NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data

Rothman, Jason S.; Silver, R. Angus

doi:10.3389/fninf.2018.00014

Cited by 221 publications

(175 citation statements)

References 63 publications

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“…Stimulus protocols and digitization were under software control (Molecular Devices, pClamp v10, RRID:SCR_011323). Data were imported using IGOR-compatible routines (Rothman & Silver, 2018) (NeuroMatic v3 0c RRID:SCR_004186). Off-line signal processing, analysis and figure creation used technical graphing and data analysis software (IGOR Pro, v8, RRID:SCR_000325).…”

Section: Statistics and Curve Fittingmentioning

confidence: 99%

Synaptic cleft microenvironment influences potassium permeation and synaptic transmission in hair cells surrounded by calyx afferents in the turtle

Contini

Holstein

Art

2019

The Journal of Physiology

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Key points In central regions of vestibular semicircular canal epithelia, the [K+] in the synaptic cleft ([K+]c) contributes to setting the hair cell and afferent membrane potentials; the potassium efflux from type I hair cells results from the interdependent gating of three conductances. Elevation of [K+]c occurs through a calcium‐activated potassium conductance, GBK, and a low‐voltage‐activating delayed rectifier, GK(LV), that activates upon elevation of [K+]c. Calcium influx that enables quantal transmission also activates IBK, an effect that can be blocked internally by BAPTA, and externally by a CaV1.3 antagonist or iberiotoxin. Elevation of [K+]c or chelation of [Ca2+]c linearizes the GK(LV) steady‐state I–V curve, suggesting that the outward rectification observed for GK(LV) may result largely from a potassium‐sensitive relief of Ca2+ inactivation of the channel pore selectivity filter. Potassium sensitivity of hair cell and afferent conductances allows three modes of transmission: quantal, ion accumulation and resistive coupling to be multiplexed across the synapse. Abstract In the vertebrate nervous system, ions accumulate in diffusion‐limited synaptic clefts during ongoing activity. Such accumulation can be demonstrated at large appositions such as the hair cell–calyx afferent synapses present in central regions of the turtle vestibular semicircular canal epithelia. Type I hair cells influence discharge rates in their calyx afferents by modulating the potassium concentration in the synaptic cleft, [K+]c, which regulates potassium‐sensitive conductances in both hair cell and afferent. Dual recordings from synaptic pairs have demonstrated that, despite a decreased driving force due to potassium accumulation, hair cell depolarization elicits sustained outward currents in the hair cell, and a maintained inward current in the afferent. We used kinetic and pharmacological dissection of the hair cell conductances to understand the interdependence of channel gating and permeation in the context of such restricted extracellular spaces. Hair cell depolarization leads to calcium influx and activation of a large calcium‐activated potassium conductance, GBK, that can be blocked by agents that disrupt calcium influx or buffer the elevation of [Ca2+]i, as well as by the specific KCa1.1 blocker iberiotoxin. Efflux of K+ through GBK can rapidly elevate [K+]c, which speeds the activation and slows the inactivation and deactivation of a second potassium conductance, GK(LV). Elevation of [K+]c or chelation of [Ca2+]c linearizes the GK(LV) steady‐state I–V curve, consistent with a K+‐dependent relief of Ca2+ inactivation of GK(LV). As a result, this potassium‐sensitive hair cell conductance pairs with the potassium‐sensitive hyperpolarization‐activated cyclic nucleotide‐gated channel (HCN) conductance in the afferent and creates resistive coupling at the synaptic cleft.

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Section: Statistics and Curve Fittingmentioning

confidence: 99%

Synaptic cleft microenvironment influences potassium permeation and synaptic transmission in hair cells surrounded by calyx afferents in the turtle

Contini

Holstein

Art

2019

The Journal of Physiology

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“…The maximal light intensity used in experiments was estimated to be 1.24 mW/mm 2 at the focal plane. The electrophysiological recordings were analyzed in IgorPro using NeuroMatic plug-in (Rothman and Silver, 2018). were usually performed in small "cohorts" of n = 3 and n = 3 mice for "control group" and "Arch group".…”

Section: Methodsmentioning

confidence: 99%

Dopamine in the basal amygdala signals salient somatosensory events during fear learning

