Caenorhabditis elegans Module


In this module, students use a variety of complementary experimental techniques to study sensory processing and behavior in the nematode Caenorhabditis elegans. This module continues the theme of using state-of-the art approaches to study and manipulate the function of neurons within the brains of intact, behaving animals. C. elegans is an excellent preparation for this task, with a complete neural wiring diagram, genetic access to each neuron, optogenetic tools for neural stimulation and activity recording by calcium imaging, detailed behavioral analysis, and an extensive library of genetic mutants. Information flow can be traced from sensory stimulus to neural signals to behavioral output, in living and behaving animals.

In the first few days of the modules, all students are trained in pairs to perform a series of complementary experiments in recording and analysis of nematode behavior, neural stimulation and imaging, and C. elegans culture. Behavioral assays are performed using machine vision cameras and MATLAB- or LabView-based quantification systems. Three distinct sensory modalities are typically used for behavioral and neural activity analyses: olfactory, mechanical, and thermal stimulation. Precise chemical stimulation is performed using microfluidic arenas and chambers. Mechanical stimulation is delivered through an Arduino controlled tapper, thermal stimuli are precisely regulated using peltier-based systems. Behavior and neural imaging systems are capable of optogenetic activation or silencing of specific neurons via multicolor LEDs. In the first few days, students are taught how to run many experiments to give them a sense for which types of experiments are best for different project questions. Students are tasked with replicating real, published experiments, to gain confidence with each system. Because these systems are well-established and their use is relatively simple, students can become facile at the core techniques within the first few days. Students continue to build their expertise with the use of MATLAB for designing stimuli, running experiments, and performing analysis. We also use the first few days of the module to familiarize students with the basics of C. elegans neurobiology and genetics, and provide mini ‘boot camps’ on genetic crosses, RNAi, molecular biology, and other relevant topics.

By the fourth day of the first week, the students are sufficiently competent to plan their own projects. The focus of these projects changes from year-to-year as the faculty endeavor to compile a list of ideas based on current research in the field as well as the interests of the students. One consistent theme over the last several years has been imaging neural activity in intact animals during sensory stimulation and behavior using genetically encoded calcium indicators. Students have worked on projects investigating sensory adaptation, synaptic plasticity, and the interplay between sensory and interneuron activity. For instance, one project in compared sensory adaptation between natural sensory stimuli and optogenetic manipulations. Another project investigated the functional importance of a plastic synaptic connection by bypassing this plasticity with a genetically encoded synthetic gap junction to artificially re-wire the C. elegans connectome. In 2018, one project assessed the role of interneurons in behavioral decision-making by tracking activity within interneurons of freely moving animals during directed migration on a thermal gradient. One of the major outcomes of this module is that students come to realize the power of molecular biology and genetics to address questions with precision and clarity. The well-established imaging and behavioral systems, in conjunction with the ability of faculty to bring a wide variety of new worm strains each year, provides a powerful foundation for students to explore discovery-driven projects based on current interest and state-of-the-art genetic tools.


2021 C. elegans Module Faculty and Teaching Assistants

Mark Alkema
University of Massachusetts Medical School

The goal of my research is to understand how the nervous system orchestrates complex behaviors and how evolutionary forces shape behavior. We are addressing this question by studying the escape response of the nematode C. elegans. We have shown that the escape response allows C. elegans increases it chances to escape from predacious fungi that use constricting rings to entrap nematodes. My lab is elucidating how neurons, neurotransmitters and ion channels define neural circuits control independent motor programs, and how these motor programs are linked temporally in the execution of a compound motor sequence. The simplicity and completely defined synaptic connectivity of C. elegans nervous system in combination with powerful genetic methods, optogenetics, calcium imaging and electrophysiology allows us to address how the nervous controls behavior with a cellular and molecular resolution that cannot be readily attained in any other system. Mark has been a faculty member since 2014.


Steve Flavell

Steve Flavell completed his undergraduate work at Oberlin College, majoring in Neuroscience. He then pursued graduate studies in Harvard University’s PhD program in Neuroscience. Working the lab of Michael Greenberg, Steve investigated the mechanisms by which neuronal activity alters gene expression to regulate synapse development and function. Steve then worked as a postdoctoral fellow in Cori Bargmann’s lab at Rockefeller University. Using a combination of behavioral recordings, genetics, in vivo calcium imaging, and optogenetics, Steve characterized a neural circuit capable of generating persistent locomotor states that last from minutes to hours. He joined the faculty of MIT in January 2016, as an assistant professor in Brain and Cognitive Sciences and the Picower Institute for Learning and Memory. His current research interests center on understanding on how neuromodulators organize large-scale patterns of neural activity to generate long-lasting behavioral states. Steve joined the C. elegans faculty in 2020.


jeremy_flormanJeremy Florman
UMass Medical

I did my graduate work in the lab of Dr. Mark Alkema at Umass Medical School where I studied peptidergic coordination of complex behavior in C. elegans. I completed my PhD in the fall of 2020 and have continued as postdoc in the Alkema lab. My current work focuses on neuromodulatory regulation of both physiological and behavioral responses to stress, with an emphasis on the role of monoamine/neuropeptide co-transmission in switching between different stress response states. I employ optical, chemical, and genetic approaches to manipulate neuronal function, in conjunction with calcium imaging, microfluidics and behavioral analysis, to address how an animal orchestrates a response to stress. Jeremy joined the C. elegans team in 2017.

nate_cNate Cermak


My interests are centered around developing better (cheaper, higher-throughput, more precise) tools for biology, especially neuroscience. I did my PhD with Scott Manalis and Martin Polz, developing new instruments for measuring single-cell biophysical properties like mass, growth, and deformability. After attending NS&B as a student in 2016, I did a postdoc with Steve Flavell studying C. elegans behavior, followed by a postdoc with Jackie Schiller studying cortical dendritic dynamics with multiphoton calcium imaging. I am currently a member of the technical staff at Neuralink, working to build a high-bandwidth, fully-implanted brain-machine interface.