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elements/neuron/presynapse.md
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@@ -7,59 +7,70 @@ include_toc: true
Qui comprendiamo: Qui comprendiamo:
- PRESYNAPSE: Presynapse - PRESYNAPSE: Presynapse
- VGCC-PRE-TUN: la modulazione della quantita' di VGCC-PRE
- VGCC-PRE: Voltage-Controlled Gated Channels - VGCC-PRE: Voltage-Controlled Gated Channels
## PRESYNAPSE: Comprehension ## PRESYNAPSE
```Gen ```Gen
PRESYNAPSE PRESYNAPSE
type: comprehension type: comprehension
expand_comprehension: expand_comprehension:
&VGCC-PRE_ALL: VGCC-PRE ( full: 10x, active: 5x, empty: 2x ) _VgccPre: VGCC-PRE [ full: 10x, active: 5x, empty: 2x ]
instantiate_container: instantiate_container:
PRESYNAPSE-BEH [] @: $BehaviorPre []
VGCC-PRE-TUN [pass: &VGCC-PRE_ALL] @: $TunVgccPre [pass: _VgccPre]
``` ```
### PRESYNAPSE-BEH: Container ### $BehaviorPre
**Tubs:** **Tubs:**
- **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 - **_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
- **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. - **_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.
- **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. - **_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.
- **NT**: Neuro Transmitter, released in the synapse by the vescicles. The release increses NT and decreases RRP - **_NT**: Neuro Transmitter, released in the synapse by the vescicles. The release increses NT and decreases RRP
- **CaTraces**: sono le tracce di permanenza della concentrazione di Ca2+. Servono alla modulazione (TUN) - **_CaTraces**: sono le tracce di permanenza della concentrazione di Ca2+. Servono alla modulazione (TUN)
- **eCB**: retrograde signal updates from postsynapsis (postsynaptic input) - **_eCB**: retrograde signal updates from postsynapsis (postsynaptic input)
```Gen ```Gen
PRESYNAPSE-BEH $BehaviorPre
type: container type: container
activity_scope: !DAY activity_scope: !DAY
tub_local: tub_local:
- Ca2+ ( full: 60x, active: 30x, empty: 0x ) _Ca2+: TUB [ full: 60x, active: 30x, empty: 0x ]
# developed_by: DEV-PRE-CA2+FULL from DEV.N _Rrp: TUB [ full: 30x, active: 15x, empty: 0x ]
- Rrp ( full: 30x, active: 15x, empty: 0x ) _Rp: TUB [ full: 30x, active: 15x, empty: 0x ]
# developed_by: DEV-PRE-RRP-FULL from DEV.N _CaTraces: TUB [ full: 50x, active: 0x, empty: 0x ]
- Rp ( full: 30x, active: 15x, empty: 0x )
# developed_by: DEV-PRE-RRP-FULL from DEV.N
- CaTraces ( full: 50x, active: 0x, empty: 0x )
tub_intricated: tub_intricated:
- NT ( contained_by: SYN ) _NT: contained_by [ SYN ]
- ATP ( contained_by: ? ) _ATP: contained_by [?]
- eCB ( contained_by: POST ) _eCB: contained_by [POST]
context_intricated: context_intricated:
- AP_ctx ( contained_by: SOMA ) $AP: contained_by [SOMA]
snippets:
# &AP
NTreleaseLow: [RF: active 12x, type: accumulator]
NTreleaseMedium [RF active 9x, type: accumulator]
NTreleaseHigh: [RF active 9x, type: accumulator]
Ca2+TracesAccLow: [RF active 3x, type: accumulator]
Ca2+TracesAccMedium: [RF active 6x, type: accumulator]
Ca2+TracesAccHigh: [RF active 10x, type: accumulator]
# NOT &AP
eCBClearence: RF [active: 24x]
``` ```
#### AP_ctx #### &AP
Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP. Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP.
@@ -77,23 +88,21 @@ NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare i
In tutti i casi di NT In tutti i casi di NT
##### NTreleaseLow: ( active: 12x ) accumulator ##### NTreleaseLow
```Gen
NTreleaseLow: ( active: 12x ) # Low
type: accumulator
contained_by: PRESYNAPSE-BEH
in_context: AP_ctx ```Gen
hypothesis: ( Ca2+ mediumness ) AND ( Rrp mediumness ) AND NOT( ATP empty ) NTreleaseLow
action: [Rrp decrease, Nt increase, ATP decrease]
in_context: &AP
hypothesis: ( _Ca2+ mediumness ) AND ( _Rrp mediumness ) AND NOT( _ATP empty )
action: [_Rrp decrease, _Nt increase, _ATP decrease]
trace: None trace: None
``` ```
##### NTreleaseMedium: ( active: 9x ) accumulatorv ##### NTreleaseMedium
```Gen ```Gen
NTreleaseMedium: ( active: 9x ) # Medium NTreleaseMedium
type: accumulator
contained_by: PRESYNAPSE-BEH
in_context: AP_ctx in_context: AP_ctx
hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR
@@ -103,11 +112,10 @@ NTreleaseMedium: ( active: 9x ) # Medium
trace: None trace: None
``` ```
##### NTreleaseHigh: ( active: 3x ) accumulator ##### NTreleaseHigh
```Gen ```Gen
NTreleaseHigh: ( active: 3x ) # High NTreleaseHigh
type: accumulator
contained_by: PRESYNAPSE-BEH
in_context: AP_ctx in_context: AP_ctx
hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND
@@ -116,9 +124,10 @@ NTreleaseHigh: ( active: 3x ) # High
trace: None trace: None
``` ```
##### Ca2+TracesAccumulationLow: accumulator ##### Ca2+TracesAccLow
Serve a: Serve a:
- fare il tuning dei VGCC - fare il tuning dei VGCC
- 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. - 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.