Tang

Kochubey

Kintscher

et al. 2019

Preprint

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2 SummaryThe amygdala is a brain area critical for the formation of threat memories. However, the nature of the teaching signal(s) that drive plasticity in the amygdala are still under debate. Here, we use optogenetic methods to investigate whether dopamine release in the amygdala contributes to fear learning. Antero-and retrograde labeling showed that a sparse, and relatively evenly distributed population of ventral tegmental area (VTA) neurons projects to the basal amygdala (BA). In-vivo optrode recordings in behaving mice showed that many VTA neurons, amongst them putative dopamine neurons, are excited by footshocks. Correspondingly, in-vivo fiber photometry of dopamine in the BA revealed robust dopamine concentration transients upon footshock presentation. Finally, silencing VTA dopamine neurons, or their axon terminals in the BA during the footshock, reduced the extent of threat memory retrieval one day later. Thus, VTA dopamine neurons projecting to the BA code for the saliency of the footshock event, and the resulting dopamine release in the BA facilitates threat memory formation.

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“…The housekeeping gene Actb (coding for β-actin) was measured 234 for all ages and LG conditions tested using primers described in Table 1. 235 236 Data Analysis 237 ABR recordings were saved as text files and analyzed using NeuroMatic in Igor Pro software 238 (WaveMetrics; Rothman and Silver, 2018). ABR thresholds were determined using an amplitude 239 criterion to detect responses that were larger than four times the standard deviation (SD) of the (1) 249 250 Where Y 0 is the minimum observed Y (i.e., the percent pups with ABR, EO, or air volume), 251…”

Section: Auditory Brainstem Response (Abr) Tracking 184mentioning

confidence: 99%

Robust range of auditory periphery development, eye opening, and brain gene expression in Wistar rat pups that experience variation in maternal backgrounds

Rodríguez-Contreras

Cardoso

Liu

et al. 2020

Preprint

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The experience of variation in maternal licking and grooming (LG) is considered a critical influence in neurodevelopment related to stress and cognition, but little is known about its relationship to early sensory development. In this study, we used a maternal selection approach to test the hypothesis that differences in LG during the first week of life influence the timing of hearing onset in Wistar rat pups. We performed a range of tests, including auditory brainstem responses (ABR), tracking of eye opening (EO), micro-CT X-ray tomography, and qRT-PCR to monitor neurodevelopmental changes in the female and male progeny of low-LG and high-LG dams. Our results show that variation in maternal LG is not overtly associated with different timing of ABR onset and EO in the progeny. However, the data provide insight on the delay between hearing onset and EO, on key functional and structural properties that define hearing onset at the auditory periphery, and on changes in brain gene expression that include the first evidence that: a) the hypoxia-sensitive pathway is regulated in subcortical and cortical auditory brain regions before hearing onset, and b) implicates maternal LG in regulation of Bdnf signaling in auditory cortex after hearing onset. Altogether, these findings provide a baseline to evaluate how factors that severely disrupt the early maternal environment may affect the expression of robust developmental sensory programs.SIGNIFICANCE STATEMENTEarly life experience during sensitive developmental periods can induce long-term effects on the neurobiological development of the offspring. In the present work we tested the hypothesis that variation in maternal licking and grooming (LG) affects the timing of hearing onset in Wistar rat pups. To our surprise the results did not support the hypothesis. Instead, we found a robust range of early and late auditory development that was independent of maternal LG. Nevertheless, the study provides new findings on the delay between hearing onset and eye opening, on key functional and structural properties that define hearing onset at the auditory periphery, and the first evidence that a) the hypoxia-sensitive pathway is regulated in the central auditory system during the sensitive period before hearing onset, and b) maternal LG is implicated in regulation of Bdnf signaling during the sensitive period after hearing onset. These findings provide a baseline to evaluate how factors that severely disrupt the early maternal environment may affect the expression of robust developmental sensory programs.

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NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data

Cited by 221 publications

References 63 publications

Synaptic cleft microenvironment influences potassium permeation and synaptic transmission in hair cells surrounded by calyx afferents in the turtle

Synaptic cleft microenvironment influences potassium permeation and synaptic transmission in hair cells surrounded by calyx afferents in the turtle

Dopamine in the basal amygdala signals salient somatosensory events during fear learning

Robust range of auditory periphery development, eye opening, and brain gene expression in Wistar rat pups that experience variation in maternal backgrounds

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