Hydrophobic patches on the surfaces of protein structures

A survey of hydrophobic patches on the surface of 112 soluble, monomeric proteins is presented. The largest patch on each individual protein averages around 400 Ų but can range from 200 to 1,200 Ų. These areas are not correlated to the sizes of the proteins and only weakly to their apolar surface fraction. Ala, Lys, and Pro have dominating contributions to the apolar surface for smaller patches, while those of the hydrophobic amino acids become more important as the patch size Increases. The hydrophilic amino acids expose an approximately constant fraction of their apolar area independent of patch size; the hydrophobic residue types reach similar exposure only in the larger patches. Though the mobility of residues on the surface is generally higher, it decreases for hydrophilic residues with Increasing patch size. Several characteristics of hydrophobic patches catalogued here should prove useful in the design and engineering of proteins. © 1996 Wiley-Liss, Inc.     

Heathland management effects on carabid beetle communities: the relationship between bare ground patch size and carabid biodiversity

Carabid beetles were sampled by pitfall trapping on Brentmoor Heath, Surrey, UK during the summers of 2009 and 2010 to determine the effects of bare ground patch size on beetle abundance, richness and diversity. Four patch sizes were investigated: 1, 4, 25 and 100?m² as well as the adjacent mown and unmown areas. A range of environmental parameters relating to soil characteristics, stones and nearby vegetation were measured at each patch and control habitat in order to distinguish the effect of patch size. Results show that bare ground is a valuable habitat for carabids, but that the response of their abundance, richness and diversity to bare ground patch size depends on a large number of environmental variables on and around the patches. When all variables are taken into account, smaller patches appear to benefit carabid abundance, richness and diversity. In the presence of Molinia caerulea at the patch edges, however, larger patches were more beneficial. Given this dependence on environmental variables, the perfect patch size for conservation of biodiversity is likely to be site specific and the best approach may be to use a variety of patch sizes at a range of successional stages.     

Nucleosome rearrangement in human cells following short patch repair of DNA damaged by bleomycin.

We have examined the structure of newly repaired regions of chromatin in intact and permeabilized human cells following exposure to bleomycin (BLM). The average repair patch size (in permeabilized cells) was six to nine bases, following doses of 1-25 micrograms/mL BLM, and greater than 80% of the total repair synthesis was resistant to aphidicolin. In both intact and permeabilized cells, nascent repair patches were initially very sensitive to staphylococcal nuclease, analogous to repair induced by "long patch" agents, and are nearly absent from isolated nucleosome core DNA. Unlike long patch repair, however, the loss of nuclease sensitivity during subsequent chase periods was very slow in intact cells, or in permeabilized cells treated with a low dose of BLM (1 microgram/mL), and was abolished by treatment with hydroxyurea (HU) or aphidicolin (APC). The rate of repair patch ligation did not correlate with this slow rate of chromatin rearrangement since greater than 95% of the patches were ligated within 6 h after incorporation (even in the presence of HU or APC). In permeabilized cells, repair patches induced by either 5 or 25 micrograms/mL BLM, where significant levels of strand breaks occur in compact regions of chromatin, lost the enhanced nuclease sensitivity at a rate similar to that observed following long patch repair. This rapid rate of rearrangement was not affected by APC. These results indicate that short patch repair in linker regions of nucleosomes, and/or "open" regions of chromatin, involves much less nucleosome rearrangement than long patch repair or short patch repair in condensed chromatin domains.     

The effective size of a metapopulation living in a heterogeneous patch network

I analyze stochastic patch occupancy models (SPOMs), which record habitat patches as empty or occupied. A problem with SPOMs has been that if the spatial structure of a heterogeneous habitat patch network is taken into account, the computational effort needed to analyze a SPOM grows as a power of 2n, where n is the number of habitat patches. I propose a computationally feasible approximation method, which approximates the behavior of a heterogeneous SPOM by an "ideal" metapopulation inhabiting a network of identical and equally connected habitat patches. The transformation to the ideal metapopulation is based on weighting the individual patch occupancies by the dynamic values of the habitat patches, which may be calculated from the deterministic mean-field approximation of the original SPOM. Conceptually, the method resembles the calculation of the effective size of a population in the context of population genetics. I demonstrate how the method may be applied to SPOMs with flexible structural assumptions and with spatially correlated and temporally varying parameter values. I apply the method to a real habitat patch network inhabited by the Glanville fritillary butterfly, illustrating that the metapopulation dynamics of this species are essentially driven by temporal variability in the environmental conditions.     

