Diversity,dynamics and reproduction in a community of small mammals in Upper Guinea,with emphasis on pygmy mice ecology

As part of a large survey on reservoirs of Lassa fever in Guinea, three villages were investigated in high endemic zone, close to Sierra Leone border. Biodiversity of the small mammal community is presented in this study through a standardized trapping in houses, cultivations and forest. Identification of the small mammals was based on morphology and by molecular technique for sibling species. Of the 1123 specimens collected in 2003–2005, we identified seventeen species (thirteen Muridae, four Soricidae), leading to high diversity (Shannon index = 1.6–1.8) and high equitability (evenness index = 0.7–0.8) in cultivations and forest. In houses conversely, the rodent community was dominated by Mastomys natalensis (95–98%), leading to low diversity and equitability. Dynamics and reproduction were investigated in two species of pygmy mice, Mus mattheyi and Mus minutoides, two species of Praomys, P. daltoni and P. rostratus, and in Mastomys erythroleucus. The pygmy mice were abundant in cultivations in early rainy season, and reproduced from rainy to dry season. Praomys daltoni was also found more abundant in cultivations and seemed to reproduce between rainy and dry season, whereas P. rostratus preferred forest and cultivations in late rainy season, and reproduced throughout the year. Finally, M. erythroleucus was more abundant in forest in dry season, and seemed to reproduce from late rainy to dry season. This species had a low occurrence (6.5%) in the Faranah’s zone, and probably lived at its southern limit in Guinea. The presence of other Murinae, such as M. natalensis, Praomys spp as possible competitors in the same habitats, is discussed. For the first time, this study relates population biology of pygmy mice with molecular identification.     

Synthetic molecules: helping to unravel plant signal transduction

The application of small molecules has played a crucial role in identifying novel components involved in plant signalling. Compared to classic genetic approaches, small molecule screens offer notable advantages in dissecting plant biological processes, such as technical simplicity, low start-up costs, and most importantly, bypassing the problems of lethality and redundancy. To identify small molecules that target a biological process or protein of interest, robust and well-reasoned high-throughput screening approaches are essential. In this review, we present a series of principles and valuable approaches in small molecule screening in the plant model system Arabidopsis thaliana. We also provide an overview of small molecules that led to breakthroughs in uncovering phytohormone signalling pathways, endomembrane signalling cascades, novel growth regulators, and plant defence mechanisms. Meanwhile, the strategies to deciphering the mechanisms of these small molecules on Arabidopsis are highlighted. Moreover, the opportunities and challenges of small molecule applications in translational biology are discussed.     

Prey consumption by phytoseiid spider mite predators as affected by diurnal temperature variations

The consumption rate of an ectothermic predator is highly temperature-dependent and is a key driver of pest-predator population interactions. Not only average daily temperature, but also diurnal temperature variations may affect prey consumption and life history traits of ectotherms. In the present study, we evaluated the impact of temperature alternations on body size, predation capacity and oviposition rate of the predatory mites Phytoseiulus persimilis Athias-Henriot and Neoseiulus californicus McGregor (Acari: Phytoseiidae) when presented with eggs of their natural prey, the two-spotted spider mite Tetranychus urticae Koch (Acari: Tetranychidae). For both predators, mean daily temperature as well as temperature alternation had a substantial impact on the number of prey consumed. At lower average temperatures, more eggs were killed under an alternating temperature regime (20 °C/5 °C and 25 °C/10 °C) than at the corresponding mean constant temperatures (15 and 20 °C). At higher average temperatures (>25 °C), however, the opposite was observed with higher numbers of prey killed at constant temperatures than at alternating temperatures. At 25 °C, temperature variation had no effect on the predation capacity. A similar trend as for the predation rates was observed for the oviposition rates of the phytoseiids. Body size of N. californicus was affected both by average daily temperature and temperature variation, with smaller adult females emerging at alternating temperatures than at constant temperatures, whereas for P. persimilis, temperature variation had no impact on its body size. Our results demonstrate that temperature variations are likely to affect biological control of T. urticae by the studied phytoseiid predators.     

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

SUMMARY: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm. AVAILABILITY: Via the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D.     

Large Intercontinental Differentiation of Moina Micrura (Crustacea: Anomopoda): One Less Cosmopolitan Cladoceran?

Moina micrura Kurz, 1874 (Crustacea: Anomopoda), commonly regarded as a cosmopolitan cladoceran species, can be found almost all over the world except for arctic and cold-temperate regions. M. micrura has been recorded from virtually all types of limnetic habitats, including temperate permanent ponds, lakes, ephemeral desert pools, and tropical brackish fishponds. Its high morphological and ecological variability has so far been considered a result of intraspecific diversity. We tested the hypothesis that genetically isolated groups exist within M. micrura with crossing experiment and DNA sequence analysis. We compared two clones originating from populations from Central Europe (area of the type locality) and Australia. As there was extremely low production of hybrid eggs, the results of the crossing experiment strongly suggest the existence of reproductive isolation. The sequence divergence of mitochondrial gene for 12S rRNA (7.9%) was comparable to intraspecific differences within Daphnia pulex group. The sequence divergence of the clones of Moina macrocopa from Europe and Central Africa was much lower (1.4%). Our results suggest that at least two sibling species exist within M. micrura complex, which is in agreement with other data questioning the cosmopolitanism of various cladoceran species.     

