organism/neuron/neuron-developer.md

# neuron-developer.md

Neuron Development - LTP-LTD Behavior:

This is critical for long-term presynaptic changes. The postsynaptic cell, upon detecting specific  activity patterns (like those for LTP/LTD), releases chemical signals  that travel backwards to the presynaptic terminal, instructing it to  change.

- For Presynaptic Strengthening (e.g., un LTP):
  - Nitric Oxide (NO):  A gas that diffuses freely. During postsynaptic LTP induction (strong  NMDAR activation), neuronal NO synthase (nNOS) is activated. NO diffuses  into the presynaptic terminal and activates soluble guanylyl cyclase  (sGC), raising cGMP levels. This enhances vesicle release via PKG,  contributing to presynaptic LTP.
  - Endocannabinoid-Mediated LTP (eLTP): In some synapses, a postsynaptic depolarization triggers production of endocannabinoids (e.g., 2-AG). These bind to presynaptic CB1 receptors, but surprisingly, can initiate a signaling cascade (involving cAMP/PKA) that increases Pr for a long period.
  - Neurotrophins (BDNF):  Released from the postsynapse in an activity-dependent manner.  Presynaptic TrkB receptors activate pathways (PI3K, MAPK) that enhance  vesicle docking and Pr.
- For Presynaptic Weakening (e.g., LTD):
  - Classical Endocannabinoid-Mediated LTD (eCB-LTD):  More common. Moderate postsynaptic activity (mGluR activation or  moderate Ca²⁺ rise) triggers 2-AG release. 2-AG binds presynaptic CB1  receptors, which inhibit VGCCs and directly inhibit the release machinery via Gi/o protein signaling, reducing Pr for a long time.
  - Other Lipid Mediators (like LPA) can also act as retrograde signals for depression.

Augmentation:

- Calcium-sensing proteins (Munc13) alter release probability (1-10s range). How?

Upregulation:

- NO/BDNF activates cascades that increase P_r, promote synaptic growth (facilitates LTP). How?
- VGCC TUN
- Potassium channel modulation ??

Downregulation:

- eCBs bind CB1 receptors, inhibit VGCCs, activate K⁺ channels → profound decrease in P_r (DSE/DSI - depolarization-induced suppression)
- CB1 receptor activation (by eCBs)
- Retrograde BDNF (brain-derived neurotrophic factor)

> Night Time Scale

```Gen
developer: NEURON-DEVELOPER
  contained_by: NEURON
```

## CA2-PRESYNAPSE-DEVELOPER: Developer

```Gen
CA2-PRESYNAPSE-DEVELOPER

type: developer

  contained_by: NEURON-DEVELOPER

  develops: NEURON/NEURON-DAY/AXON/PRESYNAPSE/tub/Ca2+ # this is the tub whose "full" must be modulated
  
  tub_dev: 
    - fullMod ( fullness: 100x, active: Ca2+/full, emptiness: 50x ) 
    # qui stiamo modulando il full di Ca2+, associandolo ad
    # active di fullMod. Cambiando active di fullMod, 
    # si cambia la full di Ca2+

  tub_local:

  tub_intricated:
    - Nox ( contained_by: EURON/NEURON-DAY/AXON/PRESYNAPSE )
    - Ecb ( contained_by: EURON/NEURON-DAY/AXON/PRESYNAPSE )
```

### :Contextor

***Tens Milliseconds Time Scale***

```Gen
CheckPreTubCa2+: ( active: 60x )

  type: contextor

  contained_by: NEURON-DEVELOPER
  in_context: Fixed

  condition: ( empty ) 
    out_context: DecreaseFull_ctx

  condition: NOT ( empty ) AND NOT ( Ca2+ full ) 
    out_context: Nothing_ctx

  condition: ( full) 
    out_context: IncreaseFull_ctx
```

### :Accumulator

```Gen
DecreaseFull: ( active: 1x )

  type: accumulator
  contained_by: DEV-PRE-FULL-CA2+

  in_context: DecreaseFull_ctx

  hypothesis: NOT ( full ) AND NOT ( empty ) 
    action: [ increase,  decrease]
    trace: None
```

### DEV-PRE-RRP-TUB: Developer

```Gen
developer: DEV-PRE-RRP-TUB
 contained_by: DEV-TUB-FLOOR

 develops: BEH-PRE/tub/Rrp # this is the tub whose "full" must be modulated
  
 tub_dev: 
   - fullMod ( fullness: 100x, active: Rrp/fullness, emptiness: 50x ) # RrpFull "contains" a number of blocks equal to the current Full.
# qui stiamo modulando la fullness di Rrp, associandola ad
# active di fullMod. Cambiando active di fullMod, 
# si cambia la fullness di Rrp

 tub_local:

 tub_intricated:
  - Nox ( contained_by: BEH-POST )
  - Ecb ( contained_by: BEH-POST )
```

#### Context1

#### Episode1

## DEV-TUB-CONCEPTUAL: Developer

Qui la PRE e la POST si predispongono per dare le condizioni a SYN di stabilire o eliminare una sinapsi. Per ora questo comportamento lo mettiamo in TUN perche’ non si tratta di creare o distruggere PRE o POST, ma di rendere disponibile a SYN la possibilita’ di creare o distruggere una SYN. Durante il Day c’e’ il TUN che mette a disposizione, durante il Night SYN crea o distrugge gli accoppiamenti PRE POST.

ATTENZIONE: Questo e POST e’ da cambiare, perche’ c’e’ il passaggio da TubPoss a TubPossSyn a TubAct. E’ la SYN che passa in TubAct.

> Minutes/hours Time Scale

```Gen
developer: DEV-TUB-CONCEPTUAL
 contained_by: NIGHT-N
```

### AXO-PRE-TUB-DEV: Developer

Qui stiamo ragionanando sulla trasformazione fra bottone presinaptico inattivo e bottone attivo, pronto a diventare parte di una sinapsi. Il ragionamento e' locale, e mette a disposizione o toglie un bottone attivo che un altro ragionamento, in TUN-WTA, fara' su questo bottone, il bottone postisinaptico e una sinapsi disponibile. Agiamo sulla fullness di BEH-PRE.

```Gen
developer: AXO-PRE-TUB-DEV
 contained_by: DEV-TUB-CONCEPTUAL
 
 develops: N/AXO/BEH-AXO/expansion/BEH-PRE
   # qui stiamo modulando fullness del tub BEH-PRE associandoli a tub_modulation prePos e PreAct. 

 tub_modulation:
  - fulMod ( fullness: 100x, active: BEH-PRE/fullness, empty: 0x )  # aumento di possible di BEH-PRE
  - actMod ( fullness: None, active: BEH-PRE/active, empty: BEH-PRE/emptiness )  # riferimento a active di BEH-PRE

 context_intricated:
  - TunPossible ( contained_by: TUN-N )

 tub_local:

 tub_intricated:
```

#### Context2

```Gen
context: CheckTunSynAxoPrePossibility
 contained_by: TUN-SYN-AXO-PRE

 in_context: TunPossible
 rf: ( active: 60x )

 condition:
  out_context: 
```

#### Episode2

```Gen
episode: TunSynAxoPre
  contained_by: TUN-SYN-AXO-PRE

  in_context: ??
  rf: 1x

  hypothesis: NOT () AND NOT ()
  action: [ increase,  decrease]
  trace: None
```

### DEV-BD-BEH-POST-TUB: Developer

```Gen
developer: DEV-BD-BEH-POST-TUB

 contained_by: DEV-TUB-CONCEPTUAL
...
```

#### Context3

#### Episode3