斑块尺度湿地植物群落多样性的维持能力

基于GIS技术和主成分分析方法,对1950、1967、1983和2000年挠力河流域湿地景观斑块特征与斑块内植物群落多样性之间的关系进行了研究.结果表明： 1950—2000年间,研究区湿地斑块平均面积逐渐减小,能够维持2种及2种以上植物群落的斑块数量逐渐减少,最小斑块面积为10.1 km²;湿地斑块面积与植物群落多样性指数和群落类型数均呈极显著正相关关系（P<0.01）,湿地斑块面积越大,维持植物群落多样性的能力越强;随着湿地斑块面积的逐渐减小,斑块破碎化指数和分维数逐渐增大,形状指数和斑块内植物群落多样性指数逐渐减小;随着湿地斑块空间分离度的增大,斑块内植物群落多样性指数呈减小趋势;主成分分析结果显示,研究区湿地斑块面积大小是影响斑块内群落多样性的最重要因素,其次为斑块的破碎化程度和分离度.     

Patch cramming: monitoring intracellular messengers in intact cells with membrane patches containing detector ion channels.

This paper introduces "patch cramming," a new procedure that utilizes an ion channel gated directly by an intracellular messenger molecule as a probe for detecting changes in the concentration of that molecule in an intact cell. A patch pipette containing the channel in a membrane patch is inserted into a recipient cell where the channel locally "senses" the intracellular messenger. In this study patches containing Ca2(+)-dependent K+ channels were inserted into Helix neurons, where they were activated by Ca2+ influx during trains of action potentials. Channels gated directly by other messengers, including cyclic nucleotides and IP3, have also been identified. Hence, by using detector channels with appropriate specificity, it may be possible to detect local intracellular fluctuations of these molecules.     

Biotic filtering and mass effects in small shrub patches: is arthropod community structure predictable based on the quality of the vegetation?

1. Community assembly is affected by four processes: dispersal, filtering effects (selection), ecological drift and evolution. The role of filtering relative to dispersal and drift should decline with patch size, hampering possibilities to predict which organisms will be observed within small‐sized patches. However, vegetation structure is known to have a marked impact on species assemblages, and plant quality may act as a biotic filter. This challenges the assumption of unpredictable species assemblages in small‐sized vegetation patches. 2. Using 32 stands of five shrub species in south‐west Finland, this study investigated whether biotic filtering effects caused by patch‐forming plants are strong enough to overcome the mixing of mobile arthropod assemblages across small patches. 3. Stochastic variation did not hide the signals of biotic filtering and dispersal in the small shrub patches. Habitat richness around the patches explained a three times larger share of variation in the species composition than did the identity of the patch‐forming plant, but it had less effect on the abundance of arthropods. A radius of 50–100 m around a patch explained the species composition best. 4. Abundance patterns varied between the feeding guilds; the patch‐forming shrub influenced the abundances of detritivores and leaf‐feeding herbivores, whereas the abundances of flower‐visiting herbivores appeared to track the flowering phenology of the plants. Shrub identity had little effect on omnivores or predators. Predator abundances were correlated with the abundance of potential prey. 5. The results of this study suggest that community composition within a vegetation patch may be predictable even if dispersal overrides local filtering effects, as suggested by the mass‐effects paradigm.     

Consequences of insular population structure: Distribution and extinction of spruce grouse populations

Summary The population structure of the spruce grouse (Canachites canadensis) was studied in the Adirondack Mountains of New York, U.S.A. Twenty-five isolated habitat patches exist and are occupied by spruce grouse, with 7 suitable but unoccupied patches existing at the periphery of the range. The regional distribution and abundance of spruce grouse is correlated with the amount of lowland coniferous forest habitat. Unoccupied patches were significantly smaller and significantly farther from occupied patches than were other occupied patches. For all patches, as distance from the nearest occupied patch increased, the percent of occupied patches decreased linearly. I incorporated birth and death rates for spruce grouse into the MacArthur-Wilson survivorship model which closely predicted the proportion of occupied patches for an average population density (2.8 spruce grouse/100ha). For the same demographic parameters, extinction times were calculated which indicate that the 15 habitat patches of a carrying capacity of 3 female spruce grouse (100 ha) would have an average extinction time of less than 6 years. This in part accounts for the high proportion of these patches which are unoccupied. Extinctions and recolonizations of patches were observed during the study. The patterns of patch occupancy can partially be predicted based on their size, spatial arrangement, and the demographic characteristics of the spruce grouse.     

