Search results for "COMPUTATION"

Practicing logical reasoning through Drosophila segmentation gene mutants.

2021

Laboratory practical sessions are critical to scientific training in biology but usually fail to promote logical and hypothesis-driven reasoning and rely heavily on the teacher's instructions. This paper describes a 2-day laboratory practicum in which students prepare and analyze larval cuticle preparations of Drosophila segmentation gene mutant strains. Embryonic segmentation involves three major classes of genes according to their loss-of-function phenotypes: the establishment of broad regions by gap genes, the specification of the segments by the pair-rule genes, and the compartments within segments by the segment polarity genes. Students are asked to sort undefined segmentation mutants …

Problems in time-intensity measurements. A case study-Bitterness evaluation in water solutions and in beers

1992

International audience

Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits

2020

In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT.

2020

AbstractDeveloping methods for accurate detection of RNA modifications remains a major challenge in epitranscriptomics. Next-generation sequencing-based mapping approaches have recently emerged but, often, they are not quantitative and lack specificity. Pseudouridine (ψ), produced by uridine isomerization, is one of the most abundant RNA modification. ψ mapping classically involves derivatization with soluble carbodiimide (CMCT), which is prone to variation making this approach only semi-quantitative. Here, we developed ‘HydraPsiSeq’, a novel quantitative ψ mapping technique relying on specific protection from hydrazine/aniline cleavage. HydraPsiSeq is quantitative because the obtained sign…

DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes

2019

Abstract Epigenomics is the study of modifications on the genetic material of a cell that do not depend on changes in the DNA sequence, since those latter involve specific proteins around which DNA wraps. The end result is that Epigenomic changes have a fundamental role in the proper working of each cell in Eukaryotic organisms. A particularly important part of Epigenomics concentrates on the study of chromatin, that is, a fiber composed of a DNA-protein complex and very characterizing of Eukaryotes. Understanding how chromatin is assembled and how it changes is fundamental for Biology. In more than thirty years of research in this area, Mathematics and Theoretical Computer Science have gai…

Correction

2019

ABSTRACT During gastrulation, embryonic cells become specified into distinct germ layers. In mouse, this continues throughout somitogenesis from a population of bipotent stem cells called neuromesodermal progenitors (NMps). However, the degree of self-renewal associated with NMps in the fast-developing zebrafish embryo is unclear. Using a genetic clone-tracing method, we labelled early embryonic progenitors and found a strong clonal similarity between spinal cord and mesoderm tissues. We followed individual cell lineages using light-sheet imaging, revealing a common neuromesodermal lineage contribution to a subset of spinal cord tissue across the anterior-posterior body axis. An initial pop…

Efficient Online Laplacian Eigenmap Computation for Dimensionality Reduction in Molecular Phylogeny via Optimisation on the Sphere

2019

Reconstructing the phylogeny of large groups of large divergent genomes remains a difficult problem to solve, whatever the methods considered. Methods based on distance matrices are blocked due to the calculation of these matrices that is impossible in practice, when Bayesian inference or maximum likelihood methods presuppose multiple alignment of the genomes, which is itself difficult to achieve if precision is required. In this paper, we propose to calculate new distances for randomly selected couples of species over iterations, and then to map the biological sequences in a space of small dimension based on the partial knowledge of this genome similarity matrix. This mapping is then used …

Interaction between odorants and proteins involved in the perception of smell: the case of odorant-binding proteins probed by molecular modelling and…

2012

A joint approach that combines molecular modelling and fluorescence spectroscopy is used to study the affinity of an odorant binding protein towards various odorant molecules. We focus on the capability of molecular modelling to rank odorants according to their affinity with this protein, which is involved in the sense of smell. Although ligand-based approaches are unable to propose an accurate model attending to the strength of the bond with the odorant-binding protein, receptor-based structures considering either static or dynamic structure of the protein perform equally to discriminate between good, medium and low affinity odorants. Such approaches will be useful for further rational des…

Visualizing Human Protein‐Protein Interactions and Subcellular Localizations on Cell Images Through CellMap

2020

Visualizing protein data remains a challenging and stimulating task. Useful and intuitive visualization tools may help advance biomolecular and medical research; unintuitive tools may bar important breakthroughs. This protocol describes two use cases for the CellMap (http://cellmap.protein.properties) web tool. The tool allows researchers to visualize human protein-protein interaction data constrained by protein subcellular localizations. In the simplest form, proteins are visualized on cell images that also show protein-protein interactions (PPIs) through lines (edges) connecting the proteins across the compartments. At a glance, this simultaneously highlights spatial constraints that prot…

MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments

2020

Multiple sequence alignments are usually phylogenetically driven. They are studied in the framework of evolution. But sometimes, it is interesting to study residue conservation at positions unconstrained by evolutionary rules. We present a supervised method to access a layer of information difficult to appreciate visually when many protein sequences are aligned. This new tool (MAGA; http://cbdm-01.zdv.uni-mainz.de/~munoz/maga/ ) locates positions in multiple sequence alignments differentially conserved in manually defined groups of sequences.