Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker

Motivation: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data. Results: We evaluated the Metaxa2 Database Builder on 11 commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality. Availability and implementation: Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/. Supplementary information: Supplementary data are available at Bioinformatics online

On deformations of 2d SCFTs

Motivated by the representation of the super Virasoro constraints as generalized Dirac-K{\"a}hler constraints $(d \pm d^\dagger)|\psi> = 0$ on loop space, examples of the most general continuous deformations $d \to e^{-W} d e^W$ are considered which preserve the superconformal algebra at the level of Poisson brackets. The deformations which induce the massless NS and NS-NS backgrounds are exhibited. Hints for a manifest realization of S-duality in terms of an algebra isomorphism are discussed. It is shown how the first order theory of 'canonical deformations' is reproduced and how the deformation operator $W$ encodes vertex operators and gauge transformations.Comment: 44 pages, no figures, discussion of relation to canonical deformations and vertex operators added, typos correcte

Taxa-area relationship of aquatic fungi on deciduous leaves

One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios.This work was supported by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569), funded by national funds through the Portuguese Foundation for Science and Technology (FCT) I.P. (http://www.fct.pt/) and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalizacao (POCI) and by the project PTDC/AAC-AMB/117068/2010, funded by national funds through FCT I.P. and the European Regional Development Funds through the Operational Competitiveness Program (FEDER-COMPETE). Support from FCT to SD (SFRH/BPD/47574/2008 and SFRH/BPD/109842/2015) and from NSERC Discovery grant program (http://www.nserc-crsng.gc.ca/index_eng.asp) to FB is also acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica

Antarctic ice-covered lakes are exceptional sites for studying the ecology of aquatic fungi under conditions of minimal human disturbance. In this study, we explored the diversity and community composition of fungi in five permanently covered lake basins located in the Taylor and Miers Valleys of Antarctica. Based on analysis of the 18S rRNA sequences, we showed that fungal taxa represented between 0.93% and 60.32% of the eukaryotic sequences. Cryptomycota and Chytridiomycota dominated the fungal communities in all lakes; however, members of Ascomycota, Basidiomycota, Zygomycota, and Blastocladiomycota were also present. Of the 1313 fungal OTUs identified, the two most abundant, belonging to LKM11 and Chytridiaceae, comprised 74% of the sequences. Significant differences in the community structure were determined among lakes, water depths, habitat features (i.e., brackish vs. freshwaters), and nucleic acids (DNA vs. RNA), suggesting niche differentiation. Network analysis suggested the existence of strong relationships among specific fungal phylotypes as well as between fungi and other eukaryotes. This study sheds light on the biology and ecology of basal fungi in aquatic systems. To our knowledge, this is the first report showing the predominance of early diverging lineages of fungi in pristine limnetic ecosystems, particularly of the enigmatic phylum Cryptomycota.National Science Foundation/[PLR1439774]/NSF/Estados UnidosNational Science Foundation/[PLR1115245]/NSF/Estados UnidosNational Science Foundation/[PLR 1543537]/NSF/Estados UnidosNational Aeronautics and Space Administration/[NNH14ZDA001N-PSTAR]/NASA/Estados UnidosUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biologí

Induction of neutralizing antibodies specific for the envelope proteins of the koala retrovirus by immunization with recombinant proteins or with DNA

Background: The koala retrovirus (KoRV) is the result of a transspecies transmission of a gammaretrovirus with fatal consequences for the new host. Like many retroviruses, KoRV induces lymphoma, leukemia and an immunodeficiency that is associated with opportunistic infections in the virus-infected animals. We recently reported the induction of neutralizing antibodies by immunization with the recombinant ectodomain of the transmembrane envelope protein p15E of KoRV. Since the neutralization titers of the p15E-specific sera were only moderate, we investigated the use of the surface envelope protein gp70 to induce neutralizing antibodies. Findings: We immunized rats and goats with the recombinant gp70 protein of the KoRV, an unglycosylated protein of 52kD (rgp70/p52) or with the corresponding DNA. In parallel we immunized with recombinant rp15E or with a combination of rp15E and rgp70/p52. In all cases binding and neutralizing antibodies were induced. The gp70-specific sera had titers of neutralizing antibodies that were 15-fold higher than the p15E-specific sera. Combining rp15E and rgp70/p52 did not significantly increase neutralizing titers compared to rgp70/p52 alone. High titers of neutralizing antibodies specific for gp70 were also induced by immunization with DNA. Since KoRV and PERV are closely related, we investigated cross-neutralization of the antisera. The antisera against p15E and gp70 of PERV and KoRV inhibited infection by both viruses. Conclusion: The envelope proteins of the KoRV may therefore form the basis of an effective preventive vaccine to protect uninfected koalas from infection and possibly an immunotherapeutic treatment for those already infected

Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada [version 1; referees: 2 approved]

Most streams receive substantial inputs of allochthonous organic material in the form of leaves and twigs (CPOM, coarse particulate organic matter). Mechanical and biological processing converts this into fine particulate organic matter (FPOM). Other sources of particles include flocculated dissolved matter and soil particles. Fungi are known to play a role in the CPOM conversion process, but the taxonomic affiliations of these fungi remain poorly studied. The present study seeks to shed light on the composition of fungal communities on FPOM and CPOM as assessed in a natural stream in Nova Scotia, Canada. Maple leaves were exposed in a stream for four weeks and their fungal community evaluated through pyrosequencing. Over the same period, four FPOM size fractions were collected by filtration and assessed. Particles had much lower ergosterol contents than leaves, suggesting major differences in the extent of fungal colonization. Pyrosequencing documented a total of 821 fungal operational taxonomic units (OTU), of which 726 were exclusive to particles and 47 to leaf samples. Characterizing fungal communities may shed some light on the origins and processing pathways of fine particles in streams and broadens our view of the phylogenetic composition of fungi in freshwater ecosystems

Tracheo-esophageal supplementary phonation: quantification of irregular vibrational patterns

Bei Laryngektomierten mit Stimmventilprothesen ist die Qualität der Ersatzstimme von der Schwingungscharakteristik des pharyngo-ösophagealen Segments (PE-Segment) abhängig. Mit digitalen Hochgeschwindigkeitsaufnahmen (HG-Aufnahmen) kann die Bewegung des PE-Segments gemessen werden. Neben der Morphologie beeinflusst die Dichte des Gewebes und die Spannungsverteilung entlang des Umfangs des PE-Segments maßgeblich die Schwingungscharakteristik. Diese Parameter sind einer direkten Messung nicht zugänglich. Deshalb wurde ein Verfahren entwickelt, bei dem die Gewebeeigenschaften des PE-Segments mit einem biomechanischen Modell nachgebildet werden. Dies wird mit Hilfe einer Inversionsprozedur ermöglicht, welche die Modelldynamik an die Bewegungen des PE-Segments anpasst. Die Inversionsprozedur unterteilt sich in eine Modellinitialisierung durch Auswertung der HG-Messung und einer Optimierung der Modellparameter. Die optimierten Parameterwerte beschreiben qualitativ die Gewebeeigenschaften des PE-Segments und ermöglichen neben der Visualisierung mit Hilfe der Bildverarbeitung eine Quantifizierung der irregulären Schwingungsmuster der tracheoösophagealen Ersatzstimme. In einer ersten Studie wird das Verfahren auf drei HG-Aufnahmen angewendet. Die Ergebnisse der optimierten Parameter erlauben eine Quantifizierung der irregulären Dynamik des PE-Segments. In weiteren Arbeiten soll der Zusammenhang zwischen den optimierten Modellparametern und der Qualität der Ersatzstimme untersucht werden