diff --git a/neuron/presynapse.md b/neuron/presynapse.md index 22b4afe..838884f 100644 --- a/neuron/presynapse.md +++ b/neuron/presynapse.md @@ -43,8 +43,13 @@ Qui comprendiamo: Qui riportiamo la struttura della espressione G e una descrizione di come leggerla (uno dei possibili modi): -- i possibili behavior della presynapsi sono espressi in due contesti. AP_ctx and NOT AP_ctx. -- i possibili behavior sono anche raggrupati in ms, sec e min, per facilitarne la verifica. Quello che conta sono gli RF specifici di ciascuno snipplet. +- i possibili behavior della presynapsi sono espressi in due contesti. AP_ctx and NOT AP_ctx. I possibili behavior sono anche raggrupati in ms, sec e min, per facilitarne la verifica. Quello che conta sono gli RF specifici di ciascuno snipplet. +- All'arrivo di un AP dal SOMA, si aprono i canali ionici VGCC. Il numero di VGCC e' soggetto a tuning a medi termine. +- i VGCC fanno entrare ioni Ca2+ nella Presynapse, in base a: + - quanto Ca2+ e' gia' presente (proxy per CDI) + - alla concentrazione di eCB (che arriva dalla Postsynapse e tende a limitare l'ingresso di Ca2+ per limitare indirettamente il rilascio di NT) + - alla concentrazione di NT (proxy per mGlur) +- il rilascio di NT avviene in base alla concetrazione di Ca2+ e la concentrazione di Rrp (readily release pool) - ```Gen @@ -119,7 +124,8 @@ container: PRESYNAPSE #### ms: AP_ctx: PRESYNAPSE -##### NTreleaseHigh: interacting + +##### NTreleaseLow: interacting Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP. @@ -135,39 +141,6 @@ Ci sono 4 casi che dipendono da RRP, Ca2+ e indirettamente da concentrazione di NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN. -```Gen -interacting: NTreleaseHigh - contained_by: PRESYNAPSE - - in_context: AP_ctx - rf: ( active: 3x ) # High - - hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND - NOT( ATP empty ) - action: [Rrp decrease, NT increase, ATP decrease] - trace: None -``` - -##### NTreleaseMediumness: interacting - -In tutti i casi di NT - -```Gen -interacting: NTreleaseMedium - contained_by: PRESYNAPSE - - in_context: AP_ctx - rf: ( active: 9x ) # Medium - - hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR - ( Ca2+ mediumness ) AND ( Rrp fullness )) AND - NOT( ATP empty ) - action: [Rrp decrease, Nt increase, ATP decrease] - trace: None -``` - -##### NTreleaseLow: interacting - In tutti i casi di NT ```Gen @@ -184,7 +157,40 @@ interacting: NTreleaseLow trace: None ``` -##### AP-CaClearanceHigh: interacting +##### NTreleaseMedium: interacting + +In tutti i casi di NT + +```Gen +interacting: NTreleaseMedium + contained_by: PRESYNAPSE + + in_context: AP_ctx + rf: ( active: 9x ) # Medium + + hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR + ( Ca2+ mediumness ) AND ( Rrp fullness )) AND + NOT( ATP empty ) + action: [Rrp decrease, Nt increase, ATP decrease] + trace: None +``` + +##### NTreleaseHigh: interacting + +```Gen +interacting: NTreleaseHigh + contained_by: PRESYNAPSE + + in_context: AP_ctx + rf: ( active: 3x ) # High + + hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND + NOT( ATP empty ) + action: [Rrp decrease, NT increase, ATP decrease] + trace: None +``` + +##### AP-CaClearanceMedium: interacting Qui