The particle size characteristics of fluvial suspended sediment: an overview

The particle size characteristics of suspended sediment are of fundamental importance in understanding its role in a variety of environmental processes. Existing knowledge concerning the spatial and temporal variability of the grain size composition of suspended sediment is, however, relatively limited. At the global scale, major contrasts may exist between individual rivers in the calibre of their suspended load and this may be related to a number of controls including climate, catchment geology and basin scale. Any attempt to understand the precise relationship between the grain size characteristics of suspended sediment and those of its source material must also take account of the selectivity of erosion and delivery processes. A local case study undertaken by the authors in the 1500 km² basin of the River Exe in Devon, UK is used to illustrate the considerable spatial variability that may occur within a relatively small area and the complexity of the associated controls.Available evidence concerning the temporal variability of the grain size characteristics of suspended sediment emphasises the diverse patterns of behaviour that may exist and the complexity of the controls involved. In some rivers the sediment may become coarser as flow increases, in others it may become finer, whilst in others it may exhibit a relatively constant grain size composition. Data from the local case study in the Exe basin are again used to highlight the considerable diversity in response to changing discharge that may occur within a relatively small area.Any attempt to understand the dynamics of sediment movement through a river system must also take account of the potential contrast between the ultimate and effective particle size distribution of suspended sediment in response to aggregation. Results from the Exe basin study indicate that even in rivers with relatively low solute concentrations, almost an order of magnitude difference may exist between the median particle size associated with the ultimate and effective grain size distributions.     

Relative importance of temporal and spatial heterogeneity in the zooplankton community of an artificial reservoir

Zooplankton samples were collected monthly at three stations in Ogochi Reservoir during 1980, and the temporal and horizontal variations in the density of dominant taxa were evaluated by a standard 2-way ANOVA with random effects. The analysis revealed that horizontal is greater than temporal variation in the warm water season (> 18 °C), whereas temporal variation is greater in the cold water season (< 18 °C). Horizontal heterogeneity of the zooplankton community found in the warm water season seems to be associated with differences in site-specific conditions.     

Microgeographic distribution of immature Ixodes dammini ticks correlated with that of deer

In order to determine whether the small-scale distribution of immature Ixodes dammini Spielman et al. corresponds closely to the activity patterns of white-tailed deer, Odocoileus virginianus (Zimmerman), these relationships were examined in a site on Long Island, New York, U.S.A. We first determined the extent and temporal pattern of adult ticks feeding on deer by examining twenty-three resident deer tranquilized during September-December 1985. I. dammini adults infested deer throughout this fall period, most abundantly during October and November. With radio-telemetry collars attached to deer we determined the relative frequency that they occupied 0.25 ha quadrats of the study site. During the following summer, we examined white-footed mice, Peromyscus leucopus (Rafinesque), that inhabited these quadrats and removed immature ticks from each. 8975 larval and 163 nymphal I. dammini were removed from 208 mice trapped in forty-three such quadrats. The frequency of deer using these quadrats was positively correlated with both the number of larval and of nymphal ticks per mouse. These results suggest that risk of I. damminiborne zoonotic disease may be decreased by locally reducing deer density in sites that experience intense human activity.     

Prediction of the packing arrangement of strands in β-sheets of globular proteins

A method is proposed for predicting the adjacency order in which strands pack in a -sheet in a protein, on the basis of its amino acid sequence alone. The method is based on the construction of a predicted contact map for the protein, in which the probability that various residue pairs are close to each other is computed from statistically determined average distances of residue pairs in globular proteins of known structure. Compact regions, i.e., portions of the sequence with many interresidue contacts, are determined on the map by using an objective search procedure. The proximity of strands in a -sheet is predicted from the density of contacts in compact regions associated with each pair of strands. The most probable -sheet structures are those with the highest density of contacts. The method has been tested by computing the probable strand arrangements in a five-strand -sheet in five proteins or protein domains, containing 62–138 residues. Of the theoretically possible 60 strand arrangements, the method selects two to eight arrangements as most probable; i.e., it leads to a large reduction in the number of possibilities. The native strand arrangement is among those predicted for three of the five proteins. For the other two, it would be included in the prediction by a slight relaxation of the cutoff criteria used to analyze the density of contacts.     

Scales and costs of habitat selection in heterogeneous landscapes

Summary Two scales of habitat selection are likely to influence patterns of animal density in heterogeneous landscapes. At one scale, habitat selection is determined by the differential use of foraging locations within a home range. At a larger scale, habitat selection is determined by dispersal and the ability to relocate the home range. The limits of both scales must be known for accurate assessments of habitat selection and its role in effecting spatial patterns in abundance. Isodars, which specify the relationships between population density in two habitats such that the expected reproductive success of an individual is the same in both, allow us to distinguish the two scales of habitat selection because each scale has different costs. In a two-habitat environment, the cost of rejecting one of the habitats within a home range can be expressed as a devaluation of the other, because, for example, fine-grained foragers must travel through both. At the dispersal scale, the cost of accepting a new home range in a different habitat has the opposite effect of inflating the value of the original habitat to compensate for lost evolutionary potential associated with relocating the home range. These costs produce isodars at the foraging scale with a lower intercept and slope than those at the dispersal scale.Empirical data on deer mice occupying prairie and badland habitats in southern Alberta confirm the ability of isodar analysis to differentiate between foraging and dispersal scales. The data suggest a foraging range of approximately 60 m, and an effective dispersal distance near 140 m. The relatively short dispersal distance implies that recent theories may have over-emphasized the role of habitat selection on local population dynamics. But the exchange of individuals between habitats sharing irregular borders may be substantial. Dispersal distance may thus give a false impression of the inability of habitat selection to help regulate population density.     

Voluntary progression order in captive rhesus macaques

The sequence in which 14 laboratory rhesus macaques left their home enclosure during a routine catching procedure was recorded on 30 occasions during 6 weeks. The animals were trained to voluntarily exit one by one and enter a transport cage for weighing and/or treatment. Mean weekly exit orders cross-correlated significantly, and individuals retained their exit positions with remarkable consistency throughout the study period. An animal's position did not depend on its sex, age, or dominance rank. The oldest female never failed to enter the transport cage as number 1. When she was prevented from taking the lead, the group was hesitant but eventually proceeded in the usual order. Food was a strong, yet not absolute, incentive for the monkeys to cooperate. If they could not expect a reward, they took more time before proceeding, but did so in the habitual order. The predictability of the exit sequence has practical managerial value because it makes it possible for a single person to quickly catch a selected group member when necessary.     

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.     

Application of a directed conformational search for generating 3-D coordinates for protein structures from alpha-carbon coordinates.

A directed conformational search algorithm using the program CONGEN (ref. 3), which samples backbone conformers, is described. The search technique uses information from the partially built structures to direct the search process and is tested on the problem of generating a full set of backbone Cartesian coordinates given only alpha-carbon coordinates. The method has been tested on six proteins of known structure, varying in size and classification, and was able to generate the original backbone coordinates with RMSs ranging from 0.30-0.87A for the alpha-carbons and 0.5-0.99A RMSs for the backbone atoms. Cis peptide linkages were also correctly identified. The procedure was also applied to two proteins available with only alpha-carbon coordinates in the Brookhaven Protein Data Bank; thioredoxin (SRX) and triacylglycerol acylhydrolase (TGL). All-atom models are proposed for the backbone of both these proteins. In addition, the technique was applied to randomized coordinates of flavodoxin to assess the effects of irregularities in the data on the final RMS. This study represents the first time a deterministic conformational search was used on such a large scale.