Multiple attractors and boundary crises in a tri-trophic food chain

The asymptotic behaviour of a model of a tri-trophic food chain in the chemostat is analysed in detail. The Monod growth model is used for all trophic levels, yielding a non-linear dynamical system of four ordinary differential equations. Mass conservation makes it possible to reduce the dimension by 1 for the study of the asymptotic dynamic behaviour. The intersections of the orbits with a Poincaré plane, after the transient has died out, yield a two-dimensional Poincaré next-return map. When chaotic behaviour occurs, all image points of this next-return map appear to lie close to a single curve in the intersection plane. This motivated the study of a one-dimensional bi-modal, non-invertible map of which the graph resembles this curve. We will show that the bifurcation structure of the food chain model can be understood in terms of the local and global bifurcations of this one-dimensional map. Homoclinic and heteroclinic connecting orbits and their global bifurcations are discussed also by relating them to their counterparts for a two-dimensional map which is invertible like the next-return map. In the global bifurcations two homoclinic or two heteroclinic orbits collide and disappear. In the food chain model two attractors coexist; a stable limit cycle where the top-predator is absent and an interior attractor. In addition there is a saddle cycle. The stable manifold of this limit cycle forms the basin boundary of the interior attractor. We will show that this boundary has a complicated structure when there are heteroclinic orbits from a saddle equilibrium to this saddle limit cycle. A homoclinic bifurcation to a saddle limit cycle will be associated with a boundary crisis where the chaotic attractor disappears suddenly when a bifurcation parameter is varied. Thus, similar to a tangent local bifurcation for equilibria or limit cycles, this homoclinic global bifurcation marks a region in the parameter space where the top-predator goes extinct. The 'Paradox of Enrichment' says that increasing the concentration of nutrient input can cause destabilization of the otherwise stable interior equilibrium of a bi-trophic food chain. For a tri-trophic food chain enrichment of the environment can even lead to extinction of the highest trophic level.     

Anatomical Organization of Multiple Modulatory Inputs in a Rhythmic Motor System

In rhythmic motor systems, descending projection neuron inputs elicit distinct outputs from their target central pattern generator (CPG) circuits. Projection neuron activity is regulated by sensory inputs and inputs from other regions of the nervous system, relaying information about the current status of an organism. To gain insight into the organization of multiple inputs targeting a projection neuron, we used the identified neuron MCN1 in the stomatogastric nervous system of the crab, Cancer borealis. MCN1 originates in the commissural ganglion and projects to the stomatogastric ganglion (STG). MCN1 activity is differentially regulated by multiple inputs including neuroendocrine (POC) and proprioceptive (GPR) neurons, to elicit distinct outputs from CPG circuits in the STG. We asked whether these defined inputs are compact and spatially segregated or dispersed and overlapping relative to their target projection neuron. Immunocytochemical labeling, intracellular dye injection and three-dimensional (3D) confocal microscopy revealed overlap of MCN1 neurites and POC and GPR terminals. The POC neuron terminals form a defined neuroendocrine organ (anterior commissural organ: ACO) that utilizes peptidergic paracrine signaling to act on MCN1. The MCN1 arborization consistently coincided with the ACO structure, despite morphological variation between preparations. Contrary to a previous 2D study, our 3D analysis revealed that GPR axons did not terminate in a compact bundle, but arborized more extensively near MCN1, arguing against sparse connectivity of GPR onto MCN1. Consistent innervation patterns suggest that integration of the sensory GPR and peptidergic POC inputs occur through more distributed and more tightly constrained anatomical interactions with their common modulatory projection neuron target than anticipated.     

