Polymorphisms of interferon-inducible genes OAS-1 and MxA associated with SARS in the Vietnamese population

We hypothesized that host antiviral genes induced by type I interferons might affect the natural course of severe acute respiratory syndrome (SARS). We analyzed single nucleotide polymorphisms (SNPs) of 2',5'-oligoadenylate synthetase 1 (OAS-1), myxovirus resistance-A (MxA), and double-stranded RNA-dependent protein kinase in 44 Vietnamese SARS patients with 103 controls. The G-allele of non-synonymous A/G SNP in exon 3 of OAS-1 gene showed association with SARS (p=0.0090). The G-allele in exon 3 of OAS-1 and the one in exon 6 were in strong linkage disequilibrium and both of them were associated with SARS infection. The GG genotype and G-allele of G/T SNP at position -88 in the MxA gene promoter were found more frequently in hypoxemic group than in non-hypoxemic group of SARS (p=0.0195). Our findings suggest that polymorphisms of two IFN-inducible genes OAS-1 and MxA might affect susceptibility to the disease and progression of SARS at each level.     

Role of the Nuclease Activities Encoded by Herpes Simplex Virus 1 UL12 in Viral Replication and Neurovirulence

Enzyme-dead mutations in the herpes simplex virus 1 UL12 gene that abolished its endo- and exonuclease activities only slightly reduced viral replication in cell cultures. However, the UL12 null mutation significantly reduced viral replication, suggesting that a UL12 function(s) unrelated to its nuclease activities played a major role in viral replication. In contrast, the enzyme-dead mutations significantly reduced viral neurovirulence in mice, suggesting that UL12 nuclease activities were critical for viral pathogenesis in vivo.     

Polychaete meets octopus: symbiotic relationship between Spathochaeta octopodis gen. et sp. nov. (Annelida: Chrysopetalidae) and Octopus sp. (Mollusca: Octopodidae)

Marine annelids in the subfamily Calamyzinae (family Chrysopetalidae) are either symbiotic or free-living forms that have been mainly reported from deep-sea chemosynthetic systems. Symbiotic calamyzines mainly live in the mantle cavity of bivalves in hydrothermal vents or cold seeps, but one species is also found to be inserted into the epidermis of polychaetes. We found a single specimen of calamyzine polychaete on the body surface of Octopus sp. collected in the Sea of Kumano (Japan), which represents the first known record of symbiotic association between polychaetes and octopuses. We described the specimen as Spathochaeta octopodis gen. et sp. nov. Spathochaeta gen. nov. can be discriminated from other genera in Calamyzinae by the presence of spatula-shaped notochaetae and dorsal chaetal lobes. We also provided the phylogenetic position of S. octopodis gen. et sp. nov. within Chrysopetalidae based on four gene markers (COI, 16S, 18S, H3). www.zoobank.org/urn:lsid:zoobank.org:pub:A8FB15C1-31A7-4487-966B-13F10E19A373.     

Unbiased identification of target antigens of CD8+ T cells with combinatorial libraries coding for short peptides

Cytotoxic CD8(+) T cells recognize the antigenic peptides presented by class I major histocompatibility complex (MHC) molecules. These T cells have key roles in infectious diseases, autoimmunity and tumor immunology, but there is currently no unbiased method for the reliable identification of their target antigens. This is because of the low affinities of antigen-specific T cell receptors (TCR) to their target MHC-peptide complexes, the polyspecificity of these TCRs and the requirement that these TCRs recognize protein antigens that have been processed by antigen-presenting cells (APCs). Here we describe a technology for the unbiased identification of the antigenic peptides presented by MHC class I molecules. The technology uses plasmid-encoded combinatorial peptide libraries and a single-cell detection system. We validated this approach using a well-characterized influenza-virus–specific TCR, MHC and peptide combination. Single APCs carrying antigenic peptides can be detected among several million APCs that carry irrelevant peptides. The identified peptide sequences showed a converging pattern of mimotopes that revealed the parent influenza antigen. This technique should be generally applicable to the identification of disease-relevant T cell antigens.     

Using food network unfolding to evaluate food–web complexity in terms of biodiversity: theory and applications

Food–web complexity often hinders disentangling functionally relevant aspects of food–web structure and its relationships to biodiversity. Here, we present a theoretical framework to evaluate food–web complexity in terms of biodiversity. Food network unfolding is a theoretical method to transform a complex food web into a linear food chain based on ecosystem processes. Based on this method, we can define three biodiversity indices, horizontal diversity (D_H), vertical diversity (D_V) and range diversity (D_R), which are associated with the species diversity within each trophic level, diversity of trophic levels, and diversity in resource use, respectively. These indices are related to Shannon's diversity index (H′), where H′ = D_H + D_V ? D_R. Application of the framework to three riverine macroinvertebrate communities revealed that D indices, calculated from biomass and stable isotope features, captured well the anthropogenic, seasonal, or other within‐site changes in food–web structures that could not be captured with H′ alone.