Herrel, A. | Search bioRxiv

bioRxiv2018

Hydrodynamics of the frontal strike in aquatic snakes: drag, added mass and the possible consequences for prey capture success.

Natural selection favors organisms that are the most successful in fitness-related behaviors such as foraging. Secondary adaptations pose the problem of re-adapting an already optimized phenotype to new constraints. When animals forage underwater, they face strong physical constraints, particularly when capturing prey. Successful prey capture requires a predator to be fast and to generate a high acceleration. This involves two main constraints due to the surrounding fluid: drag and added mass. Both constraints are related to the shape of the animal. We experimentally explore the relationship between shape and performance in the context of an aquatic snake strike. As a model, we use two different 3D- printed snake heads representing typical shapes of aquatically-foraging and non-aquatically- foraging snakes, and frontal strike kinematics based on in vivo observations. By using direct force measurements, we compare the drag and added mass faced by the aquatic and non- aquatic snake models during a strike. Our results show that both drag and added mass are optimized in aquatic snakes. Using flow field measurements with particle image velocimetry, we examine the fluid dynamical mechanisms that could be behind the reduction of hydrodynamic constraints observed for the aquatic snake head shape, which makes it well suited to capture prey under water.\n\nSummary statementThe present work explores the functional implications of head shape 15 in a group of aquatic predators using a fluid mechanics approach.

biophysics↗

bioRxiv2016

Characterizing Xenopus tropicalis endurance capacities with multilevel transcriptomics

Vertebrate endurance capacity is a phenotype with considerable genetic heterogeneity. RNA-Seq technologies are an ideal tool to investigate the involved genes and processes, but several challenges exist when the phenotype of interest has a complex genetic background. Difficulties manifest at the level of results interpretation because commonly used statistical methods are designed to identify strongly associated genes. If an observed phenotype can be achieved though multiple distinct genetic mechanisms then typical gene-centric methods come with the attached risk that signal may be lost or misconstrued.\n\nGene set analysis (GSA) methods are now widely accepted as a means to address some of the shortcomings of gene-by-gene analysis methods. We carry out both gene level and gene set level analyses on Xenopus tropicalis to identify the genetic factors that contribute to endurance heterogeneity. A typical workflow might consider gene level and pathway level analyses, but in this work we propose an additional focus at the intermediate level of functional modules. We generate functional modules for GSA testing in order to be explicit in how ontology information is used with respect to the functional genomics of Xenopus. Additionally, we make use of multiple assemblies to corroborate implicated genes and processes.\n\nWe identified 42 core genes, 10 functional modules, and 14 pathways based on gene expression differences between endurant and non-endurant frogs. The majority of the genes and processes are readily associated with muscle contraction or catabolism. A substantial number of these genes are involved in lipid metabolic processes, suggesting an important role in frog endurance heterogeneity. Unsurprisingly, many of the gene expression differences between endurant and non-endurant frogs can be distilled down to the capacity to utilize substrate for energy, but at the individual level frogs appear to make use of diverse machinery to achieve these differences.

bioinformatics↗