Multiple Environmental Controls on Cockroach Assemblage Structure in a Tropical Rain Forest

Arthropod abundance and diversity are remarkable in tropical forests, but are also spatially patchy. This has been attributed either to resources, predators, abiotic conditions or disturbances, but whether such factors may simultaneously shape arthropod assemblage structure is little known. We used cockroaches to test for multiple environmental controls on assemblage structure in 25 km² of Amazonian forest. We performed nocturnal, direct searches for cockroaches in 30 plots (250 m × 2 m) during two seasons, and gathered data on biotic and abiotic factors from previous studies. Cockroach abundance increased with dry litter mass, a measure of resource amount, while species richness increased with litter phosphorus content, a measure of resource availability. Cockroach abundance and species richness decreased with ant relative abundance. Cockroach species composition changed along the gradient of: (1) soil clay content, which correlates with a broad differentiation between flood‐prone and non‐flooded forest; (2) soil relative moisture, consistent with known interspecific variation in desiccation tolerance; and (3) according to the abundance of ants, a potential predator. Turnover in species composition was correlated with abiotic conditions—sorting species according to physiological requirements and to disturbance‐related life history traits—and to ants' selective pressure. Cockroach abundance, diversity, and composition seem to be controlled by distinct sets of environmental factors, but predators which were represented by ants, emerged as a common factor underlying cockroach distribution. Such patterns of community structure may have been previously overlooked by undue focus on single or a few factors, and may be common to tropical forest arthropods.     

Isolation of Multiple Subspecies of Bacillus thuringiensis from a Population of the European Sunflower Moth, Homoeosoma nebulella

Five subspecies of Bacillus thuringiensis were isolated from dead and diseased larvae obtained from a laboratory colony of the European sunflower moth, Homoeosoma nebulella. The subspecies isolated were B. thuringiensis subspp. thuringiensis (H 1a), kurstaki (H 3a3b3c), aizawai (H 7), morrisoni (H 8a8b), and thompsoni (H 12). Most isolates produced typical bipyramidal crystals, but the B. thuringiensis subsp. thuringiensis isolate produced spherical crystals and the B. thuringiensis subsp. thompsoni isolate produced a pyramidal crystal. Analysis of the parasporal crystals by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the crystals from the B. thuringiensis subsp. kurstaki and aizawai isolates contained a protein of 138 kDa whereas those from B. thuringiensis subsp. morrisoni contained a protein of 145 kDa. The crystals from B. thuringiensis subsp. thuringiensis contained proteins of 125, 128, and 138 kDa, whereas those from B. thuringiensis subsp. thompsoni were the most unusual, containing proteins of 37 and 42 kDa. Bioassays of purified crystals conducted against second-instar larvae of H. nebulella showed that the isolates of B. thuringiensis subspp. aizawai, kurstaki, and thuringiensis were the most toxic, with 50% lethal concentrations (LC(inf50)s) of 0.15, 0.17, and 0.26 (mu)g/ml, respectively. The isolates of B. thuringiensis subspp. morrisoni and thompsoni had LC(inf50)s of 2.62 and 37.5 (mu)g/ml, respectively. These results show that a single insect species can simultaneously host and be affected by a variety of subspecies of B. thuringiensis producing different insecticidal proteins.     

Multiple origins of European populations of the giant liver fluke Fascioloides magna (Trematoda: Fasciolidae), a liver parasite of ruminants

The giant liver fluke, Fascioloides magna, a liver parasite of free-living and domestic ruminants of Europe and North America, was analysed in order to determine the origin of European populations and to reveal the biogeography of this originally North American parasite on the European continent. The variable fragments of the mitochondrial cytochrome c oxidase subunit I (cox1; 384bp) and nicotinamide dehydrogenase subunit I (nad1; 405bp) were used. Phylogenetic trees and haplotype networks were constructed and the level of genetic structuring was evaluated using population genetic tools. In F. magna individuals originating from all European foci of infection (Italy, Czech Republic and Danube floodplain forests involving the territories of Slovakia, Hungary and Croatia) and from four of five major North American enzootic areas, 16 cox1 and 18 nad1 haplotypes were determined. The concatenated sequence set produced 22 distinct haplotypes. The European fluke populations were less diverse than those from North America in that they contained proportionately fewer haplotypes (eight), while a more substantial level of genetic diversity and a greater number of haplotypes (15) were recorded in North America. Only one haplotype was shared between the European (Italy) and North American (USA/Oregon and Canada/Alberta) flukes, supporting a western North American origin of the Italian F. magna population. Haplotypes found in Italy were distinct from those determined in the remaining European localities which indicates that introduction of F. magna to the European continent occurred more than once. In the Czech focus of infection, a south-eastern USA origin was revealed. Identical haplotypes, common to parasites from the Czech Republic and from an expanding focus in Danube floodplain forests, implies that the introduction of F. magna to the Danube region came from an already established Czech focus of infection.     

