Network theory and metapopulation persistence: incorporating node self‐connections

Network analysis is gaining increasing importance in conservation planning. However, which network metrics are the best predictors of metapopulation persistence is still unresolved. Here, we identify a critical limitation of graph theory‐derived network metrics that have been proposed for this purpose: their omission of node self‐connections. We resolve this by presenting modifications of existing network metrics, and developing entirely new metrics, that account for node self‐connections. Then, we illustrate the performance of these new and modified metrics with an age‐structured metapopulation model for a real‐world marine reserve network case study, and we evaluate the robustness of our findings by systematically varying particular features of that network. Our new and modified metrics predict metapopulation persistence much better than existing metrics do, even when self‐connections are weak. Existing metrics become good predictors of persistence only when self‐connections are entirely absent, an unrealistic scenario in the overwhelming majority of metapopulation applications. Our study provides a set of novel tools that can substantially enhance the extent to which network metrics can be employed to understand, and manage for, metapopulation persistence.     

A unified model explains commonness and rarity on coral reefs

Abundance patterns in ecological communities have important implications for biodiversity maintenance and ecosystem functioning. However, ecological theory has been largely unsuccessful at capturing multiple macroecological abundance patterns simultaneously. Here, we propose a parsimonious model that unifies widespread ecological relationships involving local aggregation, species‐abundance distributions, and species associations, and we test this model against the metacommunity structure of reef‐building corals and coral reef fishes across the western and central Pacific. For both corals and fishes, the unified model simultaneously captures extremely well local species‐abundance distributions, interspecific variation in the strength of spatial aggregation, patterns of community similarity, species accumulation, and regional species richness, performing far better than alternative models also examined here and in previous work on coral reefs. Our approach contributes to the development of synthetic theory for large‐scale patterns of community structure in nature, and to addressing ongoing challenges in biodiversity conservation at macroecological scales.     

Binding and endocytosis of cluster glycosides by rabbit hepatocytes. Evidence for a short-circuit pathway that does not lead to degradation

Synthetic cluster glycosides containing either one, two, or three galactosyl or lactosyl residues per ligand were used to test the effect of carbohydrate clustering on binding by the rabbit hepatic Gal/GalNAc-binding lectin using either isolated rabbit hepatocytes or the solubilized, affinity-purified lectin. The tris- and bis-glycosides were superior to the mono-glycosides for inhibition of 125I-asialoorosomucoid binding to rabbit hepatocytes at 0 degrees C. The concentrations of the tris-glycosides required for 50% inhibition of 125I-asialoorosomucoid binding (4-8 microM) to hepatocytes were 50-100 times lower than the concentrations of the corresponding mono-glycosides required for 50% inhibition (400-500 microM). The isolated lectin, however, did not effectively discriminate between the mono-, bis-, and tris-glycosides, possibly indicating an organizational difference between the lectin in the cell membrane and the isolated lectin. When the cluster glycosides were labeled with 125I-tyrosine, it was shown that the tris- and bis-galactosides were bound to the hepatocytes at 37 degrees C, and that binding was followed by a step that led to ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid resistance, probably internalization. The process could be specifically inhibited by the neoglycoprotein Gal44-AI-bovine serum albumin, or by IgG specific for the hepatic lectin, but not by preimmune IgG. Internalization of the cluster glycosides did not lead to accumulation of ligand inside the cell, nor to degradation. Instead, the ligands were quickly released from the cells.     

Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase

The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available, the fluorescence of 2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its environment is perturbed. We find that 2-aminopurine gives enhanced fluorescence emission not only when it is placed at the M.EcoKI methylation sites but also at a location adjacent to the target adenine. Thus it appears that 2-aminopurine fluorescence intensity is not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon addition of the cofactor S-adenosyl-methionine to the M.EcoKI:DNA complex, the 2-aminopurine fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450 nm. This change requires a fully active enzyme, the correct cofactor and the 2-aminopurine located at the methylation site. However, the new fluorescent species is not a covalently modified form of 2-aminopurine and we suggest that it represents a hitherto undetected physicochemical form of 2-aminopurine.     

Topographical control of cell behaviour: II. Multiple grooved substrata

Electronics miniaturization techniques have been used to fabricate substrata to study contact guidance of cells. Topographical guidance of three cell types (BHK, MDCK and chick embryo cerebral neurones) was examined on grooved substrata of varying dimensions (4-24 microns repeat, 0.2-1.9 microns depth). Alignment to within 10 degrees of groove direction was used as our criterion for guidance. It was found that repeat spacing had a small effect (alignment is inversely proportional to spacing) but that groove depth proved to be much more important in determining cell alignment, which increased with depth. Measurements of cell alignment and examination by scanning electron microscopy showed that BHK cells and MDCK cells interacted differently with grooved substrata, and also that the response of MDCK cells depended on whether or not the cells were isolated or part of an epithelial cell island. Guidance by a multiple topographical cue is greater than could be predicted from cells' reactions to a single cue (Clark et al. Development 99: 439-448, 1987). Substratum topography is considered to be an important cue in many developmental processes. Cellular properties such as cytoskeletal organisation, cell adhesion and the interaction with other cells are discussed as being factors determining a cells susceptibility to topography.