Experiments Summary

Theme 1: Introduction and Synaptic Plasticity

  1. Electrophysiological Recordings (General - often Patch Clamp: Voltage Clamp & Current Clamp)

    • Values Tested:

      • AMPA/NMDA Receptor Properties: Rise time, decay time of currents (EPSCs), ion permeability (by changing ion concentrations and measuring reversal potentials), voltage-dependent Mg2+ block (for NMDARs by varying holding potential).

      • Synaptic Strength/Amplitude (EPSCs/EPSPs): The magnitude of the postsynaptic current or potential change. This is the fundamental readout for plasticity.

      • Quantal Amplitude (a): Amplitude of response to a single vesicle release (often measured via miniature EPSC analysis or statistical methods).

      • Postsynaptic Potentials (PSPs): Voltage changes (EPSPs, IPSPs) in response to synaptic input (measured in current clamp).

  2. Paired-Pulse Experiments (PPR)

    • Values Tested:

      • Initial Probability of Release (p): Inferred from the Paired-Pulse Ratio (PPR = Amplitude of 2nd response / Amplitude of 1st response).

        • PPR < 1 (depression) suggests high initial 'p'.

        • PPR > 1 (facilitation) suggests low initial 'p'.

      • Short-Term Plasticity Dynamics: Nature and magnitude of facilitation or depression.

      • Locus of LTP/LTD Expression (Indirect): Changes (or lack thereof) in PPR after LTP/LTD induction can suggest pre- vs. postsynaptic mechanisms.

  3. Tetanic Stimulation / High-Frequency Stimulation (HFS)

    • Values Tested/Induced:

      • Induction of Post-Tetanic Potentiation (PTP): A short-term increase in synaptic strength.

      • Induction of NMDAR-Dependent Long-Term Potentiation (LTP): A long-lasting increase in synaptic strength.

      • Presynaptic Calcium Accumulation (Indirectly): HFS leads to significant Ca2+ buildup, which is a value being manipulated/observed.

  4. Low-Frequency Stimulation (LFS) (e.g., 1-5 Hz)

    • Values Tested/Induced:

      • Induction of NMDAR-Dependent Long-Term Depression (LTD): A long-lasting decrease in synaptic strength.

      • Modest, Prolonged Intracellular Ca2+ Elevation (Indirectly): LFS leads to a different Ca2+ dynamic than HFS.

  5. Coefficient of Variation (CV) Analysis (1/CV²)

    • Values Tested:
      • Locus of Synaptic Change (Pre- vs. Postsynaptic): Changes in 1/CV² (inversely related to variance) can distinguish between presynaptic (changes in 'n' or 'p') and postsynaptic (changes in 'a') mechanisms of plasticity, as 1/CV² is proportional to n*p.

  6. Photon Glutamate Uncaging (especially Two-Photon Excitation)

    • Values Tested:

      • Postsynaptic Receptor Sensitivity/Number: Directly probes the responsiveness of postsynaptic receptors by bypassing presynaptic release.

      • Locus of LTP/LTD Expression (Direct):

        • If natural (evoked) response increases but uncaging response doesn't change → presynaptic LTP.

        • If both natural and uncaging responses increase → postsynaptic LTP.

  7. Advanced Imaging (e.g., Calcium Imaging, Fluorescent Vesicle Reporters)

    • Values Tested:

      • Presynaptic Calcium Concentration/Dynamics: Real-time changes in [Ca2+]i.

      • Vesicle Trafficking Parameters: Docking, fusion rates, size of vesicle pools (readily releasable pool, reserve pool).

      • Structural Changes: Synapse size, spine morphology.

Theme 2: Inhibitory Synaptic Transmission

  1. Electrophysiology (Current Clamp / Voltage Clamp)

    • Values Tested:

      • Reversal Potential (E_ion, specifically E_Cl for GABA-A, E_K for GABA-B): The membrane potential at which there's no net flow of the specific ion. Crucial for determining if GABA is hyperpolarizing, shunting, or depolarizing.

      • Inhibitory Postsynaptic Currents (IPSCs): Amplitude, kinetics (rise/decay) of GABA-A and GABA-B mediated currents.

      • Inhibitory Postsynaptic Potentials (IPSPs): Amplitude, duration, and effect on membrane potential (hyperpolarization, shunting).

      • Neuronal Excitability: How IPSPs affect the likelihood of action potential firing.

      • Shunting Inhibition: Measured by observing the reduction in an EPSP's amplitude or depolarizing effect when co-activated with an IPSP near the resting potential.

  2. Pharmacological Manipulation (using specific receptor agonists/antagonists)

    • Values Tested:

      • Contribution of specific receptor subtypes (GABA-A vs. GABA-B) to inhibition: By blocking one type and observing the remaining current/potential.

      • Modulation of KCC2 function: Drugs affecting KCC2 can alter E_Cl and thus GABA's effect, which can be measured electrophysiologically.

