notes.txt

C. elegans
https://www.ncbi.nlm.nih.gov/books/NBK20086/
The mind of a worm
https://www.wormatlas.org/MoW_built0.92/MoW.html

Self-fertilizing hermaphrodite (both male and female) soil nematodes (parasitic worms). 

The pachytene region (synaptomenal complex?) contains *DTC, mitotic, meiotic
regions, *primary secondary spermatocytes, *spermatids

Sensory rays

*DTC: Distal Tip Cells, u-shaped trip, function ----
*PSS: primary is diploid, after meiosis I its haploid (secondary), grown sperm cells
*Spermatid: Product of mitosis II of spermatocytes.

wormbase:
https://wormbase.org/species/all/anatomy_term/WBbt:0000100#01--10

anatomy image:
https://upload.wikimedia.org/wikipedia/commons/4/4b/C_elegans_male.svg


Morphological structure
    A big part of the structure dates back to 1986 with 'The structure of the nervous
    system of the nematode Caenorhabditis elegans' that used electron micrographs to map it.

    It showed that it has 302 neurons with 118 classes (roughly) and have about
    5000 chemical synapses, 2000 neuromuscular (electrical impulse to activity for muscle fibers) junctions and 600 gap junctions.
    ?HOW
    
    'Structural Properties of the Caenorhabditis elegans Neuronal Network'
    Then expanded the wiring diagram with new data. This can be found (perhaps updated)
    here: 
    FILL

    This model is still not complete given that we have not information on gap junction
    rectification (diode), long range neuromodulation, etc.
    
    
    'Optimally wired subnetwork determines neuroanatomy of Caenorhabditis elegans' shows
    84% of the neurons are optimally wired with 5% position error.
    This variance is mostly explained by economical wiring cost.
    EXPAND

    However, several assumptions are made:
        -one axon -> many synapses becomes many synapses -> many axons
        CONTINUE

    Datasets:
    Midbody bend and speeds + segmentation ~5 TB of video data and numbers.


Behavior:
    Due to individual variability and, perhaps, missing data, the C. Elegans' functions
    can't be exactly mapped, however, with recordings (segmented), we can try to identity
    different behavioral patterns.

    Paper: 'A database of Caenorhabditis elegans behavioral phenotypes',
    https://www.dropbox.com/s/tqr3abcrr8dt3bi/A%20database%20of%20Caenorhabditis%20elegans%20behavioral%20phenotypes.%20-%20Yemini%20et%20al.%20-%202013.pdf# 

    Film with 20 per strained for mins (with 20-30 fps) behaving on food at about 2.5 x 2 mm^2.
    Available on both 'C.elegans Behavioural Database' channel and 'openworm'

    C. Elegans exhibits touch induced movement pathway with 6 touch receptors, five pairs of interneurons, and 69 motor neurons.


  
Genetic expressions:
    Datasets:
        wormbase.org (a bit confusing)
        contribute @ openworm github

 
Intra, Inter variability of morphology and behavior:
    Figures of behavioral phenotypes vs mutation q values

mysteries (to me):
    distal tip cells function