Molecular phylogenetic evidence that the phylum Haplosporidia has an alveolate ancestry

The phylogenetic position of the phylum Haplosporidia among other protists was investigated with the complete 16S-like rRNA gene sequences from two species in the phylum: Haplosporidium nelsoni, a parasite of oysters, and Minchinia teredinis, a parasite of shipworms. Because the lack of obvious morphological homologies with other protists hampered decisions regarding taxonomic composition for sequence alignment and phylogenetic analysis, the complete sequences for these two haplosporidians were directed as search queries to the blast/ncbi.nlm.nih.gov electronic mail server. The results of this heuristic similarity search provided a basis for constructing a preliminary higher-taxonomic-level analysis comparing the haplosporidians with species from the slime molds, fungi, algae, amoebae, ciliates, dinoflagellates, and apicomplexans. Maximum parsimony yielded equivocal results, whereas transversionally weighted parsimony suggested an affinity with the alveolates (i.e., the ciliates, dinoflagellates, and apicomplexans). Multiple alignment of the two haplosporidian sequences against 17 taxa in a secondary analysis focusing on the alveolates and subsequent parsimony analysis placed the phylum Haplosporidia as a monophyletic group within the Alveolata and as a taxon of equal rank with the other three alveolate phyla. The precise placement within the Alveolata was sensitive to weighting.      

Local IL-13 gene transfer prior to immune-complex arthritis inhibits chondrocyte death and matrix-metalloproteinase-mediated cartilage matrix degradation despite enhanced joint inflammation

During immune-complex-mediated arthritis (ICA), severe cartilage destruction is mediated by Fcγ receptors (FcγRs) (mainly FcγRI), cytokines (e.g. IL-1), and enzymes (matrix metalloproteinases (MMPs)). IL-13, a T helper 2 (Th2) cytokine abundantly found in synovial fluid of patients with rheumatoid arthritis, has been shown to reduce joint inflammation and bone destruction during experimental arthritis. However, the effect on severe cartilage destruction has not been studied in detail. We have now investigated the role of IL-13 in chondrocyte death and MMP-mediated cartilage damage during ICA. IL-13 was locally overexpressed in knee joints after injection of an adenovirus encoding IL-13 (AxCAhIL-13), 1 day before the onset of arthritis; injection of AxCANI (an empty adenoviral construct) was used as a control. IL-13 significantly increased the amount of inflammatory cells in the synovial lining and the joint cavity, by 30% to 60% at day 3 after the onset of ICA. Despite the enhanced inflammatory response, chondrocyte death was diminished by two-thirds at days 3 and 7. The mRNA level of FcγRI, a receptor shown to be crucial in the induction of chondrocyte death, was significantly down-regulated in synovium. Furthermore, MMP-mediated cartilage damage, measured as neoepitope (VDIPEN) expression using immunolocalization, was halved. In contrast, mRNA levels of MMP-3, -9, -12, and -13 were significantly higher and IL-1 protein, which induces production of latent MMPs, was increased fivefold by IL-13. This study demonstrates that IL-13 overexpression during ICA diminished both chondrocyte death and MMP-mediated VDIPEN expression, even though joint inflammation was enhanced.     

Determination of expander apparatus displacements and contact pressures on the mucosa using FEM modelling considering mandibular asymmetries

This paper presents a method for prediction of forces and displacements in the expansion screw of a modified mandibular Schwarz appliance and the contact pressure distributions on the mucosa during malocclusions treatment. A 3D finite element biomechanical model of the complete mandible–mucosa–apparatus set was built using computerised tomographic images of a patient's mandible and constructive solid geometry by computer software. An iterative procedure was developed to handle a boundary condition that takes into account the mandibular asymmetries. The results showed asymmetries in the contact pressure distributions that indicated with precision the patient's malocclusion diagnosis. In vivo measurements of contact pressure using piezoelectric sensors agreed with the computational results. It was shown that the left and right ends of the expansion screw move differently with respect to the patient mandible, even though the expansion screw has an opening mechanism to ensure equal stretching at both ends. The contact pressures between the apparatus and the mucosa vary linearly with applied forces, which can simplify the analysis of the biomechanical behaviour of the expander mandible apparatus. The biomechanical modelling proposed in this paper can be a useful tool to improve malocclusions treatment, safely avoiding the use of forces acting on live structures beyond the biological tolerance, which could result in traumatic effects.     

Mobster: accurate detection of mobile element insertions in next generation sequencing data

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users.     

Allometric models for aboveground biomass estimation of the mangrove Avicennia schaueriana

As mangroves become recognized as important carbon storages, the need for reducing the uncertainty of carbon inventories becomes increasingly emphasized. Accordingly, the objective of this study was to develop allometric models to estimate the total aboveground biomass (AGB) and the biomass per compartment of Avicennia schaueriana and to compare them with other models previously published for the genus Avicennia. Fifty three A. schaueriana trees, with different diameters at breast height (DBH) and height, were felled in a mangrove from Southeastern Brazil and their dry weight determined. Simple linear regression analysis was used to develop the equations after log-transformation, using the following independent variables: DBH and DBH² * height. All the equations were significant and presented high R _a ² (adjusted coefficient of determination). DBH provided the lowest SEE (standard error of estimation) in the regressions associated to leaves and total AGB, while DBH² * height generated the most precise regressions for trunk, branches, and twigs. In comparison with other 11 equations previously developed for the genus Avicennia, the equation developed in the present study for total AGB showed the lowest mean deviation in relation to trees with known biomass, underscoring the importance of developing species- and site-specific equations.     

Chemical characterization of Azadirachta indica grafted on Melia azedarach and analyses of azadirachtin by HPLC‐MS‐MS (SRM) and meliatoxins by MALDI‐MS

Introduction – Melia azedarach adapted to cool climates was selected as rootstocks for vegetative propagation of Azadirachta indica. Cleft grafting of A. indica on M. azedarach rootstock showed excellent survival. Little is known about the chemistry of grafting. Objective – The roots, stems, leaves and seeds of this graft were examined in order to verify if grafted A. indica would produce limonoids different from those found in non‐grafted plants. Intact matured fruits were also studied to verify if they were free of meliatoxins. Methodology – After successive chromatographic separations the extracts afforded several limonoids. HPLC‐MS/MS and MALDI‐MS were used to develop sensitive methods for detecting azadirachtin on all aerial parts of this graft and meliatoxins in fruits, respectively. Results – The stem afforded the limonoid salannin, which was previously found in the oil seeds of A. indica. Salannin is also found in the root bark of M. azedarach. Thus, the finding of salannin in this study suggests that it could have been translocated from the M. azedarach rootstock to the A. indica graft. HPLC‐MS/MS analyses showed that azadirachtin was present in all parts of the fruits, stem, flowers and root, but absent in the leaves. The results of MALDI‐MS analyses confirmed the absence of meliatoxins in graft fruits. Conclusion – This study showed that A. indica grafted onto M. azedarach rootstock produces azadirachtin, and also that its fruits are free of meliatoxins from rootstocks, confirming that this graft forms an excellent basis for breeding vigorous Neem trees in cooler regions. Copyright © 2010 John Wiley & Sons, Ltd.     

Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait−gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.