Maser, M. | Search bioRxiv

bioRxiv2025

Replication of seizure-suppressing effects of alpha-linolenic acid on the Drosophila melanogaster paraShudderer mutant

Voltage-gated sodium channels are essential for healthy nervous system function. Mutations in voltage-gated sodium channels are associated with a range of seizure conditions. The genetics of seizure conditions are complex and often challenging to study or replicate in animal models. The Drosophila melanogaster gene paralytic (para) is the sole voltage-gated sodium channel gene in flies. The paraShudderer allele causes dominant seizure activity manifest in adult morphology and behavior. In this study we replicated previous findings of paraShudderer hyperexcitability and the ability to suppress this activity with dietary supplementation of an omega-3 fatty acid, alpha-linolenic acid (ALA). Our results support the robustness of the paraShudderer phenotype and the replicability of findings across separate lab environments.

neuroscience↗

bioRxiv2023

Mixed structure- and sequence-based approach for protein graph neural networks with application to antibody developability prediction

There are hundreds of thousands of known proteins but significantly fewer unique protein folds. Furthermore, proteins often have conserved and even repeating geometric patterns, which can be captured by models of protein structure and function. In this work, we use Delaunay tessellations and -shapes, which capture these conserved geometric patterns, to define graph adjacency in Graph Convolutional Networks (GCN). We demonstrate the utility of the resulting GCN model on antibody developability prediction. Compared to the frequently used graph adjacencies based on k-nearest-neighbors or a fixed cutoff radius, the Delaunay tessellation and -shapes better capture residue-specific interactions at a lower computational cost for a given system size. The resulting models achieve state-of-the-art performance on an antibody developability prediction task. Finally, we propose an extension of the model which does not require known or predicted structures but uses an "archetypical" antibody structure to infer likely contacts.

biophysics↗