eliminiamo Ca2+. Non comprendiamo per ora: @@ -198,6 +204,20 @@ Abbiamo il caso di clearance nel contesto di un AP e non nel contesto di AP, per --- +```Gen +interacting: AP-CaClearanceMedium + contained_by: PRESYNAPSE + + in_context: AP_ctx + rf: ( active: 6x ) # mediumness + + hypothesis: (Ca2+ mediumness) + action: [Ca2+ decrease] + trace: None +``` + +##### AP-CaClearanceHigh: interacting + ```Gen interacting: AP-CaClearanceHigh contained_by: PRESYNAPSE @@ -210,20 +230,6 @@ interacting: AP-CaClearanceHigh trace: None ``` -##### AP-CaClearanceMediumness: interacting - -```Gen -interacting: AP-CaClearanceMediumness - contained_by: PRESYNAPSE - - in_context: AP_ctx - rf: ( active: 6x ) # mediumness - - hypothesis: (Ca2+ mediumness) - action: [Ca2+ decrease] - trace: None -``` - ### NOT AP_ctx: PRESYNAPSE #### ms: NOT AP_ctx: PRESYNAPSE @@ -242,7 +248,7 @@ interacting: NotAP-CaClearance trace: None ``` -##### CaTracesAccumulationFast: interacting +##### CaTracesAccumulationLow: interacting Serve a dare la velocita' al trasporto di vesicles da RP a RRP. 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. @@ -252,30 +258,30 @@ The result is that Tr_Ca encodes not the instantaneous calcium level but the rec --- -Qui le tracce CaTrace si accumulano di piu' perche' RF e' minore, se c'e' la condizione, perche' va a fare il controllo piu' spesso. - ```Gen -interacting: CaTracesAccumulationFast +interacting: CaTracesAccumulationLow contained_by: PRESYNAPSE in_context: NOT AP_ctx - rf: ( active: 12x ) # fast + rf: ( active: 24x ) # Low - hypothesis: (Ca2+ fullness) + hypothesis: (Ca2+ mediumness) action: [CaTrace increase] trace: None ``` -##### CaTracesAccumulationSlow: interacting +##### CaTracesAccumulationHigh: interacting + +Qui le tracce CaTrace si accumulano di piu' perche' RF e' minore, se c'e' la condizione, perche' va a fare il controllo piu' spesso. ```Gen -interacting: CaTracesAccumulationSlow +interacting: CaTracesAccumulationHigh contained_by: PRESYNAPSE in_context: NOT AP_ctx - rf: ( active: 24x ) # Slow + rf: ( active: 12x ) # high - hypothesis: (Ca2+ mediumness) + hypothesis: (Ca2+ fullness) action: [CaTrace increase] trace: None ``` @@ -316,7 +322,7 @@ interacting: CaTracesClearance trace: None ``` -##### RPShuttleSlow: interacting +##### RPShuttleLow: interacting This happens in the seconds loop, once per second. @@ -480,9 +486,11 @@ container: VGCC-PRE ### AP_ctx: VGCC-PRE +Da rivedere le condizioni per aggiungere mGluR che ha come proxy NT concentration!!!!! + #### ms: AP_ctx: VGCC-PRE -##### Ca2+enterOpen: interacting +##### Ca2+enterLow: interacting Here we comprehend the breaking activity on VGCC by: CDI, eCB and mGluR: @@ -524,8 +532,8 @@ interacting: Ca2+enterMedium rf: ( active: 6x ) # Medium hypothesis: (Ca2+ mediumness) OR - (eCB mediumness) AND (Ca2+ empty) OR - (eCB full) AND (Ca2+ empty) AND (NT empty) + ((eCB mediumness) AND (Ca2+ empty)) OR + ((eCB full) AND (Ca2+ empty) AND (NT empty)) action: [Ca2+ increase, ATP decrease] trace: None ``` @@ -540,7 +548,7 @@ interacting: Ca2+enterHigh rf: ( active: 3x ) # High hypothesis: (Ca2+ mediumness) AND (eCB full) OR - (eCB mediumness)) + (eCB mediumness) action: [Ca2+ increase, ATP decrease] trace: None ```