# Milliseconds Time Scale 

## N-SPK

### Presynapse

#### 1 - Ca+ Clearance: \[AP\], \[Ca+\], \[CaFullnessTraces\], \[CaNotEmptyTraces\]

*Questa e’ una novita’ per evitare di fare controlli sempre. Invece viene attivato il contesto allo Spike, e invece di sparire alla fine dello spike, sparisce da solo (ContextSelf)*

- **RF**: 1
- **InContext**: Action potential depolarization (to \~+30 mV)
- **Context Self** 
  - **Condition: IF** \[Ca+\] **FULLNESS**
    - **OutContext**: {Ca+ FULLNESS}
    - **Consequence:** Ca+ clearance fast
    - **Tracce:** \[CaFullnessTraces\]
  - **Condition: IF** \[Ca+\] **NOT EMPTY AND \[**Ca+\] **NOT FULLNESS**
    - **OutContext**: {Ca+ NOT EMPTY}
    - **Consequence:** Ca+ clearance slow
    - **Tracce:** \[CaNotEmptyTraces\]
  - **Condition: IF** \[Ca+\] **EMPTY**
    - **EndContext**: Self

#### 2 - VGCC open: \[AP\], \[Ca+\], \[CaFullnessTraces\]

- **RF**: 1
- **InContext**: Action potential depolarization (to \~+30 mV)
  - **Consequence**: \[Ca+\] concentration increase 
  - **Tracce**: Se Ca+ FULLNESS, lascio tracce di overflow per modulazione DOWN, da capire UP

#### 3 - Vescicle release: \[Ca+\], \[RRP\], \[NT\]

*Il rilascio di NT avviene solo se Ca+ FULLNESS? Ovviamente se ci sono Vesciche. O dipende da altro? Cioe’ cosi’ rilascerebbe tutte le vesciche se c’e’ fullness. Dovremmo mettere un tag, o una discesa improvvisa di Ca+ al release di una vescica. Perche’ potremmo avere il caso che i VGGC sia talmente tanti da far entrare tanto calcio da far si che la prima vescica consumi CA ma non abbastanza da andare sotto FULLNESS*

- **RF**: 1
- **InContext**: Action potential depolarization (to \~+30 mV)
  - **Condition: IF** Ca+ **FULLNESS** **AND** RRP **NOT EMPTY (AND NOT** VES)
    - **Consequence**: Glutamate vescicle release. 
    - **Consequence:** Si consumano i Ca+?
    - **Traces**: Lascio tracce di non possibilita’ per la modulazione UP, da capire DOWN

#### 4 - Lactate uptake

Il Lactate viene mandato da Astro che ha fatto re-uptake di Glutamate, trasformato in Glutamine e poi Lactate. Il Lactate serve a fare ATP

- **Timing**: > 10 ms

#### 5 - Vescicle moved to RRP

From **The Reserve Pool** and **Recently Endocytosed Vesicles**

- **For Presynaptic Strengthening (e.g., 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.


- **Mechanism**: 
  - **residual calcium →** The key sensor is **Calmodulin (CaM)**. When bound to calcium, its structure changes → This Ca²⁺/Calmodulin complex then binds to and activates **Munc13**, the master regulator of vesicle priming.
  - **Munc13** is the essential protein that "primes" vesicles, making them release-ready (part of the SNARE complex assembly).
  - In its activated state (by Ca²⁺/CaM), Munc13's activity increases dramatically—by an order of magnitude or more.
  - This turns the normal, slow "drip-feed" of vesicles into a **high-speed conveyor belt**.
  - Superpriming requires ATP for phosphorylation reactions and for molecular motors that move vesicles. If the reserve pool is depleted or ATP is low, the superpriming "conveyor belt" has nothing to feed into the RRP. (Astrocyte)
  - The **vesicle reserve pool is a strictly private, local resource of each individual presynaptic bouton.** What is shared between synapses on the same axon are **signals (neuromodulators)** and **metabolic resources (energy)**, but **not the synaptic vesicles themselves.** This ensures both independent computation and cooperative metabolic support within the axonal branch.
  - ATP mostly comes from lactate from Atrocyte
- **Timing**: < 10 ms
- **InContext**: Ca+ **NOT EMPTY**
  - **Condition: IF** ATP **NOT EMPTY** **AND** RP **NOT EMPTY**
    - **Consequence:** Vescicles moved slow
    - **Tracce**: se non c’e’ abbastanza ATP o non ci sono abbastanza RP, lascio tracce per la modulazione UP, devo capire modulazione DOWN
- **InContext**: Ca+ **FULLNESS**
  - **Condition: IF** ATP **NOT EMPTY** **AND** RRP **NOT EMPTY**
    - **Consequence:** Vescicles moved fast
    - **Tracce**: se non c’e’ abbastanza ATP o non ci sono abbastanza RP, lascio tracce per la modulazione UP, devo capire modulazione DOWN

