Date of Award

Fall 2017

Project Type


Program or Major


Degree Name

Doctor of Philosophy

First Advisor

William Hersman

Second Advisor

David Mattingly

Third Advisor

Kai Germaschewski


The pre-Bötzinger complex (pre-BötC) is an essential rhythmogenic brainstem nucleus located in the ventrolateral medulla. Rhythmic output from the pre-BötC is relayed through premotor and motor neurons to the diaphragm and intercostal muscles to drive the active inspiratory phase of breathing. The specific biophysical mechanisms responsible for generating rhythmic bursting and network synchronization are not well understood and remain a highly debated topic within the field. Through extensive experimental and theoretical work two plausible rhythmogenic mechanisms have emerged. One mechanism is based on a slowly inactivating persistent sodium current (INaP) and the other on a calcium activated non-selective cation current (ICAN) that is coupled to intracellular calcium transients. Despite this effort, the specific role of these two mechanisms in rhythm generation and the source(s) of intracellular calcium transients remains unclear.

This thesis addresses these challenges by first systematically investigating the role of INaP, ICAN and two general sources of intracellular calcium transients in a biophysically based model of pre-BötC neurons. The results show that simulated blockade of ICAN in a heterogeneous population of excitatory neurons produces a large reduction in network amplitude, when CaSyn is the primary source of intracellular calcium. Furthermore, activation of ICAN by CaSyn functions as a mechanism to amplify the inspiratory drive potential and recruit follower neurons. The results of these simulations are quantitatively consistent with experimental data. This study suggests that rhythm generation in the pre-BötC arises from a group of INaP dependent pacemaker neurons which form a rhythmogenic kernel. Output from these neurons triggers post-synaptic calcium transients, ICAN activation, and subsequent membrane depolarization, which drives bursting in follower neurons.

The second part of this thesis explores the use of optogenetics to probe mechanisms of rhythm generation within the pre-BötC. This was accomplished by incorporating the light activated hyperpolarizing and depolarizing channels, Archaerhodopsin-3 and Channelrhodopsin-2, respectively, into the model developed in the first part of the thesis. The results of these simulations are consistent with available experimental data and provide testable mechanism-specific predictions to guide future optogenetic experiments.