Muere C, Neumueller S, Miller J, Olesiak S, Hodges MR, Pan L, Forster HV. Atropine microdialysis within or near the pre-Bötzinger Complex increases breathing frequency more during wakefulness than during NREM sleep. J Appl Physiol 114: 694-704, 2013. First published December 27, 2012 doi:10.1152/japplphysiol.00634.2012.-Normal activity of neurons within the medullary ventral respiratory column (VRC) in or near the pre-Bötzinger Complex (preBötC) is dependent on the balance of inhibitory and excitatory neuromodulators acting at their respective receptors. The role of cholinergic neuromodulation during awake and sleep states is unknown. Accordingly, our objective herein was to test the hypotheses that attenuation of cholinergic modulation of VRC/ preBötC neurons in vivo with atropine would: 1) decrease breathing frequency more while awake than during non-rapid-eye-movement (NREM) sleep and 2) increase other excitatory neuromodulators. To test these hypotheses, we unilaterally dialyzed mock cerebrospinal fluid (mCSF) or 50 mM atropine in mCSF in or near the preBötC region of adult goats during the awake (n ϭ 9) and NREM sleep (n ϭ 7) states. Breathing was monitored, and effluent dialysate was collected for analysis of multiple neurochemicals. Compared with dialysis of mCSF alone, atropine increased (P Ͻ 0.05) breathing frequency while awake during the day [ϩ10 breaths (br)/min] and at night (ϩ9 br/min) and, to a lesser extent, during NREM sleep (ϩ5 br/min). Atropine increased (P Ͻ 0.05) effluent concentrations of serotonin (5-HT), substance P (SP), and glycine during the day and at night. When atropine was dialyzed in one preBötC and mCSF in the contralateral preBötC, 5-HT and SP increased only at the site of atropine dialysis. We conclude: 1) attenuation of a single neuromodulator results in local changes in other neuromodulators that affect ventilatory control, 2) effects of perturbations of cholinergic neuromodulation on breathing are state-dependent, and 3) interpretation of perturbations in vivo requires consideration of direct and indirect effects.neuromodulators; control of breathing; acetylcholine; non-rapid-eyemovement sleep THE NEUROMODULATOR ACETYLCHOLINE (ACh) is involved in a variety of central and peripheral neural circuits, including the control of breathing and sleep (7,12,16,19,25,39). The effects of ACh are mediated through either nicotinic or muscarinic receptors coupled to second messenger pathways (6, 10, 13, 42). There are five known muscarinic ACh receptor (mAChR) subtypes (M 1 to M 5 ) expressed in the brain stem, differing in expression profiles and in effects on breathing (2,9,11,13,33,34). For example, the pontine respiratory group (PRG) nuclei express M 1 -M 3 mAChRs (34). The predominant effect of cholinergic modulation of PRG neurons within the Kölliker-Fuse Nucleus (KFN) appears to be excitatory, since reverse dialysis of the nonselective mAChR antagonist atropine reduced minute ventilation (V I ) and breathing frequency in both the awake state and during non-rapid-eye-movement (NREM...