RNA Relics and Origin of Life

A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells

An oracle based method to compute a coupled equilibrium in a model of international climate policy

This paper proposes a computational game-theoretic model for the international negotiations that should take place at the end of the period covered by the Kyoto protocol. These negotiations could lead to a self-enforcing agreement on a burden sharing scheme given the necessary global emissions limit that will be imposed when the real extent of climate change is known. The model assumes a non-cooperative behavior of the parties except for the fact that they will be collectively committed to reach a target on total cumulative emissions by the year 2050. The concept of normalized equilibrium, introduced by J.B. Rosen for concave games with coupled constraints, is used to characterize a family of dynamic equilibrium solutions in an m-player game where the agents are (groups of) countries and the payoffs are the welfare gains obtained from a Computable General Equilibrium (CGE) model. The model deals with the uncertainty about climate sensitivity by computing an S-adapted equilibrium. These equilibria are computed using an oracle-based method permitting an implicit definition of the payoffs to the different players, obtained through simulations performed with the global CGE model GEMINI-E

Transmission enhancement through square coaxial apertures arrays in metallic film: when leaky modes filter infrared light

We consider arrays of square coaxial apertures in a gold layer and study their diffractive behavior in the far infrared region. These structures exhibit a resonant transmission enhancement that is used to design tunable bandpass filters. We provide a study of their spectral features and show by a modal analysis that the resonance peak is due to the excitation of leaky modes of the open photonic structure. Fourier transform infrared (FTIR) spectrophotometry transmission measurements of samples deposited on Si substrate show good agreement with numerical results and demonstrate angular tolerance up to 30 degrees of the fabricated filters.Comment: 4 pages, 3 figure

Controlling the Biological Effects of Spermine Using a Synthetic Receptor

Polyamines play an important role in biology, yet their exact function in many processes is poorly understood. Artificial host molecules capable of sequestering polyamines could be useful tools for studying their cellular function. However, designing synthetic receptors with affinities sufficient to compete with biological polyamine receptors remains a huge challenge. Binding affinities of synthetic hosts are typically separated by a gap of several orders of magnitude from those of biomolecules. We now report that a dynamic combinatorial selection approach can deliver a synthetic receptor that bridges this gap. The selected receptor binds spermine with a dissociation constant of 22 nM, sufficient to remove it from its natural host DNA and reverse some of the biological effects of spermine on the nucleic acid. In low concentrations, spermine induces the formation of left-handed DNA, but upon addition of our receptor, the DNA reverts back to its right-handed form. NMR studies and computer simulations suggest that the spermine complex has the form of a pseudo-rotaxane. The spermine receptor is a promising lead for the development of therapeutics or molecular probes for elucidating spermine’s role in cell biology.

An Oracle method to couple climate and economic dynamics

This paper deals with an oracle method to couple economic and climate models. The approach permits a dialogue between two models pertaining to two different scientific domains, the climate module being a fully-coupled ocean-atmosphere-ice model, whereas the economic module is an adaptation of the neo-classical optimal economic growth paradigm. The paper explains how the Analytic Centre Cutting Plane Method (ACCPM) is implemented to integrate in the optimal economic growth model a constraint on climate change that is computed from the climate model runs. Several experiments show the usefulness of the approach to build new types of integrated assessment meta-model

Sea ice thickness and elastic properties from the analysis of multimodal guided wave propagation measured with a passive seismic array

Field data are needed for a better understanding of sea ice decline in the context of climate change. The rapid technological and methodological advances of the last decade have led to a reconsideration of seismic methods in this matter. In particular, passive seismology has filled an important gap by removing the need to use active sources. We present a seismic experiment where an array of 247 geophones was deployed on sea ice, in the Van Mijen fjord near Sveagruva (Svalbard). The array is a mix of 1C and 3C stations with sampling frequencies of 500 and 1000 Hz. They recorded continuously the ambient seismic field in sea ice between 28 February and 26 March 2019. Data also include active acquisitions on 1 and 26 March with a radar antenna, a shaker unit, impulsive sources, and artificial sources of seismic noise. This data set is of unprecedented quality regarding sea ice seismic monitoring, as it also includes thousands of microseismic events recorded each day. By combining passive seismology approaches with specific array processing methods, we demonstrate that the multimodal dispersion curves of sea ice can be calculated without an active source and then used to infer sea ice properties. We calculated an ice thickness, Young's modulus, and Poisson's ratio with values h=543 cm, E=3.90.15 GPa, and nu=0.340.02 on 1 March, and h=583 cm, E=4.4 +/- 0.15 GPa, and nu=0.32 +/- 0.02 on 5 March. These values are consistent with in situ field measurements and observations.Peer reviewe

Oleic Acid Biosynthesis in Plasmodium falciparum: Characterization of the Stearoyl-CoA Desaturase and Investigation as a Potential Therapeutic Target

BACKGROUND:Plasmodium falciparum parasitization of erythrocytes causes a substantial increase in the levels of intracellular fatty acids, notably oleic acid. How parasites acquire this monounsaturated fatty acid has remained enigmatic. Here, we report on the biochemical and enzymatic characterization of stearoyl-CoA desaturase (SCD) in P. falciparum. METHODOLOGY/PRINCIPAL FINDINGS:Metabolic labeling experiments allowed us to demonstrate the production of oleic acid from stearic acid both in lysates of parasites incubated with [(14)C]-stearoyl-CoA and in parasite-infected erythrocytes labeled with [(14)C]-stearic acid. Optimal SCD activity was detected in schizonts, the stage of maximal membrane synthesis. This activity correlated with a late trophozoite stage-specific induction of PFE0555w transcripts. PFE0555w harbors a typical SCD signature. Similar to mammalian SCDs, this protein was found to be associated with the endoplasmic reticulum, as determined with PFE0555w-GFP tagged transgenic P. falciparum. Importantly, these parasites exhibited increased rates of stearic to oleic acid conversion, providing additional evidence that PFE0555w encodes the plasmodial SCD (PfSCD). These findings prompted us to assess the activity of sterculic acid analogues, known to be specific Delta9-desaturase inhibitors. Methyl sterculate inhibited the synthesis of oleic acid both with parasite lysates and infected erythrocytes, most likely by targeting PfSCD. This compound exhibited significant, rapid and irreversible antimalarial activity against asexual blood stages. This parasiticidal effect was antagonized by oleic acid. CONCLUSION/SIGNIFICANCE:Our study provides evidence that parasite-mediated fatty acid modification is important for blood-stage survival and provides a new strategy to develop a novel antimalarial therapeutic based on the inhibition of PfSCD

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species