Monocular microsaccades are visual-task related

During visual fixation, we constantly move our eyes. These microscopic eye movements are composed of tremor, drift, and microsaccades. Early studies concluded that microsaccades, like larger saccades, are binocular and conjugate, as expected from Hering's law of equal innervation. Here, we document the existence of monocular microsaccades during both fixation and a discrimination task, reporting the location of the gap in a foveal, low-contrast letter C. Monocular microsaccades differ in frequency, amplitude, and peak velocity from binocular microsaccades. Our analyses show that these differences are robust to different velocity and duration criteria that have been used previously to identify microsaccades. Also, the frequency of monocular microsaccades differs systematically according to the task: monocular microsaccades occur more frequently during fixation than discrimination, the opposite of their binocular equivalents. However, during discrimination, monocular microsaccades occur more often around the discrimination threshold, particularly for each subject's dominant eye and in case of successful discrimination. We suggest that monocular microsaccades play a functional role in the production of fine corrections of eye position and vergence during demanding visual tasks

Gigwa—Genotype investigator for genome-wide analyses

Background Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Description Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. Conclusions The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers. (Résumé d'auteur

High quality phased assembly of grape genome offer new opportunities in chimera detection

In perennial plants and especially those propagated through cuttings, several genotypes can coexist in a single individual, thus leading to chimeras. When the variant induces a noticeable phenotype modification, it can lead to a new cultivar. Viticulture already took economic advantage of this natural phenomenon: for instance, the berry skin of ‘Pinot gris’ derived from ‘Pinot noir’ by the selection of a chimera. Chimeras could also impact other crucial traits without being visually identified. Periclinal chimera where the variant has entirely colonized a cell layer is the most stable and can be propagated through cuttings. In grapevine, two functional cell layers are present in leaves, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves could allow chimera detection. In this study we used new generation Hifi long reads sequencing and recent bioinformatics tools applied to ‘Merlot’ to detect periclinal chimeras. Sequencing of ‘Magdeleine Noire des Charentes’ and ‘Cabernet franc’, the parents of ‘Merlot’, allowed haplotype resolved assembly. Pseudomolecules were built with few contigs, in some occasions only one per chromosome. This high resolution allowed haplotype comparison. Annotation from PN40024 was transferred to all pseudomolecules. Through variant detection, periclinal chimeras were found on both haplotypes. These results open new perspectives on chimera detection, which is an important resource to improve cultivars through clonal selection or breed new ones. Detailed results will be presented and discussed