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50 protocols using axoscope software

1

Electrophysiological Monitoring of Fish Behavior

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After the pairing phase was completed, fish were temporarily separated, and behavioral testing was performed on a single fish following the protocol described elsewhere (Issa et al., 2011 (link)). Each fish was placed in a testing chamber (dimensions: 11 × 4 × 3 cm). A pair of conductive electrodes placed on either side of the chamber recorded the electric field potentials. Bare electrodes were 1 mm in thickness with 3–5 mm metal exposure. Electrodes were connected to an AC differential amplifier (AM-Systems model 1700, Carlsborg, WA, United States), and signals were amplified 1,000-fold. Electrical signals were low-pass filtered at 300 Hz and high-pass filtered at 1 KHz. Electrical field potentials are generated by muscle contractions when the fish moves (Issa et al., 2011 (link)). These signals were digitized using a Digidata-1322A digitizer then stored using Axoscope software (Molecular Devices, Inc., Sunnyvale, CA, United States). The experimental animals were acclimatized for 30 min before behavioral testing was initiated. Swimming behavior was recorded immediately following acclimation. Immediately after, startle escape responses were recorded.
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2

Extracellular Recordings of Electric Fish

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The surgical techniques used were identical to those previously described in the studies by Marsat et al. (2009) (link) and Marsat and Maler (2010) (link). Cells of the lateral segment (LS) of the ELL were targeted. A. albifrons brain anatomy is very similar to that of A. leptorhynchus, so major landmark blood vessels described in the study by Maler et al. (1991) (link) and electrode depth served as an adequate guide to locate LS pyramidal cells (see Histology). In vivo recordings were made via metal-filled extracellular electrodes (Frank and Becker, 1964 ) and amplified with a Model 1700 Amplifier (A-M Systems). Data were recorded (Axon Digidata 1500 data acquisition system and AxoScope software, Molecular Devices) at a 20 kHz sampling rate. ON and OFF cells were identified using known response properties, particularly responses to sinusoidal stimulation and spike-triggered average waveforms calculated from responses to 0–60 Hz noise (Saunders and Bastian, 1984 (link)).
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3

Extracellular Nerve Activity Recording

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We used custom-made suction electrodes to record extracellularly the activity of the 5A nerves, unless stated otherwise. To record the pro-mesothoracic connective, we used a hook electrode. Recordings started 5 min before and lasted for at least 40 min after pilocarpine bath-application. Data were acquired and stored on the computer for off-line analysis using two four-channel differential amplifiers (Model 1700, A-M Systems, USA) and Axon Digidata 1440A A-D board with Axo-Scope software (Molecular Devices, Sunnyvale, CA, USA).
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4

Respiratory Airflow Analysis During Hypercapnia

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Respiratory airflow was recorded using the plethysmograph chamber (Data Science International, St. Paul, MN) attached to flow transducers connected to an A/D board that transmitted signals to the computer. Volume calibrations for these chambers were performed by repeated known volume air injections. Flow transducer readings were digitized at 1 kHz and recorded using Axoscope software (Molecular Devices, Foster City, CA, USA). The flow signals were analyzed offline for respiratory rate, tidal volume, and ventilation using software to automatically detect the peaks and troughs of each breath (Matlab, Mathworks Inc., Natick, MA). Trials for a particular condition (with and without Laser-ON) were ensemble averaged. We then compared the respiratory variables for three breaths before hypercapnia to that during hypercapnia just prior to waking in response to CO2 (shown in Fig. S4; respiratory data shown relates to Fig. 2 in the main text).
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5

Electrophysiological Assessment of Fictive Locomotion

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For whole spinal cord preparations in which locomotor-related activity was induced pharmacologically, glass suction electrodes were attached to the upper lumbar segment roots (L1–3) on both the left and right side of the isolated spinal cords to assess left-right alternation and flexor-related activity. Fictive locomotion was induced with 5-HT (10 μM), NMDA (5 μM) and DA (50 μM). Preparations displaying stable fictive locomotion for ~20 min during control periods were used for full experiments with the addition of additional drugs. Data were amplified and filtered (band-pass filter 10–5,000 Hz, A-M Systems Model 1700) and acquired at a sampling frequency of 6 kHz with a Digidata 1440A analog-digital converter and Axoscope software (Molecular Devices, Sunnyvale, CA, USA). For hemisected spinal cord experiments with simultaneous Ca2+ imaging, only one root was attached (L1–L3). Data were amplified and filtered (30–3,000 Hz; Qjin Design) and then acquired at a sampling frequency of 6 kHz using a Digidata 1440A A/D board and Axoscope software.
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Isometric Force Measurement of Airway Smooth Muscle