- le tracce vengono eliminate quando il neurone e' in pausa, lontano da uno spike train, TunPossible_ctx - le tracce vengono eliminate quando il neurone e' in pausa, lontano da uno spike train, TunPossible_ctx
@@ -127,13 +136,8 @@ Serve a:
- 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. - 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.
- 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. - 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.
---
##### Ca2+TracesAccumulationLow: ( active: 10x ) accumulator
```Gen ```Gen
Ca2+TracesAccumulationLow: ( active: 10x ) Ca2+TracesAccuLow
type: accumulator
contained_by: PRESYNAPSE-BEH
in_context: AP_ctx in_context: AP_ctx
hypothesis: (Ca2+ emptiness) hypothesis: (Ca2+ emptiness)
@@ -141,11 +145,10 @@ Ca2+TracesAccumulationLow: ( active: 10x )
trace: None trace: None
``` ```
##### Ca2+TracesAccumulationMedium: ( active: 6x ) accumulator ##### Ca2+TracesAccMedium
```Gen ```Gen
Ca2+TracesAccumulationMedium: ( active: 6x ) # medium Ca2+TracesAccMedium
type: accumulator
contained_by: PRESYNAPSE-BEH
in_context: AP_ctx in_context: AP_ctx
hypothesis: (Ca2+ mediumness) hypothesis: (Ca2+ mediumness)
@@ -153,11 +156,10 @@ Ca2+TracesAccumulationMedium: ( active: 6x ) # medium
trace: None trace: None
``` ```
##### Ca2+TracesAccumulationHigh: ( active: 10x ) accumulator ##### Ca2+TracesAccHigh
```Gen ```Gen
Ca2+TracesAccumulationHigh: ( active: 10x ) # high Ca2+TracesAccumulationHigh
type: accumulator
contained_by: PRESYNAPSE-BEH
in_context: AP_ctx in_context: AP_ctx
hypothesis: (Ca2+ fullness) hypothesis: (Ca2+ fullness)
@@ -165,7 +167,7 @@ Ca2+TracesAccumulationHigh: ( active: 10x ) # high
trace: None trace: None
``` ```
#### NOT AP_ctx #### NOT &AP
##### eCB clearance: accumulator ##### eCB clearance: accumulator
@@ -174,6 +176,7 @@ eCB dipende da POST. Tende a modulare l'entrata di Ca2+ degli VGCC.
Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un RF di questo episodio. Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un RF di questo episodio.
##### eCBClearance: ( active: 24x ) accumulator ##### eCBClearance: ( active: 24x ) accumulator
```Gen ```Gen
eCBClearance: ( active: 24x ) # Slow eCBClearance: ( active: 24x ) # Slow
type: accumulator type: accumulator
@@ -299,6 +302,7 @@ Ca2+TracesClearance: ( active: 30x ) # Slow
``` ```
### VGCC-PRE-TUN: Container ### VGCC-PRE-TUN: Container
```Gen ```Gen
VGCC-PRE-TUN VGCC-PRE-TUN
@@ -323,7 +327,9 @@ VGCC-PRE-TUN
#### TunPossible_ctx #### TunPossible_ctx
##### CheckVgccPreTun: ( active: 60x ) contexting ##### CheckVgccPreTun: ( active: 60x ) contexting
Qui controlliamo che ci siano le condizioni per aumentare o diminuire la quantita' di VGCC Qui controlliamo che ci siano le condizioni per aumentare o diminuire la quantita' di VGCC
```Gen ```Gen
CheckVgccPreTun: ( active: 60x ) CheckVgccPreTun: ( active: 60x )
type: contexting type: contexting
@@ -338,6 +344,7 @@ CheckVgccPreTun: ( active: 60x )
``` ```
##### PossibleUpPreVgccTun: ( active: 10x ) accumulator ##### PossibleUpPreVgccTun: ( active: 10x ) accumulator
```Gen ```Gen
PossibleUpPreVgccTun: ( active: 10x ) PossibleUpPreVgccTun: ( active: 10x )
type: accumulator type: accumulator
@@ -350,6 +357,7 @@ PossibleUpPreVgccTun: ( active: 10x )
``` ```
##### PossibleDownPreVgccTun: ( active: 10x ) accumulator ##### PossibleDownPreVgccTun: ( active: 10x ) accumulator
```Gen ```Gen
PossibleDownPreVgccTun: ( active: 10x ) PossibleDownPreVgccTun: ( active: 10x )
type: accumulator type: accumulator
@@ -414,6 +422,7 @@ Qui semplifichiamo:
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. 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.
