Description of a new species of coral-inhabiting barnacle, Darwiniella angularis sp. n. (Cirripedia, Pyrgomatidae) from Taiwan

The present study has identified a new species from the previously monotypic genus Darwiniella Anderson, 1992. Darwiniella angularissp. n. is similar to Darwiniella conjugatum (Darwin, 1854) in external shell morphology and arthropodal characters. Darwiniella conjugatum, however, has a sharper tergal spur and a less obvious adductor plate angle when compared to Darwiniella angularissp. n. Molecular analyses on mitochondrial DNA 12S rDNA and COI regions also support the morphological differences. Sequence divergences in 12S rDNA and COI between Darwiniella conjugatum and Darwiniella angularissp. n. are 5% and 13% respectively, which are equivalent to the inter-specific sequence divergences in other barnacles. Both Darwiniella species are common on Cyphastrea Milne-Edwards and Haime, 1848 corals and Darwiniella angularissp. n. is also collected from Astreopora de Blainville, 1830 corals in Taiwan.     

Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior

The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs). In mammals, sGCs function as alpha/beta heterodimers activated by gaseous ligands binding to a haem prosthetic group. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian beta than alpha subunits. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior. We show that GCY-35 and GCY-36 act as alpha-like and beta-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid.     

Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces

Macromolecular oligomeric assemblies are involved in many biochemical processes of living organisms. The benefits of such assemblies in crowded cellular environments include increased reaction rates, efficient feedback regulation, cooperativity and protective functions. However, an atom‐level structural determination of large assemblies is challenging due to the size of the complex and the difference in binding affinities of the involved proteins. In this study, we propose a novel combinatorial greedy algorithm for assembling large oligomeric complexes from information on the approximate position of interaction interfaces of pairs of monomers in the complex. Prior information on complex symmetry is not required but rather the symmetry is inferred during assembly. We implement an efficient geometric score, the transformation match score, that bypasses the model ranking problems of state‐of‐the‐art scoring functions by scoring the similarity between the inferred dimers of the same monomer simultaneously with different binding partners in a (sub)complex with a set of pregenerated docking poses. We compiled a diverse benchmark set of 308 homo and heteromeric complexes containing 6 to 60 monomers. To explore the applicability of the method, we considered 48 sets of parameters and selected those three sets of parameters, for which the algorithm can correctly reconstruct the maximum number, namely 252 complexes (81.8%) in, at least one of the respective three runs. The crossvalidation coverage, that is, the mean fraction of correctly reconstructed benchmark complexes during crossvalidation, was 78.1%, which demonstrates the ability of the presented method to correctly reconstruct topology of a large variety of biological complexes. Proteins 2015; 83:1887–1899. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

New records of water mites of the family Torrenticolidae (Acari, Hydrachnidia) with descriptions of two new species from Nanshih River system in Taiwan and redescription of Torrenticola ussuriensis (Sokolow, 1940) from the Russian Far East

New records of torrenticolid water mites (Acari: Hydrachnidia, Torrenticolidae) from Nanshih River, Taiwan, are presented. Two new species are described: Torrenticola nanshihensis and Torrenticola taiwanicus; the latter species is compared with Torrenticola ussuriensis (Sokolow, 1940), a poorly known species which is re-described based on a new material from the Russian Far East; Monatractides cf. circuloides (Halík, 1930)is reported for the first time for Taiwan.     

Differential requirement for cathepsin D for processing of the full length and C-terminal fragment of the malaria antigen MSP1

Merozoite Surface Protein 1 is expressed on the surface of malaria merozoites and is important for invasion of the malaria parasite into erythrocytes. MSP1-specific CD4 T cell responses and antibody can confer protective immunity in experimental models of malaria. In this study we explore the contributions of cathepsins D and E, two aspartic proteinases previously implicated in antigen processing, to generating MSP1 CD4 T-cell epitopes for presentation. The absence of cathepsin D, a late endosome/lysosomal enzyme, is associated with a reduced presentation of MSP1 both following in vitro processing of the epitope MSP1 from infected erythrocytes by bone marrow-derived dendritic cells, and following in vivo processing by splenic CD11c+ dendritic cells. By contrast, processing and presentation of the soluble recombinant protein fragment of MSP1 is unaffected by the absence of cathepsin D, but is inhibited when both cathepsin D and E are absent. The role of different proteinases in generating the CD4 T cell repertoire, therefore, depends on the context in which an antigen is introduced to the immune system.     

The antibacterial activity of biogenic silver and its mode of action

In a previous study, biogenic silver nanoparticles were produced by Lactobacillus fermentum which served as a matrix preventing aggregation. In this study the antibacterial activity of this biogenic silver was compared to ionic silver and chemically produced nanosilver. The minimal inhibitory concentration (MIC) was tested on Gram-positive and Gram-negative bacteria and was comparable for biogenic silver and ionic silver ranging from 12.5 to 50 mg/L. In contrast, chemically produced nanosilver had a much higher MIC of at least 500 mg/L, due to aggregation upon application. The minimal bactericidal concentration (MBC) in drinking water varied from 0.1 to 0.5 mg/L for biogenic silver and ionic silver, but for chemically produced nanosilver concentrations, up to 12.5 mg/L was needed. The presence of salts and organic matter decreased the antimicrobial activity of all types of silver resulting in a higher MBC and a slower inactivation of the bacteria. The mode of action of biogenic silver was mainly attributed to the release of silver ions due to the high concentration of free silver ions measured and the resemblance in performance between biogenic silver and ionic silver. Radical formation by biogenic silver and direct contact were found to contribute little to the antibacterial activity. In conclusion, biogenic nanosilver exhibited equal antimicrobial activity compared to ionic silver and can be a valuable alternative for chemically produced nanosilver.     

Syncephalis aggregata, a new species from the semiarid region of Brazil

A new species of Syncephalis (Zoopagales) was isolated from soil in a semiarid area of northeastern Brazil. Syncephalis aggregata is distinguished from the other species of the genus by the production of merosporangiophores in dense tufts and with randomly spaced, irregular swellings and simple merosporangia produced over the upper 50% of a globose to ovoid vesicle. An identification key for the species of Syncephalis found in Brazil is provided.     

Factors determining plant–neighbour interactions on different spatial scales in young species-rich grassland communities

In naturally colonised species-rich grassland communities, we examined the properties of a plant’s aboveground neighbourhood that affect its performance (aboveground biomass). To this end a range of neighbourhood parameters were measured: number, biomass and species richness of the neighbours, number and biomass of the conspecific neighbours, and light availability at the base of the target plant. We also determined at which neighbourhood size the strongest target plant–neighbour interactions occurred, and whether conspecific neighbours affected competitively stronger or weaker target species differently. Target plant performance varied with target identity, and was significantly affected by light availability and the number of neighbouring plants (neighbourhood density). Depending on the target species, there was also an effect of total neighbour biomass on plant performance. The target plants were most strongly affected by their neighbours within a 3-cm distance, which could account for 78% of the variance in target biomass. Number or biomass of the conspecific neighbours did not contribute to the explanation of target performance in any of the target species. Whereas in an 8-cm neighbourhood the amount of light penetration was the strongest predictor of target performance, the number of neighbours was more important in a 3-cm neighbourhood. These experimental results might be useful to extend existing neighbourhood competition models for one or two species to multi-species competition models.