浑善达克沙地榆树疏林自然保护区核心区设计的初步研究

为了保护浑善达克沙地榆树(Ulmus pumila)疏林景观,拟建立自然保护区。基于榆树疏林植被图,运用ArcGIS分析榆树疏林斑块数量、面积、破碎化程度,发现该区榆树疏林斑块大小差异较大,小斑块较多,斑块边界割裂严重,破碎化程度高,需要及时加以保护。按照景观生态学原理、生物岛屿地理学设计自然保护区原则,选择疏林斑块集中分布区,作为潜在核心区,运用ArcGIS的缓冲区分析功能,设计不同的宽度,发现斑块边界向外延伸3 km能够连接较多的斑块,而占用较少的非疏林斑块土地面积。同时调查斑块外不同距离样方与疏林斑块的群落相似度,发现1 km以内能够包含大于10%相似度的群落。由此而初步确定的核心区分布在正蓝旗23个嘎查,面积1 531 km²,约占全旗总面积的13%。     

Scale of spatial pattern: four methods compared

Four methods of pattern analysis were compared using simulated data. Simulated transects were of five types: 1) equal patch-equal gap, in which gap and patch length were equal, 2) unequal but fixed patch-fixed gap, in which patch length was approximately one sixth gap length, and transects in which 3) the length of the patch, or 4) gap, or 5) both varied randomly. The first peak of the variance-block size graph was used to identify patch size, instead of the more commonly used highest peak. The random pairing method estimated patch size more accurately than hierarchical ANOVA, two-term local variance, or spectral analysis. The average position of the first peak (calculated from eight replicate random pairing analyses) detected correct average patch size, even when simulated patches were randomly placed or patch size followed a uniform distribution with a range twice the mean. Hierarchical ANOVA and two-term local variance confounded patch and gap lengths and therefore overestimated the patch size. The highest peak of spectral analysis detected the full cycle (patch + gap) of the pattern but was unable to partition the components of grain. The expected variance of an independent, random pattern is suggested as a reference point for identifying meaningful peaks and troughs in random pairing analyses of field data. The method is illustrated by analysis of a transect through submersed aquatic vegetation.     

Trade-offs between social behaviour and foraging by sheep in heterogeneous pastures

In heterogeneous pastures, groups of sheep may have to alter their social behaviour in order to graze patches of preferred vegetation. In this event, patch size, inter-patch distance and the contrast between patch and background vegetation are likely to affect behaviour. In this experiment, groups of five female Scottish Blackface sheep grazed for 2-h periods in 0.1ha grass plots containing seven 1.5mx1.5m patches of improved vegetation, with inter-patch distances of 1.5, 6 or 11.5m. Background vegetation was of either medium or poor quality. Control plots contained no patches. On average, sheep spent 44% of the time grazing patches, although patches comprised only 1.6% of the total plot area. Inter-patch distance did not affect accumulated time spent grazing patches during the first 30min, but patch residence time and the number of sheep on a patch increased with inter-patch distance. The distribution of nearest neighbour distances was altered when patches were 6 or 11.5m apart, compared to no patches. Accumulated time spent grazing patches and the number of sheep on a patch were greater with poor than medium backgrounds. Sheep visited patches frequently and for short periods and it is suggested that sheep often moved off patches as a result of competition. The results provide evidence that sheep make trade-offs between social and foraging behaviour and demonstrate the importance of interactions between social spacing and the size and spacing of vegetation patches, when sheep forage in heterogeneous pastures.     

Spatial and Temporal Dynamics of a Restored Population of Oryza rufipogon in Huli Marsh, South China

Studying the process of population restoration is helpful for managing and preserving endangered species. A population of Oryza rufipogon (wild rice), an endangered species, was reintroduced in 1993 into Huli Marsh. We conducted a detailed survey over a 5‐year period (1997–2001) to evaluate the present status of the population and to further our understanding of its habitat requirements and the population model. The population was surveyed using 2 × 2–m quadrats in mid‐September of each year. In total, 2,683 quadrats were surveyed covering the whole O. rufipogon reserve during each survey. The population's spatial distribution was mapped, and the maps were used to examine the relationship between patch replacement and water depth. The individual number of O. rufipogon increased steadily from 1993 to 2001. The patch number, patch area, mean patch size, and largest patch size increased over this time period, and Korcak patchiness exponents decreased. On average, 83% of the patches persisted from one year to the next. There was a significant positive correlation between the initial patch size and the size the following year. The probability of patch disappearance decreased as patch size increased. Fifty‐eight percent of the patches were located at water depths between 20 and 30 cm. Water depth had no significant effect on the patch transition from O. rufipogon to other species. The loss and gain of O. rufipogon patches were statistically correlated with the patch areas in different water depths. Our results show that the population of O. rufipogon can successfully be reintroduced to the original habitat after appropriate environmental conditions have been restored. We recommend the following transplantation practices: transplant many smaller patches rather than a few larger patches, use transplant patch sizes of at least 20 m², and transplant into sites vegetated with species with different regeneration niches from the transplanted species.     

