Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

International audienceBackground: With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus

Synergic coordination of stem cells is required to induce a regenerative response in anthozoan cnidarians

Little is known about the origin of the inductive signal that translates the amputation stress into a cooperative cellular response. By studying the process underlying the reformation of lost body parts in the anthozoan cnidarian Nematostella vectensis, we identified a regeneration-inducing structure that, via a tissue crosstalk, is responsible for the initiation of the repair program. We further revealed for the first time in anthozoan cnidarians, that fast and slow-cycling/quiescent stem cells respond to the amputation stress and actively participate in the reformation of lost body parts. Importantly, a synergic interaction of both stem cell populations is required to complete the regeneration process. Our findings suggest that the emergence/loss of structure complexity/compartmentalization influences the proprieties of tissue plasticity, changes the competence of a tissue to reprogram and, in the context of regeneration, the capacity of the tissue to emit or respond to a regeneration-inducing signal

Facilitating Hydrogen Dissociation over Dilute Nanoporous Ti-Cu Catalysts

The dissociation of H2 is an essential elementary step in many industrial chemical transformations, typically requiring precious metals. Here, we report a hierarchical nanoporous Cu catalyst doped with small amounts of Ti (npTiCu) that increases the rate of H2-D2 exchange by approximately one order of magnitude compared to the undoped nanoporous Cu (npCu) catalyst. The promotional effect of Ti was measured via steady-state H2-D2 exchange reaction experiments under atmospheric pressure flow conditions in the temperature range of 300─523 K. Pretreatment with flowing H2 is required for stable catalytic performance and two temperatures, 523 K and 673 K, were investigated. The experimentally-determined H2-D2 exchange rate is 5-7 times greater for npTiCu vs. the undoped Cu material under optimized pretreatment and reaction temperatures. The H2 pretreatment leads to full reduction of Cu oxide and partial reduction of surface Ti oxide species present in the as-prepared catalyst as demonstrated using in-situ ambient pressure X-ray photoelectron spectroscopy and X-ray absorption spectroscopy. The apparent activation energy and pre-exponential factors measured for H2-D2 exchange are substantially different for Ti-doped vs. undoped npCu catalysts. DFT calculations suggest that isolated, metallic Ti atoms on the surface of the Cu host can act as the active surface sites for hydrogen recombination. The increase in the rate of exchange above that of pure Cu is caused primarily by a shift in the rate-determining step from dissociative adsorption on Cu to H/D atom recombination on Ti-doped Cu, with the corresponding decrease in activation entropy that it produces

TRF2-Mediated Control of Telomere DNA Topology as a Mechanism for Chromosome-End Protection.

International audienceThe shelterin proteins protect telomeres against activation of the DNA damage checkpoints and recombinational repair. We show here that a dimer of the shelterin subunit TRF2 wraps ∼ 90 bp of DNA through several lysine and arginine residues localized around its homodimerization domain. The expression of a wrapping-deficient TRF2 mutant, named Top-less, alters telomeric DNA topology, decreases the number of terminal loops (t-loops), and triggers the ATM checkpoint, while still protecting telomeres against non-homologous end joining (NHEJ). In Top-less cells, the protection against NHEJ is alleviated if the expression of the TRF2-interacting protein RAP1 is reduced. We conclude that a distinctive topological state of telomeric DNA, controlled by the TRF2-dependent DNA wrapping and linked to t-loop formation, inhibits both ATM activation and NHEJ. The presence of RAP1 at telomeres appears as a backup mechanism to prevent NHEJ when topology-mediated telomere protection is impaired