Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?

Summary The feasibility of determining the relative populations of multi-conformer structures from NOE-derived distances alone is assessed. Without cross-validation of the NOE restraints, any population ratio can be refined to a similar quality of the fit. Complete cross-validation provides a less biased measure of fit and allows the estimation of the correct population ratio when used in conjunction with very tight distance restraints. With the qualitative distance restraints most commonly used in NMR structure determination, cross-validation is unsuccessful in providing the correct answer. Other experimental sources are therefore needed to determine relative populations of multi-conformer structures.To whom correspondence should be addressed.     

Effect of forest landscapes composition and configuration on bird community and its functional traits in a hotspot of biodiversity of Chile

Understanding the effect of landscape configuration on the bird species richness and their functional traits (dietary preferences) is important to link the conservation and restoration plans to the production of the crops. Our aims were: 1) to study the influence of forest types (native, mixed and plantations) on the bird species richness in two agroforestry landscapes (heterogeneous/homogeneous); 2) to assess the effect of size/density of forest patches in the birds’ functional traits; 3) to evaluate the effect of isolated trees on them, and 4) to discuss conservation and restoration measures for the birds’ functional traits in agroforestry landscapes. We used hierarchical occupancy models to evaluate the effect of different landscape metrics and detectability measures on bird communities. We recorded a total of 64 bird species. The estimated species richness was considerable higher in homogeneous landscape (31.7 ± 2.7) than heterogeneous (27.3 ± 2.5). Our results showed the bird assemblage had a positive trend with native forests, negative with mixed forests and neutral trend for plantations. The granivores and insectivore’s species showed significant preferences for homogeneous landscape, while omnivores had significant preferences for heterogeneous landscape. Carnivores/Piscivores and herbivores/frugivores species did not show preferences by any landscape type. The response of functional traits depended on different forests attributes. The isolated trees had a significant effect on the birds’ functional traits. In conclusion, it is necessary a deep knowledge about the relationship between the landscape configuration and the bird species richness/functional traits. These findings could help in the future with the conservation, restoration, and rewilding policies in this important hotspot of biodiversity, avoiding alterations in the ecosystem services.     

Enzyme occupancy measurement of intracellular protein tyrosine phosphatase 1B using photoaffinity probes

Protein tyrosine phosphatase 1B (PTP1B) is believed to be one of the enzymes involved in down-regulating the insulin receptor and is a drug target for the treatment of type II diabetes. To better understand the in vitro and in vivo behavior of PTP1B inhibitors, a cell-based assay to directly measure enzyme occupancy of PTP1B by inhibitors using photoaffinity labeling was developed. Two photoaffinity probes were synthesized containing the photolabile diazirine moiety. These photoprobes were specific for PTP1B and T-cell protein tyrosine phosphatase over CD45, with the most potent photoprobe having an IC(50) value of 0.2nM for PTP1B. Activation of the photoprobes with a 40-W UV lamp in the presence of purified AspTyrLysAspAspAspAspLys (Flag)-PTP1B formed a 1:1 irreversible adduct with the enzyme. The photolabeling was competed by known PTP1B inhibitors, vanadate, and the peptide inhibitor N-benzoyl-l-glutamyl-[4-phosphono(difluoromethyl)]-l-phenylalanyl-[4-phosphono(difluoromethyl)]l-phenylalanineamide (BzN-EJJ-amide). In HepG2 (human hepatoma cell line) cells, endogenous PTP1B was labeled by the UV-activated photoprobes in both lysed and intact cells. Enzyme occupancy measurements were conducted with a series of PTP1B inhibitors using the photoprobe affinity assay. Several compounds were shown to bind to endogenous PTP1B in the HepG2 intact cells.     

Relative importance of host plant patch geometry and habitat quality on the patterns of occupancy,extinction and density of the monophagous butterfly <Emphasis Type="Italic">Iolana iolas</Emphasis>

Habitat fragmentation is a major cause of species rarity and decline because it increases local population extinctions and reduces recolonisation rates of remnant patches. Although two major patch characteristics (area and connectivity) have been used to predict distribution patterns in fragmented landscapes, other factors can affect the occurrence of a species as well as the probability of it becoming extinct. In this paper, we study the spatial structure and dynamics of the butterfly Iolana iolas in a 75-patch network of its host plant (Colutea hispanica) to determine the relative importance of patch area, connectivity and habitat quality characteristics on occupancy, extinction and density over the period 2003–2006. Occupancy in 2003, incidence (proportion of years occupied) and probability of extinction were mostly affected by patch area. Smaller patches were less likely to be occupied because they had a higher probability of extinction, partly due to environmental stochasticity. The density of I. iolas was negatively related to patch area in all study years. Only in 2004 was the density of I. iolas positively influenced by fruit production per plant. Our results suggest that for I. iolas, and probably for other specialist butterflies with clearly delimited resource requirements, metapopulation dynamics can be satisfactorily predicted using only geometric variables because most habitat characteristics are subsumed in patch area. However, this hypothesis should be subject to further testing under diverse environmental conditions to evaluate the extent of its generalisation.     