Support for the habitat amount hypothesis from a global synthesis of species density studies

Decades of research suggest that species richness depends on spatial characteristics of habitat patches, especially their size and isolation. In contrast, the habitat amount hypothesis predicts that (1) species richness in plots of fixed size (species density) is more strongly and positively related to the amount of habitat around the plot than to patch size or isolation; (2) habitat amount better predicts species density than patch size and isolation combined, (3) there is no effect of habitat fragmentation per se on species density and (4) patch size and isolation effects do not become stronger with declining habitat amount. Data on eight taxonomic groups from 35 studies around the world support these predictions. Conserving species density requires minimising habitat loss, irrespective of the configuration of the patches in which that habitat is contained.     

On the importance of body size in the colonisation of ephemeral resource patches by vagile consumers

A study on the colonisation of leaf detritus patches by vagile macroinvertebrates in a brackish lagoon is presented in the framework of a conceptual model where a body size-related constraint on patch use behaviour is explicitly considered. Abundance patterns of dominant macroinvertebrate taxa were characterised by short-term, non-random fluctuations, showing significant site-dependent variations. Yet, a site-independent covariation was observed between patterns’ fractal dimension and the average body mass of each taxon, indicating that, while the temporal scales characterising the colonisation patterns may be highly species-specific, cross-species generalisations are possible based on body size. The generality of these results was supported by literature data on temporal patterns of carcass colonisation by bathyal fish. The importance of size-related mechanisms in regulating the aggregation of vagile consumers on resource patches and, ultimately, their coexistence at both an inter- and intra-specific level, is discussed.     

Dissecting protein-protein recognition sites

The recognition sites in 70 pairwise protein-protein complexes of known three-dimensional structure are dissected in a set of surface patches by clustering atoms at the interface. When the interface buries <2000 A2 of protein surface, the recognition sites usually form a single patch on the surface of each component protein. In contrast, larger interfaces are generally multipatch, with at least one pair of patches that are equivalent in size to a single-patch interface. Each recognition site, or patch within a site, contains a core made of buried interface atoms, surrounded by a rim of atoms that remain accessible to solvent in the complex. A simple geometric model reproduces the number and distribution of atoms within a patch. The rim is similar in composition to the rest of the protein surface, but the core has a distinctive amino acid composition, which may help in identifying potential protein recognition sites on single proteins of known structures.     

Quantitative predictions for patch occupancy of capercaillie in fragmented habitats

A major conclusion of studying metapopulation biology is that species conservation should favor regional rather than local population persistence. Regional persistence is tightly linked to size, spatial configuration and quality of habitat patches. Hence it is important for the management of endangered species that priority patches can be identified. We developed a predictive model of patch occupancy by capercaillie, a threatened grouse species, based on a single snapshot of data. We used logistic regression to predict patch occupancy as a function of patch size, isolation, connectivity, relative altitude, and biogeographical area. The probability of a patch being occupied increased with patch size and increasing altitude, and decreased with increasing distance to the next occupied patch. Patch size was the most important predictor although occupied patches varied considerably in size. Our model only uses data on the number, size and spatial configuration of habitat patches. It is a useful tool to designate priority areas for conservation, i.e. large core patches with high resilience in habitat quality, smaller island‐patches that still have high probability of being inhabited or becoming recolonised, and patches functioning as “stepping stones”. If capercaillie is to be preserved, habitat suitability needs to be maintained in a functional network of patches that account for size and inter‐patch distance thresholds as found in this study. We suggest that similar area‐isolation relationships are valid for almost any region within the distribution range of capercaillie. The thresholds for occupancy are however likely to depend on characteristics of the respective landscape. The outcome of our study emphasises the need for future investigations that explore the relationship between patch occupancy, matrix quality and its resistance to dispersing individuals.     

Is spotted knapweed (<Emphasis Type="Italic">Centaurea stoebe</Emphasis> L.) patch size related to the effect on soil and vegetation properties?