Identifying marginal suppliers of construction materials: consistent modeling and sensitivity analysis on a Belgian case

Purpose

The identification of marginal suppliers is a key element of consequential LCA. This study investigates how systematically the identification of marginal suppliers can be performed across different products, while maintaining consistent modeling choices. Some products relevant for the Belgian construction sector are taken as a case study.

Methods

To gain insight in the current practice of identifying marginal suppliers, 30 recent studies have been reviewed. Based on the findings of the review, a method was proposed to identify geographical market boundaries from trade data and sensitive suppliers from production data. Both retrospective and prospective approaches to anticipate the future effect of a change in demand were taken into account. The method was applied to compute both a retrospective and a prospective marginal supplier’s mix per product. Finally, the effect of the modeling choices on the size of geographical market boundaries and marginal mixes was estimated via regression analysis.

Results and discussion

The forecasts and marginal mixes obtained matched with those from the existing literature, although clear differences in results are observed between the retrospective and prospective approach. Deviations from default assumptions in LCA were observed as well, such as large regional geographical markets for cement and aggregates instead of local ones. The statistical sensitivity analysis showed that identifying geographical market boundaries has the largest effect on the final marginal mix and that these markets are relative stable over time.

Conclusions

The proposed method and corresponding sensitivity analysis is an attempt to gain insight into the effect of modeling choices in the context of the identification of marginal suppliers for consequential LCA. It can in principle be applied to any product for which trade and production data are available. The proposed method helps to identify marginal mixes on a consistent and transparent way, to improve the robustness of the results in future consequential LCAs.

     

Effect of the mycotoxin deoxynivalenol on grain aphid <Emphasis Type="Italic">Sitobion avenae</Emphasis> and its parasitic wasp <Emphasis Type="Italic">Aphidius ervi</Emphasis> through food chain contamination

We investigated the influence of the Fusarium mycotoxin deoxynivalenol on the English grain aphid Sitobion avenae (Hemiptera: Aphididae) and its parasitic wasp Aphidius ervi (Hymenoptera: Braconidae) using in vitro laboratory experiments. In this tritrophic interaction, deoxynivalenol caused lethal (declined survival) and sublethal (prolonged nymphal development and reduced reproduction) effects on S. avenae aphids and consequentially led to a decreased production of parasitoid offspring resulting from parasitized deoxynivalenol-contaminated aphids. This paper highlights that the presence of mycotoxins should be considered in environmental risk assessment tests because they may alter the efficiency of biological control agents such as parasitoids through food chain contamination.     

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

Graphlets are small subgraphs, usually containing up to five vertices, that can be found in a larger graph. Identification of the graphlets that a vertex in an explored graph touches can provide useful information about the local structure of the graph around that vertex. Actually finding all graphlets in a large graph can be time-consuming, however. As the graphlets grow in size, more different graphlets emerge and the time needed to find each graphlet also scales up. If it is not needed to find each instance of each graphlet, but knowing the number of graphlets touching each node of the graph suffices, the problem is less hard. Previous research shows a way to simplify counting the graphlets: instead of looking for the graphlets needed, smaller graphlets are searched, as well as the number of common neighbors of vertices. Solving a system of equations then gives the number of times a vertex is part of each graphlet of the desired size. However, until now, equations only exist to count graphlets with 4 or 5 nodes. In this paper, two new techniques are presented. The first allows to generate the equations needed in an automatic way. This eliminates the tedious work needed to do so manually each time an extra node is added to the graphlets. The technique is independent on the number of nodes in the graphlets and can thus be used to count larger graphlets than previously possible. The second technique gives all graphlets a unique ordering which is easily extended to name graphlets of any size. Both techniques were used to generate equations to count graphlets with 4, 5 and 6 vertices, which extends all previous results. Code can be found at https://github.com/IneMelckenbeeck/equation-generator and https://github.com/IneMelckenbeeck/graphlet-naming.     

Spatio-temporal dynamics of the parasitic nematode Anguillicola crassus in Flanders, Belgium

Despite Egusa's earlier warning of the damage that the parasitic nematode Anguillicola crassus could inflict on the European eel Anguilla anguilla, its introduction in Europe was a fact in the early 1980s. Based on an elaborate dataset on Anguillicola crassus infection of 11 river catchments, this paper presents the results of a detailed study on the dispersal of the parasite in Flanders, Belgium, and the host-parasite relationship. In addition, data from 1986 and 1997 are used for comparative purposes, providing a perspective on the temporal infection pattern over 15 yr. The presence of A. crassus in Flanders was first discovered in 1985; 2 yr later a survey revealed a prevalence of 34.1% and a mean infection intensity of 5.5, based on adult nematodes only, and 10 yr later the parasite was present at all 11 sites sampled. Prevalence had increased to 62.5 % but the mean infection intensity had decreased to 3.9 adults per infected eel. Finally, in the year 2000, a third study revealed that A. crassus was present in 139 of 140 investigated sites; a further increase in prevalence to 68.7% and a decrease in mean infection intensity to 3.4 adults per infected eel was observed. When all larval stages were taken into account, mean prevalence amounted to 88.1% and mean intensity to 5.5 adults. The high infection level in Flanders is thought to be the result of restocking with glass eel and yellow eel, both of which are susceptible to A. crassus. The general infection parameters were similar in all 11 river catchments. It is possible that in Flanders both prevalence and mean infection intensity are stabilizing due to density-dependent regulation of the parasite infrapopulation. Fibrotic swimbladder walls were observed, mainly in large eels, and 20% of the total number of nematodes consisted of encapsulated larvae in the surveys of 1997 and 2000; 8 cases of swimbladder regeneration were observed.