Category Archives: Nematode

New Pristionchus polyphenism paper out!

ErikblogLong time friend and fellow Sommer Lab postdoc just had a great paper come out in the most recent issue of Cell. Though I didn’t contribute anything intellectually to the paper, I was able at least to help them out with a couple images for Figure 1. I think the paper is a good demonstration of why one shouldn’t be afraid of working with non-standard model organisms.

Erik (along with Manuela Müller and Christian Rödelsperger, also in the lab) explores the mechanisms by which developmental plasticity Continue reading

Pristionchus on the cover of Evolution & Development

EvoDevoCover001One of the groups in our lab, headed up by postdoc Erik Ragsdale, is investigating the genetics and evolution of a feeding polyphenism in Pristionchus. They just had a nice paper come out in Evolution & Development entitled: “Feeding plasticity in the nematode Pristionchus pacificus is influenced by sex and social context and is linked to developmental speed.” Once it was accepted, they asked me to help design a cover submission. I used some still captures from some of my predatory feeding movies, and the cover was accepted! Score another point for my artistic career! Check out the paper, and expect more cool work from this group on the same polyphenism to be coming out later this year.

An artistic contribution to worm neuroanatomy.

sideview4Bumbargercover1In annotating all of the connectivity for my recent comparative connectomics papers, one of the byproducts was a massive 3D model of the anatomy of all the cells in the nervous system. For me, these models are fascinating to look at and  I enjoy when I get a chance to admire some of the beauty in the data I generate. I spent some time making some 3D rendering of the models using Blender (www.blender.org) in order to submit them as possible covers for the issue in which the paper was published… they weren’t chosen for the cover, but I still want to share them with the world!  Click the images to see them larger on my FLICKR page, and let me know what you think!

Data is online at Open Connectome

brainsectionWhen image stacks are acquired for generating connectivity datasets, there is so much information in the micrographs that does not make it into the first manuscript. As these datasets are extremely difficult to acquire, I think it is important that we try and make the data as openly available as possible. This, however, is not an easy task… it requires you to spend quite a bit of time developing a resource… time that could be spent generating more data or writing papers. As such, I am terribly thankful that the folks at openconnecto.me have developed a resource for making easy for people such as myself to host their image data in a useful way. Right now, one of the Continue reading

Journal Club: Connecting a Connectome to Behavior

0yks_X4B3uHScKQYMpmLDzl72eJkfbmt4t8yenImKBVaiQDB_Rd1H6kmuBWtceBJAn obvious goal of connectomics is to use it is a tool for better understanding complex network function. As new data are becoming available it is  not entirely clear what the best methods are for extracting useful information out of connectivity matrices. Part of the problem lies in the fact that while a wiring diagram is necessary for understanding nervous system function, it is hardly sufficient. The painful reality is that in complex systems like networks of neurons, small details of neuron and synapse function can dramatically alter system behavior. A recent Plos Computational Biology paper by Eduardo Izquierdo and Randall Beer at Indiana University makes what I think is a useful contribution to the problem by Continue reading

Pristionchus pacificus predatory feeding video

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.

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 (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.