revisione sintassi
This commit is contained in:
@@ -7,59 +7,70 @@ include_toc: true
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Qui comprendiamo:
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- PRESYNAPSE: Presynapse
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- VGCC-PRE-TUN: la modulazione della quantita' di VGCC-PRE
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- VGCC-PRE: Voltage-Controlled Gated Channels
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## PRESYNAPSE: Comprehension
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## PRESYNAPSE
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```Gen
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PRESYNAPSE
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type: comprehension
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expand_comprehension:
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&VGCC-PRE_ALL: VGCC-PRE ( full: 10x, active: 5x, empty: 2x )
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_VgccPre: VGCC-PRE [ full: 10x, active: 5x, empty: 2x ]
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instantiate_container:
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PRESYNAPSE-BEH []
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VGCC-PRE-TUN [pass: &VGCC-PRE_ALL]
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@: $BehaviorPre []
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@: $TunVgccPre [pass: _VgccPre]
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```
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### PRESYNAPSE-BEH: Container
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### $BehaviorPre
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**Tubs:**
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- **Ca2+**: Calcium Ion entering the Presynapse when VCGG open that influence NT release. Normally returns to ~0 between spikes; stays elevated when pumps fail. They are key to check the concentration, release NT and modulation
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- **Rrp**: Readily Releasable Pool: The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse. This pool is very small (usually only about 0.5% to 5% of total vesicles) and can be exhausted quickly during high-frequency firing, leading to "short-term depression" of the signal. Here we consider them as NT ready to be released.
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- **Rp**: Reserve Pool: The bulk of the vesicles held further back in the terminal, often tethered by a protein called synapsin. These are only mobilized during intense, prolonged stimulation. This makes up the vast majority of the vesicles (up to 80% or 90%). Here we consider them NT in reserve that can be transfered to RRP and created using Glutamine from Astorcyte.
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- **NT**: Neuro Transmitter, released in the synapse by the vescicles. The release increses NT and decreases RRP
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- **CaTraces**: sono le tracce di permanenza della concentrazione di Ca2+. Servono alla modulazione (TUN)
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- **eCB**: retrograde signal updates from postsynapsis (postsynaptic input)
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- **_Ca2+**: Calcium Ion entering the Presynapse when VCGG open that influence NT release. Normally returns to ~0 between spikes; stays elevated when pumps fail. They are key to check the concentration, release NT and modulation
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- **_Rrp**: Readily Releasable Pool: The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse. This pool is very small (usually only about 0.5% to 5% of total vesicles) and can be exhausted quickly during high-frequency firing, leading to "short-term depression" of the signal. Here we consider them as NT ready to be released.
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- **_Rp**: Reserve Pool: The bulk of the vesicles held further back in the terminal, often tethered by a protein called synapsin. These are only mobilized during intense, prolonged stimulation. This makes up the vast majority of the vesicles (up to 80% or 90%). Here we consider them NT in reserve that can be transfered to RRP and created using Glutamine from Astorcyte.
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- **_NT**: Neuro Transmitter, released in the synapse by the vescicles. The release increses NT and decreases RRP
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- **_CaTraces**: sono le tracce di permanenza della concentrazione di Ca2+. Servono alla modulazione (TUN)
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- **_eCB**: retrograde signal updates from postsynapsis (postsynaptic input)
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```Gen
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PRESYNAPSE-BEH
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$BehaviorPre
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type: container
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activity_scope: !DAY
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tub_local:
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- Ca2+ ( full: 60x, active: 30x, empty: 0x )
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# developed_by: DEV-PRE-CA2+FULL from DEV.N
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- Rrp ( full: 30x, active: 15x, empty: 0x )
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# developed_by: DEV-PRE-RRP-FULL from DEV.N
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- Rp ( full: 30x, active: 15x, empty: 0x )
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# developed_by: DEV-PRE-RRP-FULL from DEV.N
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- CaTraces ( full: 50x, active: 0x, empty: 0x )
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_Ca2+: TUB [ full: 60x, active: 30x, empty: 0x ]
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_Rrp: TUB [ full: 30x, active: 15x, empty: 0x ]
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_Rp: TUB [ full: 30x, active: 15x, empty: 0x ]
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_CaTraces: TUB [ full: 50x, active: 0x, empty: 0x ]
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tub_intricated:
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- NT ( contained_by: SYN )
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- ATP ( contained_by: ? )
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- eCB ( contained_by: POST )
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_NT: contained_by [ SYN ]
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_ATP: contained_by [?]
