Beyond seek and destroy: How to generate allelic series using genome editing tools

Genome editing tools have greatly facilitated the functional analysis of genes of interest by targeted mutagenesis. Many usable genome editing tools, including different site-specific nucleases and editor databases that allow single-nucleotide polymorphisms (SNPs) to be introduced at a given site, are now available. These tools can be used to generate high allelic diversity at a given locus to facilitate gene function studies, including examining the role of a specific protein domain or a single amino acid. We compared the effects, efficiencies and mutation types generated by our LbCPF1, SpCAS9 and base editor (BECAS9) constructs for the OsCAO1 gene. SpCAS9 and LbCPF1 have similar efficiencies in generating mutations but differ in the types of mutations induced, with the majority of changes being single-nucleotide insertions and short deletions for SpCAS9 and LbCPF1, respectively. The proportions of heterozygotes also differed, representing a majority in our LbCPF1, while with SpCAS9, we obtained a large number of biallelic mutants. Finally, we demonstrated that it is possible to specifically introduce stop codons using the BECAS9 with an acceptable efficiency of approximately 20%. Based on these results, a rational choice among these three alternatives may be made depending on the type of mutation that one wishes to introduce, the three systems being complementary. SpCAS9 remains the best choice to generate KO mutations in primary transformants, while if the desired gene mutation interferes with regeneration or viability, the use of our LbCPF1 construction will be preferred, because it produces mainly heterozygotes. LbCPF1 has been described in other studies as being as effective as SpCAS9 in generating homozygous and biallelic mutations. It will remain to be clarified in the future, whether the different LbCFP1 constructions have different efficiencies and determine the origin of these differences. Finally, if one wishes to specifically introduce stop codons, BECAS9 is a viable and efficient alternative, although it has a lower efficiency than SpCAS9 and LbCPF1 for creating KO mutations

New hippotragini (Bovidae, Mammalia) from the Late Miocene of Toros-Menalla (Chad)

International audienceUntil now, the pre-Pleistocene record of the bovid tribe Hippotragini was rather poor. We describe here two new taxa from the late Miocene of Toros-Menalla in northern Chad, which yielded the earliest known hominid, Sahelanthropus tchadensis. Tchadotragus sudrei n.gen. n.sp. is known by complete skulls and numerous horn-cores. It has typical hippotragine features such as long slender, curved horn-cores, weak cranial flexure, large frontal sinus, and hippotragine-like dentition, and is here taken as a basal member of the tribe, branching before the divergence between Oryx-Praedamalis and Hippotragus s.l. Saheloryx solidus n.gen. n.sp. is less well-known; it differs mainly by the lack of sinus in the frontal and horn-cores, shorter horn-cores, and rounded brain-case, but it shares with Tchadotragus a large number of features that prompt us to classify it also at the base of the hippotragine tree, perhaps as the sister-taxon of Tchadotragus. No other African taxon looks like Saheloryx, and the only one similar to Tchadotragus is from Sahabi, Libya. The abundance of hippotragines sharply distinguishes Toros-Menalla from the East African late Miocene bovid faunas

The Grid Observatory

International audienceThe goal of the Grid Observatory project (GO) is to contribute to an experimental theory of large grid systems by integrating the collection of data on the behaviour of the flagship European Grid Infrastructure (EGI) and its users, the development of models, and an ontology for the domain knowledge. The GO gives access to a database of grid usage traces available to the wider computer science community without the need of grid credentials. The paper presents the architecture of the digital curation process enacted by the GO and examples of their exploitation.L'objectif du projet Grid Observatoiry (GO) est de contribuer à une théorie expérimentale de systèmes globalisés à grande échelle en intégrant l'acquisition de données sur le comportement de l'infrastructure de la grille européenne phare (EGI) et de ses utilisateurs, avec le développement de modèles, et d'une ontologie du domaine. Le GO donne accès à une base de données des traces d'utilisation de la grille, mise à la disposition de la communauté scientifique. L'article présente l'architecture du processus de conservation numérique adoptée par le GO et des exemples de l'exploitation des traces collectées

Specificity of Resistance and Tolerance to Cucumber Vein Yellowing Virus in Melon Accessions and Resistance Breaking with a Single Mutation in VPg

Altres ajuts: CERCA Programme/Generalitat de CatalunyaCucumber vein yellowing virus (CVYV) is an emerging virus on cucurbits in the Mediterranean Basin, against which few resistance sources are available, particularly in melon. The melon accession PI 164323 displays complete resistance to isolate CVYV-Esp, and accession HSD 2458 presents a tolerance, i.e., very mild symptoms despite virus accumulation in inoculated plants. The resistance is controlled by a dominant allele Cvy-11, while the tolerance is controlled by a recessive allele cvy-2, independent from Cvy-11. Before introducing the resistance or tolerance in commercial cultivars through a long breeding process, it is important to estimate their specificity and durability. Upon inoculation with eight molecularly diverse CVYV isolates, the resistance was found to be isolate-specific because many CVYV isolates induced necrosis on PI 164323, whereas the tolerance presented a broader range. A resistance-breaking isolate inducing severe mosaic on PI 164323 was obtained. This isolate differed from the parental strain by a single amino acid change in the VPg coding region. An infectious CVYV cDNA clone was obtained, and the effect of the mutation in the VPg cistron on resistance to PI 164323 was confirmed by reverse genetics. This represents the first determinant for resistance-breaking in an ipomovirus. Our results indicate that the use of the Cvy-11 allele alone will not provide durable resistance to CVYV and that, if used in the field, it should be combined with other control methods such as cultural practices and pyramiding of resistance genes to achieve long-lasting resistance against CVYV

Magnetic nano-fluctuations in a frustrated magnet

Frustrated systems exhibit remarkable properties due to the high degeneracy of their ground states. Stabilised by competing interactions, a rich diversity of typically nanometre-sized phase structures appear in polymer and colloidal systems, while the surface of ice pre-melts due to geometrically frustrated interactions. Atomic spin systems where magnetic interactions are frustrated by lattice geometry provide a fruitful source of emergent phenomena, such as fractionalised excitations analogous to magnetic monopoles. The degeneracy inherent in frustrated systems may prevail all the way down to absolute zero temperature, or it may be lifted by small perturbations or entropic effects. In the geometrically frustrated Ising--like magnet Ca3Co2O6, we follow the temporal and spatial evolution of nanoscale magnetic fluctuations firmly embedded inside the spin--density--wave magnetic structure. These fluctuations are a signature of a competing ferrimagnetic phase with an incommensurability that is different from, but determined by the host. As the temperature is lowered, the fluctuations slow down into a super-paramagnetic regime of stable spatiotemporal nano-structures

ACO2 mutations: A novel phenotype associating severe optic atrophy and spastic paraplegia

International audienc