The causes of insect endemicity with the example of Madagascar

Abstract Biodiversity is disappearing at an exceptional rate, engendering a considerable effort of the scientific community to conserve the rarest and most threatened species. Biodiversity Hotspots were designed for this purpose and Madagascar, showing the highest levels of endemism and imbalance across taxa, rapidly became their flagship. The processes that lead to such exceptional biodiversity patterns on the island remain poorly understood and the lack of efficacy of traditional taxonomy to catalogue tropical endemic biodiversity hinders the scientific advances in this domain. This study tackles insect endemism in Madagascar, aiming at identifying the evolutionary and ecological factors responsible for their present diversity patterns. Aquatic beetles, living in standing or running water, submit to differences in habitat stability, potentially affecting dispersal patterns and hence endemism patterns. We chose them as a target group for these reasons, and first achieved a DNA level inventory of the fauna. We identified 169 species, showing high congruence with the morphological taxonomy and corresponding to 74% of the total estimated species richness. The mitochondrial dataset revealed high spatial turnover at the species and haplotype levels. A phylogenetic tree from three gene markers was used for ancestral state character reconstruction and suggested the dependent evolution of endemism and habitat use. Secondly, our results highlight a combination of low dispersal activity and important climatic constraints for the lotic fauna, explaining the local scale endemism in this group, whereas the lentic species turnover correlated the least to both climate and geographic distance. Last, a distribution modelling approach revealed the uniqueness of Malagasy climate niches and the absence of conservation of environmental envelopes at higher phylogenetic levels. We conclude that endemism in Madagascar is best explained locally by the dependence to environmental variability of the lotic species, and that dispersal capacities are the primary hindrance to colonising external suitable habitats

Encoding folding paths of RNA switches

RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and intermolecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.Comment: 9 pages, 6 figure

Commercial Applications of Microalgae

The first use of microalgae by humans dates back 2000 years to the Chinese, who used Nostoc to survive during famine. However, microalgal biotechnology only really began to develop in the middle of the last century. Nowadays, there are numerous commercial applications of microalgae. For example, (1) microalgae can be used to enhance the nutritional value of food and animal feed owing to their chemical composition, (2) they play a crucial role in aquaculture and (3) they can be incorporated into cosmetics. Moreover, they are cultivated as a source of highly valuable molecules. For example, polyunsaturated fatty acid oils are added to infant formulas and nutritional supplements and pigments are important as natural dyes. Stable isotope biochemicals help in structural determination and metabolic studies. Future research should focus on the improvement of production systems and the genetic modification of strains. Microalgal products would in that way become even more diversified and economically competitive

Localized Joule heating produced by ion current focusing through micron-size holes

We provide an experimental demonstration that the focusing of ionic currents in a micron size hole connecting two chambers can produce local temperature increases of up to $100^\circ$ C with gradients as large as $1^\circ$ K$\mu m^{-1}$. We find a good agreement between the measured temperature profiles and a finite elements-based numerical calculation. We show how the thermal gradients can be used to measure the full melting profile of DNA duplexes within a region of 40 $\mu$m. The possibility to produce even larger gradients using sub-micron pores is discussed.Comment: 3 pages, accepted to Appl. Phys. Lett

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at