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LMS contractility data were acquired with an HSE-HA isometric force transducer F30 (Harvard Apparatus, United States). 72 h after culture, each LMS was removed from their chamber and stretcher, and placed in a Petri dish filled with culture media preheated to 37 C. One of the holders on the side of the slice was attached to a hook and the other one to the spring hook of the force transducer. The slices were gradually stretched until maximum amplitude of contractility was obtained and subjected to a constant field stimulation of 30–40 V voltage, 1.0 Hz frequency and 30–40 m width. Data were recorded and analysed using AxoScope software (Molecular Devices LLC, United States).
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7

Measuring Myocardial Slice Contractility

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Slice contractility was assessed using a force transducer (Harvard Apparatus, USA). To assess the contractility of fresh slices (0 h) and those cultured without electromechanical stimulation (unloaded), the areas with the most highly aligned myofibrils were selected and custom-made rings were attached as described above. Slices cultured with electromechanical stimulation (SL = 1.8, 2.0, 2.2 and 2.4 μm) were carefully removed from the culture chamber and then removed from stretchers. The slices were then attached to the force transducer using the attached rings. Rat myocardial slices were field stimulated at 1 Hz, 10 ms and 10–30 V and human HF and donor slices were field stimulated at 0.5 Hz, 10 ms and 10–30 V. The slices were continuously superfused in 37 °C oxygenated Tyrode’s solution. The slices were progressively stretched in a stepwise manner, until maximum isometric contraction was obtained. Data were recorded using AxoScope software and peak amplitude analyses were conducted using Clampfit software (both Molecular Devices, USA). A video of the contraction of human HF and rat myocardial slices can be found here: https://images.nature.com/original/nature-assets/nprot/journal/v12/n12/extref/nprot.2017.139-sv8.mp4
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8

Correlating rILN Photometry and Reward

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To directly correlate rILN→DS photometric activity to reward consumption, mice were placed under a reverse 12 hour light cycle (lights off at 0900) for 2 weeks before rILN photometry recordings were collected while given access to 2 and 8% (wt/vol) sucrose water connected to a custom lickometer (Patton et al., 2021 (link)). Licks were recorded using Axoscope software (Molecular Devices), and rILN→DS photometry signal was aligned via custom MATLAB code to the start of lick bouts. Bouts were defined as two or more licks with an inter-lick interval of less than 2 s.
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9

Extracellular Recordings of Cardiac Cells

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Extracellular recordings were performed with an MEA data-acquisition system (Multi Channel Systems, Reutlingen, Germany). The MEA plates contained a matrix of 60 titanium nitride electrodes (30 μm in diameter) with an inter-electrode distance of 200 μm. The signal recorded with one of the extracellular electrodes reflects local changes of the membrane potential. The MEA plates were sterilized and coated with polyornithine/laminin/fibronectin. Standard measurements were acquired at 5 kHz (at 37°C). Recordings were performed 48 hr after plating, for 100 s at baseline, and at 5 min after 100 nM isoprenaline. The parameters including filed potential duration (ms), peak amplitude (μV) inter-spike interval duration (ms), and beating rate (beats/min) were analyzed using AxoScope software (Molecular Devices) and CardioMDA.
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10

Intracellular Voltage Recording in Mouse Cerebral Endothelium

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Recording of Vm in mouse cerebral endothelium has been previously described and illustrated [5, 7, 21, 22 (link)]. Briefly, Vm of isolated endothelial tubes was recorded with Axoclamp electrometers (2B and/or 900A; Molecular Devices, Sunnyvale, CA) using microelectrodes pulled (P-97, Sutter Instruments) from glass capillary tubes (GC100F-10, Warner Instruments, Holliston, MA, USA). Under continuous superfusion with PSS, an endothelial cell was penetrated with a microelectrode backfilled with 2 mol/L KCl (tip resistance: ∼150 MΩ) while viewing the endothelial tube at 400×magnification. Amplifier outputs were connected to a data acquisition system (Digidata 1550A; Molecular Devices), whereby all data were acquired at a 10 Hz frequency on a Hewlett-Packard personal computer using Axoscope software (Molecular Devices). Each experiment included a continuous intracellular Vm recording for ∼2 h.
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