Python meets systems neuroscience: affordable, scalable and open-source electrophysiology in awake, behaving rodents

Mukherjee, Narendra; Wachutka, Joseph; Katz, Donald B.

doi:10.25080/shinma-7f4c6e7-00e

Cited by 16 publications

(19 citation statements)

References 7 publications

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“…Voltage signals from the micro-electrodes were sampled at 30 kHz, digitally amplified and filtered, and saved to the hard drive of an Ubuntu computer connected to an Intan recording system (RHD2000 Evaluation System and Amplifier Boards; Intan Technologies, LLC, LA). From these raw voltage signals, we retained all waveforms and sorted the resulting waveforms into distinct units on the basis of S:N (>3:1) and distinctiveness of wave shape, using customized python scripts (for details see Mukherjee et al, 2017). A total of 185 single units were isolated for the experiments across 10 sessions.…”

Section: Acquisition Of Electrophysiological Datamentioning

confidence: 99%

Single and population coding of taste in the gustatory-cortex of awake mice

Levitan

Lin

Wachutka

et al. 2019

Preprint

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A great deal is known about the broad coding and neural ensemble dynamics characterizing forebrain taste processing in awake rats, and about the relationship between these firing rate dynamics and behavior. With regard to mice, in contrast, data concerning cortical taste coding are few, inconclusive, and largely restricted to imaging, which lacks the temporal sensitivity necessary for evaluation of fast response dynamics. Here we have recorded the spiking activity of ensembles of gustatory cortical (GC) single neurons while presenting representatives of the basic taste modalities (sweet, salty, sour and bitter) to awake mice. Our results reveal deep similarities between rat and mouse taste processing. Many recorded murine GC neurons (~66%) responded distinctly to different tastes, and entropy analysis (which measures the breadth of taste coding) further confirmed that the majority of taste neurons in fact responded to 3 or 4 tastes. Temporal coding analyses revealed that single mouse GC neurons sequentially coded taste identity and palatability-the latter responses emerging ~0.5s after the former-a dynamic that population analysis suggested reflects a reliable sequence of network states activated by taste delivery (i.e., ensembles of simultaneously-recorded neurons transitioned suddenly and coherently from coding taste identity to coding taste palatability). All of the above results held across the anterior-posterior and dorsal-ventral axes of GC-neither between-nor within-mouse mapping revealed regions of narrow or temporally simple taste responses. In conclusion, our data indicates that mouse GC, like rat GC, codes multiple aspects of taste in a coarse, time-varying manner.

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Section: Acquisition Of Electrophysiological Datamentioning

confidence: 99%

Single and population coding of taste in the gustatory-cortex of awake mice

Levitan

Lin

Wachutka

et al. 2019

Preprint

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“…Neuron signals were isolated in Offline Sorter (Plexon, Dallas, TX) or through a semisupervised spike sorting Python program (Pl2_sort) modified from Mukherjee et al (2017). The Pl2_sort program contained three scripts of which the user interacted with (Pl2_preprocessing.py, Pl2_postprocessing.py, and Convert_to_nex.py) and a handful of scripts that were called upon; PyPl2 scripts (containing Clustering.py, Pl2_waveforms_datashader.py, pypl2api.py, pypl2lib.py, PL2FileReader.dll, and PL2FileReader64.dll) and a Pl2_processing.py script.…”

Section: Electrophysiological Recording and Light Stimulationmentioning

confidence: 99%

“…The Pl2_preprocessing script was used to obtain sorting criteria from the user, select Pl2 files, obtain continuous data and event information from Pl2 files, and save the generated information as an HDF5 file. It then called on the Pl2_processing script using multicore processing and units were isolated from each channel as described in Mukherjee et al (2017) with slight modifications. The first five principal components were used to determine isolation instead of 3, threshold for significant waveforms was set at 2.5 standard deviations from average voltage value, sampling rate was performed at 40 kH, and 3-7 clusters were generated for the user to select from.…”

