Search found 45 matches

by davidhubbardmd
Tue Aug 22, 2023 11:03 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Jui-Yun Chang, PhD and her colleagues at Duke have studied calmodulin (CaM) and proposed a model in their 2019 paper: Chang, J. Y., Nakahata, Y., Hayano, Y., & Yasuda, R. (2019). Mechanisms of Ca2+/calmodulin-dependent kinase II activation in single dendritic spines. Nature communications, 10(1)...
by davidhubbardmd
Fri Aug 18, 2023 10:36 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

I have not added a GABA receptor on the spine-head or neck because I believe they are found only on the pre-synaptic side of the synaptic cleft. Ted may disagree; I cite his 2013 paper (Chiu, C. Q., Lur, G., Morse, T. M., Carnevale, N. T., Ellis-Davies, G. C., & Higley, M. J. (2013). Compartment...
by davidhubbardmd
Tue Aug 15, 2023 10:57 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

We have the best modeling minds at Yale, U Montreal and USC but no calcium influx into sensory spine-necks. I suspect that in addition to AMPA, NMDA, and VGCC model processes, there may also need to be a 5HT-2A receptor process that indirectly increases calcium influx near but not in the postsynapti...
by davidhubbardmd
Mon Aug 07, 2023 10:11 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Jean-marie Bouteiller at USC has also agreed to help me figure out why I can't get a decent calcium flow into sensory spine-necks.
by davidhubbardmd
Mon Jun 19, 2023 10:15 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Thank you Professor. That 1981 reference was an “hallucination” by BARD AI. No such reference exists, although I believe the 100 ms spine-neck duration is correct. I have written to the Montreal lab again asking if they could look at the following list of NEURON hoc file commands and see if their mo...
by davidhubbardmd
Fri Jun 02, 2023 10:26 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

I asked BARD* again: Prompt: In response to a 16 ms visual stimulus, what will be the duration of visual cortex pyramidal spine neck calcium influx. BARD* Response: The duration of visual cortex pyramidal spine neck calcium influx in response to a 16 ms visual stimulus is approximately 100 ms. This ...
by davidhubbardmd
Fri May 12, 2023 12:09 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

I asked Bard, “In my NEURON program simulation of a pyramidal neuron spine neck calcium ion concentration, which mechanisms are needed in the segment?” Bard responded: // Define the spine neck. spine_neck = compartment(name='spine_neck', length=100.0, diameter=10.0) // Define the membrane. spine_nec...
by davidhubbardmd
Fri Apr 28, 2023 11:15 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Soledad Miranda-Rottman PhD, an author and team member, has sent me the Tazerart et al 2022 reprint and will visit the Forum. Ty Soledad.
by davidhubbardmd
Tue Apr 04, 2023 9:11 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

I opened ModelDB.science in my browser > entered Chiu into the filter, found Chiu et al Compartmentalization …2013 > Files > Mod folder > I found 12 mod files, some already in my spine_neck model, some I did not recognize: ca.mod, ca_a1g.mod, ca_a1h.mod, cad.mod, constant.mod, distr.mod, exp2syncur....
by davidhubbardmd
Mon Apr 03, 2023 3:26 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

NEURON does seem to be the best neuronal simulator and it's shareable. The shoulders of giants! Ty sir and permit the revision 'play with your own blocks'.
by davidhubbardmd
Sat Apr 01, 2023 12:44 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

I am looking forward to the research group’s input on their model. In the meantime, I note another group has reported that a single action potential generates a calcium influx into the spine of about 20 uM, Higley, M. J., & Sabatini, B. L. (2008). Calcium signaling in dendrites and spines: pract...
by davidhubbardmd
Wed Mar 29, 2023 1:37 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Just to be sure, I ran a longer train of synaptic transmissions https://docs.google.com/document/d/1Iu95s4B4xmyK1jOoXiqQn2adWchVaAyQfq8-4M9bklA/edit?usp=sharing But I still got no response in the intracellular calcium concentration. I wonder if I need voltage-gated calcium channels distributed in th...
by davidhubbardmd
Sat Mar 25, 2023 10:26 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Sensory Spine model-Araya Mitchell et al 2023, and Tazerart et al 2022 (referenced in link) describe the following mechanisms and parameters: spine-neck length 1 um. spine axial resistance, neck, head 500, 150 MΩ. spine-head volume 0.18 um3. V = ℼ* D3/6 diam = 0.7 um connected to basilar dendrite 17...
by davidhubbardmd
Thu Mar 23, 2023 8:40 am
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Thank you. I'm waiting to hear back from Dr. Tazerart.
by davidhubbardmd
Thu Mar 16, 2023 4:58 pm
Forum: Other questions
Topic: pyramidal spine-neck EPSPs
Replies: 70
Views: 5337362

Re: pyramidal spine-neck EPSPs

Good plan. A good model of calcium in sensory spine_necks needs a good launch with a model that's recently published. I am reaching out to the team that created it.