C. elegans: Connectome to behaviour

Between discussions of Young’s modulus, neurochemical equations and hydrodynamics algorithms; I managed to get the gist of the biophysics of C. elegans behaviour.

Well, as an amateur in this field, I’d like to say I got the gist of the biophysics of C. elegans behaviour.

However, I was told knowledge is like butter, and it comes on in layers. At first, you would not understand what is going on. However, when you expose yourself to it again and again. It will start to make sense (this is relieving to say the least, there is hope!).

At the conference they had 2D and 3D models of various aspects in the C. elegans. But, first, what is a model?

 

What is the purpose of a model?

Models are used to create a predictive model to increase insight and help direct experiment and experimental methodology. Basically, we are looking for the patterns, looking for those rules that guide the C. elegans.

However, the models and maps, like a tube map or a satellite map; depends on the question we are asking. Models that are created are often restricted by the questions one is asking. Some models are created to understand locomotor behaviour in C. elegans; while others can be used to understand proprioception. The question brought up during the conference was, how can these different models be used to complement one another and answer ‘classical’ questions.

Barbasi introduced an interesting twist to the way we understand models; he suggested that networks can not only be used to qualify and predict, but to also control a system. However, there are certain aspects that modelling does not take into account such as extra synaptic signalling.

In a utopian world – or maybe in the far future – we would be able to create a model of the whole organisms, that takes into account the hubs and nodes.

 

Types of models

The following are examples of models that were presented in the conference:

  • Neural model to match elctrophysiology (understanding how traces generate movement)
  • Using computational high-throughput to understand behaviour
  • Modelling proprioception and feed-forward circuits (they are often seen or modelled as separate entities)

 

Open online tools

We got an assignment to identify the greatest advancement in developmental neuroscience; one would normally look for new conceptual advancements in biology; however, technological advancements are just as important. The following are (open source) technologies that were presented in the conference:

  • Wormtracker: single worm tracker
  • NeuroML: creating computational models of neural systems
  • NeuroElectro: a centralised database compiling the electrophysiological properties of different neurons
  • Wormbrowser: using the literature to create 3D models of C. elegans
  • DevoWorm: understanding embryonic development, morphogenesis and plasticity
  • Gapetto: open source platform to explore and stimulate models. There is a virtual fly brain that allows one to see the 3D structure of neurons.

 

Expansion microscopy and other advancements

One of the most fascinating thing was a poster on expansion microscopy in C. elegans. The first thing to enter my mind was ‘THIS IS SO COOL’. The second thought was ‘science in Africa’.

C. elegans as a model organism would be convenient to undertake experiments in Africa, specifically East-Africa because of my  personal experience. When I first came across expansion microscopy by the Ed Boyden laboratory  when I was in Nairobi. I immediately looked up the protocol and thought that this was an amazing feat to get higher resolutions. But unfortunately, some of the chemicals were harder to get my hands on than others.

There was an interesting visualisation method called neuroPal by Yemini. NeuroPal has more than 50 transgenes that labels cells in the C. elegans. It can be used to identify different cells in the organism according to colour and location in the ganglion. A paper I want to read; Hamet et al., holistic modelling.

 

I would like to thank the organisers of the discussion meeting on their excellent effort; Dr. John White, Dr. Stephen Larson, Dr. André Brown, Dr. William Schafer and Professor Netta Cohen.

Beautiful scenery on the way to the conference

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