Interspecific abundance-occupancy relationships and the effects of disturbance: a test using microcosms

The effects of disturbance on interspecific relationships between abundance and occupancy are tested using the results of a factorial experiment carried out with microcosm communities of protists. A positive relationship was documented whether marked disturbance was present or not; the pattern was neither a product of disturbance, nor was it destroyed by disturbance. Coefficients of determination, and the slopes and intercepts of abundance-occupancy relationships did not appear to change systematically with treatment. This robustness of the relationship may reflect the tendency for species to maintain approximately the same relative abundances and levels of occupancy in a broad range of circumstances. Received: 4 October 1996 / Accepted: 29 April 1997     

Habitat and landscape factors associated with neotropical waterbird occurrence and richness in wetland fragments

Habitat destruction alters the structure and spatial arrangement of remnants and creates a novel matrix, affecting the structure of biological communities. This study evaluated the contribution of patch, class and landscape level attributes of 42 wetland fragments and surrounding landscapes on the richness, abundance and presence of waterbird species. Twelve monthly censuses identified 55 species––ranging from 3 to 40 among fragments, and a total of 84,286 birds––ranging from 15 to 19,322. Wetland areas varied from 0.2 ha to 145.2 ha. The presence of 37 out of 42 species could be predicted from the structure of the fragments and the landscapes. The most important predictors were the wetland area (22 models), the rice field matrix permeability (13 models), the microhabitat richness (7 models), the wetland connectivity (5 models), and the wetland isolation (5 models). Discriminant analysis showed that fragments richer in species than expected from their areas, are found in landscapes with greater connectivity and matrix permeability than the species-poor fragments. The total area of rice fields was not related to the richness, abundance or presence of waterbirds in the wetlands fragments. The results suggest that the maintenance of the connectivity among fragments and the matrix permeability through rice-fields could be managed to foster the waterbird conservation at the landscape scale.     

A threshold response to habitat disturbance by forest birds in the Choco Andean corridor, Northwest Ecuador

Understanding how organisms use disturbed habitats and how that use can be increased is a pivotal question in conservation biology. We analyzed the relationship between upper canopy cover, a measure of disturbance, and habitat occupancy and use by 18 forest bird species in northwest Ecuador. From May 22 to June 28, 2006 we conducted five, 10-min 50 m-radius point counts at each of the 28 sites (140 total) representing a gradient of habitat disturbance from 1,285 to 1,787 m in elevation. Both habitat occupancy and use showed strong threshold responses at 21–40% upper canopy cover with the probability of occupancy increasing from about 0 to 1 and emigration (the probability that a species would stop using the site during the study period) decreasing from about 1 to 0. Bird surveys ended near the beginning of the driest time of year and high levels of emigration in more disturbed areas imply that forest birds stopped using these areas as the dry season approached, possibly due to a shift in food resources. Patterns of habitat use and occupancy suggest that disturbed habitat in the region (which is primarily abandoned pasture) may only be valuable to forest birds after a specific level of regeneration and during certain times of the year.     

Long-term population trends in widespread British moths

The Rothamsted Insect Survey has operated a Great Britain-wide network of light-traps since 1968. From these data we estimated the first ever national abundance indices and 35-year population trends for 338 species of common macro-moths. Although the number of trap sites which run each year is not constant, there is a representative, well-distributed core of traps that have run for 15 years. The proportion of operating sites catching a species and the annual geometric mean catch of successful traps were used to provide estimates of species range and absolute abundance. T, an index of long-term population trends, was used to compare trends among species. T was not biased by trap site turnover. The percentage of species displaying significant decreases (54%) was more than double that displaying increases (22%). Species found throughout Great Britain are decreasing most rapidly in the south and especially the southeast but species with a southerly distribution are increasing. Results of a preliminary overview suggest habitat and climate change may both play a role in changing species dynamics. The existence of estimates of abundances and trends for such a large species pool opens the way for much further research, linking trends with land-use changes, climate change and inter-specific dynamics.     

Population turnover and habitat dynamics in Notonecta (Hemiptera: Notonectidae) metapopulations

Simple metapopulation models assume that local populations occur in patches of uniform quality habitat separated by non-habitat. However field metapopulations tend to show considerable spatial and temporal variation in patch quality, and hence probability of occupancy. This may have implications for the adequacy of simple metapopulation models in describing and predicting regional population dynamics of natural systems. This study investigated the effects of habitat characteristics on landscape-scale occupancy dynamics of two species of backswimmer (Notonecta, Hemiptera: Notonectidae) in small freshwater ponds. The results demonstrated clear links between habitat, pond occupancy and population turnover, particularly local extinction. There were considerable changes in the habitat of individual ponds between years, but local changes were not spatially correlated and the frequency distribution of habitat conditions at the landscape level remained similar in different years. Stable occupancy levels of Notonecta species appears to result from a balance of the rates of creation and loss of suitable habitat due to spatially uncorrelated habitat change. Systems such as this, where turnover is driven by habitat dynamics, demonstrate the potential value of incorporating the dynamics of habitat change into metapopulation models. Such developments are likely to improve predictions of landscape-scale occupancy dynamics, whilst also allowing patch-level predictions of occupancy, based on local habitat conditions. Received: 18 August 1999 / Accepted: 3 December 1999