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Varshney et al. 2011

Structural Properties of the Caenorhabditis elegans Neuronal Network

Lav R. Varshney, Beth L. Chen, Eric Paniagua, David H. Hall, Dmitri B. Chklovskii
PLOS Computational Biology 7(2): e1001066
Published: February 3, 2011

Datasets

Data Acquisition

  • Assembled wiring diagram by consolidating existing data from both published and unpublished sources

White et al- The Mind of a Worm (MOW) (starting point)

  • extracted wiring data from diagrams, figures, tables and text
  • connectivity of each neuron, its synaptic partner, and synaptic type was manually entered into an electronic database
  • in the ventral cord, determining this level of synaptic specification was complicated by the fact that connections were recorded by neuron class
  • assigned proper connections to the appropriate left/right neuronby referring to White and coworker's original laboratory notebooks and original EMs

R.M. Durbin- the anterior portion of the worm

  • Anterior connections needed an update as MOW did not specify the location of syanpses, integration proved difficult
  • For these neurons, they obtained positional information by cross-referencing Durbin's data against original EMs and his handwritten annotations in White's laboratory notebooks
  • Only synapses located in regions addressed by Durbin were included
  • Connections in the middle and tail region of the worm were mostly unaffected by these updates.

Differences in data and gaps

  • [Hobert O and Hall DH, unpublished] differences between GFP neurons and White's work have been observed
    • anterior processes of DVB and PVT could have been mistakenly switched in MOW
    • so they reversed the connections for neurons DVB and PVT anterior to the vulva
  • reconstructions of neurons in the mid-body of the wor are incomplete
  • from a combination of these published works
    • White et al 1986
    • Durbin RM 1987
    • Hall DH, Russel RL 1991
    • White et al 1976
  • wiring data for 64 neurons had large gaps or were missing entirely
    • 61 of these were motor neurons in the ventral cord
  • 2 were excretory neurons (CANL/R) that do not appear to make any synapses
    • RID is the only process in the dorsal cord that extends over the length of the animal

Updates to previous data

  • Using a White et al laboratory notebooks, they identified notes for full reconstructions of 24 of the aforementioned neurons
  • Partial connectivity data for the remaining 38 were also available where 22 neurons have partial/missing dorsal side connections and 6 neurons have partial ventral side connections
  • 600 updates were made to the original notes and published reconstructions -additions of previously missed NMJs between ventral cord motor neurons and body wall muscles -large section on the dorsal side of the worm was never EM at high power magnification
  • produced new high power EMs of this dorsal region
  • 3 neurons (DA5,DB4,DD3) were obtained from these EMs
  • resource constraints prevented them from covering the entire dorsal gap
  • reconciliation of discrepancies -561 synapses for 108 neurons (49% chemical "sends", 31% chemical "receives" and 20% for electrical junctions)