Spatial Variation in Army Ant Swarm Raiding and its Potential Effect on Biodiversity

Invertebrate communities of the tropical rain forest floor are highly diverse, characterized by patchy species distribution patterns and high variation in species density. Spatial variation in the foraging activity of swarm raiding army ants, prime invertebrate predators in tropical rain forests, is discussed as a mechanism contributing to these patterns, but highly resolved long‐term data on army ant raiding on the local and landscape scale are hitherto lacking. In this study, 196 positions in 11 study sites in a tropical rain forest in western Kenya were continuously monitored over ~4 mo for the occurrence of swarm raids of army ants. Using population simulation analyses, the consequences of army ant raiding for prey communities were assessed. We found an unexpectedly high variation in raid rates at the study site and landscape scale. The weekly chance of communities to become raided by army ants was on average 0.11, but ranged from 0 to 0.50 among the 196 positions. Simulating population developments of two Lotka–Volterra species—showing slight trade‐offs between competitive strength and resistance to army ant raids—in the real raiding landscapes showed that the observed spatial variation in raid rates may produce high prey diversity at larger spatial scales (due to high β‐diversity) and strong variation in species density. Our results indicate that high spatial variation in army ant swarm raiding is a mechanism capable of generating patchy species distribution patterns and maintaining the high biodiversity of invertebrate communities of the tropical rain forest floor.     

Loss of plant biodiversity eliminates stimulatory effect of elevated CO2 on earthworm activity in grasslands

Earthworms are among the world’s most important ecosystem engineers because of their effects on soil fertility and plant productivity. Their dependence on plants for carbon, however, means that any changes in plant community structure or function caused by rising atmospheric CO₂ or loss of plant species diversity could affect earthworm activity, which may feed back on plant communities. Production of surface casts measured during three consecutive years in field experimental plots (n = 24, 1.2 m²) planted with local calcareous grassland species that varied in plant species richness (diversity levels: high, 31 species; medium, 12; low, 5) and were exposed to ambient (356 μl CO₂ l^?1) or elevated (600 μl CO₂ l^?1) CO₂ was only consistently stimulated in high diversity plots exposed to elevated CO₂ (+120 %, 31 spp: 603 ± 52 under ambient CO₂ vs. 1,325 ± 204 g cast dwt. m^?2 year^?1 under elevated CO₂ in 1996; +77 %, 940 ± 44 vs. 1,663 ± 204 g cast dwt. m^?2 year^?1 in 1998). Reductions in plant diversity had little effect on cast production in ecosystems maintained at ambient CO₂, but the stimulatory effect of elevated CO₂ on cast production disappeared when plant species diversity was decreased to 12 and 5 species. High diversity plots were also the only communities that included plant species that an earlier field study showed to be among the most responsive to elevated CO₂ and to be most preferred by earthworms to deposit casts near. Further, the +87 % CO₂-induced increase in cast production measured over the 3 years corresponded to a parallel increase in cumulative total nitrogen of 5.7 g N m^?2 and would help explain the large stimulation of aboveground plant biomass production observed in high-diversity communities under elevated CO₂. The results of this study demonstrate how the loss of plant species from communities can alter responses of major soil heterotrophs and consequently ecosystem biogeochemistry.     

Analysis of the Fungal Flora in Environmental Dust Samples by PCR–SSCP Method

Conventional microbiological techniques yield only limited information on the composition of fungal communities in dust. The aim of this study was to establish and optimize PCR-single strand conformation polymorphism (PCR–SSCP) analysis for investigation of fungal diversity in rural dust samples. Three different DNA extraction protocols were tested on 38 fungal cultures. A total of six known universal fungal primer pairs were tested targeting the 18S rRNA gene, the 28S rRNA gene and the ITS region, respectively. Objective evaluation was performed with respect to the following parameters: efficiency to amplify all 38 strains; separation of seven species from different phylogenetic groups on the SSCP gel; additional bands in PCR–SSCP analysis; possibility to classify the amplified gene fragments to species level. Primer ITS1/ITS4 and PowerSoil? DNA isolation showed the best performance in most cases and were chosen for further analysis. The detection limit of the developed system was 200 CFU/g dust. Moreover, the reproducibility of the system could be demonstrated, leading to average profile similarities of 94.94 % [SD = 2.51] within gels, 93.03 % [SD = 4.69] between different days and 87.66 % [SD = 6.62] between different gels when testing shed and mattress dust samples. Sequencing allowed identification on species level, in detail: Alternaria alternata, Cladosporium sphaerospermum, Cladosporium cladosporioides as well as the yeasts Candida cabralensis and Candida catenulata. This demonstrates the adaptability of the method. In this study, a standardized system for fungal community analysis was developed that provides reproducible results applicable for epidemiological purposes.     

