Reconstructing 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!
It is not so often that some piece of software comes out that gets me as excited as what the folks at eyewire.org are doing. What they are attempting to do is to take one of the most difficult aspects of generating synapse-level “Connectomes” and speed it up by crowd sourcing the labor. By breaking the task into pieces that can be completed in short periods of time and adding some game-like elements, they hope they can dramatically speed up their reconstructions of the human retina connectome. But how useful is it really? Continue reading
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.
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 (www.wormatlas.org) 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.
I’ve been working with Christian Rödelsperger on some new methods for asking specific question about networks, and using the C. elegans nervous system data as a test case. I just wanted to share an early version of the kind of network graph that will be resulting from the analysis. Pretty cool! The center node is what the analysis focuses on, above it is all of the information flowing into it, and below it all of the information flowing out of it. The graph was made using Graphviz and then modified using Adobe Illustrator. For a larger version, look HERE.
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…
A review I did with Ralf on nematode models in Evolutionary and Developmental biology just came out in WIRES Developmental Biology. http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WDEV33.html
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!