Cheating on the edge

We present the results of an individual agent-based model of antibiotic resistance in bacteria. Our model examines antibiotic resistance when two strategies exist: "producers"--who secrete a substance that breaks down antibiotics--and nonproducers ("cheats") who do not secrete, or carry the machinery associated with secretion. The model allows for populations of up to 10,000, in which bacteria are affected by their nearest neighbors, and we assume cheaters die when there are no producers in their neighborhood. Each of 10,000 slots on our grid (a torus) could be occupied by a producer or a nonproducer, or could (temporarily) be unoccupied. The most surprising and dramatic result we uncovered is that when producers and nonproducers coexist at equilibrium, nonproducers are almost always found on the edges of clusters of producers.     

Living on the edge

A report on the Second EMBL/EMBO Symposium on Functional Genomics: 'Exploring the Edges of Omics', European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, 16-19 October 2004.     

Bioinformatics: living on the edge

A report on the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012.     

Living on the edge: The use of fruit-feeding butterflies to evaluate edge effect on subtropical assemblages

This study evaluated how the edge effect influences the structuration of fruit-feeding butterfly assemblages in swamp forest fragments of the subtropical Atlantic Forest, Southern Brazil. Sampling was carried out twice in 10 fragments using baited traps placed in sampling units both at the forest edge and 50 m within the forest interior, with the habitats being defined by a set of environmental variables. Richness and abundance were higher for edge habitats with an effect of temperature depending on humidity and luminosity. The subfamily/tribe composition of fruit-feeding butterflies was segregated between edge and interior and was predicted by wind speed and the interaction between humidity and luminosity. Fifty meters within the forest interior is not sufficient to cause homogenization of butterfly composition between the edge and interior of swamp forest fragments, indicating distinct assemblages in each habitat. The interior harboured forest-loving butterfly groups while the edge harboured generalist sun-loving and common butterflies associated with disturbed areas, suggesting resistance to the effects of habitat fragmentation. We highlight the importance of using fruit-feeding butterfly groups, instead of species, to evaluate edge effects. We also suggest that a heterogeneous matrix with native habitats and distinct semi-natural land-use systems be maintained to manage subtropical areas by increasing connectivity within the landscape. Considering the impacts that the Atlantic Forest suffers, increased knowledge of modifications caused at small and regional scales is crucial for the maintenance of ecological processes and represents a tool for conservation planning and environmental agendas.     

Life on the edge: gastrointestinal parasites from the forest edge and interior primate groups

Humans are responsible for massive changes to primate habitats, and one unanticipated consequence of these alterations may be changes in host-parasite interactions. Edges are a ubiquitous aspect of human disturbance to forest landscapes. Here we examine how changes associated with the creation of edges in Kibale National Park, Uganda, alter the parasite community that is supported by two species of African colobines: the endangered red colobus (Piliocolobus tephrosceles) and the black-and-white colobus (Colobus guereza). An analysis of 822 fecal samples from edge and forest interior groups revealed no difference in the richness of parasite communities (i.e., the number of parasite species recovered from the host's fecal sample). However, for both species the proportion of individuals with multiple infections was greater in edge than forest interior groups. The prevalence of specific parasites also varied between edge and forest interior groups. Oesophagostomum sp., a potentially deleterious parasite, was 7.4 times more prevalent in red colobus on the edge than in those in the forest interior, and Entamoeba coli was four times more prevalent in red colobus on the edge than in animals from the forest interior. Environmental contamination with parasites (measured as parasite eggs/gm feces) by red colobus from the edge and forest interior differed in a similar fashion to prevalence for red colobus, but it did not differ for black-and-white colobus. For example, egg counts of Oesophagostomum sp. were 10 times higher in red colobus from the edge than in those from the interior. The less severe infections in the black-and-white colobus relative to the red colobus may reflect the fact that black-and-white colobus raid agricultural crops while red colobus do not. This nutritional gain may facilitate a more effective immune response to parasites by the black-and-white colobus. The fact that animals on the edge are likely not nutritionally stressed raises an intriguing question as to what facilitates the elevated infections in edge animals. We speculate that interactions with humans may be linked to the observed patterns of infections, and hence that understanding the ecology of infectious diseases in nonhuman primates is of paramount importance for conservation and potentially for human-health planning.     

农田-荒地边缘地带中蝗虫边缘反应分析

探讨了中华蚱蜢等10种蝗总科昆虫对农田－荒地的边缘反应。研究发现,就同一边缘而言,有些物种的多度在靠近边缘时上升,而有些物种则下降。从科的水平上分析的结果与物种水平上的分析有差异。为了更精确地了解边缘对蝗虫的分布格局的影响,从物种水平上对其进行分析是 很有必要的。     

Mating system shifts on the trailing edge

BACKGROUND: The trailing edges of species ranges are becoming a subject of increasing interest as the environment changes due to global warming. Trailing edge populations are likely to face extinction because of a decline in numbers and an inability to evolve new adaptations with sufficient speed. Discussions of character change in the trailing edge have focused on physiological, exomorphic and phenological traits. The mating pattern within populations has not been part of the discourse, in spite of the fact that the mating pattern may affect the ability of populations to respond to environmental change and to maintain their sizes. In this paper, the case is made that a substantial increase in self-fertilization rates may occur via plastic responses to stress. SCOPE AND CONCLUSIONS: Small populations on the trailing edge are especially vulnerable to environmental change because of inadequate levels of cross-fertilization. Evidence is presented that a deficiency of cross-seed production is due to inadequate pollinator services and a paucity of self-incompatibility alleles within populations. Evidence also is presented that if plants are self-compatible, self-fertilization may compensate in part for this deficiency through a stress-induced increase in levels of self-compatibility and stress-induced alterations in floral morphology that elevate self-pollination. Whereas increased self-fertility may afford populations the time to adapt to their changing environments, it can be concluded that increased selfing is not a panacea for the ills of environmental change, because it will lead to substantial reductions in genetic diversity, which may render adaptation unlikely.     

