The principal structure of male genital sclerites and muscles of bombycoid moths, with special reference to Anthelidae (Lepidoptera: Bombycoidea)

Male genital structures and muscles of bombycoid moths have repeatedly been misidentified in the literature. Furthermore, the genital structures of some bombycoid families, such as the poorly known Australo-New Guinean Anthelidae, have essentially remained unstudied. Based on comparative morphology, this study details the principal arrangements of male genital sclerites and muscles in all bombycoid families, with particular focus on basic structures and their modifications in Anthelidae. Emphasis is placed on the homology of and fusions between these structures and their function, providing a basis for the interpretation of modifications in future phylogenetic and taxonomic studies. This includes the unique fusion of gnathos and valvae in several bombycoid families, the arrangement and extent of the fused tegumen and vinculum, as well as the homology of the "transtilla". Further, a modification of the valve adductor muscle (the segment IX sternum to valva muscle, m4) widely regarded as a synapomorphy of Bombycoidea is demonstrated to be non-existent, as is the presumed presence of the valve abductor muscle (the segment IX tergum to valva muscle, m2) in Saturniidae.     

MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study

Background  

The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have been done to identify and quantify the importance of multi-SNP interactions, few of them could handle the genome wide data due to the combinatorial explosive search space and the difficulty to statistically evaluate the high-order interactions given limited samples.     

Relationship between Antibody 2F5 Neutralization of HIV-1 and Hydrophobicity of Its Heavy Chain Third Complementarity-Determining Region

The membrane-proximal external region (MPER) of the HIV-1 gp41 transmembrane glycoprotein is the target of the broadly neutralizing antibody 2F5. Prior studies have suggested a two-component mechanism for 2F5-mediated neutralization involving both structure-specific recognition of a gp41 protein epitope and nonspecific interaction with the viral lipid membrane. Here, we mutationally alter a hydrophobic patch on the third complementarity-determining region of the heavy chain (CDR H3) of the 2F5 antibody and assess the abilities of altered 2F5 variants to bind gp41 and to neutralize diverse strains of HIV-1. CDR H3 alterations had little effect on the affinity of 2F5 variants for a peptide corresponding to its gp41 epitope. In contrast, strong effects and a high degree of correlation (P < 0.0001) were found between virus neutralization and CDR H3 hydrophobicity, as defined by predicted free energies of transfer from water to a lipid bilayer interface or to octanol. The effect of CDR H3 hydrophobicity on neutralization was independent of isolate sensitivity to 2F5, and CDR H3 variants with tryptophan substitutions were able to neutralize HIV-1 ∼10-fold more potently than unmodified 2F5. A threshold was observed for increased hydrophobicity of the 2F5 CDR H3 loop beyond which effects on 2F5-mediated neutralization leveled off. Together, the results provide a more complete understanding of the 2F5 mechanism of HIV-1 neutralization and indicate ways to enhance the potency of MPER-directed antibodies.The membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 (HIV-1) gp41 transmembrane glycoprotein is the target of three broadly neutralizing anti-HIV-1 antibodies, 2F5, Z13e, and 4E10, and is thus a potential site of HIV-1 vulnerability to the humoral immune response (21, 24, 27, 48). The MPER encompasses ∼25 residues at the carboxyl-terminal end of the predicted gp41 ectodomain, just before the transmembrane region, and is rich in aromatic residues, typical of bilayer-interfacial regions of membrane proteins (26, 36, 40). Mutation of selected MPER tryptophans abrogates gp41-mediated fusion of the viral and target cell membranes, indicating that this region is crucial for HIV-1 infectivity (23, 28). Structural studies of unbound forms of the gp41 MPER both in solution and in lipid contexts have demonstrated that it adopts a number of conformations, many of which are α-helical, and electron-paramagnetic resonance measurements have indicated lipid bilayer immersion depths for MPER residues that range from acyl to phospholipid headgroup regions (4, 7, 8, 19, 32, 37). The binding of neutralizing antibodies, such as 2F5, to the MPER must therefore account for the membrane milieu in which the epitope is found.The 2F5 antibody has been shown to exhibit ∼100-fold-enhanced binding to its epitope on uncleaved gp140s when presented in the context of lipid proteoliposomes (11, 25), and other studies have shown that 2F5 can contact phospholipids directly in the absence of gp41 (1, 3, 12, 22, 29, 30). The latter finding has led to the suggestion that 2F5 might be autoreactive (12), although passive transfusion of 2F5 does not appear to have deleterious effects (38) and 2F5 failed to react in some clinically based assays for autoreactive lipid antibodies (31, 39). The crystal structures of the 2F5 antibody in complex with its gp41 MPER epitope revealed that, despite the 22-residue length of the 2F5 heavy chain third complementarity-determining region (CDR H3) loop, contacts with the gp41 MPER peptide are made predominantly at the loop base. In some crystal structures, the tip of the loop protrudes away from gp41, while in others, it is disordered (9, 14, 25). A unique feature of the tip of the CDR H3 loop is that it contains a patch of hydrophobic residues, including residues L100_A, F100_B, V100_D, and I100_F (Kabat numbering), which, with the exception of I100_F, do not contact gp41 (9, 10, 14, 25) (Fig. ​(Fig.1).1). While a prior study revealed the importance of residue F100_B of the CDR H3 loop in 2F5-neutralizing activity, nonconservative residue substitutions at this position also appeared to diminish 2F5 binding to the immobilized MPER peptide and gp41 in enzyme-linked immunosorbent assay (ELISA) formats (47). Conversely, a more recent study has shown that alanine mutations in the 2F5 CDR H3 loop can affect neutralization without affecting gp41 binding (2).Open in a separate windowFIG. 1.2F5 CDR H3 loop mutagenesis. (A) Structure of 2F5 Fab (blue and gray) in complex with a gp41 peptide (red). The 2F5 CDR H3 (purple) contacts gp41 only at its base, while the tip extends away from the peptide. (B) Close-up view of the 2F5 CDR H3 loop, with hydrophobic residues at the loop tip shown in stick representation and colored green. (C) Mutations introduced into the tip of the 2F5 CDR H3 (100_A to 100_F) are defined, along with a plot of the Wimley-White predicted free energies of transfer to a lipid bilayer interface (black) or to octanol (gray) for each of the mutations.In this study, we sought to examine the role of the chemical nature of residues at the tip of the 2F5 CDR H3 loop in neutralization of HIV-1. Mutations were introduced into the 2F5 CDR H3 loop that altered its hydrophobicity, and the resulting 2F5 mutants were tested both for binding to a gp41 epitope peptide and for neutralization of HIV-1. The results showed that the tip of the 2F5 CDR H3 loop, and specifically its hydrophobic nature, is required for 2F5-mediated neutralization of HIV-1 by means that appear to be independent both of gp41 affinity and of isolate-specific sensitivity to neutralization by 2F5.     

