Galaxy Training: A powerful framework for teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.

Dispersal between shallow and abyssal seas and evolutionary loss and regain of compound eyes in cylindroleberidid ostracods: conflicting conclusions from different comparative methods.

Complex organs such as eyes are commonly lost during evolution, but the timescale on which lost phenotypes could be reactivated is a matter of long-standing debate, with important implications for the molecular mechanisms of trait loss. Two phylogenetic approaches have been used to test whether regain of traits has occurred. One way is by comparison of nested, continuous-time Markov models of trait evolution, approaches that we term tree-based tests. A second way to demonstrate statistical support for trait regain is through use of node-based tests that employ explicit estimation of ancestral node states. Here, we estimate new molecular and morphological phylogenies and use them to examine the possibility of eye regain and dispersal between abyssal and shallow seas during the history of cylindroleberidid ostracods, a family of about 200 species, comprising both eyeless and sighted species. First, we confirmed that eye presence/absence is correlated with habitat depth. Parameter estimates from a phylogenetic model indicate that speciation is more rapid in deep-sea eyeless clades compared with shallow-water sighted clades. In addition, we found that tree-based statistical tests usually indicated reversals, including both transitions from deep to shallow seas and regain of eyes. In contrast, node-based statistical tests usually failed to show significant support for reversals. These results also hold for simulated phylogenies, indicating that they are not unique to the current data set. We recommend that both tree-based and node-based tests should be examined before making conclusions about character reversal and that ideally, alternative character histories should be tested using additional data, besides just the phylogenetic distribution of presence/absence of the characters.

Sequestrate species of Agaricus and Macrolepiota from Australia: new species and combinations and their position in a calibrated phylogeny.

Australian collections of sequestrate Agaricaceae were examined with morphological and molecular data (nuclear DNA from ITS and LSU), and the majority were found to belong to the genera Agaricus and Macrolepiota. Previously described Australian species of Endoptychum are transferred to the appropriate agaricoid genera and several new combinations proposed. Descriptions and illustrations are provided for these and eight new species: Agaricus eburneocanus sp. nov., A. chartaceus sp. nov., A. erythrosarx sp. nov., A. inilleasper sp. nov., A. pachydermus sp. nov., Macrolepiota gasteroidea sp. nov., M. vinaceofibrillosa sp. nov. and M. turbinata sp. nov. The sequestrate genus Barcheria is retained as a distinct taxon. Timing of evolution of sequestrate sporocarp forms in Macrolepiota, Chlorophyllum and Agaricus seems to have occurred in the past 15 000 000 y, and a stem age is approximately 65 000 000 y for Barcheria.

Full spectroscopic model and trihybrid experimental-perturbative-variational line list for CN.

Accurate line lists are important for the description of the spectroscopic nature of small molecules. While a line list for CN (an important molecule for chemistry and astrophysics) exists, no underlying energy spectroscopic model has been published, which is required to consider the sensitivity of transitions to a variation of the proton-to-electron mass ratio. Here we have developed a Duo energy spectroscopic model as well as a novel hybrid style line list for CN and its isotopologues, combining energy levels that are derived experimentally (Marvel), using the traditional/perturbative approach (Mollist), and the variational approach (from a Duo spectroscopic model using standard ExoMol methodology). The final Trihybrid ExoMol-style line list for 12C14N consists of 28 004 energy levels (6864 experimental, 1574 perturbative, the rest variational) and 2285 103 transitions up to 60 000 cm-1 between the three lowest electronic states (X 2Σ+, A 2Π, and B 2Σ+). The spectroscopic model created is used to evaluate CN as a molecular probe to constrain the variation of the proton-to-electron mass ratio; no overly promising sensitive transitions for extragalactic study were identified.

Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha.

Organelle genomes are typically represented as single, static, circular molecules. However, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found that different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths.

Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach.

BACKGROUND: Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design; and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we examine the rates and patterns of gene duplication and loss evident in 19 metazoan genomes, including that of Daphnia pulex - the first completely sequenced crustacean genome. This is of particular interest because the pancrustaceans (hexapods+crustaceans) have more optical designs than any other major clade of animals, allowing us to test specifically whether the high amount of disparity in pancrustacean eyes is correlated with a higher rate of duplication and retention of vision genes. RESULTS: Using protein predictions from 19 metazoan whole-genome projects, we found all members of 23 gene families known to be involved in eye development or phototransduction and deduced their phylogenetic relationships. This allowed us to estimate the number and timing of gene duplication and loss events in these gene families during animal evolution. When comparing duplication/retention rates of these genes, we found that the rate was significantly higher in pancrustaceans than in either vertebrates or non-pancrustacean protostomes. Comparing patterns of co-duplication across Metazoa showed that while these eye-genes co-duplicate at a significantly higher rate than those within a randomly shuffled matrix, many genes with known functional relationships in model organisms did not co-duplicate more often than expected by chance. CONCLUSIONS: Overall, and when accounting for factors such as differential rates of whole-genome duplication in different groups, our results are broadly consistent with the hypothesis that genes involved in eye development and phototransduction duplicate at a higher rate in Pancrustacea, the group with the greatest variety of optical designs. The result that these genes have a significantly high number of co-duplications and co-losses could be influenced by shared functions or other unstudied factors such as synteny. Since we did not observe co-duplication/co-loss of genes for all known functional modules (e.g. specific regulatory networks), the interactions among suites of known co-functioning genes (modules) may be plastic at the temporal scale of analysis performed here. Other factors in addition to gene duplication - such as cis-regulation, heterotopy, and co-option - are also likely to be strong factors in the diversification of eye types.

