Documentation: References
These data provide details of the experimental protocols and techniques used
in the plasticity studies, as well as the numerical results of the experiments.
In total, the plasticity data is derived from 338 papers. 124 of these (37%)
have been curated in detail in the manner explained here.
Contents
Background
Reference
Citation
PMID
Experiment Number
Gene
Gene Name
Mutation Type
Tissue
Culture
Protocol
Recording Chamber or In Vivo
Temperature (degrees C)
Ca2+ Concentration (mM)
Stimulation
Protocol
Baseline Stimulus Intensity (%)
Induction Stimulus Intensity (%)
No. of Series
Interseries Interval (s)
No. of Trains
Intertrain Interval (s)
No. of Pulses
Interpulse Interval (ms)
Total Pulse Duration (s)
Pulse Frequency (Hz)
Recording
Protocol
fEPSP/EPSP/EPSC/Population spike recorded
Intracellular/Extracellular Pairing
Time Post-Stimulation (min)
Drug(s)
used
Drug(s)
Drug Concentration (microM)
Method of Drug Application
Mouse
Details and Results
Mouse Age
Number of Mice Used
Number of Slices Used
Number of Cells Used
Number (Mice/Slices Not Specified)
Mean Amplitude
Standard Error
P-Value
Paired-Pulse
Facilitation
PPF Interstimulus Range (ms)
PPF Wild-Type Number
PPF Mutant Number
Result
Other
Experiments
NMDA/AMPA-related Tests Undertaken and Results
Depotentiation/Dedepression/Extra Information
Background
Reference
The reference for the paper: the journal name, issue, volume and year are given.
Citation
The full citation for the paper, including the authors and the title.
PMID
The PubMed ID for the paper. The ID acts as a link to the paper's entry on PubMed.
Experiment Number
Each paper typically contains more than one experiment. Each experiment is assigned
a number (generally reflecting the order in which they are reported in the paper),
to serve as an identifier.
Gene Name
The common gene name.
Mutation Type
The type of mutation the gene has been subjected to in the paper. Mutations
were classified as belonging to one of the following categories:
| Mutation type |
Code |
| Knockout |
1ko |
| Over-Expression |
1ov |
| Point |
1po |
| Truncation |
1tr |
| Conditional |
1co |
| Other |
1ot |
Tissue
Name of the brain region in which synaptic plasticity was studied. Brain regions
were classified as belonging to one of the following categories:
| Hippocampal Regions |
Non-Hippocampal Regions |
| CA1-CA3 Schaffer Collateral / Commisural |
Cerebellum |
| Dentate Gyrus |
Striatum |
| Mossy Fibres |
Cortex |
| Other Hippocampal |
Amygdala |
| |
Other |
Recording Chamber or In Vivo
The environment in which the electrophysiological experiments were carried out.
Experiments may have been conducted in vivo or in a recording chamber.
Such chambers may be further classified as 'submerged' (in which the slice is
entirely submerged in medium) or 'interface' (in which only a thin layer of
medium covers the slice).
Temperature (degrees C)
The temperature at which the experiment was maintained. Where the temperature
was kept within a certain range, this is indicated. In some cases, the experimenters
report only that the experiment was kept at 'room temperature', in which case
this is stated.
Ca2+ Concentration (mM)
The concentration of calcium ions in the medium, measured in milliMoles per
litre.
Baseline Stimulus Intensity (%)
The 'baseline' stimulation intensity used to stimulate the slice in order to
elicit a response, measured as a percentage of the stimulus intensity required
to achieve the maximum EPSP response.
Induction Stimulus Intensity (%)
The 'induction' stimulation intensity used specifically during the plasticity
induction protocol, measured as a percentage of the stimulus intensity required
to achieve the maximum EPSP response.
No. of Series
The number of series (of trains) delivered.
Interseries Interval (s)
The interval between the end of one series and the beginning of the next one,
measured in seconds. Where only one series was delivered, this field reads 'N/A'.
