Biology subjects

Porto, D.

Publications and source records attributed to Porto, D..

2 recordsLinked to original sources

bioRxiv2023

rphenoscate: An R package for semantic-aware evolutionary analyses of anatomical traits

O_LIOrganismal anatomy is a complex hierarchical system of interconnected anatomical entities often producing dependencies among multiple morphological characters. Ontologies provide a formalized and computable framework for representing and incorporating prior biological knowledge about anatomical dependencies in models of trait evolution. Further, ontologies offer new opportunities for assembling and working with semantic representations of morphological data. C_LIO_LIIn this work we present a new R package--rphenoscate--that enables incorporating ontological knowledge in evolutionary analyses and exploring semantic patterns of morphological data. In conjunction with rphenoscape it also allows for assembling synthetic phylogenetic character matrices from semantic phenotypes of morphological data. We showcase the new package functionalities with three data sets from bees and fishes. C_LIO_LIWe demonstrate that ontology knowledge can be employed to automatically set up ontologyinformed evolutionary models that account for trait dependencies in the context of stochastic character mapping. We also demonstrate how ontology annotations can be explored to interrogate patterns of morphological evolution. Finally, we demonstrate that synthetic character matrices assembled from semantic phenotypes retain most of the phylogenetic information of the original data set. C_LIO_LIOntologies will become an increasingly important tool not only for enabling prior anatomical knowledge to be integrated into phylogenetic methods but also to make morphological data FAIR compliant--a critical component of the ongoing phenomics revolution. Our new package offers key advancements toward this goal. C_LI

evolutionary biology↗

bioRxiv2021

Conformational changes in twitchin kinase in vivo revealed by FRET imaging of freely moving C. elegans

The force-induced unfolding and refolding of proteins is speculated to be a key mechanism in the sensing and transduction of mechanical signals in the living cell. Yet, little evidence has been gathered for its existence in vivo. Prominently, stretch-induced unfolding is postulated to be the activation mechanism of the twitchin/titin family of autoinhibited sarcomeric kinases linked to the mechanical stress response of muscle. To test the occurrence of mechanical kinase activation in living working muscle, we generated transgenic C. elegans expressing twitchin containing FRET moieties flanking the kinase domain and developed a quantitative technique for extracting FRET signals in freely moving C. elegans, using tracking and simultaneous imaging of animals in three channels (donor fluorescence, acceptor fluorescence, and transmitted light). Computer vision algorithms were used to extract fluorescence signals and muscle contraction states in each frame, in order to obtain fluorescence and body curvature measurements with spatial and temporal precision in vivo. The data revealed statistically significant periodic changes in FRET signals during muscle activity, consistent with a periodic change in the conformation of twitchin kinase. We conclude that stretch-unfolding of twitchin kinase occurs in the active muscle, whereby mechanical activity titrates the signalling pathway of this cytoskeletal kinase. We anticipate that the methods we have developed here could be applied to obtaining in vivo evidence for force-induced conformational changes or elastic behavior of other proteins not only in C. elegans but in other animals in which there is optical transparency (e.g zebrafish).

biophysics↗