  3. Paired-Pulse Experiments (at inhibitory synapses)

    • Values Tested:

      • Initial GABA Release Probability (p_GABA): Similar to excitatory synapses, PPR at inhibitory synapses can indicate high or low initial p_GABA.

      • Short-Term Plasticity of Inhibitory Transmission: Facilitation or depression of IPSCs/IPSPs.

  4. Optogenetic/Chemogenetic Manipulation of Interneuron Subtypes (e.g., PV, CCK, VIP, SST cells)

    • Values Tested:

      • Specific Role of Interneuron Subtypes in Circuit Function: By selectively activating/silencing them and recording from target neurons (e.g., principal cells or other interneurons).

      • Connectivity Patterns: Mapping inputs and outputs of specific interneuron types.

      • Impact on Network Oscillations: How specific interneurons contribute to rhythms like gamma.

Theme 3: Learning and Memory (Many experiments overlap with Theme 1, as synaptic plasticity is a core mechanism)

  1. Behavioral Paradigms (e.g., Morris water maze, fear conditioning, novel object recognition)

    • Values Tested:

      • Memory Formation/Acquisition: Learning curves, time to criterion.

      • Memory Recall/Retrieval: Performance on a test phase (e.g., time in target quadrant, freezing behavior).

      • Memory Extinction/Consolidation: Changes in memory strength over time or with new learning.

      • Working Memory Capacity/Duration: Performance on tasks requiring active maintenance and manipulation of information (e.g., delayed non-match to sample).

  2. Engram Tagging & Manipulation (e.g., c-fos based, activity-dependent reporters + opto/chemogenetics)

    • Values Tested:

      • Necessity of Engram Cells for Recall: Silencing tagged cells and observing impaired memory.

      • Sufficiency of Engram Cells for Recall: Activating tagged cells and observing memory recall/expression (e.g., artificial fear memory).

      • Excitability of Neurons for Engram Allocation: Correlating pre-learning excitability with likelihood of being part of an engram.

  3. In Vivo Electrophysiology (Single-unit, Multi-unit, LFP recordings in behaving animals)

    • Values Tested:

      • Place Cell Firing Fields: Location-specific firing of hippocampal neurons.

      • Grid Cell Firing Patterns: Hexagonal firing patterns in MEC.

      • Neuronal Firing Rate Changes with Learning/Attention: Correlation between task performance/attention and neuronal activity.

      • Memory Reactivation/Replay (during sleep/rest): Coordinated firing sequences mirroring waking experience.

      • Neural Correlates of Attention: Increased firing for attended stimuli, decreased for unattended; changes in synchrony/oscillations.

  4. Lesion Studies / Pharmacological Inactivation of Brain Regions (e.g., Hippocampus, mPFC, Amygdala)

    • Values Tested:

      • Necessity of a Brain Region for Specific Memory Types/Processes: Observing deficits in learning/memory after inactivation.

  5. EEG/LFP Recordings

    • Values Tested:

      • Brain Wave Frequencies and Power (Delta, Theta, Alpha, Beta, Gamma): Correlation with behavioral states (sleep, wakefulness, attention, task performance), memory consolidation processes.

Theme 5: Development and Neurodevelopmental Disorders

  1. Ocular Dominance Plasticity Paradigms (e.g., Monocular Deprivation - MD)

    • Values Tested (using techniques below):

      • Shift in Ocular Dominance: The relative strength of input from the open vs. deprived eye to visual cortex neurons.

      • Extent of LTD at Deprived Eye Synapses / LTP at Open Eye Synapses.

  2. Recording Techniques for ODP:

    • Single-Unit Extracellular Recordings (in visual cortex):

      • Value Tested: Firing rate responses of individual neurons to visual stimuli presented to each eye separately; calculation of Ocular Dominance Index (ODI).

    • Calcium Fluorescence Imaging (in visual cortex):

      • Value Tested: Population activity (Ca2+ transients) in response to monocular/binocular visual stimuli over time.

    • Visually-Evoked Potentials (VEPs):

      • Value Tested: Gross electrical response of visual cortex to stimulation of each eye.

  3. Pharmacological/Genetic Manipulation during Critical Periods

    • Values Tested:

      • Role of Specific Molecules (e.g., GABA, NMDA receptor subunits, LTD machinery) in opening/closing critical periods or mediating ODP: By blocking/enhancing their function and observing effects on ODP.

      • Chloride Reversal Potential (E_Cl) changes: Measured electrophysiologically to track GABAergic maturation.

  4. Dark Rearing Experiments (Metaplasticity)

    • Values Tested:

      • Baseline Plasticity State: How experience (or lack thereof) alters the subsequent capacity for LTP/LTD induction.

      • NMDA Receptor Subunit Composition: Biochemical analysis.

  5. Animal Models of Neurodevelopmental Disorders (e.g., genetic KOs/KIs, pharmacological models like NMDAR hypofunction for Schizophrenia, PTZ for epilepsy)

    • Values Tested (using electrophysiology, EEG, behavioral tests):

      • Gamma Oscillation Power/Coherence: Often impaired in schizophrenia models.

