Corcoran AE, Richerson GB, Harris MB. Functional link between the hypocretin and serotonin systems in the neural control of breathing and central chemosensitivity. J Neurophysiol 114: 381-389, 2015. First published April 15, 2015 doi:10.1152/jn.00870.2013.-Serotonin (5-HT)-synthesizing neurons of the medullary raphe are putative central chemoreceptors, proposed to be one of potentially multiple brain stem chemosensitive cell types and loci interacting to produce the respiratory chemoreflex. Hypocretin-synthesizing neurons of the lateral hypothalamus are important contributors to arousal state, thermoregulation, and feeding behavior and are also reportedly involved in the hypercapnic ventilatory response. Recently, a functional interaction was found between the hypocretin system and 5-HT neurons of the dorsal raphe. The validity and potential significance of hypocretin modulation of medullary raphe 5-HT neurons, however, is unknown. As such, the purpose of this study was to explore functional interactions between the hypocretin system and 5-HT system of the medullary raphe on baseline respiratory output and central chemosensitivity.To explore such interactions, we used the neonatal in vitro medullary slice preparation derived from wild-type (WT) mice (normal 5-HT function) and a knockout strain lacking all central 5-HT neurons (Lmx1b f/f/p mice). We examined effects of acidosis, hypocretin-1, a hypocretin receptor antagonist (SB-408124), and the effect of the antagonist on the response to acidosis. We confirmed the critical role of 5-HT neurons in central chemosensitivity given that the increased hypoglossal burst frequency with acidosis, characteristic of WT mice, was absent in preparations derived from Lmx1b f/f/p mice. We also found that hypocretin facilitated baseline neural ventilatory output in part through 5-HT neurons. Although the impact of hypocretin on 5-HT neuronal sensitivity to acidosis is still unclear, hypocretins did appear to mediate the burst duration response to acidosis via serotonergic mechanisms.hypocretin; serotonin; ventilation; chemosensitivity THE BRAIN'S RESPONSIVENESS to pH/CO 2 (central chemosensitivity) has been proposed to be a distributed network function involving multiple chemoreceptive sites in the brain stem (Nattie and Li 2009). Growing evidence identifies a distinct subset of 5-HT neurons of the medullary raphe as critical for chemosensitivity (Brust et al. 2014;Corcoran et al. 2009Corcoran et al. , 2013Richerson 2004). Much effort has been directed at understanding how multiple chemoreceptive cells and loci interact and modulate each other and/or the respiratory rhythm itself (Dias et al. 2008(Dias et al. , 2009Iceman et al. 2014;Li et al. 2006;Mulkey et al. 2007).Recently, neurons containing hypocretin neuropeptides (hypocretin-1/orexin A and hypocretin-2/orexin B) were proposed to influence CO 2 sensitivity (Dias et al. 2009;Nakamura et al. 2007). The hypocretin system is anatomically linked with central chemosensory and respiratory nuclei (Fung et al. 2001;Hagan et al. ...