No. of Trains
The number of trains (of pulses) delivered.
Intertrain Interval (s)
The interval between the end of one train and the beginning of the next one,
measured in seconds. Where only one train was delivered, this field reads 'N/A'.
No. of Pulses (stated or calculated)
The number of electrical pulses within each train. This figure is not necessarily
stated in the paper, in which case we have (where possible) calculated it from
other figures supplied. We state whether the figure was stated in the paper
or whether we have calculated it ourselves.
Interpulse Interval (msec)
The interval between the end of one pulse and the beginning of the next one,
measured in milliseconds
Total Pulse Duration (s) (stated or calculated)
The total duration of the pulses, calculated as the total number of pulses delivered
multiplied by the duration of an individual pulse. This figure is not necessarily
stated in the paper, in which case we have (where possible) calculated it from
other figures supplied. We state whether the figure was stated in the paper
or whether we have calculated it ourselves.
Pulse Frequency (Hz)
The frequency at which the pulses were delivered, measured in Hertz (Hz). 1Hz
is equivalent to one pulse per second. In some papers, the precise frequency
is not stated and is instead replaced by a statement such as 'theta stimulation';
in such cases we have reproduced the statement from the paper.
fEPSP/EPSP/EPSC/Population spike Recorded
The type of excitatory post synaptic potentials/currents recorded. fEPSP is
an extracellular field EPSP, so is a measure of the activity of many cells.
EPSP is an intracellular recording of the membrane potential of one neurone.
EPSC is a recording of intracellular current in one neurone under voltage-clamp.
Population spike is an extracellular field recording in the stratum pyramidale
or granule cell body layer representing sum of somatic action potentials.
Intracellular/Extracellular Pairing
Intracellular pairing is an injection of a depolarising pulse during plasticity
induction. Extracellular pairing is an antidromic stimulation of neurones concomitant
with the synaptic stimulation.
Time Post-Stimulation (min)
At what time (in minutes), following the stimulation protocol, were recordings
taken?
Drug(s)
The name(s) of the drug(s) used, if any.
| Drug |
Drug Action |
| 1400W |
Selective iNOS inhibitor |
| 4-AP |
A-type potassium channel blocker |
| 6-APB |
D1 dopamine receptor agonist |
| 6-Br-APB |
D1-D5 receptor agonist |
| ACPD |
Selective agonist for mGluRs (groups I and II) |
| Aminoguanidine |
Irreversible inhibitor of iNOS |
| Amyloid beta protein |
Neurotrophic and neurotoxic effects |
| Amyloid beta protein 1-42 |
Downregulator of bcl-2, increases level of bax, neurotoxic |
| Anisomycin |
Protein synthesis inhibitor |
| AP5 |
NMDAR antagonist |
| ARMKVAKNPQ |
Control for KAMKVAKNPQ |
| Baclofen |
Selective GABAB receptor antagonist |
| BAPTA |
Ca2+ chelator |
| Bicuculline |
GABA-A antagonist |
| Bicuculline methiodide |
Water-soluble, more stable salt of bicuculline |
| Bicuculline methochloride |
Water-soluble, more stable salt of bicuculline |
| Calyculin A |
PP1/2A inhibitor |
| Catalase |
Scavenger of hydrogen peroxide, converting it to oxygen and water |
| Chelerythrine |
Protein kinase C inhibitor |
| CHPG |
Selective mGluR5 agonist |
| CNQX |
AMPA/kainate receptor antagonist |
| CPCCOEt |
hmGlu1 subtype selective non-competitive antagonist |
| CXCL10 |
Chemoattractant for several types of leukocyte |