Spotted knapweed (Centaurea stoebe L. subsp. Micranthos (Gugler) Hayek) was first introduced in the 1890s from Europe into western North America, where it now occupies over three million hectares of rangeland and pasture in 14 states and two Canadian provinces, reducing forage production and causing economic damage. Despite many reported effects spotted knapweed can have on soils and native vegetation, it is not known whether patch size is correlated with these ecosystem-level effects. The objective of our study was to determine whether the effects of spotted knapweed on plant composition and soil properties was related to spotted knapweed patch size. We asked the following questions: (1) Are there differences in plant species richness and diversity between small and large knapweed patches? and (2) Do soil water and soil mineral nutrient properties change depending on knapweed patch size? Twenty-four knapweed patches, and paired natural grassland plots, were randomly selected within Lac du Bois Provincial Park, British Columbia, Canada. Knapweed patch size ranged from 6 to 366 m². Sampling and analysis revealed a significant effect of knapweed patch size on soil and vegetation properties. Soil P, soil temperature, and total dry plant biomass (g/0.25 m²) increased, while soil N, soil C, and soil moisture decreased with patch size. Since our results show that spotted knapweed patch size is related to degree of soil alteration, it is important to consider size of patch when modeling the impact of spotted knapweed in North America. Since large patches of spotted knapweed seem to have a proportionately greater effect on soil chemistry properties, large patches may move the system further away from a point where it is possible to restore the site to pre-invasion conditions.     

Effects of flowering plant's patch size on species composition of pollinator communities,foraging strategies,and resource partitioning in bumblebees (Hymenoptera: Apidae)

Summary In 4 common Middle-European mainly bumblebee-pollinated plant species (Impatiens glandulifera, Echium vulgare, Aconitum napellus, Symphytum officinale) the influence of patch size on species composition of the pollinator community was studied. Short-tongued species were most dominant in large patches, while small patches were frequented by middle- and long-tongued bumblebees. This phenomenon was extremely obvious in Symphytum officinale and Aconitum napellus, where short-tongued species had bitten a hole in nearly every flower of large patches. Long-tongued species were forced to small patches, where nectarrobbing occurred only exceptionally. In small patches visitationrate (Number of visits per flower per hour) was not lower but either equal or even higher then in large patches. Nectar measurements in Echium vulgare showed, that not only the mean quantity of nectar but also the variance was lower in small patches. As a result, the possible gain can be predicted much more precisely in a small patch than in a large one, and bumblebees have less difficulties in making the right foraging decisions. According to this, foraging strategies depend on patch size. This was confirmed by a computer simulation. The conclusion can be drawn, that many bumblebee species are able to share the same resource by using different patch sizes. Since large flower patches occur mainly in man-made habitats, the dominance of short-tongued species in many bumblebee communities studied by other authors may be unnatural.Supported by the Landesgraduiertenförderung Baden-Württemberg     

A model for estimating the extent of variegation in mosaic tissues

A method is described which allows the size of patches of like cells in mosaic tissues to be estimated from the frequency with which small samples taken from the tissue contain both of the mosaic cell types. The mosaic patches are represented as close-packed geometric figures arranged in twoor three-dimensional tissues. Small samples drawn at random from these tissues will include portions of one or more patches; only those samples which include portions of two or more dissimilar patches (mixed samples) will contain both cell types. The expected frequency of mixed samples is calculated as a function of the shape of the mosaic patches, the frequency of the two mosaic cell types and the sample to patch size ratio. This expected frequency is not strongly dependent on patch shape for triangular, square and hexagonal patches in two dimensions or for cubic and orthotetrakaidekahedral patches in three dimensions. Elongation of square patches along one axis or of cubic patches along one or two axes results in slight increases in the expected frequency of mixed samples for given sample to patch size ratio.     

The evolution of patch selection in stochastic environments

A null model for habitat patch selection in spatially heterogeneous environments is the ideal free distribution (IFD), which assumes individuals have complete knowledge about the environment and can freely disperse. Under equilibrium conditions, the IFD predicts that local population growth rates are zero in all occupied patches, sink patches are unoccupied, and the fraction of the population selecting a patch is proportional to the patch's carrying capacity. Individuals, however, often experience stochastic fluctuations in environmental conditions and cannot respond to these fluctuations instantaneously. An evolutionary stability analysis for fixed patch-selection strategies reveals that environmental uncertainty disrupts the classical IFD predictions: individuals playing the evolutionarily stable strategy may occupy sink patches, local growth rates are negative and typically unequal in all patches, and individuals prefer higher-quality patches less than predicted by their carrying capacities. Spatial correlations in environmental fluctuations can enhance or marginalize these trends. The analysis predicts that continually increasing environmental variation first selects for range expansion, then selects for persisting coupled sink populations, and ultimately leads to regional extinction. In contrast, continually increasing habitat degradation first selects for range contraction and may select for persisting coupled sink populations before regional extinction. These results highlight the combined roles of spatial and temporal heterogeneity on the evolution of habitat selection.