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Talk in Köln

On February 6th, I gave a talk in Cologne entitled “Dense neural circuit reconstruction and graph theoretical analysis of nematode nervous systems.” In it, I emphasized primarily some of the graph theory I have been using to try and understand circuit function. I was invited by Einhard Schierenberg, who works on cell lineage evolution in nematodes. His postdoc, Jens Schulz, took the time to give me a bit of a tour of the city and had me try a bit of Kölsch at a local brewery.  I was also had a great chat (though a little short) with Johannes Berg, a physicist who is interested in network statistics. I’ll have to go back and check out more of the city when it is a bit warmer…


Brand new publication in a brand new journal!

A review I did with Ralf on nematode models in Evolutionary and Developmental biology just came out in WIRES Developmental Biology.

In it we describe how a number of nematode species (not just C. elegans and P. pacificus!) have contributed to our understanding of evo-devo. The paper is interesting, but the publication venue is also interesting… WIRES Developmental Biology, which is a new (only 1 issue so far) online-only publication put out by Wiley. It is intended to be “a state of the art online reference resource for all of developmental biology, one that will cover basic concepts as well as specific topics, and will collect and integrate the findings and insights of our field in a comprehensive, authoritative manner.” Kind of like a peer-reviewed encyclopedia of state-of-the-art knowledge about development. I’m hoping this is just the first paper in  a very good publication year!

Talk at the Max Planck Institute

This past Tuesday I was able to present my work to our institute at our Tuesday seminar. I’ve progressed further with analyzing data, so it was a pleasure to present some of the newer results I’ve been getting. I’ve been performing a more detailed network analysis, looking at things like centrality measures to see what I can learn about both C. elegans and P. pacificus. Turns out, I’m able to use them to make some predictions about functional shifts in different parts of the neural circuitry making up the nervous systems of the two worms. Now to test them!

Pristionchus pharynx connectome!

The image to the left is a network graph showing all of the synaptic connections in the pharynx of the nematode Prisitonchus pacificus. The pharyngeal nervous system in nematodes is almost entirely independent from the rest of the body, so this is essentially a map of the pharynx “brain”. The data are still unpublished, so I can’t put in the cell names yet. Still, it is a thing of beauty that I wanted to share! There are only 20 neurons in the pharynx, so it is a relatively small neural system. There are some very interesting differences in pharynx behavior between different nematode species, and eventually we would like to use such diagrams to help understand the neural basis for evolutionary changes in behavior. From this network we are already learning some very interesting and unexpected things. I’ll be presenting these data for the first time at a meeting on C. elegans neuroscience at the end of this month in Madison, Wisconsin. I am really very excited to be sharing this, and can’t wait until it moves into publication! I used the open source software Gephi ( to make the graph. It is a pretty awesome package that is under active development that allows me to make some pretty nice looking representations of the data as well as do some basic analysis.

New Editor, Journal of Nematology

I’ve been notified this week that I’ll be serving as an editor for the Journal of Nematology. It makes me very happy to have the opportunity to serve the Society of Nematologists, which has been an important part of my career since my first work on nematodes (my first scientific meeting was the 1997 SON meeting in Tucson) and will undoubtedly continue to be in the future. Though it adds a little to a busy schedule, it is going to be interesting to be on this side of the review process. I’ll be serving as the subject editor for taxonomy papers submitted to the journal.  Pictured to the left is a bad scan of one of the old-school orange covers, for those nostalgic nematologists out there.

Nematode Brain!

Metta and I are still in the process of collecting images of a serial section dataset through the front end of our nematode. I am hoping it will eventually become the second species for which we have a complete connectome, or “wiring” diagram of all the synaptic connections in the nervous system. We have now imaged everything from the tip of the nose to the brain of the animal, which is called the nerve ring as it wraps around the pharynx making a ring shape. Everything is going exceptionally well, and we only need a few hundred more images to have a very complete and useful dataset showing all of the connections. The above image is a cross section of the nematode. The pharynx is in the middle, and you can see the neuropil wrapping around in a circle, forming synapses as they pass each other. All of these images are taken at much higher resolution than is shown here. Click HERE for a Flickr gallery showing the same image at different magnifications.

New publication!

Finally, the last paper from my PhD work has been published in the journal of comparative neurology. Really feels great to get this one out! If anyone wants a pdf, just email me and let me know. Here is the citation:

Bumbarger, DJ, S Wijeratne, C Carter, J Crum, MH Ellisman and JG Baldwin. 2008. Three-Dimensional Reconstruction of the Amphid Sensilla in the Microbial Feeding Nematode, Acrobeles Complexus (Nematoda: Rhabditida). J Comp Neurol 512:271-281.

In other lab news, our institute will be purchasing an obscenely expensive digital camera for our electron microscope to replace a less than desirable one that I am currently using. It should make a big difference in my work. Also, Ralf has agreed that if I can find a qualified person I can get a graduate student of my very own! That would add much to my life quality and would allow me to think more ambitiously about what I can do here.

Below is an image of the main figure in the paper, which shows the sensory endings of all the amphid dendrites (colored textured things), the amphid socket (transparent red) and sheath (transparent green) cells, a bit of one of the epidermal cells (transparent grey) and a bit of the pharymx (solid grey). The amphids are the primary sensory structures in nematodes. Enjoy!