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_eCB: contained_by [POST]
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context_intricated:
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- AP_ctx ( contained_by: SOMA )
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$AP: contained_by [SOMA]
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snippets:
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# &AP
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NTreleaseLow: [RF: active 12x, type: accumulator]
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NTreleaseMedium [RF active 9x, type: accumulator]
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NTreleaseHigh: [RF active 9x, type: accumulator]
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Ca2+TracesAccLow: [RF active 3x, type: accumulator]
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Ca2+TracesAccMedium: [RF active 6x, type: accumulator]
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Ca2+TracesAccHigh: [RF active 10x, type: accumulator]
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# NOT &AP
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eCBClearence: RF [active: 24x]
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```
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#### AP_ctx
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#### &AP
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Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP.
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@@ -77,23 +88,21 @@ NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare i
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In tutti i casi di NT
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##### NTreleaseLow: ( active: 12x ) accumulator
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```Gen
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NTreleaseLow: ( active: 12x ) # Low
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type: accumulator
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contained_by: PRESYNAPSE-BEH
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##### NTreleaseLow
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in_context: AP_ctx
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hypothesis: ( Ca2+ mediumness ) AND ( Rrp mediumness ) AND NOT( ATP empty )
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action: [Rrp decrease, Nt increase, ATP decrease]
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```Gen
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NTreleaseLow
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in_context: &AP
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hypothesis: ( _Ca2+ mediumness ) AND ( _Rrp mediumness ) AND NOT( _ATP empty )
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action: [_Rrp decrease, _Nt increase, _ATP decrease]
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trace: None
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```
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##### NTreleaseMedium: ( active: 9x ) accumulatorv
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##### NTreleaseMedium
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```Gen
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NTreleaseMedium: ( active: 9x ) # Medium
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type: accumulator
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contained_by: PRESYNAPSE-BEH
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NTreleaseMedium
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in_context: AP_ctx
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hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR
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@@ -103,11 +112,10 @@ NTreleaseMedium: ( active: 9x ) # Medium
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trace: None
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```
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##### NTreleaseHigh: ( active: 3x ) accumulator
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##### NTreleaseHigh
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```Gen
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NTreleaseHigh: ( active: 3x ) # High
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type: accumulator
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contained_by: PRESYNAPSE-BEH
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NTreleaseHigh
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in_context: AP_ctx
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hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND
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@@ -116,24 +124,20 @@ NTreleaseHigh: ( active: 3x ) # High
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trace: None
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```
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##### Ca2+TracesAccumulationLow: accumulator
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##### Ca2+TracesAccLow
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Serve a:
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Serve a:
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- fare il tuning dei VGCC
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- dare la velocita' al trasporto di vesicles da RP a RRP, anche se non avendo ancora compreso ATP, la velocita' non cambia molto la sostanza.
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- dare la velocita' al trasporto di vesicles da RP a RRP, anche se non avendo ancora compreso ATP, la velocita' non cambia molto la sostanza.
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- le tracce vengono eliminate quando il neurone e' in pausa, lontano da uno spike train, TunPossible_ctx
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- Abbiamo 3 tracce, high, medium and low. Andiamo a verificare una combinazione di queste per fare la modulazione
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- RF e' a 10, questo dovrebbe essere un RF di campionamento durante AP_ctx context che dovremmo assicurarci sia tipo 100. Il che implicherebbe 10 campionamenti.
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- The biological meaning is that a synapse that has just been through a burst is primed for fast recovery — the molecular machinery for vesicle docking is already engaged, calcium-dependent priming factors are still elevated, and the system is in a ready state. A synapse that has been silent for several seconds has cooled down and replenishes slowly.
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- So after one second of silence CaTrace has fallen to ~37% of its peak value, after two seconds to ~14%, after three seconds to ~5%. It asymptotes toward zero but never exactly reaches it. Between spikes, Ca2+ falls toward zero as the pumps clear it. The result is that CaTrace encodes not the instantaneous calcium level but the recent history of calcium activity — a smoothed, time-averaged measure of how active the synapse has been over the past one to two seconds.