Section: Electrophysiological Recording and Light Stimulationmentioning

confidence: 99%

Enhancing GABAergic Tone in the Rostral Nucleus of the Solitary Tract Reconfigures Sensorimotor Neural Activity

Sammons

Bass

Victor

et al. 2020

Preprint

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Recent work has shown that most cells in the rostral, gustatory portion of the nucleus tractus solitarius (rNTS) in awake, freely licking rats show lick-related firing. However, the relationship between taste-related and lick-related activity in rNTS remains unclear. Here, we tested if GABA-derived inhibitory activity regulates the balance of lick-and taste-driven neuronal activity. Combinatorial viral tools were used to restrict expression of ChR2-EYFP to GAD1+ GABAergic neurons. Viral infusions were bilateral in rNTS. 2-4wks later, an optical fiber attached to 8-16 drivable microwires was implanted into the rNTS. After recovery, waterdeprived rats were presented with taste stimuli in an experimental chamber. Trials were 5 consecutive taste licks [NaCl, KCl, NH4Cl, sucrose, MSG/IMP, citric acid, quinine, or artificial saliva (AS)] separated by 5 AS licks on a VR5 schedule. Each taste lick triggered a 1s train of laser light (25Hz; 473nm; 8-10mW) in a random half of the trials. In all, 113 cells were recorded in the rNTS, 50 responded to one or more taste stimuli without GABA enhancement. Selective changes in response magnitude (spike count) within cells shifted across unit patterns but preserved inter-stimulus relationships. Cells where enhanced GABAergic tone increased lick coherence conveyed more information distinguishing basic taste qualities and different salts than other cells. In addition, GABA activation significantly amplified the amount of information that discriminated palatable vs. unpalatable tastants. By dynamically regulating lick coherence and remodeling the across-unit response patterns to taste, enhancing GABAergic tone in rNTS reconfigures the neural activity reflecting sensation and movement.

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“…For every taste delivery, the laser was turned on 850ms before a solenoid valve opened to release a taste onto the tongue and turned off 2500ms later (see Figure 5C; Mukherjee et al 2017).…”

Section: Tpe/wpe Sessionsmentioning

confidence: 99%

The role of the gustatory cortex in incidental experience-evoked enhancement of later taste learning

Flores

Parmet

Mukherjee

et al. 2018

Preprint

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The strength of learned associations between pairs of stimuli is affected by multiple factors, the most extensively studied of which is prior experience with the stimuli themselves. In contrast, little data is available regarding how experience with incidental stimuli (independent of any conditioning situation) impacts later learning. This lack of research is striking given the importance of incidental experience to survival. We have recently begun to fill this void using conditioned taste aversion (CTA), wherein an animal learns to avoid a taste that has been associated with malaise. We previously demonstrated that incidental exposure to salty and sour tastes (taste pre-exposure-TPE) enhances aversions learned later to sucrose.Here, we investigate the neurobiology underlying this phenomenon. First, we use immediate early gene (c-Fos) expression to identify gustatory cortex (GC) as a site at which TPE specifically increases the neural activation caused by taste-malaise pairing (i.e., TPE did not change c-Fos induced by either stimulus in isolation). Next, we use site-specific infection with the optical silencer Archaerhodopsin-T to show that GC inactivation during TPE inhibits the expected enhancements of both learning and CTA-related c-Fos expression, a full day later. Thus, we conclude that GC is almost certainly a vital part of the circuit that integrates incidental experience into later associative learning.

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Python meets systems neuroscience: affordable, scalable and open-source electrophysiology in awake, behaving rodents

Cited by 16 publications

References 7 publications

Single and population coding of taste in the gustatory-cortex of awake mice

Single and population coding of taste in the gustatory-cortex of awake mice

Enhancing GABAergic Tone in the Rostral Nucleus of the Solitary Tract Reconfigures Sensorimotor Neural Activity

The role of the gustatory cortex in incidental experience-evoked enhancement of later taste learning

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