Diversity of lactic acid bacteria of the bioethanol process

Background  

Bacteria may compete with yeast for nutrients during bioethanol production process, potentially causing economic losses. This is the first study aiming at the quantification and identification of Lactic Acid Bacteria (LAB) present in the bioethanol industrial processes in different distilleries of Brazil.     

Unifying the theories of inclusive fitness and reciprocal altruism

Inclusive fitness and reciprocal altruism are widely thought to be distinct explanations for how altruism evolves. Here we show that they rely on the same underlying mechanism. We demonstrate this commonality by applying Hamilton's rule, normally associated with inclusive fitness, to two simple models of reciprocal altruism: one, an iterated prisoner's dilemma model with conditional behavior; the other, a mutualistic symbiosis model where two interacting species differ in conditional behaviors, fitness benefits, and costs. We employ Queller's generalization of Hamilton's rule because the traditional version of this rule does not apply when genotype and phenotype frequencies differ or when fitness effects are nonadditive, both of which are true in classic models of reciprocal altruism. Queller's equation is more general in that it applies to all situations covered by earlier versions of Hamilton's rule but also handles nonadditivity, conditional behavior, and lack of genetic similarity between altruists and recipients. Our results suggest changes to standard interpretations of Hamilton's rule that focus on kinship and indirect fitness. Despite being more than 20 years old, Queller's generalization of Hamilton's rule is not sufficiently appreciated, especially its implications for the unification of the theories of inclusive fitness and reciprocal altruism.     

Scirtes hemisphaericus uses macrophyte snorkels to pupate under water. With notes on pupae of additional European genera of Scirtidae (Coleoptera)

Morphological and behavioural adaptations enable Scirtes hemisphaericus to pupate under water, using emergent macrophytes as snorkels to breathe atmospheric air. The last instar larva bites into emergent macrophytes until the aerenchym is exposed. The pupa pushes its fore body into the wound, becoming surrounded by an air film in continuity with intracellular and atmospheric air. The pupa lacks normal ecdysial sutures, instead, its cuticle ruptures between the pro- and mesothorax. The fore body cuticle remains in place, preserving the connection to atmospheric air for the immature beetle. Pupation in earthen cells is known only in Elodes. Several other genera pupate under some cover, or freely exposed. Most pupae have 2–4 horn-like pronotal processes and 2–4 caudal attachment organs which differ between genera and sexes. Hydrocyphon (which pupates under water) and S. hemisphaericus pupae lack pronotal horns and attachment organs.     

Australian edwardsina (Diptera: Blephariceridae), new and rediscovered species

Edwardsina (Tonnoirina) confusa sp. n. is described from New South Wales. Previous records of E. (T.) spinosa Zwick from Barrington Tops were erroneous. The presumedly extinct E. (T.) lasmaniensis Tonnoir has been rediscovered in SW Tasmania.     

Notes on the genus Agnetina (= Phasganophora) (Plecoptera: Perlidae)

Genus Agnetina Klapálek, 1907 is removed from synonymy with Dinocras Klapálek, 1907 and synonymy between Agnetina and Phasganophora Klapálek, 1914 is established. A list of presently recognised nominal species of Agnetina is provided. For all west palaearctic species, i.e., A. elegantula (Klapálek), A. senilis Klapálek, A. werneri (Kempny), comb, n., lectotypes are designated. Distinctive characters of these three species are described, external male genitalia and eggs are illustrated. Asian A. brevipennis (Navás), comb, n., is briefly compared. A. dubia nom. n. is proposed to replace A. brevipennis Klapálek, 1921 (not Navás, 1912), a doubtful Asian species. A. pedata (Koponen, 1949) and A. undaata (Klapálek, 1921) are considered possible synonyms of A. senilis. which is for the first time recorded from Central Asia (Baikal area).