On Wednesday I was at the IMP in vienna to deliver a talk about my recent paper.Manuel Zimmer, my host, put together a great schedule of people to meet with and I had a great time delivering the talk .. the audience was highly engaged and asked a lot of very good questions. I spent the rest of the day having some great discussions with members of top-notch labs Continue reading
Much to my amusement, I found out that the local newspaper, the Schwäbisches Tagblatt, picked up on our press release and published a nice little story. The title “Räubuerischer Schlund” translates to “Predatory Mouth”, referring to the toothy mouth Pristionchus pacificus uses to puncture its prey. Pretty cool! The image on this post is the same one used in the press release, and shows P. pacificus chomping down on C. elegans. Click HERE for a link to the article. It’s in German, so if you need to you can have a look at it in google translate.
Finally, after years of blood sweat and tears our comparative connectomics paper has been published. This represents a huge victory for myself and all of the people who have helped me along the way. It is rather humbling to have this work get the kind of exposure it gets by being published in Cell. It is the culmination of years of work, complete with with heart-breaking failures, long grinding hours on the microscope and in front of the computer, and the occasional adrenaline-inducing discovery. In the paper, we compare a wiring diagram(or connectome) of the pharyngeal nervous system of the nematode Pristionchus pacificus to that of the well-known model organism C. elegans. The data are obtained by Continue reading
Posted in Connectome, Electron Microscopy, Pristionchus pacificus, Science, Sommer Lab
Tagged Behavior, C. elegans, Caenorhabditis, Connectome, connectomics, graph theory, Nematode, Neural Circuit, P. pacificus, Pristionchus
One of the things that interests me about the nematode Pristionchus pacificus is that it is capable of taking advantage of many different food sources. Like it’s cousin and well known model organism Caenorhabditis elegans, this nematode can be raised on agar plates seeded with bacteria. Pristionchus can additionally feed on other sources, including other nematodes! These predatory feeding behaviors are quite distinct from bacterial feeding. For instance, Pristionchus has tooth-like denticles in its mouth opening that are highly active during predatory but not bacterial feeding. This increase in the complexity of the P. pacificus
behavioral palette is most interesting when you consider that the nervous systems are composed of a nearly identical set of neurons. So how do you teach an old nervous system to do new tricks? This is one of my primary motivations for comparing networks of synaptic connectivity between these two species.
Posted in Caenorhabditis elegans, Connectome, Nematode, Pristionchus pacificus, Science, Sommer Lab
Tagged Behavior, Caenorhabditis elegans, Connectome, Nematode, Pristionchus pacificus, Video
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
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.