#### Observed 1 - Upregulation of Pr

- **Timing**: > 10 ms
- **Upregulation (Facilitation):** Residual Ca²⁺ from previous spikes increases P_r for next release

#### Observed 2 - Downregulation of Pr

- **Timing**: > 10 ms
- **Downregulation (Depression):** High-frequency firing depletes readily releasable vesicle pool, decreasing P_r

### Postsynapse

#### 1 - AMPA Opening

- **Timing**: < 1 ms
- **InContext:** Glutamate > **FULLNESS** 
- **OutContext:** AMPA receptor opening

#### 2 - Ca+ influx by AMPA

- **Timing**: < 1 ms
- **InContext:** AMPA receptor opened 
- **Consequence:** Na⁺ influx 
- **Consequence:** addition to local depolarization (EPSP) from AMPA activation

#### 3 - Limited Ca+ influx by NMDA

- **Timing**: > 1 ms


- **InContext:** local depolarization (EPSP) **NOT** **FULLNESS** (requires depolarization > -40mV)
- **Consequence:** Glutamate binding to NMDA receptors (Mg²⁺-blocked initially)
- **Consequence:** limited NMDA receptor opening → Ca²⁺ influx
- **Consequence:** limited addition to local depolarization (EPSP) from NMDA activation

#### 4 - Depolarization by bAP

- **Timing**: > 1 ms
- **InContext:** bAP backpropagating action potential
- **Consequence:** addition to local depolarization (EPSP) from bAP

#### 5 - Mg²⁺ NMDA unblock

- **Timing**: > 1 ms


- **InContext:** local depolarization (EPSP) > **FULLNESS** (requires depolarization > -40mV)
- **OutContext:** NMDA Mg²⁺ unblock

#### 6 - Full Ca+ influx by NDMA

- **Timing**: < 1 ms
- **InContext:** NMDA Mg²⁺ unblock 
- **Consequence:** Na⁺ influx 
- **Consequence:** addition to local depolarization (EPSP) from Full NMDA activation

#### Observed 1 - Upregulation

- **Upregulation:** Depolarization relieves NMDA Mg²⁺ block → Ca²⁺ influx amplification

#### Observed 2 - Downregulation

- **Downregulation:** AMPA desensitization acts as low-pass filter

### Dendrite

### Soma

### AIS

# Seconds Time Scale

## N-CHAN - LTP/LTD

Qui si modulano i canali ionici, sia quelli voltage (PRE/POST) che quelli Neuro (POST). Non si creano o si distruggono, ma si rendono attivi disattivi quelli presenti.

### Presynapse

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., 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.

#### 1 - **Augmentation:** 

- Calcium-sensing proteins (Munc13) alter release probability (1-10s range)
- Astrocyte gliotransmitters (ATP, D-serine, glutamate)
- ATP and Vescicle production

  Qui dobbiamo vedere su che scala temporale mettere questo comportamento
  - **Timing**: > 1s?

#### 2 - **Upregulation:** 

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

#### 3 - **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)

#### 

### Postsynapse

#### 1 - NO Signalling

### Dendrite

### Soma

### AIS

# Hours/Day Time Scale

## N-Meta - Structural

Qui si modula la possibilita’ di potenza di fuoco, sia come nuovi recettori (voltage e neuro) sia come grandezza di RP, RRP e velocita’ di spostamento.

### Presynapse

Long-lasting presynaptic strengthening requires **new proteins**:

- More vesicles
- More active zone proteins (e.g., RIM, Munc13)
- More mitochondria (for energy)
- More synaptic vesicle components (synaptobrevin, synaptotagmin)
- More cytoskeletal elements for structure

The neuron must **detect a sustained need for strengthening at a specific synapse**, send a signal to its nucleus, transcribe genes, and then deliver the new proteins back to that specific presynaptic bouton.

