Category Archives: Sommer Lab

Faces in the worm.

2975_Montage Acquisition0001Reconstructing neurons from thousands of images is typically a very dull, repetitive and labor intensive task. Some would say that the long periods of monotony, broken by occasional excitement caused by an unexpected discovery, is enough to drive you insane. Yet it is how I spent much of my time. Either because I have gone crazy or more likely out of a need to amuse myself with the task I have started to notice faces in the micrographs. This is not all that surprising really. As humans we are really pre-programmed to recognize anything that has the same proportions as a face… all we need are two dots for eyes  something that looks like a mouth in the right places. As mitochondria are typically tube shaped they can very easily substitute for a mouth or a pair of eyes in an image, so most of them time these are what construct the features of the face. Sometimes, the inner membranes of the mitochondria even stain in such a way as to resemble teeth in the mouth! Perhaps it is a reflection of optimism that the vast majority of faces that I notice are smiley faces. For anyone that is amused, I’ve started collecting them and have uploaded them to a Flickr gallery. Click HERE for the link!


Gilberto Bento in town


Gilberto Bento, former Sommer Lab member best know for his 2010 Nature paper on the Pristionchus pacificus mouth form polyphenism, managed to make a return visit to Tübingen this weekend. A few of us went out for dinner and beers during his all-to-brief stay. In the photo, left-right, is Gilberto, Akira Ogawa (our esteemed Japanese postdoc who is soon leaving the lab) and Matthias Herrmann, our resident beetle taxonomist. Bento can now be found working on the genetics of Daphnia magna in the lab of Dieter Ebert in Basel, Switzerland.

Neural Circuit Meeting at CSHL, and a trip to Albert einstein to boot.

During the last week of March, I made a trip to the good ol’ U.S.A. to attend the Neuronal Circuits meeting at Cold Spring Harbor Laboratory out on Long Island. There, I presented a talk entitled “Comparative Graph Theoretical Analysis of Networks of Identified Neurons.” During the talk, I summarized the Pristionchus connectivity project as well as introduced some of the graph theory methods I’ve been working on for asking questions of connectivity networks. For me, the meeting was outstanding. All of the talks were well presented and of a very high standard… you can count on your mind being blown at least a couple of times a day at these meetings! CSHL is an excellent (though expensive) venue for meetings, and the  meeting itself was structured to allow plenty of time to talk with people. There weren’t so many worm people there, but Scott Emmons presented his connectivity dataset for the male in C. elegans, Julie Cho from Paul Sternberg’s lab presented a nice talk on her work dealing with lethargic (“sleep”) and a couple of awesome grad students from Mark Alkema’s lab had posters (Christopher Clark and Jennifer Pirri). They look at locomotion circuits, including examining how C. elegans avoids nematode trapping fungi. I’ve always been a fan of Arthrobotrys! Prior to the meeting, I went out to the Albert Einstein College of Medicine in the Bronx to visit the labs of David Hall and Scott Emmons. Their work on the male tail is impressive, available already online ( and should be published this year. I always like visiting David’s lab because it is kind of an electron microscopy museum, containing many of the early and important electron micrographs for C. elegans. This time around, there was a new addition: the original wooden models constructed by, I think, John White in order to investigate vulva development! Apparently, Dave saved them from being discarded. Dave is also an Avid birder and an active conservationist, so in between lab visits I had a chance to tag along to some of his birding sites. Truly an action packed trip! To see some additional photos, look at my Flickr page HERE.

Talk at the INI/ETH in Zürich

This past week I was invited to speak about my work at the Institute for Neuroinformatics in Zürich, and presented a talk entitled “Comparative connectomics: Synaptic connectivity in the nematodes Caenorhabditis elegans and Pristionchus pacificus.” It was exciting for me as it as a place where there are some pretty interesting neuroscience projects going on. I talked with people doing such things as neuromorphic computing (essentially using sensors or processors that recreate vision or other senses in a similar way that our neurons do…) , large scale synaptic connectivity reconstruction and correlated LM/EM. Some of the more interesting work relates to studying the neural circuitry involved in bird song. It was also great to spend some time with my host, Albert Cardona, who works on mapping synaptic connectivity in Drosophila and is responsible for some of the software that makes what I do possible. The talk was, as far as I could tell, well received and generated a significant amount of interest… though I think maybe some of the grad students found my American accent a little humorous. It was the first time that I presented the work in essentially the way that I hope it will end up in the first paper to come out of the project… looks like I better get writing!

Amphid commissure

We are continuing to experience great success in acquiring data for our Prisitonchus connectome project. Here’s an image showing how far into the worm we are with our current dataset. In it you can see the terminal bulb of the pharynx, and if you look very closely you can see the amphid commissures, which contain most of the nose sensory organs. The image is taken very close to the duct for the secretory/excretory system, which can also be seen very nicely in the image. It looks like we should be able to switch to worrying about the tremendous task of describing all of the synaptic connectivity in January. Metta and I have been working very hard to collect these data as fast as we can.. in fact I’m sitting at the electron microscope while typing this post! I’ve added a couple of images to my Pristionchus Flickr album HERE.

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.

Synapses at last.

Finally, after years of tedious work, we have our first very high quality thin section series through synapses in Pristionchus pacificus. This image is of the nerve ring in the pharynx, which controls many aspects of feeding behavior in the nematode and is like a mini-brain. It is very difficult to obtain such data and few groups have done it, so this is no small victory for me. We have a long way to go though, as the “real” brain of the animal is still hundreds of sections away, but if things continue to go well we could finish this in January or early February. The triangular white structure you see in the middle is the lumen of the pharynx, through which all of the food passes. In fact, there is rather conveniently a bacteria in the center in the process of being swallowed by the worm. Clusters of black spheres in the smaller cells are synaptic vesicles, and the black blotches on the cell membrane adjacent to the synaptic vesicles are pre-synaptic densities.. on the other side of each synaptic density is the cell each neuron is “talking” to. The two irregularly shaped holes near the pharynx lumen are gland cell ducts, that fuse with the lumen a few microns from this image and likely secrete digestive enzymes. Filamentous structures radiating out from the lumen are muscle cell filaments, used to open and close the lumen. Beautiful, isn’t it?