Horan, S. | Search bioRxiv

bioRxiv2021

High throughput measurement of Arabidopsis thaliana fitness traits using transfer learning

O_LIRevealing the contributions of genes to plant phenotype is frequently challenging because the effects of loss of gene function may be subtle or be masked by genetic redundancy. Such effects can potentially be detected by measuring plant fitness, which reflects the cumulative effects of genetic changes over the lifetime of a plant. However, fitness is challenging to measure accurately, particularly in species with high fecundity and relatively small propagule sizes such as Arabidopsis thaliana. C_LIO_LIAn image segmentation-based (ImageJ) and a Faster Region Based Convolutional Neural Network (R-CNN) approach were used for measuring two Arabidopsis fitness traits: seed and fruit counts. C_LIO_LIAlthough straightforward to use, ImageJ was error-prone (correlation between true and predicted seed counts, r2=0.849) because seeds touching each other were undercounted. In contrast, Faster R-CNN yielded near perfect seed counts (r2=0.9996) and highly accurate fruit counts (r2=0.980). C_LIO_LIBy examining seed counts, we were able to reveal fitness effects for genes that were previously reported to have no or condition-specific loss-of-function phenotypes. C_LIO_LIOur study provides models to facilitate the investigation of Arabidopsis fitness traits and demonstrates the importance of examining fitness traits in the study of gene functions. C_LI

bioinformatics↗

bioRxiv2019

The Kaufman oculocerebrofacial syndrome protein Ube3b regulates synapse number by ubiquitinating Ppp3cc.

Kaufman oculocerebrofacial syndrome (KOS) is a severe autosomal recessive disorder characterized by intellectual disability, developmental delays, microcephaly and characteristic dysmorphisms. Biallelic mutations of UBE3B, encoding for a ubiquitin ligase E3B are causative for KOS. In this report, we characterize neuronal functions of its murine ortholog Ube3b. We show that Ube3b regulates dendritic branching in a cell-autonomous manner. Moreover, Ube3b knockout (KO) neurons exhibit increased density and aberrant morphology of dendritic spines, altered synaptic physiology and changes in hippocampal circuit activity. Dorsal forebrain-specific Ube3b KO animals show impaired spatial learning and alterations in social interactions. We further demonstrate that Ube3b ubiquitinates the catalytic {gamma}-subunit of calcineurin (Ppp3cc), the overexpression of which phenocopies the loss of Ube3b with regard to dendritic spine density. This work provides insights into the molecular pathologies underlying intellectual disability-like phenotypes in a genetic mouse model for KOS.

neuroscience↗