##### Ca2+enterLow: ( active: 12x ) accumulator ##### Ca2+enterLow: ( active: 12x ) accumulator
```Gen ```Gen
Ca2+enterLow: ( active: 12x ) # Low Ca2+enterLow: ( active: 12x ) # Low
type: accumulator type: accumulator
@@ -426,6 +435,7 @@ Ca2+enterLow: ( active: 12x ) # Low
``` ```
##### Ca2+enterMedium: ( active: 6x ) accumulator ##### Ca2+enterMedium: ( active: 6x ) accumulator
```Gen ```Gen
Ca2+enterMedium: ( active: 6x ) # Medium Ca2+enterMedium: ( active: 6x ) # Medium
type: accumulator type: accumulator
@@ -440,6 +450,7 @@ Ca2+enterMedium: ( active: 6x ) # Medium
``` ```
##### Ca2+enterHigh: ( active: 3x ) accumulator ##### Ca2+enterHigh: ( active: 3x ) accumulator
```Gen ```Gen
Ca2+enterHigh: ( active: 3x ) # High Ca2+enterHigh: ( active: 3x ) # High
type: accumulator type: accumulator
@@ -457,16 +468,19 @@ Ca2+enterHigh: ( active: 3x ) # High
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). 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).
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: 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:
- PMCA: primary, ATP-dependent - PMCA: primary, ATP-dependent
- NCX: fast, NOT ATP-dependent - NCX: fast, NOT ATP-dependent
- SERCA: slowest, ATP-dependent - SERCA: slowest, ATP-dependent
Qui disinguiamo: Qui disinguiamo:
- Ca+2 fullness che si puo' verificare alla fine di un AP - Ca+2 fullness che si puo' verificare alla fine di un AP
- NOT ca2+ fullness che svuota piu' lentamente - NOT ca2+ fullness che svuota piu' lentamente
- da capire se serve veramente questa distinzione per il tempo di svuotamento. - da capire se serve veramente questa distinzione per il tempo di svuotamento.
##### Ca2+ClearanceLow: ( active: 24x ) accumulator ##### Ca2+ClearanceLow: ( active: 24x ) accumulator
```Gen ```Gen
Ca2+ClearanceLow: ( active: 24x ) # Low Ca2+ClearanceLow: ( active: 24x ) # Low
type: accumulator type: accumulator
@@ -479,6 +493,7 @@ Ca2+ClearanceLow: ( active: 24x ) # Low
``` ```
##### Ca2+ClearanceHigh: ( active: 4x ) accumulator ##### Ca2+ClearanceHigh: ( active: 4x ) accumulator
```Gen ```Gen
Ca2+ClearanceHigh: ( active: 4x ) # High Ca2+ClearanceHigh: ( active: 4x ) # High
type: accumulator type: accumulator
organs/tectum/tectum.md
+5 -4
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@@ -14,7 +14,7 @@ TECTUM
../../modules/winnertakeall.md ../../modules/winnertakeall.md
../../elements/astrocyte.md ../../elements/astrocyte.md
expansion: expand_comprehension:
# Modules # Modules
@WTA-001: WINNERTAKEALL [] @WTA-001: WINNERTAKEALL []
@@ -24,6 +24,10 @@ TECTUM
@AST-001: ASTROCYTE [] @AST-001: ASTROCYTE []
@AST-002: ASTROCYTE [] @AST-002: ASTROCYTE []
@: bind [@WTA-001, @AST-001]
istantiate_container:
# Qui l'interprete deve controllare che due o piu' "in" non sono ammessi, perche' potrebbero riguardare ASTROCYTE diversi. Da capore come fare il controllo. # Qui l'interprete deve controllare che due o piu' "in" non sono ammessi, perche' potrebbero riguardare ASTROCYTE diversi. Da capore come fare il controllo.
# external intrication # external intrication
@@ -35,7 +39,4 @@ TECTUM
@: EXCITATION [out: @WTA-001.@OUT-EXCI-001, in: @WTA-003.@IN-EXCI-002] @: EXCITATION [out: @WTA-001.@OUT-EXCI-001, in: @WTA-003.@IN-EXCI-002]
@: INHIBITION [out: @WTA-002.@OUT-INHI-001, in: @WTA-003.@IN-INHI-004] @: INHIBITION [out: @WTA-002.@OUT-INHI-001, in: @WTA-003.@IN-INHI-004]
bind: [@WTA-001, @AST-001]
``` ```