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

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

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

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

Probing complex RNA structures by mechanical force

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure

Effect of an electric field on a floating lipid bilayer: a neutron reflectivity study

We present here a neutron reflectivity study of the influence of an alternative electric field on a supported phospholipid double bilayer. We report for the first time a reproducible increase of the fluctuation amplitude leading to the complete unbinding of the floating bilayer. Results are in good agreement with a semi-quantitative interpretation in terms of negative electrostatic surface tension.Comment: 12 pages, 7 figures, 1 table accepted for publication in European Physical Journal E Replaced with with correct bibliograph

Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n^2) clustering algorithm which computes time averages over a continously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 100,000-fold for short multistable molecules (<150 bases). We performed extensive folding statistics on random and natural RNA sequences, and found that pseudoknots are unevenly distributed amongst RNAstructures and account for up to 30% of base pairs in G+C rich RNA sequences (Online RNA folding kinetics server including pseudoknots : http://kinefold.u-strasbg.fr/ ).Comment: 6 pages, 5 figure