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Cory Root


Sensory systems detect features of the external world, which are represented in the activity of ensembles of neurons in the brain. My lab seeks to understand how sensory information is represented in the brain and how internal representations acquire meaning that can be used to inform behavior. Animals have evolved neural circuits that drive innate behavioral responses to environmental cues that have been essential to the survival of a species over long periods of evolutionary time. However, most stimuli do not have innate significance. Rather, meaning is acquired over the lifetime of an animal through learning. We exploit the sense of smell to investigate how sensory representations afford meaning for innate and experience-dependent behavior. We use endoscopic 2-photon calcium imaging to monitor neuronal activity, and molecular genetics, viral tracing and optogenetics to trace and manipulate the neural circuits of the mouse brain.

The Olfactory System

Olfactory perception is initiated upon the recognition of odorants by a large repertoire of receptors in the sensory epithelium. Neurons expressing a given receptor are randomly distributed within zones of the epithelium but project with precision to two spatially invariant glomeruli in the olfactory bulb. This invariant glomerular map in the bulb is transformed in the representations in higher olfactory centers. For instance, the piriform cortex receives distributed input from seemingly random sets of glomeruli in the olfactory bulb, and is implicated in learned associations. In contrast, the cortical amygdala receives topographically organized input from the olfactory bulb, and in recent work I have demonstrated that the neurons in this pathway mediate innate behaviors.

The Cortical Amygdala Mediates Innate Behavior

The higher order circuits mediating innate behaviors have not been well defined, however, anatomic tracing experiments implicated the cortical amygdala in determined behaviors. With Richard Axel at Columbia University, I devised experiments to directly determine if the cortical amygdala is involved in innate odor-driven behavior. We found that the stereotyped circuits from the olfactory bulb to the cortical amygdala are required for innate aversive and appetitive responses to odor. Moreover, we identified and manipulated the activity of these neurons by exploiting the promoter of the activity-dependent gene, arc, to express channelrhodopsin in neurons of the cortical amygdala activated by odors that elicit innate behaviors. Optical activation of these neurons leads to appropriate behaviors that recapitulate the responses to odors. Together these data demonstrate that the cortical amygdala contains distinct neurons that are necessary and sufficient for the generation of innate, odor-driven behaviors (Root et al., Nature 2014). Moreover, we have revealed that neurons mediating aversive and appetitive behaviors have distinct projections to downstream targets. The identification of neural circuits that elicit innate behaviors provides a foundation for dissecting sites of plasticity to afford behavioral flexibility.

Select Publications

  • Lee D, Liu L, Luo N., Root CM. (2023) Transformation of valence signaling in a striatopallidal circuit. eLife 90976.1
  • Stern DB, Root CM. (2023) Anatomical connectivity of the intercalated cells of the amygdala. eNeuro 10:0238
  • Root CM, Denny CA, Hen R, Axel R. (2014) The participation of cortical amygdala in innate, odor-driven behavior. Nature 515:269-273.


Dr. Root received his B.A. in Biology and Chemistry from Whitman College and his Ph.D. in Biology from UC San Diego. He did postdoctoral research with Dr. Richard Axel at Columbia University. Dr. Root joined the faculty in 2016 and has been the recipient of the Elkins Memorial Award for an outstanding doctoral thesis in the field of Drosophila Neurobiology and a K99/R00 Pathway to Independence Award from the NIDCD.

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