Environmental factors influencing herb layer productivity in Central European oak forests: insights from soil and biomass analyses and a phytometer experiment

Habitat productivity and vegetation biomass are important factors affecting species diversity and ecosystem function, but factors determining productivity are still insufficiently known, especially in the forest herb layer. These factors are difficult to identify because different methods often yield different results. We sampled the herb layer biomass and assessed soil nutrients, moisture and light availability in 100 m² plots in Czech oak forests. Habitat productivity was estimated independently from nutrient content in the soil, herb layer biomass and using a bioassay experiment (growing phytometer plants of Raphanus sativus under standardised conditions in soil samples taken from forest plots). The generalised linear model for herb layer biomass showed it to increase with light, soil phosphorus and moisture availability, but only 10.7% of its variation was explained by these factors. The phytometer biomass increased mainly with soil pH and phosphorus availability; together with soil C/N ratio these factors explained 56.1% of the phytometer biomass variability. Combined evidence based on different approaches indicates that canopy shading and soil phosphorus tend to be the most important factors influencing the herb layer productivity of the studied oak forests.     

Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay

Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, background-free ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5′ and 3′ ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10⁴. A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.Clinical diagnostics and disease management strategies increasingly require fast and accurate methods for the detection and identification of multiple pathogenic microorganisms from complex samples. Conventional techniques used to detect and identify pathogenic microorganisms have typically relied upon culture-based morphological approaches. Unfortunately, these methods are often time-consuming, laborious, and restricted to those microorganisms that can be cultured routinely.Several recently developed molecular techniques, such as conventional and real-time PCRs, circumvent some of these drawbacks. PCR-based detection mechanisms are sensitive, accurate, and relatively fast and allow the detection of difficult-to-culture microorganisms. This last aspect is of considerable importance, given the fact that the majority of the microorganisms present in environmental samples still elude conventional cultivation efforts (1, 21). Although PCR-based methods for microbial identification and detection offer several advantages over conventional microbiological approaches, they still often have serious limitations. The attainable level of multiplexing is relatively low and is typically restricted to the detection of only a few target pathogens per assay (15, 40). Adding multiple specific primer pairs to a single reaction mixture can result in undesired amplification products (16), and for TaqMan PCR, the attainable level of multiplexing is low due to the limited number of fluorescent probes (8, 34, 41). Reliable detection and identification of several pathogens in a single sample, therefore, requires separate reaction mixtures, making large-scale screening of samples more laborious, time-consuming, and expensive. To increase efficiency and reduce expenses, it is desirable to develop simple and rapid multiplex assays that can specifically detect and identify several pathogens simultaneously.DNA microarray- and macroarray-based technologies offer the possibility of adding a highly multiplexed aspect to PCR-based pathogen detection and identification (9, 37, 54, 58). Array-based pathogen detection strategies typically involve PCR amplification of universal phylogenetic target genes (e.g., 16S, 18S, and 23S rRNA genes) or a number of microorganism-specific genetic markers (10, 19, 58) or random amplification of genomic DNA (gDNA) fragments (54). The combination of nucleic acid amplification strategies with array-based detection has resulted in the development of sensitive, high-throughput microbial diagnostic microarrays (MDMs) (4, 38, 50, 60). Although several array-based detection technologies have been realized to detect pathogens, only a minority of these methods can discriminate target pathogens from closely related nontarget organisms, which may differ from the target organisms by only a single nucleotide in the probe-binding region (36). Designing sufficiently discriminating oligonucleotide detectors for arrays, however, is relatively complicated, requiring extensive hybridization specificity testing. Moreover, the oligonucleotide detectors spotted onto the microarray are target organism specific, making it necessary to redesign microarrays if accommodation of additional probes is required for the detection of new targets.DNA ligase requires a double-stranded match to allow ligation, facilitating the development of ligation-based systems to discriminate point mutations (29). This feature of ligation detection (LD) has led to the development of