Circuitry Rewiring Directly Couples Competence to Predation in the Gut Dweller Streptococcus salivarius

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Individual identification and marking techniques for zebrafish

In laboratory fish research, the zebrafish Danio rerio (Cyprinidae) represents the equivalent of the mouse in mammalian research. This species has become a major model for studies in developmental and behavioural genetics, neurophysiology, biomedicine, ecotoxicology, and behavioural and evolutionary ecology. To meet the need for accurate and reproducible data in both fundamental and applied sciences, it is of primary importance to be able to tag and/or recognize individual zebrafish. However, classic methods used in fish ecology and aquaculture are generally difficult to apply to such small fish. Recently, various new tagging methods have been developed. This paper presents a first review of current identification and marking methods applied to zebrafish, from external observation methods (such as skin pattern recognition, fin clipping, scale regeneration, colour and transgenic methods) to the most advanced technological developments in electronic (low- and high- radio-frequencies PIT tags, microchip) and image analysis methods (video tracking). This review aims to help researchers and zebrafish facility managers select the identification method (ID) best adapted to their needs. The main characteristics of each ID method are examined (including detection range, durability, speed and repetitiveness, ID code combination, size dependence and ethical considerations), and their pros and cons are summarized in a decision table to help select the most appropriate option for a research or management program. Finally, contextual applications of these ID methods and future developments are discussed.     

Conservation of a domestic metapopulation structured into related and partly admixed strains

Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1,828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Bu?a strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Bu?a metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronized maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenization process. This study collected and evaluated samples, data and genomewide information and developed genome‐assisted cross‐border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semiprivate alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.     

Mononuclear-cell-derived microparticles attenuate endothelial inflammation by transfer of miR-142-3p in a CD39 dependent manner

Plasma microparticles (MP) bear functional active ectonucleotidases of the CD39 family with implications in vascular inflammation. MP appear to be able to fuse with cells and transfer genetic information. Here, we tested whether levels of different immunomodulatory microRNAs (miRs) in plasma MP are modulated by CD39 after experimental hepatectomy. We further investigated whether horizontal transfer of miR-142-3p between mononuclear (MNC) and endothelial cells via MP is regulated by purinergic signaling. Partial hepatectomy was performed in C57BL/6 wild type and Cd39 null mice. MP were collected via ultracentrifugation. MNC were stimulated with nucleotides and nucleosides, in vitro, and tested for miR-142-3p levels. Fusion of MNC-derived MP and endothelial cells with subsequent transfer of miR-142-3p was imaged by flow cytometry and confocal microscopy. Endothelial inflammation and apoptosis were quantified after transfection with miR-142-3p. Significantly lower miR-142-3p levels were observed in plasma MP of Cd39 null mice after partial hepatectomy, when compared to C57BL/6 wild types (p?<?0.05). In contrast to extracellular nucleotides, anti-inflammatory adenosine significantly increased miR-142-3p levels in MNC-derived MP, in vitro (p?<?0.05). MNC-derived MP are able to transfer miR-142-3p to endothelial cells by fusion. Transfection of endothelial cells with miR-142-3p decreased TNF-α levels (p?<?0.05) and endothelial apoptosis (p?<?0.05). MiR-142-3p levels in MNC-derived MP are modulated by nucleoside signaling and might reflect compensatory responses in vascular inflammation. Our data suggest the transfer of genetic information via shed MP as a putative mechanism of intercellular communication—with implications in organ regeneration.     

Following the course of human leptospirosis: evidence of a critical threshold for the vital prognosis using a quantitative PCR assay

In order to follow the course of acute human leptospirosis, an ELISA microtiter plate hybridization method was developed for the quantitative determination of Leptospira spp. in biological samples after PCR. The biotin-labelled amplified product (331 bp from the rrs gene) was hybridized with a complementary capture probe covalently linked onto aminated polystyrene wells, and detected using a colorimetric reaction. The mean detection limit was 50 copies per 10 microl. In a prospective study of human leptospirosis cases, we obtained evidence that a density of 10(4) leptospires per ml of blood is a critical threshold for the vital prognosis of the patients. The practicability of the method makes it suitable for use in tropical areas for multicentric studies. Such studies could lead to a better knowledge of the natural history of the human disease. The method is also suitable for experimental evaluation of improved antibiotic treatments for leptospirosis.     

Proteins

Proteins continue to surprise and amaze us in the myriad of ways in which they achieve biological function. The Proteins section in this issue of Current Opinion in Structural Biology highlights several proteins in which large conformational changes and evolutionary divergence in structure and function, play essential roles in their adaptation to a variety of biological functions. In addition, fundamental advances have been made in research, spurred on by industrial interest in the use of proteins as drug targets or as catalysts. All of the reviews in this section document the fact that multiple crystal structures of a protein in different functional states, and of different members of protein families, are necessary for the composition of a complete structural picture.