.) representing a wide range of surface complexities. I adapt existing techniques for quantifying movement in two dimensions to the study of movement on natural plant structures in three dimensions. These experiments indicate that plant structure and insect size are significant factors affecting the movement ability of P. maculiventris. Changes in movement ability due to factors of ontogeny and different habitat structures suggest that the scale of an individual’s ambit or ecological sphere of influence may vary within its lifespan. Considering the influence of ontogeny and habitat structure on movement ability may be useful to investigations of population dynamics, foraging behavior, and pest management. Received: 14 July 1999 / Accepted: 23 March 2000     

pH Biosensing by PI4P Regulates Cargo Sorting at the TGN

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Distinct feeding strategies of generalist and specialist spiders

1. Feeding behaviour of generalist and specialist predators is determined by a variety of trophic adaptations. Specialised prey‐capture adaptations allow specialists to catch relatively large prey on a regular basis. As a result, specialists might be adapted to exploit each item of prey more thoroughly than do generalists. 2. It was expected that obligatory specialist cursorial spiders would feed less frequently than generalists but for a longer time and, thus, that their foraging pause would be longer. First, the feeding frequencies of three generalist spider species (Cybaeodamus taim, Harpactea hombergi, Hersiliola sternbergsi) were compared with those three phylogenetically related specialist species: myrmecophagous Zodarion rubidum, and araneophagous Nops aff. variabilis and Palpimanus orientalis. 3. Generalists captured more prey, exploited each item of prey for a significantly shorter time, and had a shorter foraging pause than was the case for specialists. Generalists also gained significantly less relative amount of prey mass than did specialists. 4. Second, the study compared the prey DNA degradation rate in the gut of generalists and specialists by means of PCR. The degradation rate was not significantly different between specialists and generalists: the detectability half‐life was estimated to exist for 14.3 days after feeding. 5. This study shows that the feeding strategies of cursorial generalist and obligatory specialist spiders are different. Obligatory specialists have evolved a feeding strategy that is based on thorough exploitation of a few large prey, whereas generalists have evolved a strategy that is based on short exploitation of multiple small items of prey.     

Uptake and distribution of calcium, magnesium and potassium in cucumber of different age

Uptake and distribution of Ca⁺, Mg²⁺ and K²⁺ were investigated in plants of cucumber ( Cucumis sativus L. var. Cila) which had been cultivated for 12, 19, 32, or 53 days in complete nutrient solution with 1.0 m M Ca²⁺, 2.0 m M Mg²⁺ and 2.0 m M K⁺. The ⁺ concentration was about the same in roots and shoots, while the Ca²⁺ and Mg²⁺ concentrations were low in roots compared to shoots. The K⁺ concentration decreased with increasing leaf age, while the Ca²⁺ and Mg²⁺ concentrations increased, except in older plants with flowers and fruits, where an increased concentration was found in the youngest leaves. This is discussed in connection with increased indoleacetic acid (IAA) synthesis in the shoot. Excision of leaves at different levels from 21-day-old plants, followed by uptake for 24 h from the nutrient solution on days 22 and 23, resulted in no immediate reduction in Ca²⁺ (⁴⁵Ca) uptake. Transport of Ca²⁺ increased to leaves above and below the excision point and total Ca²⁺ uptake remained at the same level as for the intact plant. It is suggested that regulation of Ca²⁺ uptake is primarily achieved in the root while the distribution in the shoot is regulated by the accessability of negative binding sites.     

The role of context, colour and location cues in socially learned novel food source preferences in starlings, Sternus vulgaris

Although the opportunity for errors in social learning is widely recognised, as yet little research has been directed towards understanding specific inaccuracies, biases and limitations in social learning and the mechanisms that give rise to them. In two experiments I ask how starlings, Sternus vulgaris, identify exemplars of novel feeders previously learned about socially. I find that starlings have a stronger response to feeders in the same context as that in which social learning took place, compared to identical and nonidentical feeders in a different context. Within a context that matches where social learning took place, starlings prefer feeders that show the same location and colour as the feeder demonstrated by the demonstrator starling, and show no preference when colour and location cues are dissociated. This suggests that starlings are relatively accurate social learners, since they show strong responses to novel foraging options only if they match the context, colour and location of options learned about socially, and they do so after very few trials. Furthermore, the responses of the subjects were compatible with conditioned learning-like mechanisms, which provide a useful basis for the further investigation of the origins and implications of errors in social learning.     

Influence of intertree distance on foraging behaviour of Rhagoletis pomonella in the field

Abstract. 1. We tested a prediction from contemporary foraging theory that animals should decrease their allocation of energy to the searching of individual patches when interpatch travel costs decrease.
2. We used individual Rhagoletis pomonella Walsh (Diptera: Tephritidae) females foraging for oviposition sites (= Crataegus fruit) in a host tree which was surrounded by four other trees at varying distances.
3. We found that flies generally invested less search, measured as time spent searching a tree or number of leaves visited on a tree, when neighbouring trees were nearby than when farther away.
4. Under our test conditions, flies appeared to have difficulty locating neighbouring trees at a distance of more than 1.6 m.
5. Our study calls into question the interpretation of search effort by insects within resource patches in the absence of information on interpatch distances.     

The use of breeding sites of Tilapia congica (Thys & van Audenaerde 1960) to delineate conservation sites in the Lake Tumba,Democratic Republic of Congo: toward the conservation of the lake ecosystem

To guide the zoning process in Lake Tumba, Democratic Republic of Congo, breeding sites of Tilapia congica were studied. Physical metrics measured were: nest depths, exposure to sun rays, distance from the edges, site spreads, and habitat types. Mean nest depth = 0.23 m ± 0.08 (SD), range = 0.04–2.2 m (n = 553 nests); 100% (n = 70 sites) sites were exposed to the sun and the polynomial regression analysis showed 90% sites were within the range 51–250 m from the lake shores (y = ?1.7143x² + 10.371x? 1.8; R² = 0.597, n = 70 sites), with 60% clumped within the range of 51–150 m, indicating a relationship between nesting sites and the distance from edges. The largest group spread group was 300 m, and among the four breeding sites identified, one was ～10 km long, meaning a zonal spatial spread ∏ = 300 ha and a core reproduction zone ∏′ = 100 ha. T. congica built 87.30% of their nest in habitats where Hippo grass Vossia cuspidata (48.20%) and Water lily Nympheae stellata (39.10%) dominated. T. congica shared 41.81% of its nesting sites with other fish species, leading to the conclusion that protecting the species habitats would provide the umbrella for the conservation of other species.     

Tubes and foraging behavior in larval Chironomidae: implications for predator avoidance

Summary In laboratory experiments, I studied differential susceptibility of four co-occurring species of chironomids to a predatory damselfly. The chironomids differed in foraging behavior and could be ranked according to the amount of time they spent outside of their tubes. In choice experiments, the predator consistently selected the prey which spent more time out of the tube, and time out of tube was a significant predictor of the predation rate coefficient. Electivity indices, calculated from field samples and diet analyses of the predator, supported the laboratory results. The data suggest that exposure to predators in a heterogeneous prey community is largely determined by tubedwelling behavior.