<Emphasis Type="Italic">H2r</Emphasis>: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments

Background  

A multiple sequence alignment (MSA) generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues.     

Photosynthetic parameters of birch (Betula pendula Roth) leaves growing in normal and in CO2- and O3- enriched atmospheres

Two silver birch (Betula pendula Roth) clones K1659 and V5952 were grown in open‐top chambers over 3 years (age 7–9 years). The treatments were increased CO₂ concentration (+CO₂, 72 Pa), increased O₃ concentration (+O₃, 2 × ambient O₃ with seasonal AOT40 up to 28 p.p.m. h) and in combination (+CO₂ + O₃). Thirty‐seven photosynthetic parameters were measured in the laboratory immediately after excising leaves using a computer‐operated routine of gas exchange and optical measurements. In control leaves the photosynthetic parameters were close to the values widely used in a model (Farquhar, von Caemmerer and Berry, Planta 149, 78–90, 1980). The distribution of chlorophyll between photosystem II and photosystem I, intrinsic quantum yield of electron transport, uncoupled turnover rate of Cyt b₆f, Rubisco specificity and K_m (CO₂) were not influenced by treatments. Net photosynthetic rate responded to +CO₂ with a mean increase of 17% in both clones. Dry weight of leaves increased, whereas protein, especially Rubisco content and the related photosynthetic parameters decreased. Averaged over 3 years, eight and 17 mechanistically independent parameters were significantly influenced by the elevated CO₂ in clones K1659 and V5952, respectively. The elevated O₃ caused a significant decrease in the average photosynthetic rate of clone V5952, but not of clone K1659. The treatment caused changes in one parameter of clone K1659 and in 11 parameters of clone V5952. Results of the combined treatment indicated that +O₃ had less effect in the presence of +CO₂ than alone. Interestingly, changes in the same photosynthetic parameters were observed in chamberless grown trees of clone V5952 as under +O₃ treatment in chambers, but this was not observed for clone K1659. These results suggest that during chronic fumigation, at concentrations below the threshold of visible leaf injuries, ozone influenced the photosynthetic parameters as a general stress factor, in a similar manner to weather conditions that were more stressful outside the chambers. According to this hypothesis, the sensitivity of a species or a clone to ozone is expected to depend on the growth conditions: the plant is less sensitive to ozone if the conditions are close to optimal and it is more sensitive to ozone under conditions of stress.     

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.     

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.     

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.     

Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?

This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa×26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.     

IDKK1 inhibits canonical Wnt signaling in human papillomavirus-positive penile cancer cells

Penile squamous cell cancer (PSCC) is the most frequent penile malignant disease. Infections with human papillomaviruses (HPV) are a major etiologic driver of PSCC. However, the molecular details of the underlying carcinogenesis are understudied because of rare clinical specimens and missing cell lines. Here, we investigated if the expression of high-risk HPV16 oncogenes causes an augmentation of the Wnt pathway using unique HPV-positive penile cancer (PeCa) cell lines in monolayer and organotypic 3D raft cultures as well as tissue micro arrays containing clinical tissue specimens. The HPV oncoproteins enhanced the expression of Leucine-rich repeat-containing G-protein coupled receptor 6 (LGR6) and the HPV-positive PeCa cells expressed a signature of Wnt target and stemness-associated genes. However, the notable lack of nuclear β-catenin in vitro and in situ raised the question if the enhanced expression of Wnt pathway factors is tantamount to an active Wnt signaling. Subsequent TOP-flash reporter assays revealed Wnt signaling as absent and not inducible by respective Wnt ligands in PeCa cell lines. The HPV-positive PeCa cells and especially HPV-positive PeCa specimens of the tumor core expressed the Wnt antagonist and negative feedback-regulator Dickkopf1 (DKK1). Subsequent neutralization experiments using PeCa cell line-conditioned media demonstrated that DKK1 is capable to impair ligand-induced Wnt signaling. While gene expression analyses suggested an augmented and active canonical Wnt pathway, the respective signaling was inhibited due to the endogenous expression of the antagonist DKK1. Subsequent TMA stainings indicated Dkk1 as linked with HPV-positivity and metastatic disease progression in PeCa suggesting potential as a prognostic marker.     

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.