Xenon isotopes in Archean and Proterozoic insoluble organic matter: a robust indicator of syngenecity?

Insoluble organic materials (kerogens) isolated from ancient sedimentary rocks provide unique insights into the evolution of early life. However, establishing whether these kerogens are indeed syngenetic with the deposition of associated sedimentary host rocks, or contain contribution from episodes of secondary deposition, is not straightforward. Novel geochemical criterions are therefore required to test the syngenetic origin of Archean organic materials. On one hand, the occurrence of mass-independent fractionation of sulphur isotopes (MIF-S) provides a tool to test the Archean origin of ancient sedimentary rocks. Determining the isotope composition of sulphur within kerogens whilst limiting the contribution from associated minerals (e.g., nano-pyrites) is however challenging. On the other end, the Xe isotope composition of the Archean atmosphere has been shown to present enrichments in the light isotopes relative to its modern composition, together with a mono-isotopic deficit in ¹²⁹Xe. Given that the isotopic composition of atmospheric Xe evolved through time by mass dependent fractionation (MDF) until ∼2.5-2.0 Ga, the degree of MDF of Xe isotopes trapped in kerogens could provide a time stamp for the last chemical equilibration between organic matter and the atmosphere. However, the extent to which geological processes could affect the signature of Xe trapped in ancient kerogen remains unclear. In this contribution, we present new Ar, Kr and Xe isotopic data for four kerogens isolated from 3.4 to 1.8 Gy-old cherts and confirm that Xe isotopes from the Archean atmosphere can be retained within kerogens. However, new Xe-derived model ages are lower than expected from the ages of host rocks, indicating that initially trapped Xe components were at least partially lost and/or mixed together with some Xe carried out by younger generations of organic materials, therefore complicating the Xe-based dating method. Whilst non-null Δ³³S values and ¹²⁹Xe deficits relative to modern atmosphere constitute reliable imprints from the Archean atmosphere, using Xe isotopes to provide information on the syngenetic origin of ancient organic matter appears to be a promising - but not unequivocal - tool that calls for further analytical development

Cemracs 2017: numerical probabilistic approach to MFG

This project investigates numerical methods for solving fully coupled forward-backward stochastic differential equations (FBSDEs) of McKean-Vlasov type. Having numerical solvers for such mean field FBSDEs is of interest because of the potential application of these equations to optimization problems over a large population, say for instance mean field games (MFG) and optimal mean field control problems. Theory for this kind of problems has met with great success since the early works on mean field games by Lasry and Lions, see [29], and by Huang, Caines, and Malhamé, see [26]. Generally speaking, the purpose is to understand the continuum limit of optimizers or of equilibria (say in Nash sense) as the number of underlying players tends to infinity. When approached from the probabilistic viewpoint, solutions to these control problems (or games) can be described by coupled mean field FBSDEs, meaning that the coefficients depend upon the own marginal laws of the solution. In this note, we detail two methods for solving such FBSDEs which we implement and apply to five benchmark problems. The first method uses a tree structure to represent the pathwise laws of the solution, whereas the second method uses a grid discretization to represent the time marginal laws of the solutions. Both are based on a Picard scheme; importantly, we combine each of them with a generic continuation method that permits to extend the time horizon (or equivalently the coupling strength between the two equations) for which the Picard iteration converges

Verticalization of bacterial biofilms

Biofilms are communities of bacteria adhered to surfaces. Recently, biofilms of rod-shaped bacteria were observed at single-cell resolution and shown to develop from a disordered, two-dimensional layer of founder cells into a three-dimensional structure with a vertically-aligned core. Here, we elucidate the physical mechanism underpinning this transition using a combination of agent-based and continuum modeling. We find that verticalization proceeds through a series of localized mechanical instabilities on the cellular scale. For short cells, these instabilities are primarily triggered by cell division, whereas long cells are more likely to be peeled off the surface by nearby vertical cells, creating an "inverse domino effect". The interplay between cell growth and cell verticalization gives rise to an exotic mechanical state in which the effective surface pressure becomes constant throughout the growing core of the biofilm surface layer. This dynamical isobaricity determines the expansion speed of a biofilm cluster and thereby governs how cells access the third dimension. In particular, theory predicts that a longer average cell length yields more rapidly expanding, flatter biofilms. We experimentally show that such changes in biofilm development occur by exploiting chemicals that modulate cell length.Comment: Main text 10 pages, 4 figures; Supplementary Information 35 pages, 15 figure

RNA fusions involving CD28 are rare in peripheral T-cell lymphomas and concentrate mainly in those derived from follicular helper T cells.