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---
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##### Ca2+TracesAccumulationLow: ( active: 10x ) accumulator
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```Gen
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Ca2+TracesAccumulationLow: ( active: 10x )
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type: accumulator
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contained_by: PRESYNAPSE-BEH
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Ca2+TracesAccuLow
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in_context: AP_ctx
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hypothesis: (Ca2+ emptiness)
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@@ -141,11 +145,10 @@ Ca2+TracesAccumulationLow: ( active: 10x )
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trace: None
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```
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##### Ca2+TracesAccumulationMedium: ( active: 6x ) accumulator
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##### Ca2+TracesAccMedium
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```Gen
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Ca2+TracesAccumulationMedium: ( active: 6x ) # medium
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type: accumulator
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contained_by: PRESYNAPSE-BEH
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Ca2+TracesAccMedium
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in_context: AP_ctx
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hypothesis: (Ca2+ mediumness)
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@@ -153,11 +156,10 @@ Ca2+TracesAccumulationMedium: ( active: 6x ) # medium
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trace: None
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```
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##### Ca2+TracesAccumulationHigh: ( active: 10x ) accumulator
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##### Ca2+TracesAccHigh
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```Gen
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Ca2+TracesAccumulationHigh: ( active: 10x ) # high
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type: accumulator
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contained_by: PRESYNAPSE-BEH
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Ca2+TracesAccumulationHigh
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in_context: AP_ctx
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hypothesis: (Ca2+ fullness)
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@@ -165,7 +167,7 @@ Ca2+TracesAccumulationHigh: ( active: 10x ) # high
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trace: None
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```
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#### NOT AP_ctx
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#### NOT &AP
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##### eCB clearance: accumulator
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@@ -174,6 +176,7 @@ eCB dipende da POST. Tende a modulare l'entrata di Ca2+ degli VGCC.
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Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un RF di questo episodio.
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##### eCBClearance: ( active: 24x ) accumulator
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```Gen
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eCBClearance: ( active: 24x ) # Slow
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type: accumulator
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@@ -299,6 +302,7 @@ Ca2+TracesClearance: ( active: 30x ) # Slow
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```
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### VGCC-PRE-TUN: Container
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```Gen
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VGCC-PRE-TUN
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@@ -323,7 +327,9 @@ VGCC-PRE-TUN
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#### TunPossible_ctx
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##### CheckVgccPreTun: ( active: 60x ) contexting
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Qui controlliamo che ci siano le condizioni per aumentare o diminuire la quantita' di VGCC
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```Gen
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CheckVgccPreTun: ( active: 60x )
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type: contexting
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@@ -338,6 +344,7 @@ CheckVgccPreTun: ( active: 60x )
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```
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##### PossibleUpPreVgccTun: ( active: 10x ) accumulator
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```Gen
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PossibleUpPreVgccTun: ( active: 10x )
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type: accumulator
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@@ -350,6 +357,7 @@ PossibleUpPreVgccTun: ( active: 10x )
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```
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##### PossibleDownPreVgccTun: ( active: 10x ) accumulator
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```Gen
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PossibleDownPreVgccTun: ( active: 10x )
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type: accumulator
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@@ -414,6 +422,7 @@ Qui semplifichiamo:
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Devo controllare che le condizioni sotto siano esaustive. Qui ho confuso high con low, e inoltre ho messo NT per mGluR che devo controllare che abbia senso.
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##### Ca2+enterLow: ( active: 12x ) accumulator
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```Gen
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Ca2+enterLow: ( active: 12x ) # Low
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type: accumulator
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@@ -426,6 +435,7 @@ Ca2+enterLow: ( active: 12x ) # Low
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```
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##### Ca2+enterMedium: ( active: 6x ) accumulator
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```Gen
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Ca2+enterMedium: ( active: 6x ) # Medium
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type: accumulator
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@@ -440,6 +450,7 @@ Ca2+enterMedium: ( active: 6x ) # Medium
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```
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##### Ca2+enterHigh: ( active: 3x ) accumulator
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```Gen
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Ca2+enterHigh: ( active: 3x ) # High
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type: accumulator
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@@ -457,16 +468,19 @@ Ca2+enterHigh: ( active: 3x ) # High
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Qui eliminiamo Ca2+. Il tempo che ci mette ad eliminare il Ca2+ dovrebbe essere minoe dell'inervallo fra un AP_ctx e un'altra. Siccome non comprendiamo per ora ATP, non c'e' accumulo di Ca2+ per mancanza di ATP (stanchezza).
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Non non comprendiamo anche il ristabilimento del Voltage, con altri Ioni entranti e uscenti, per ora tutto dipende da AP del SOMA. Non comprendiamo per ora:
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- PMCA: primary, ATP-dependent
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- NCX: fast, NOT ATP-dependent
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- SERCA: slowest, ATP-dependent
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Qui disinguiamo:
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- Ca+2 fullness che si puo' verificare alla fine di un AP
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- NOT ca2+ fullness che svuota piu' lentamente
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- da capire se serve veramente questa distinzione per il tempo di svuotamento.
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##### Ca2+ClearanceLow: ( active: 24x ) accumulator
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```Gen
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Ca2+ClearanceLow: ( active: 24x ) # Low
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type: accumulator
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@@ -479,6 +493,7 @@ Ca2+ClearanceLow: ( active: 24x ) # Low
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```
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##### Ca2+ClearanceHigh: ( active: 4x ) accumulator
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```Gen
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Ca2+ClearanceHigh: ( active: 4x ) # High
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type: accumulator
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