Microbial growth on the edge of desiccation

The availability of water, which can be expressed in terms of water activity (a(w)), is one of the most important determinants for microbial homeostasis and growth on surface to air interfaces. Here we show, using an environmental control chamber containing a precisely controlled temperature/a(w) gradient in combination with a mathematical approach, that the environmental a(w) growth limit of a microorganism can be lower than its intracellular a(w) limit. This internal limit represents the point at which microbial cells cannot lower their internal a(w) any further in response to low external a(w) values without interfering with essential intracellular processes. To grow at external a(w) values below their internal limit, microbes need to generate more water metabolically than they lose to their environment. This internal a(w) limit can be calculated by measuring the a(w) growth limit of an organism at different water vapour diffusivities using barometric pressure as a variable. Fascinating morphological changes, such as rope-like superstructures formed by B. subtilis, are furthermore observed in response to low external a(w) values in particular around the calculated intracellular a(w) limit. The intracellular a(w) limit of an organism is a decisive parameter for water limitation-induced adaptations in cellular hydrophilicity and morphogenesis.     

Extremotolerance in fungi: evolution on the edge

Our planet offers many opportunities for life on the edge: high and low temperatures, high salt concentrations, acidic and basic conditions and toxic environments, to name but a few extremes. Recent studies have revealed the diversity of fungi that can occur in stressful environments that are hostile to most eukaryotes. We review these studies here, with the additional purpose of proposing some mechanisms that would allow for the evolutionary adaptation of eukaryotic microbial life under extreme conditions. We focus, in particular, on life in ice and life at high salt concentrations, as there is a surprising similarity between the fungal populations in these two kinds of environments, both of which are characterized by low water activity. We propose steps of evolution of generalist species towards the development of specialists in extreme habitats. We argue that traits present in some fungal groups, such as asexuality, synthesis of melanin-like pigments and a flexible morphology, are preadaptations that facilitate persistence and eventual adaptation to conditions on the ecological edge, as well as biotope switches. These processes are important for understanding the evolution of extremophiles; moreover, they have implications for the emergence of novel fungal pathogens.     

Bilateral edge filter: photometrically weighted, discontinuity based edge detection

Edge-detection algorithms have the potential to play an increasingly important role both in single particle analysis (for the detection of randomly oriented particles), and in tomography (for the segmentation of 3D volumes). However, the majority of traditional linear filters are significantly affected by noise as well as artefacts, and offer limited selectivity. The Bilateral edge filter presented here is an adaptation of the Bilateral filter [Jiang, W., Baker, M.L., Wu, Q., Bajaj, C., Chiu, W., 2003. Applications of a bilateral denoising filter in biological electron microscopy. J. Struct. Biol. 144, 114-122] designed for enhanced edge detection. It uses photometric weighting to identify significant discontinuities (representing edges), minimizing artefacts and noise. Compared with common edge-detectors (LoG, Marr-Hildreth) the Bilateral edge filter yielded significantly better results. Indeed data was of a similar quality to that of the Canny edge-detector, which is considered as a leading standard in edge detection [Basu, M., 2002. Gaussian-based edge-detection methods-a survey. IEEE Trans. Syst. Man Cybern. C Appl. Rev. 32, 252-260]. Compared to the Canny edge-detector the Bilateral edge-detector has the advantages that it only requires the adjustment of a single parameter, is theoretically faster for reasonably sized images, and can be used in selective contrast enhancement of images. The simplicity and speed of the filter for single particle and tomographic analysis are discussed.     

Positive edge effects on forest-interior cryptogams in clear-cuts

Biological edge effects are often assessed in high quality focal habitats that are negatively influenced by human-modified low quality matrix habitats. A deeper understanding of the possibilities for positive edge effects in matrix habitats bordering focal habitats (e.g. spillover effects) is, however, essential for enhancing landscape-level resilience to human alterations. We surveyed epixylic (dead wood inhabiting) forest-interior cryptogams (lichens, bryophytes, and fungi) associated with mature old-growth forests in 30 young managed Swedish boreal forest stands bordering a mature forest of high conservation value. In each young stand we registered species occurrences on coarse dead wood in transects 0-50 m from the border between stand types. We quantified the effect of distance from the mature forest on the occurrence of forest-interior species in the young stands, while accounting for local environment and propagule sources. For comparison we also surveyed epixylic open-habitat (associated with open forests) and generalist cryptogams. Species composition of epixylic cryptogams in young stands differed with distance from the mature forest: the frequency of occurrence of forest-interior species decreased with increasing distance whereas it increased for open-habitat species. Generalists were unaffected by distance. Epixylic, boreal forest-interior cryptogams do occur in matrix habitats such as clear-cuts. In addition, they are associated with the matrix edge because of a favourable microclimate closer to the mature forest on southern matrix edges. Retention and creation of dead wood in clear-cuts along the edges to focal habitats is a feasible way to enhance the long-term persistence of epixylic habitat specialists in fragmented landscapes. The proposed management measures should be performed in the whole stand as it matures, since microclimatic edge effects diminish as the matrix habitat matures. We argue that management that aims to increase habitat quality in matrix habitats bordering focal habitats should increase the probability of long-term persistence of habitat specialists.