      • PV Interneuron Function/Number/Connectivity: Histology, electrophysiology.

      • Excitatory/Inhibitory Balance: Measured via synaptic currents or network activity.

      • Seizure Threshold/Severity: In epilepsy models.

      • KCC2 Expression/Function: Biochemical or electrophysiological assessment (E_Cl).

      • Cognitive/Behavioral Deficits: Relevant to human symptoms.

Theme 6: Neurodegeneration

  1. Biomarker Assays:

    • PET Imaging (with specific radiotracers):

      • Value Tested: Brain load/distribution of fibrillary Aβ plaques or tau tangles.

    • Cerebrospinal Fluid (CSF) Analysis:

      • Value Tested: Levels of Aβ42, Aβ42/Aβ40 ratio, total tau (t-tau), phosphorylated tau (p-tau), Neurofilament light chain (NfL).

    • Blood Biomarker Tests:

      • Value Tested: Plasma levels of p-tau181, p-tau217, Aβ42/Aβ40 ratio, NfL, GFAP.

  2. Neuropathological Staging (Post-mortem or in animal models using histology/immunohistochemistry)

    • Values Tested:

      • Density and Distribution of Pathological Proteins: Amyloid plaques (Thal phases), neurofibrillary tangles (Braak stages), Lewy bodies, TDP-43 inclusions, prion plaques.

      • Neuronal Loss/Dysfunction in Specific Regions.

  3. Genetic Testing (for familial forms or risk alleles)

    • Values Tested:

      • Presence of Mutations: In APP, PSEN1, PSEN2 (familial AD), HTT (Huntington's CAG repeats), PINK1/Parkin (PD).

      • ApoE Genotype (ε2, ε3, ε4): Risk factor for late-onset AD.

  4. Animal Models of Neurodegenerative Diseases (transgenic, knock-in, toxin-induced, protein seed injection)

    • Values Tested:

      • Rate of Pathological Protein Aggregation & Spread.

      • Degree of Neuronal Dysfunction/Loss.

      • Severity of Behavioral/Motor Deficits (e.g., cognitive tests for AD models, motor tests for PD models).

      • Mitochondrial Function: Assays for respiratory chain activity, ROS production, mitophagy.

  5. Real-Time Quaking-Induced Conversion (RT-QuIC)

    • Values Tested:

      • Presence and Seeding Activity of Misfolded Proteins (PrPSc, α-synuclein, tau) in biological samples (CSF, skin): Provides diagnostic value by amplifying these specific aggregates.

  6. Deep Brain Stimulation (DBS) (as a treatment that underwent experimental testing)

    • Values Tested (during clinical trials/optimization):

      • Improvement in Motor Scores (e.g., UPDRS for PD).

      • Optimal Stimulation Parameters (frequency, amplitude, location).

  7. Cell-Replacement Therapy Studies (preclinical and clinical trials)

    • Values Tested:

      • Graft Survival and Integration.

      • Restoration of Neurotransmitter Levels (e.g., dopamine in PD).

      • Functional Motor/Cognitive Improvement.

Theme 7: Motor and Sensory Neuroscience

  1. Electrophysiology of Sensory Receptors (e.g., Photoreceptors in retina)

    • Values Tested:

      • Receptor Potential: Graded potential change in response to stimulus (e.g., light hyperpolarizing photoreceptors).

      • Signal Transduction Cascade Activity: e.g., levels of cGMP in photoreceptors.

      • Neurotransmitter Release Modulation: e.g., reduced glutamate release from hyperpolarized photoreceptors.

  2. Electromyography (EMG)

    • Values Tested:

      • Muscle Activity/Contraction Strength & Timing.

      • Motor Unit Action Potentials (MUAPs): To define motor units.

  3. Nerve Conduction Studies / Motor Evoked Potentials (MEPs)

    • Values Tested:

      • Integrity and Conduction Velocity of Motor/Sensory Nerves.

      • Excitability of Corticospinal Tract (using Transcranial Magnetic Stimulation - TMS to elicit MEPs).

  4. Reflex Testing (e.g., tapping patellar tendon for myotatic reflex)

    • Values Tested:

      • Reflex Latency and Amplitude.

      • Integrity of Monosynaptic/Polysynaptic Reflex Arcs.

      • Muscle Spindle Sensitivity.

  5. Animal Models of Movement Disorders (e.g., MPTP model for Parkinson's)

    • Values Tested:

      • Degree of Dopamine Neuron Loss (for PD models).

      • Severity of Motor Deficits (bradykinesia, rigidity, tremor).

      • Activity Changes in Basal Ganglia Nuclei (via electrophysiology or c-fos mapping).

This list covers a wide range of experimental approaches. The specific "value" being tested often depends on the precise experimental design and the question being asked, but this gives a good overview based on your notes.