Research lette

Common Peptides Study of Aminoacyl-tRNA Synthetases

Aminoacyl tRNA synthetases (aaRSs) constitute an essential enzyme super-family, providing fidelity of the translation process of mRNA to proteins in living cells. They are common to all kingdoms and are of utmost importance to all organisms. It is thus of great interest to understand the evolutionary relationships among them and underline signature motifs defining their common domains.We utilized the Common Peptides (CPs) framework, based on extracted deterministic motifs from all aaRSs, to study family-specific properties. We identified novel aaRS–class related signatures that may supplement the current classification methods and provide a basis for identifying functional regions specific to each aaRS class. We exploited the space spanned by the CPs in order to identify similarities between aaRS families that are not observed using sequence alignment methods, identifying different inter-aaRS associations across different kingdom of life. We explored the evolutionary history of the aaRS families and evolutionary origins of the mitochondrial aaRSs. Lastly, we showed that prevalent CPs significantly overlap known catalytic and binding sites, suggesting that they have meaningful functional roles, as well as identifying a motif shared between aaRSs and a the Biotin-[acetyl-CoA carboxylase] synthetase (birA) enzyme overlapping binding sites in both families.The study presents the multitude of ways to exploit the CP framework in order to extract meaningful patterns from the aaRS super-family. Specific CPs, discovered in this study, may play important roles in the functionality of these enzymes. We explored the evolutionary patterns in each aaRS family and tracked remote evolutionary links between these families

Angioimmunoblastic T-cell lymphoma is the most common T-cell lymphoma in two distinct French information data sets.

International audienceno abstrac

Kinetic Pathway of Pyrophosphorolysis by a Retrotransposon Reverse Transcriptase

DNA and RNA polymerases use a common phosphoryl transfer mechanism for base addition that requires two or three acidic amino acid residues at their active sites. We previously showed, for the reverse transcriptase (RT) encoded by the yeast retrotransposon Ty1, that one of the three conserved active site aspartates (D211) can be substituted by asparagine and still retain in vitro polymerase activity, although in vivo transposition is lost. Transposition is partially restored by second site suppressor mutations in the RNAse H domain. The novel properties of this amino acid substitution led us to express the WT and D211N mutant enzymes, and study their pre-steady state kinetic parameters. We found that the kpol was reduced by a factor of 223 in the mutant, although the Kd for nucleotide binding was unaltered. Further, the mutant enzyme had a marked preference for Mn2+ over Mg2+. To better understand the functions of this residue within the Ty1 RT active site, we have now examined the in vitro properties of WT and D211N mutant Ty1 RTs in carrying out pyrophosphorolysis, the reverse reaction to polymerization, where pyrophosphate is the substrate and dNTPs are the product. We find that pyrophosphorolysis is efficient only when the base-paired primer template region is >14 bases, and that activity increases when the primer end is blunt-ended or recessed by only a few bases. Using pre-steady state kinetic analysis, we find that the rate of pyrophosphorolysis (kpyro) in the D211N mutant is nearly 320 fold lower than the WT enzyme, and that the mutant enzyme has an ∼170 fold lower apparent Kd for pyrophosphate. These findings indicate that subtle substrate differences can strongly affect the enzyme's ability to properly position the primer-end to carry out pyrophosphorolysis. Further the kinetic data suggests that the D211 residue has a role in pyrophosphate binding and release, which could affect polymerase translocation, and help explain the D211N mutant's transposition defect