several strategies for genotyping single-nucleotide polymorphisms (SNPs) and detecting pathogens (6, 7, 11, 46). However, current LD assays require two adjacent detection oligonucleotide probes with the same melting temperature (T_m) for each target sequence, although the use of intramolecular ligation, as in padlock probe (PLP) technologies, has been demonstrated to hold clear advantages (44, 45, 51). PLPs are long oligonucleotides, ∼100 bases long, containing target complementary arms at both termini of the probe. In the assay developed in this study, the target complementary arms are connected via a compound linker sequence containing spacer sequences, a thymine-linked desthiobiotin moiety for specific capture and release (25, 53), deoxyuracil nucleotides for probe cleavage, and a unique sequence identifier, the so-called ZipCode, for standardized microarray hybridization (18) (Fig. ​(Fig.1A).1A). The unimolecular nature of the PLP allows asymmetric target complementary arm design, whereby a long 5′ arm serves as an anchor sequence and the short 3′ arm, with a low T_m, facilitates extremely specific target detection (17, 51, 53). Microarray-based PLP technology was previously shown to provide reliable detection of multiple pathogenic microorganisms, but PCR amplification of residual, unligated PLPs resulted in significant background signals, thereby complicating data analysis and decreasing the overall dynamic range of reliable detection (3, 51).Open in a separate windowFIG. 1.Schematic overview of the novel single-molecule LD system. (A) PLP design. T1a and T1b are asymmetric target complementary regions. Each PLP contains a unique ZipCode sequence for universal array hybridization, two spacer sequences (S1 and S2), a desthiobiotin moiety (dBio) for probe capture, a polyoligo(dT) linker sequence, and a polydeoxyuracil sequence for probe cleavage. (B) Multiple target-specific PLPs are ligated to PCR-preamplified DNA samples. T1a and T1b bind to adjacent sequences of the target, and in the case of a perfect match, the probe is circularized by enzymatic ligation. The PLPs are reversibly captured and washed via the desthiobiotin moiety with magnetic streptavidin-coated beads. Next, the washed probes are cleaved at the polydeoxyuracil sequences with UNG and endonuclease enzymes. The sample containing the cleaved PLPs is hybridized on a universal microarray. Finally, only the hybridized PLPs that were originally ligated can be labeled and visualized with streptavidin R-PE by using the desthiobiotin moiety.Here, we describe the development, testing, and implementation of a novel, background-free, LD-dependent strategy in which multiple PLPs are ligated on fragmented, PCR-preamplified DNA sequences. The target complementary regions recognize adjacent sequences on the target DNA, and ligation occurs only if the end nucleotides perfectly match their target, resulting in a circular molecule (Fig. ​(Fig.1B).1B). Next, the probes are captured with streptavidin-coupled magnetic beads, allowing separation from the rest of the sample. Subsequently, the washed probes are eluted from the beads and cut at the internal polydeoxyuracil probe region by enzymatic cleavage. Thus, the desthiobiotin moiety needed for fluorescent labeling of unligated PLPs is removed, while the ligated probes are linearized (Fig. ​(Fig.1B).1B). Finally, the sample is hybridized on a universal complementary ZipCode (cZipCode) microarray (18) and visualized via fluorescent labeling of the desthiobiotin moiety (Fig. ​(Fig.1B1B).In this paper, we report the development and application of cleavable PLPs combined with LD for the simultaneous, background-free detection and identification of multiple plant pathogens in environmental samples. The specificity, sensitivity, and dynamic range of detection of the developed assay were determined by using nine target-specific PLPs, and the robustness of the assay was evaluated by using samples collected from hydroponic horticultural water recirculation systems.     

Environmental factors driving the effectiveness of European agri‐environmental measures in mitigating pollinator loss – a meta‐analysis

In Europe, agri‐environmental schemes (AES) have been introduced in response to concerns about farmland biodiversity declines. Yet, as AES have delivered variable results, a better understanding of what determines their success or failure is urgently needed. Focusing on pollinating insects, we quantitatively reviewed how environmental factors affect the effectiveness of AES. Our results suggest that the ecological contrast in floral resources created by schemes drives the response of pollinators to AES but that this response is moderated by landscape context and farmland type, with more positive responses in croplands (vs. grasslands) located in simple (vs. cleared or complex) landscapes. These findings inform us how to promote pollinators and associated pollination services in species‐poor landscapes. They do not, however, present viable strategies to mitigate loss of threatened or endangered species. This indicates that the objectives and design of AES should distinguish more clearly between biodiversity conservation and delivery of ecosystem services.     

