From 4ad9fe50f0d1af0a99fc33f300334d476674d985 Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Tue, 27 May 2025 16:41:51 -0400 Subject: [PATCH 1/3] Standardized README to Markdown format --- README.md | 32 ++++++++++++++++++++++++++ readme.txt | 67 ------------------------------------------------------ 2 files changed, 32 insertions(+), 67 deletions(-) create mode 100644 README.md delete mode 100644 readme.txt diff --git a/README.md b/README.md new file mode 100644 index 0000000..36773f9 --- /dev/null +++ b/README.md @@ -0,0 +1,32 @@ +# Readme for the models associated with the paper: + +Melnick, Igor V., Sonia F. A. Santos, Karolina Szokol, Peter Szucs, and Boris V. Safronov. Ionic basis of tonic firing in spinal substantia gelatinosa neurons of rat. *J Neurophysiol* 91: 646-655, 2004. First published October 1, 2003; 10.1152/jn.00883.2003. + +## Abstract: +Ionic conductances underlying excitability in tonically firing neurons (TFNs) from substantia gelatinosa (SG) were studied by the patch-clamp method in rat spinal cord slices. Ca2+-dependent K+ (KCA) conductance sensitive to apamin was found to prolong the interspike intervals and stabilize firing evoked by a sustained membrane depolarization. Suppression of Ca2+ and KCA currents, however, did not abolish the basic pattern of tonic firing, indicating that it was generated by voltage-gated Na+ and K+ currents. Na+ and K+ channels were further analyzed in somatic nucleated patches. Na+ channels exhibited fast activation and inactivation kinetics and followed two-exponential time course of recovery from inactivation. The major K+ current was carried through tetraethylammonium (TEA)-sensitive rapidly activating delayed-rectifier (KDR) channels with a slow inactivation. The TEA-insensitive transient A-type K+ (KA) current was very small in patches and was strongly inactivated at resting potential. Block of KDR rather than KA conductance by 1 mM TEA lowered the frequency and stability of firing. Intracellular staining with biocytin revealed at least three morphological groups of TFNs. Finally, on the basis of present data, we created a model of TFN and showed that Na+ and KDR currents are sufficient to generate a basic pattern of tonic firing. It is concluded that the balanced contribution of all ionic conductances described here is important for generation and modulation of tonic firing in SG neurons. + +## How to run model: + +- Auto-launch from ModelDB (if NEURON is installed) + +or + +- Download and extract archive and compile the mod files with + `mknrndll` (mswin or MAC), `nrnivmodl` (unix/linux). Then start with + `nrngui mosinit.hoc` (linux) or by double clicking `mosinit.hoc` (mswin) + +------------------------------ + +Once the model has started press **Init&Run** to generate fig 7A (left). +Click on the **IClamp** button and adjust the current to **0.030 nA** and press **Init&Run** for the middle fig 7A, and then **0.12 nA** and press **Init&Run** for fig 7A (right). + +5/17/2017 Revised by N.T. Carnevale. As noted by the senior author in the readme.html file for ModelDB entry 62284 which is associated with the paper + +Melnick IV, Santos SF, Safronov BV (2004) +Mechanism of spike frequency adaptation in substantia gelatinosa neurones of rat. *J Physiol* 559:383-95 + +In the original implementation of this model assigning a value of 6.3 to the parameter "celsius" corresponded to an actual operating temperature of 23 deg C. In this new revision of the model, the value assigned to celsius is identical to the operating temperature, i.e. a value of 23 means 23 deg C. The motivation for the current revision is to facilitate future attributed reuse of this model and the mechanisms that it employs by promoting conceptual clarity and making sure that this code "plays nicely" with other models that involve temperature-dependent mechanisms. + +--- + +2025-05-27 – Standardized to Markdown. \ No newline at end of file diff --git a/readme.txt b/readme.txt deleted file mode 100644 index 385967e..0000000 --- a/readme.txt +++ /dev/null @@ -1,67 +0,0 @@ -Readme for the models associated with the paper: - -Melnick, Igor V., Sonia F. A. Santos, Karolina Szokol, Peter -Szucs, and Boris V. Safronov. Ionic basis of tonic firing in spinal -substantia gelatinosa neurons of rat. J Neurophysiol 91: 646-655, -2004.. First published October 1, 2003; First published October 1, -2003; 10.1152/jn.00883.2003. - -Abstract: -Ionic conductances underlying excitability in tonically firing neurons -(TFNs) from substantia gelatinosa (SG) were studied by the patch-clamp -method in rat spinal cord slices. Ca2+-dependent K+ (KCA) conductance -sensitive to apamin was found to prolong the interspike intervals and -stabilize firing evoked by a sustained membrane -depolarization. Suppression of Ca2+ and KCA currents, however, did not -abolish the basic pattern of tonic firing, indicating that it was -generated by voltage-gated Na+ and K+ currents. Na+ and K+ channels -were further analyzed in somatic nucleated patches. Na+ channels -exhibited fast activation and inactivation kinetics and followed -two-exponential time course of recovery from inactivation. The major -K+ current was carried through tetraethylammonium (TEA)-sensitive -rapidly activating delayed-rectifier (KDR) channels with a slow -inactivation. The TEA-insensitive transient A-type K+ (KA) current was -very small in patches and was strongly inactivated at resting -potential. Block of KDR rather than KA conductance by 1 mM TEA lowered -the frequency and stability of firing. Intracellular staining with -biocytin revealed at least three morphological groups of -TFNs. Finally, on the basis of present data, we created a model of TFN -and showed that Na+ and KDR currents are sufficient to generate a -basic pattern of tonic firing. It is concluded that the balanced -contribution of all ionic conductances described here is important for -generation and modulation of tonic firing in SG neurons. - -How to run model: - -Auto-launch from ModelDB (if NEURON is installed) - -or - -download and extract archive and compile the mod files with -mknrndll (mswin or MAC), nrnivmodl (unix/linux). Then start -with nrngui mosinit.hoc (linux) or by double clicking mosinit.hoc -(mswin) - ------------------------------- -Once the model has started press Init&Run to generate fig 7A (left). -Click on the IClamp button and adjust the current to 0.030 nA -and press Init&Run for the middle fig 7A, and then 0.12 nA and press -Init&Run for fig 7A (right). - -5/17/2017 Revised by N.T. Carnevale. As noted by the senior author -in the readme.html file for ModelDB entry 62284 which is associated -with the paper - -Melnick IV, Santos SF, Safronov BV (2004) -Mechanism of spike frequency adaptation in substantia gelatinosa -neurones of rat. J Physiol 559:383-95 - -in the original implementation of this model assigning a value of 6.3 -to the parameter "celsius" corresponded to an actual operating temperature -of 23 deg C. In this new revision of the model, the value assigned to -celsius is identical to the operating temperature, i.e. a value of 23 -means 23 deg C. The motivation for the current revision is to facilitate -future attributed reuse of this model and the mechanisms that it employs -by promoting conceptual clarity and making sure that this code "plays nicely" -with other models that involve temperature-dependent mechanisms. - From ff6e40c3a77cd1b84fc32c175ad999aedfd3fcc6 Mon Sep 17 00:00:00 2001 From: rsakai Date: Thu, 29 May 2025 14:44:03 -0400 Subject: [PATCH 2/3] Update README.md --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 36773f9..96216f5 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,7 @@ or Once the model has started press **Init&Run** to generate fig 7A (left). Click on the **IClamp** button and adjust the current to **0.030 nA** and press **Init&Run** for the middle fig 7A, and then **0.12 nA** and press **Init&Run** for fig 7A (right). +--- 5/17/2017 Revised by N.T. Carnevale. As noted by the senior author in the readme.html file for ModelDB entry 62284 which is associated with the paper Melnick IV, Santos SF, Safronov BV (2004) @@ -27,6 +28,4 @@ Mechanism of spike frequency adaptation in substantia gelatinosa neurones of rat In the original implementation of this model assigning a value of 6.3 to the parameter "celsius" corresponded to an actual operating temperature of 23 deg C. In this new revision of the model, the value assigned to celsius is identical to the operating temperature, i.e. a value of 23 means 23 deg C. The motivation for the current revision is to facilitate future attributed reuse of this model and the mechanisms that it employs by promoting conceptual clarity and making sure that this code "plays nicely" with other models that involve temperature-dependent mechanisms. ---- - -2025-05-27 – Standardized to Markdown. \ No newline at end of file +2025-05-27 – Standardized to Markdown. From 88ed7ffcbde7c18f179e9fdc9323edbc5bbd25ff Mon Sep 17 00:00:00 2001 From: rsakai Date: Thu, 29 May 2025 14:45:03 -0400 Subject: [PATCH 3/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 96216f5..2979403 100644 --- a/README.md +++ b/README.md @@ -28,4 +28,4 @@ Mechanism of spike frequency adaptation in substantia gelatinosa neurones of rat In the original implementation of this model assigning a value of 6.3 to the parameter "celsius" corresponded to an actual operating temperature of 23 deg C. In this new revision of the model, the value assigned to celsius is identical to the operating temperature, i.e. a value of 23 means 23 deg C. The motivation for the current revision is to facilitate future attributed reuse of this model and the mechanisms that it employs by promoting conceptual clarity and making sure that this code "plays nicely" with other models that involve temperature-dependent mechanisms. -2025-05-27 – Standardized to Markdown. +5/27/2025 Standardized to Markdown.