1. **Detection:**  Sustained high-frequency firing at the presynaptic terminal → elevated  Ca²⁺ and/or neuromodulator release (dopamine, norepinephrine).
2. **Signal to Nucleus:** Activation of kinases (PKA, CaMKIV) and retrograde importin signaling → **CREB phosphorylation** in the nucleus.
3. **Transcriptional Program:** CREB induces expression of:
   - **Immediate Early Genes** (e.g., *c-Fos*, *Arc*) that regulate further transcription.
   - **Effector Genes:** Presynaptic proteins (synapsins, RIM, Munc13), BDNF, cytoskeletal proteins.
4. **Delivery:** Newly synthesized mRNAs/proteins are actively transported down the axon, **targeted to the active synapses** that initiated the signal.
5. **Local Implementation:**
   - Assembly of new active zones.
   - Expansion of vesicle pools.
   - Possible local translation.
   - Bouton enlargement or new bouton formation.
6. **Stabilization:** Epigenetic modifications and continued autocrine/paracrine signaling (BDNF→TrkB) lock in the changes.

**In  essence, the neuron "knows" to strengthen a presynapse long-term  because the synapse's own sustained activity creates a biochemical  signature that reaches the nucleus, triggering a gene program  specifically designed to build a bigger, better release machine. This is  a fundamental mechanism underlying long-term memory storage at the  synaptic level.**

#### 1

- ATP-dependent vesicle cycling
- **Metabolic veto:** Insufficient ATP prevents vesicle release despite adequate Ca²⁺

#### 2

- Glutamine→glutamate conversion (via glutaminase). Glutamine from astrocytes (glutamate-glutamine cycle)

#### 3

- Vesicle refilling with glutamate

#### 3

- Maintenance of ion gradients

**Incoming Signals:**

- Astrocyte-supplied lactate (via monocarboxylate transporters)
- Metabolic state indicators (ATP levels, NAD/NADH ratio)

**Outgoing Signals:**

- Metabolic demand signals to astrocyte ??

**Modulation:**

- Lactate availability determines sustained release capacity during high activity ??

### Postsynapse

#### 1

#### 2

### Dendrite

### Soma

### AIS

## Astrocyte

- **Onset:** Astrocytic glutamate transporters (primarily GLT-1 and GLAST) start working **within milliseconds** of glutamate release into the synaptic cleft. They compete with postsynaptic receptors for binding glutamate.
- **Clearance Duration:** The complete clearance of synaptically released glutamate typically takes:
  - **Tens to hundreds of milliseconds (\~20-100 ms)** at a single synapse after a single synaptic event.
  - **Up to several seconds**  during and after a high-frequency spike train, as the total glutamate  load is higher and transporters can become temporarily saturated.

#### 2. **Timing Relative to Spike Trains: During and Between**

- **During the Train:**  With each pulse in a spike train, glutamate builds up in the cleft.  Astrocytes begin uptake immediately with each release. However, during  high-frequency stimulation (e.g., 50-100 Hz), release can temporarily  outpace clearance, leading to **glutamate spillover** and activation of peri- or extrasynaptic receptors.
- **Between Spikes (Inter-pulse Intervals):**  This is a critical period for uptake. The \~10-20 ms between spikes in a  high-frequency train is when transporters actively work to lower  glutamate concentration before the next pulse arrives. This helps  prevent excessive receptor desensitization and controls the temporal  fidelity of synaptic transmission.
- **After the Train:**  Uptake continues for hundreds of milliseconds to seconds to fully clear  the extracellular space, reset the synapse, and stop activation of  extrasynaptic NMDA or metabotropic glutamate receptors (mGluRs).

### Milliseconds Time Scale

#### 1

#### 2

### Seconds Time Scale

#### 1

#### 2

### Minutes Time Scale

#### 1

#### 2

## N-SYN - Creation/destruction SYN

### Presynapse

#### 1

- Structural growth/retraction of presynaptic bouton. Terminal size increases/decreases (Questo lo fa con SYN del NETWORK)

#### 2

- Changes in active zone size. Development percui la PRE si specializza. Puo’ essere anche modulation senza cambiare tipo di PRE.

#### 3

- Alterations in vesicle pool size

**Incoming Signals??:**

- Retrograde trophic factors (BDNF, sustained)
- Homeostatic scaling signals from soma

**Outgoing Signals??:**

- Modified synaptic strength through structural change

### Postsynapse

#### 1

#### 2

### Dendrite

### Soma

### Astrocyte

#### 1

#### 2