Environmental determinism of year-to-year recruitment variability of European eel Anguilla anguilla in a small coastal catchment, the Frémur River, north-west France

The influence of environmental factors (mainly the river flow) on the year-to-year variability of European eel Anguilla anguilla fluvial recruitment in a small coastal catchment, the Frémur River (north-west France) was examined. A comprehensive survey of catches from fixed traps at two weirs located at 4·5 km (Pont es Omnes Dam) and 6·0 km (Bois Joli Dam) above the river mouth was carried out between 1997 and 2004. Young pigmented elvers (mean ± s.d. total length, 133·7 ± 29·6 mm) were recruited in eel-passes from February to October, but the main runs followed a modal curve from April to September with a peak centred in May to June. Catches varied greatly between years, from 381 to 26 765 elvers. For each trap, a positive linear relationship between monthly mean river flow that preceded the maximal intensity of captures and annual total catches was observed. These relationships explained 73·1% ( P < 0.01) and 89·0% ( P < 0.001) of the year-to-year variability of the recruitment observed in the Pont es Omnes and Bois Joli traps respectively. A significant increase in river flow at the beginning of the migration peak would thus trigger a greater proportion of A. anguilla settled in the estuary and in the downstream zone of the Fremur River to begin their freshwater colonization. The physicochemical roles of changes in river discharge in stimulating upstream migration are discussed. It is concluded that fluvial recruitment in the Fremur River is mainly determined by environmental factors.     

Environmental risk assessment for the small tortoiseshell Aglais urticae and a stacked Bt-maize with combined resistances against Lepidoptera and Chrysomelidae in central European agrarian landscapes

The cultivation of Lepidoptera‐resistant Bt‐maize may affect nontarget butterflies. We assessed the risk posed by event MON89034 × MON88017 (expressing Cry1A.105 and Cry2Ab2 against corn borers) to nontarget Lepidoptera. Using the small tortoiseshell Aglais urticae, a butterfly species common in central Europe, as a test organism we (i) assessed the toxicity of Bt‐maize pollen on butterfly larvae; (ii) measured pollen deposition on leaves of the host plant Urtica dioica; (iii) mapped the occurrence and distribution of host plants and larvae in two arable landscapes in Germany during maize anthesis; and (iv) described the temporal occurrence of a 1‐year population of A. urticae. (i) Larvae‐fed 200 Bt‐maize pollen grains/cm² had a reduced feeding activity. Significant differences in developmental time existed at pollen densities of 300 Bt‐maize pollen grains/cm² and in survival at 400 grains/cm². (ii) The highest pollen amount found was 212 grains/cm² at the field margin. Mean densities were much lower. (iii) In one region, over 50% of A. urticae nests were located within 5 m of a maize field, while in the other, all nests were found in more than 25 m distance to a maize field. (iv) The percentage of larvae developing during maize anthesis was 19% in the study area. The amount of pollen from maize MON89034 × MON88017 found on host plants is unlikely to adversely affect a significant proportion of larvae of A. urticae. This paper concludes that the risk of event MON89034 × MON88017 to populations of this species is negligible.     

Research scientists surveyed on ethical issues in genetic medicine: a comparison of attitudes of US and European researchers

Abstract

This paper compares the attitudes of European and US scientists engaged in human genetics research about some of the ethical issues raised by recent advances in genetic testing, by the increasing likelihood of subsequent genetic therapies, and by hovering threats to the privacy of those tested in the face of concerns raised by individual and institutional third parties. Surveys of both groups indicate strong and fairly uniform support for attempts to discern and cure serious diseases or disorders and decisions to terminate pregnancies in which fetuses have serious genetic defects. But the data also indicate a number of issues where European and US respondents disagree and where that disagreement is characterised by a more cautious approach on the part of the European scientists. These data should provide a foundation for subsequent reflection and discussion within the scientific communities as well as within the society at large.