Evaluation of the Unsteady Effects for a Class of Wind Turbines

An investigation of a class of vertical axis wind turbines is carried out with the unsteady effects due to the rotating blade motion fully taken into account. The work is composed of two parts. In part one, a hydromechanical theory is developed which proceeds from the point of view of unsteady airfoil theory. A rotor comprised of a single blade is used and a two-dimensional analysis is applied to a cross section of the rotor in the limiting mode of operation wherein U « ΩR. Use of linearized theory and of the acceleration potential allows the problem to be expressed in terms of a Riemann-Hilbert boundary value problem. The method of characteristics is used to solve for the remaining unknown function. A uniformly valid first order solution is obtained in closed form after some approximation based on neglecting the variations in the curvature of the path. Explicit expressions of the instantaneous forces and moments acting on the blade are given and the total energy lost by the fluid and the total power input to the turbine are determined. In part two, the lift acting on a wing crossing a vortex sheet is evaluated by application of a reciprocity theorem in reverse flow. This theorem follows from Green's integral theorem and relates the circulation around a blade having impulsively crossed a vortex wake to the lift acting on a blade continuously crossing a vortex wake. A solution is obtained which indicates that the lift is composed of two parts having different rates of growth, each depending on the apparent flow velocity before and after the crossing.</p

Contamination detection in genomic data: more is not enough

The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last six years, 18 programs have been pub-lished, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algo-rithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selec-tion of appropriate tools for specific applications. Finally, we present future chal-lenges in the developing field of contamination detection.BCCM GEN-ER

AMAW: automated gene annotation for non-model eukaryotic genomes

peer reviewedBackground: The annotation of genomes is a crucial step regarding the analysis of new genomic data and resulting insights, and this especially for emerging organisms which allow researchers to access unexplored lineages, so as to expand our knowledge of poorly represented taxonomic groups. Complete pipelines for eukaryotic genome annotation have been proposed for more than a decade, but the issue is still challenging. One of the most widely used tools in the field is MAKER2, an annotation pipeline using experimental evidence (mRNA-seq and proteins) and combining different gene prediction tools. MAKER2 enables individual laboratories and small-scale projects to annotate non-model organisms for which pre-existing gene models are not available. The optimal use of MAKER2 requires gathering evidence data (by searching and assembling transcripts, and/or collecting homologous proteins from related organisms), elaborating the best annotation strategy (training of gene models) and efficiently orchestrating the different steps of the software in a grid computing environment, which is tedious, time-consuming and requires a great deal of bioinformatic skills. Methods: To address these issues, we present AMAW (Automated MAKER2 Annotation Wrapper), a wrapper pipeline for MAKER2 that automates the above-mentioned tasks. Importantly, AMAW also exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2. Use case: The performance of AMAW is illustrated through the annotation of a selection of 32 protist genomes, for which we compared its annotations with those produced with gene models directly available in AUGUSTUS. Conclusions: Importantly, AMAW also exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER

BCCM/ULC public collection of cyanobacteria: A tool for microbial research and innovation.

editorial reviewedCyanobacteria represent an ancient group of morphologically diverse oxyphototrophic bacteria. Their long and complex evolutionary history is considered to have contributed to the successful colonization of a wide range of habitats including those, which are, from an anthropocentric point of view, hostile to life and are known as ‘extreme’ environments. Cyanobacteria thriving in mesophilic environments have been extensively studied in respect to their taxonomy. However, little is known about the diversity and taxonomy of extremophilic cyanobacteria. Nonetheless, the discovery of several new taxa through the investigation of just a limited number of extreme habitats suggests a high degree of novel biological diversity that remains unexplored. The BCCM/ULC public culture collection, funded by the Belgian Science Policy Office since 2011, currently hosts more than 500 cyanobacterial strains, of which approximately 140 derive from polar, subpolar, and alpine environments, followed by tropical, subtropical and mediterranean biotopes. In addition, strains of Belgian origin (lakes, soils) are also represented in the collection. All strains are studied by applying a polyphasic approach workflow, which includes a combination of morphological (microscopy), molecular (16S rRNA gene and ITS region) and ecological data. Cyanobacteria are also known producers of a variety of natural products. Indeed, there have been more than 2000 functionally diverse and structurally complex bioactive metabolites identified from cyanobacteria, including alkaloids, cyclic and linear peptides, polyketides and nonribosomal peptides. These metabolites range from toxins to biologically active molecules showing promise as potential drug leads. As part of an ongoing effort to discover new molecules with potential pharmaceutical applications, the strains are being evaluated for their antibacterial and/or antifungal activities. Furthermore, whole-genome sequencing is applied to study taxonomically interesting morphotypes and bioactive metabolite-producing strains. Genome sequencing has already been performed for 25 strains, 10 of them being currently analysed within the collection. The bioinformatic analysis of genomes of the strains ULC007, ULC065 and ULC129 revealed the presence of biosynthetic gene clusters encoding for a wide range of natural products with potential biomedical applications. Polar strains of the recently described genus Laspinema are also studied from a phylogenomic and comparative genomic perspective to understand the basis of adaptations to cold environments. Lastly, the collection has developed a series of containerized bioinformatics workflows that correspond to the open science practices

