Xander: employing a novel method for efficient gene-targeted metagenomic assembly

BACKGROUND: Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes. RESULTS: We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences. CONCLUSION: Xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-015-0093-6) contains supplementary material, which is available to authorized users

Spins and magnetic moments of 58,60,62,64Mn ground states and isomers

The odd-odd 54,56,58,60,62,64Mn isotopes (Z = 25) were studied using bunched-beam collinear laser spectroscopy at ISOLDE, CERN. From the measured hyperfine spectra the spins and magnetic moments of Mn isotopes up to N = 39 were extracted. The previous tentative ground state spin assignments of 58,60,62,64Mn are now firmly determined to be I = 1 along with an I = 4 assignment for the isomeric states in 58,60,62Mn. The I = 1 magnetic moments show a decreasing trend with increasing neutron number while the I = 4 moments remain quite constant between N = 33 and N = 37. The results are compared to large-scale shell-model calculations using the GXPF1A and LNPS effective interactions. The excellent agreement of the ground state moments with the predictions from the LNPS calculations illustrates the need for an increasing amount of proton excitations across Z = 28 and neutron excitations across N = 40 in the ground state wave functions from N = 37 onwards.status: publishe

Quadrupole moments of odd-A Mn53-63: Onset of collectivity towards N=40

The spectroscopic quadrupole moments of the odd–even Mn isotopes between N=28 and N=38 have been measured using bunched-beam collinear laser spectroscopy at ISOLDE, CERN. In order to increase sensitivity to the quadrupole interaction, the measurements have been done using a transition in the ion rather than in the atom, with the additional advantage of better spectroscopic efficiency. Since the chosen transition is from a metastable state, optical pumping in ISOLDE's cooler and buncher (ISCOOL) was used to populate this state. The extracted quadrupole moments are compared to large-scale shell model predictions using three effective interactions, GXPF1A, LNPS and modified A3DA. The inclusion of both the 1νg9/2 and 2νd5/2 orbitals in the model space is shown to be necessary to reproduce the observed increase in the quadrupole deformation from N=36 onwards. Specifically, the inclusion of the 2νd5/2 orbital induces an increase in neutron and proton excitations across the reduced gaps at N=40 and Z=28, leading to an increase in deformation above N=36.publisher: Elsevier articletitle: Quadrupole moments of odd-A 53−63Mn: Onset of collectivity towards N=40 journaltitle: Physics Letters B articlelink: http://dx.doi.org/10.1016/j.physletb.2016.07.016 content_type: article copyright: © 2016 The Author(s). Published by Elsevier B.V.status: publishe

An experimental study on the causal relationships between (ecto-)parasites, testosterone and sexual signalling

<p>Bird song is considered to have evolved via sexual selection and should as such honestly signal aspects of the quality of its bearer. To ensure honesty, the immunocompetence handicap hypothesis proposed a dual role of testosterone, having positive effects on sexual signalling but suppressive effects on immune function. However, recent studies showed that it is rather an immune activation that suppresses the androgen production. This reversed chain of causation may significantly alter the pathways, which translate the effects of parasites and pathogens into changes in the expression of male sexual traits. We infested male canaries with Ixodes ricinus tick nymphs to investigate the causal relationships between (ecto-)parasites, testosterone and sexual signalling, here singing behaviour. We focused on flexible song traits, which may quickly reflect changes in the infestation status, and tested whether these effects relate to changes in the plasma testosterone levels or health state. The experimental tick infestation altered the males' song performance by reducing song consistency, a trait that had previously been identified to reflect male quality. The tick infestation lowered the plasma testosterone levels and had a negative effect on the health status in terms of a reduced hematocrit. Our pathway analysis then revealed that it is the parasite-induced reduction of the plasma testosterone levels but not of the health state that caused the changes in song consistency. Thus, our study supports the view that it is the effect of parasites and immune activation on plasma testosterone levels that generates the trade-off between immunocompetence and sexual signalling.</p>