Yim et al. 2024

Comparative connectomics of dauer reveals developmental plasticity

Hyunsoo Yim, Daniel T. Choe, J. Alexander Bae, Myung-kyu Choi, Hae-Mook Kang, Ken C. Q. Nguyen, Soungyub Ahn, Sang-kyu Bahn, Heeseung Yang, David H. Hall, Jinseop S. Kim & Junho Lee
Nature Communications 2024, 15:1546
Published: 27 February 2024

Datasets incorporated

• Yim et al. 2024 - Directed synaptic connections; Normalized weights
• Yim et al. 2024 - Directed synaptic connections; Non-normalized
• Yim et al. 2024 - Contactome; Normalized weights
• Yim et al. 2024 - Contactome; Non-normalized

Summary

• Reconstruction of chemical connectome of the dauer, a distinct developmental stage of C. elegans
• Uses volumetric reconstruction and automated synapse detection
• Theoretical analysis shows a considerable rearrangement of sensory neuron connections and an increase in clustering within motor neurons during this developmental stage
• Two distinct types of connection information are used from this paper:

A) Synaptic connectivity: A directed matrix, with rows presynaptic and columns postsynaptic. Presynaptic active zones were detected by a convolutional neural network, reconstructed in 3D and proofread; postsynaptic partners and each partner's share of an active zone were assigned by simulating neurotransmitter diffusion. Weights are the summed volume (nm³) of active zone material attributed to a pre/post pair.

B) Contact area/Contactome: A symmetric matrix, as physical apposition has no pre/post polarity, measured from the volumetric segmentation rather than from synapses. Weights are the summed area (nm²) of contact between two cells.