Experimental energy levels of 12C14N through marvel analysis.

The cyano radical (CN) is a key molecule across many different factions of astronomy and chemistry. Accurate, empirical rovibronic energy levels with uncertainties are determined for eight doublet states of CN using the marvel (Measured Active Rotational-Vibrational Energy Levels) algorithm. 40 333 transitions were validated from 22 different published sources to generate 8083 spin-rovibronic energy levels. The empirical energy levels obtained from the marvel analysis are compared to current energy levels from the mollist line list. The mollist transition frequencies are updated with marvel energy level data which brings the frequencies obtained through experimental data up to 77.3 per cent from the original 11.3 per cent, with 92.6 per cent of the transitions with intensities over 10-23 cm molecule-1 at 1000 K now known from experimental data. At 2000 K, 100.0 per cent of the partition function is recovered using only marvel energy levels, while 98.2 per cent is still recovered at 5000 K.

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.

BACKGROUND: Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, especially if they want to adopt good programming practices. Even experienced developers do not always follow best practices. This results in the proliferation of poorer-quality bioinformatics software, leading to limited scalability and inefficient use of resources; lack of reproducibility, usability, adaptability, and interoperability; and erroneous or inaccurate results. FINDINGS: We have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages. The resulting software is functional, carrying out a prototypical bioinformatics task, and thus serves as both a working example and a template for building new tools. Key features include command-line argument parsing, error handling, progress logging, defined exit status values, a test suite, a version number, standardized building and packaging, user documentation, code documentation, a standard open source software license, software revision control, and containerization. CONCLUSIONS: Bionitio serves as a learning aid for beginner-to-intermediate bioinformatics programmers and provides an excellent starting point for new projects. This helps developers adopt good programming practices from the beginning of a project and encourages high-quality tools to be developed more rapidly. This also benefits users because tools are more easily installed and consistent in their usage. Bionitio is released as open source software under the MIT License and is available at https://github.com/bionitio-team/bionitio.

Capacity To Utilize Raffinose Dictates Pneumococcal Disease Phenotype.

Streptococcus pneumoniae is commonly carried asymptomatically in the human nasopharynx, but it also causes serious and invasive diseases such as pneumonia, bacteremia, and meningitis, as well as less serious but highly prevalent infections such as otitis media. We have previously shown that closely related pneumococci (of the same capsular serotype and multilocus sequence type [ST]) can display distinct pathogenic profiles in mice that correlate with clinical isolation site (e.g., blood versus ear), suggesting stable niche adaptation within a clonal lineage. This has provided an opportunity to identify determinants of disease tropism. Genomic analysis identified 17 and 27 single nucleotide polymorphisms (SNPs) or insertions/deletions in protein coding sequences between blood and ear isolates of serotype 14 ST15 and serotype 3 ST180, respectively. SNPs in raffinose uptake and utilization genes (rafR or rafK) were detected in both serotypes/lineages. Ear isolates were consistently defective in growth in media containing raffinose as the sole carbon source, as well as in expression of raffinose pathway genes aga, rafG, and rafK, relative to their serotype/ST-matched blood isolates. Similar differences were also seen between serotype 23F ST81 blood and ear isolates. Analysis of rafR allelic exchange mutants of the serotype 14 ST15 blood and ear isolates demonstrated that the SNP in rafR was entirely responsible for their distinct in vitro phenotypes and was also the determinant of differential tropism for the lungs versus ear and brain in a mouse intranasal challenge model. These data suggest that the ability of pneumococci to utilize raffinose determines the nature of disease.IMPORTANCES. pneumoniae is a component of the commensal nasopharyngeal microflora of humans, but from this reservoir, it can progress to localized or invasive disease with a frequency that translates into massive global morbidity and mortality. However, the factors that govern the switch from commensal to pathogen, as well as those that determine disease tropism, are poorly understood. Here we show that capacity to utilize raffinose can determine the nature of the disease caused by a given pneumococcal strain. Moreover, our findings provide an interesting example of convergent evolution, whereby pneumococci belonging to two unrelated serotypes/lineages exhibit SNPs in separate genes affecting raffinose uptake and utilization that correlate with distinct pathogenic profiles in vivo This further underscores the critical role of differential carbohydrate metabolism in the pathogenesis of localized versus invasive pneumococcal disease.

A supplementary description of Cypridina mariae and rediagnosis of the genus Cylindroleberis (Ostracoda: Myodocopa: Cylindroleberididae).

The ostracod family Cylindroleberididae is based on the genus Cylindroleberis Brady, 1868, and has a complicated nomenclatural history. The type species of Cylindroleberis is Cypridina mariae Baird, 1850. Baird described only the carapace, which had been considered lost. Thus, there was no reference point for the concept C. mariae or the genus Cylindroleberis. Baird's material has now been found in the Natural History Museum, London, U.K., and is illustrated here. To clarify the taxonomic status of C. mariae and Cylindroleberis, specimens were obtained from near the type locality, and a supplementary description is presented. This includes description of appendages, particularly the first antenna and mandible, which contain important diagnostic characters. This supplementary description provides important information about C. mariae, allowing a revision of the genus Cylindroleberis, and establishing a framework for future biological research on this ostracod group.