Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.

Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples.

Genetic identification and reiterated captures suggest that the El Pachón cavefish population is closed and declining.

The sizes of blind cavefish populations of North-East Mexico are demographic parameters of great importance for investigating a variety of ecological, evolutionary, and conservation issues. However, few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but their feasibility and interpretation of results depend on several assumptions that must be carefully examined.

Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions.

In 2020, the world faced the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic that drastically altered people's lives. Since then, many countries have been forced to suspend public gatherings, leading to many conference cancellations, postponements, or reorganizations. Switching from a face-to-face to a remote conference became inevitable and the ultimate solution to sustain scientific exchanges at the national and the international levels.

Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals.

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes.

Reflections on a journey: a retrospective of the ISCB Student Council symposium series.

This article describes the motivation, origin and evolution of the student symposia series organised by the ISCB Student Council. The meeting series started thirteen years ago in Madrid and has spread to four continents. The article concludes with the highlights of the most recent edition of annual Student Council Symposium held in conjunction with the 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology, in Prague, in July 2017.

Evidence for late Pleistocene origin of Astyanax mexicanus cavefish.

Background: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations.

Mutations at the Darkener of Apricot locus modulate pheromone production and sex behavior in Drosophila melanogaster.

Mutations at the Darkener of Apricot (Doa) locus of Drosophila melanogaster alter sexual differentiation by disrupting sex-specific splicing of doublesex pre-mRNA, a key regulator of sex determination. Here, we study the effect of seven Doa alleles and several trans-heterozygous combinations on pheromones and courtship behavior. The cuticular hydrocarbon (CHC) profile was slightly masculinized in females, with an accumulation of shorter compounds (C23 and C25) and a reduction in longer compounds (C27 and C29).

[ENCODE apophenia or a panglossian analysis of the human genome].

In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published.

Lens defects in Astyanax mexicanus Cavefish: evolution of crystallins and a role for alphaA-crystallin.

The fish Astyanax mexicanus presents, within the same species, populations of river-dwelling surface fish (SF) and blind cave-living fish. In cavefish (CF), the eyes develop almost normally during embryogenesis. But 40 h after fertilization, the lens enters apoptosis, triggering the progressive degeneration of the entire eye.