Evaluation of the bioactive potential of polar cyanobacterial strains from BCCM/ULC

Antibiotic and antifungal resistance has become a major public health problem worldwide, with significant clinical and economic consequences. Over the past few years, some publications have highlighted cyanobacteria isolated from extreme environments as a promising source of bioactive compounds. Biondi et al. (2008) tested methanolic extracts obtained from 48 polar strains available at the BCCM/ULC Culture Collection, from which 17 proved to be bioactive against Escherichia coli, Aspergillus fumigatus, and Cryptococcus neoformans. Accordingly, as a follow-up of Biondi’s work, an evaluation of 41 polar cyanobacterial strains from the BCCM/ULC was undertaken. Briefly, the selected cyanobacterial strains were grown, and the obtained biomasses were frozen, freeze-dried and used for methanolic extraction. The methanolic extracts were then tested against E. coli ATCC25922, Staphylococcus aureus ATCC25923 as well as Candida albicans IHEM10266 and A. fumigatus IHEM28083. The results of this study showed that the methanolic extracts from the strains Phormidesmis priestleyi ULC007 and Microcoleus attenuatus ULC371 demonstrated significant antifungal activity against C. albicans and A. fumigatus. These results open up new prospects for further research aiming at isolating and identifying the compound(s) responsible for the observed antifungal activity. In addition, genomics studies are also promising for the search of the operons/clusters related to the production of these compounds, especially for the strain P. priestleyi ULC007, which was already sequenced. In this context, the BCCM/ULC Collection, that harbors more than 400 cyanobacterial strains (~160 from polar regions), reinforces its potential as an important source of cyanobacterial diversity for taxonomic, genomic, and applied research.3. Good health and well-bein

ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies

peer reviewedTQMD is a tool for high-performance computing clusters which downloads, stores and produces lists of dereplicated prokaryotic genomes. It has been developed to counter the ever-growing number of prokaryotic genomes and their uneven taxonomic distribution. It is based on word-based alignment-free methods (k-mers), an iterative single-linkage approach and a divide-and-conquer strategy to remain both efficient and scalable. We studied the performance of TQMD by verifying the influence of its parameters and heuristics on the clustering outcome. We further compared TQMD to two other dereplication tools (dRep and Assembly-Dereplicator). Our results showed that TQMD is primarily optimized to dereplicate at higher taxonomic levels (phylum/class), as opposed to the other dereplication tools, but also works at lower taxonomic levels (species/strain) like the other dereplication tools. TQMD is available from source and as a Singularity container at [https://bitbucket.org/phylogeno/tqmd ]

The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex

Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity.

peer reviewedSnodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee's microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms (BCCM) were studied, resulting in the GEN-ERA toolbox, a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). This public toolbox is designed for researchers without a specific training in bioinformatics (launched by a single command line). Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. All the workflows are based on Singularity containers and Nextflow to increase reproducibility. The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales (Cyanobacteria). This study is published at https://doi.org/10.1093/gigascience/giad022GENER

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

peer reviewed[en] BACKGROUND: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). FINDINGS: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. TECHNICAL DETAILS: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TESTING: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. CONCLUSION: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales