Ten simple rules to host an inclusive conference.

Conferences are spaces to meet and network within and across academic and technical fields, learn about new advances, and share our work. They can help define career paths and create long-lasting collaborations and opportunities. However, these opportunities are not equal for all. This article introduces 10 simple rules to host an inclusive conference based on the authors' recent experience organizing the 2021 edition of the useR! statistical computing conference, which attracted a broad range of participants from academia, industry, government, and the nonprofit sector. Coming from different backgrounds, career stages, and even continents, we embraced the challenge of organizing a high-quality virtual conference in the context of the Coronavirus Disease 2019 (COVID-19) pandemic and making it a kind, inclusive, and accessible experience for as many people as possible. The rules result from our lessons learned before, during, and after the organization of the conference. They have been written mainly for potential organizers and selection committees of conferences and contain multiple practical tips to help a variety of events become more accessible and inclusive. We see this as a starting point for conversations and efforts towards building more inclusive conferences across the world. * Translated versions of the English abstract and the list of rules are available in 10 languages in S1 Text: Arabic, French, German, Italian, Japanese, Korean, Portuguese, Spanish, Tamil, and Thai.

Changes in arbuscular mycorrhizal fungal communities, mycorrhizal soil infectivity, and phosphorus availability under Chromolaena odorata (Asteraceae) invasions in a West-African forest-savanna ecotone.

Substantial areas of agricultural lands in Sub-Saharan Africa have been invaded by Chromolaena odorata (Asteraceae), but the consequences for arbuscular mycorrhiza fungi (AMF) remains poorly understood. This study explores changes in diverse AMF community attributes and soil available phosphorus following C. odorata invasion in forest and savanna fragments in Côte d'Ivoire (West Africa). Invaded-forest (COF) and savanna (COS) sites were compared to adjacent natural forest (FOR) and savanna (SAV) fragments, respectively. Physico-chemical variables and AMF spore density parameters were determined for soil samples from 0-20 cm depth. An 18S ribosomal RNA metabarcoding analysis of AMF communities was conducted. In addition, cowpea (Vigna unguiculata) was grown on soils collected from these sites under greenhouse conditions for determination of soil mycorrhizal infectivity. Noticeable changes in the composition of AMF communities in C. odorata relative to nearby forest and savanna non-invaded sites were observed. AMF-specific richness in COS (47 species) was lower than that in SAV (57 species) while it was higher in COF (68 species) than in FOR (63 species). COF and COS differed in AMF specific composition (Dissimilarity index = 50.6%). Chromolaena odorata invasions resulted in increased relative abundances of the genera Claroideoglomus and Glomus in COF, a decreased relative abundance of Paraglomus in COS and decreased relative abundances of Ambispora in both COF and COS. Total and healthy spore densities, cowpea root colonization intensity and soil available P were all higher in invaded sites than in natural ecosystems. Remarkably, although these values were different in FOR and SAV, they turned out to be similar in COF and COS (4.6 and 4.2 total spores g-1 soil, 2.3 and 2.0 healthy spores g-1 soil, and 52.6 and 51.6% root colonization, respectively) suggesting a C. odorata-specific effect. These findings indicate that soil mycorrhizal potential and phosphorus availability have improved following C. odorata invasion.

bioSyntax: syntax highlighting for computational biology.

BACKGROUND: Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the data structure complexity. RESULTS: bioSyntax ( https://biosyntax.org/ ) is a freely available suite of biological syntax highlighting packages for vim, gedit, Sublime, VSCode, and less. bioSyntax improves the legibility of low-level biological data in the bioinformatics workspace. CONCLUSION: bioSyntax supports computational scientists in parsing and comprehending their data efficiently and thus can accelerate research output.

The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones.

The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.

Proteomic insight into the venom composition of the largest European rear-fanged snake, Malpolon monspessulanus monspessulanus.

Snake envenomations constitute a worldwide neglected tropical disease, with the vast majority of lethal bites inflicted by front-fanged snakes from the viperid and elapid groups. Rear-fanged snakes (colubrids) were often considered harmless and as a result, are much less studied, but several documented deaths have suggested potent venom in this group as well. The largest European snake (Malpolon monspessulanus monspessulanus), known as the "Montpellier snake", is such a rear-fanged snake that belongs to the Lamprophiidae family. Its venom remains largely unknown but cases of envenomation with neurological symptoms have been reported. Here, we provide the first insights into the composition of its venom using mass spectrometry methods. First, liquid chromatography coupled mass spectrometry analysis of the manually collected venom samples reveals a complex profile, with the majority of masses encompassing the range 500-3000 Da, 4000-8000 Da, and 10 000-30 000 Da. Next, shotgun proteomics allowed the identification of a total of 42 different known families of proteins, including snake venom metalloproteinases, peptidase M1, and cysteine-rich secretory proteins, as the most prominent. Interestingly, three-finger toxins were not detected, suggesting that neurotoxicity may occur via other, yet to be determined, toxin types. Overall, our results provide the basis for a better understanding of the effects of a peculiar snake venom on human symptomatology, but also on the main prey consumed by this species.

Improved prediction of conopeptide superfamilies with ConoDictor 2.0.

Motivation: Cone snails are among the richest sources of natural peptides with promising pharmacological and therapeutic applications. With the reduced costs of RNAseq, scientists now heavily rely on venom gland transcriptomes for the mining of novel bioactive conopeptides, but the bioinformatic analyses often hamper the discovery process. Results: Here, we present ConoDictor 2.0 as a standalone and user-friendly command-line program. We have updated the program originally published as a web server 10 years ago using novel and updated tools and algorithms and improved our classification models with new and higher quality sequences. ConoDictor 2.0 is now more accurate, faster, multiplatform and able to deal with a whole cone snail venom gland transcriptome (raw reads or contigs) in a very short time. The new version of Conodictor also improves the identification and subsequent classification for entirely novel or relatively distant conopeptides. We conducted various tests on known conopeptides from public databases and on the published venom duct transcriptome of Conus geographus, and compared previous results with the output of ConoDictor 2.0, ConoSorter and BLAST. Overall, ConoDictor 2.0 is 4 to 8 times faster for the analysis of a whole transcriptome on a single core computer and performed better at predicting gene superfamily. Availability and implementation: ConoDictor 2.0 is available as a python 3 git folder at https://github.com/koualab/conodictor. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Combined Proteotranscriptomic-Based Strategy to Discover Novel Antimicrobial Peptides from Cone Snails.

Despite their impressive diversity and already broad therapeutic applications, cone snail venoms have received less attention as a natural source in the investigation of antimicrobial peptides than other venomous animals such as scorpions, spiders, or snakes. Cone snails are among the largest genera (Conus sp.) of marine invertebrates, with more than seven hundred species described to date. These predatory mollusks use their sophisticated venom apparatus to capture prey or defend themselves. In-depth studies of these venoms have unraveled many biologically active peptides with pharmacological properties of interest in the field of pain management, the treatment of epilepsy, neurodegenerative diseases, and cardiac ischemia. Considering sequencing efficiency and affordability, cone snail venom gland transcriptome analyses could allow the discovery of new, promising antimicrobial peptides. We first present here the need for novel compounds like antimicrobial peptides as a viable alternative to conventional antibiotics. Secondly, we review the current knowledge on cone snails as a source of antimicrobial peptides. Then, we present the current state of the art in analytical methods applied to crude or milked venom followed by how antibacterial activity assay can be implemented for fostering cone snail antimicrobial peptides studies. We also propose a new innovative profile Hidden Markov model-based approach to annotate full venom gland transcriptomes and speed up the discovery of potentially active peptides from cone snails.

The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire.

Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d'Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina's MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.

Proteotranscriptomic Insights into the Venom Composition of the Wolf Spider Lycosa tarantula.

Spider venoms represent an original source of novel compounds with therapeutic and agrochemical potential. Whereas most of the research efforts have focused on large mygalomorph spiders, araneomorph spiders are equally promising but require more sensitive and sophisticated approaches given their limited size and reduced venom yield. Belonging to the latter group, the genus Lycosa ("wolf spiders") contains many species widely distributed throughout the world. These spiders are ambush predators that do not build webs but instead rely strongly on their venom for prey capture. Lycosa tarantula is one of the largest species of wolf spider, but its venom composition is unknown. Using a combination of RNA sequencing of the venom glands and venom proteomics, we provide the first overview of the peptides and proteins produced by this iconic Mediterranean spider. Beside the typical small disulfide rich neurotoxins, several families of proteins were also identified, including cysteine-rich secretory proteins (CRISP) and Hyaluronidases. Proteomic analysis of the electrically stimulated venom validated 30 of these transcriptomic sequences, including nine putative neurotoxins and eight venom proteins. Interestingly, LC-MS venom profiles of manual versus electric stimulation, as well as female versus male, showed some marked differences in mass distribution. Finally, we also present some preliminary data on the biological activity of L. tarantula crude venom.