| Cyclosporin A |
Inhibits phosphatase activity of Calcineurin |
| Cyto-D |
Depolymerises actin |
| D-AP5 |
Competitive NMDA antagonist, more active form of AP5 |
| DCG-IV |
Presynaptic depressant, agonist for group 2 mGluR |
| DHPG |
Selective group 1 mGluR agonist |
| DL-AP5 |
NMDA antagonist |
| Dopamine |
Neurotransmitter |
| Doxycycline |
Regulator of Rap1B expression |
| DPI |
Inhibitor of superoxide production by NADPH |
| Forskolin |
Cell-permeable activator of adenylyl cyclase |
| Galanin (1-29) |
GalR1/GalR2 agonist |
| Galanin (2-11) |
High-affinity GalR2 agonist |
| Gallamine |
M2 receptor-preferring antagonist |
| GluR2 cDNA |
GluR2 DNA synthesised from mature mRNA |
| GluR3 Q-R |
Pore mutant form of GluR3 |
| GluR3 Q-R NSF+ |
Pore mutant form of GluR3 with NSF binding site |
| GYKI 53655 |
Selective non-competitive AMPA receptor antagonist |
| IBMX |
Phosphodiesterase inhibitor |
| Jagged |
Notch ligand |
| KAMKVAKNPQ |
Disruptor of GluR2-NSF interaction |
| KT5720 |
PKA selective inhibitor |
| L-AP4 |
Selective group III metabotropic glutamate receptor antagonist |
| Latrunculin B |
'Actin-perturbing agent' |
| L-CCG1 |
Group 2 metabotropic glutamate receptor agonist |
| LY-17555 |
D2 dopamine receptor agonist |
| LY-367385 |
Selective mGlu1a |
| MCPG |
Non-selective group I/group II mGluR agonist |
| Minocycline |
Tetracycline-derived inhibitor of microglial activation |
| MPEP |
Selective non-competitive mGluR5 antagonist |
| Nifedipine |
L-type calcium channel blocker |
| NL-ARG |
NOS inhibitor |
| NOArg |
NOS inhibitor |
| Okadaic acid |
PP1/2A inhibitor |
| PDA |
Protein kinase C activator |
| PDBu |
Protein kinase C activator |
| Picrotoxin |
GABA-A antagonist |
| PKCalpha-carrying plasmid |
Transfection vector |
| PKCbeta-carrying plasmid |
Transfection vector |
| PKCgamma-carrying plasmid |
Transfection vector |
| PKI |
PKA inhibitor peptide |
| Propranolol |
Beta-adrenergic antagonist |
| Rapamycin |
Immunosuppressant |
| Rp-cAMPS |
Competitive agonist of cAMP-induced activation of PKA |
| RS-4CPG |
Group 1 mGluR antagonist |
| SCH-23390 |
D1 dopamine receptor antagonist |
| sc-Jag-1 |
Control for Jagged |
| SL327 |
Selective inhibitor of MEK1 and MEK2 |
| SNAP |
Source of NO, does not induce tolerance |
| SOD |
Catalyst of the removal of superoxide |
| Sp-8CPT-cAMP-S |
cAMP analogue: PKA activator |
| Sp-cAMPS |
PKA agonist |
| SQ22536 |
Cell-permeable adenylate cyclase inhibitor |
| Sulpiride |
D2 dopamine receptor antagonist |
| U0126 |
Selective, non-competitive MAP kinase kinase inhibitor |
| Unaggregated Amyloid beta protein 1-42 |
Less neurotoxic than aggregated version |
| Y-27632 |
Selective inhibitor of p160ROCK |
| Zaprinast |
Phosphodiesterase inhibitor (PDE5/6/9) |
Drug Concentration (microM)
The concentration of the drug used, in microMoles per litre.
Method of Drug Application
The method by which the drug was applied to the tissue samples.
This section provides as much information as is available on the numbers of
mice used and the results obtained, for both wild-type and mutant mice.
Mouse Age
The ages of the mice when they were used for the experiments. Ages are measured
variously in days, weeks and months: in almost all cases, we have simply followed
the statements made in the paper. In some cases, mice were simply described
as 'adult' or some other term; in these cases, the term has been reproduced.
Number of Mice Used
Where specified, the number of individual mice used in the experiments.
Number of Slices Used
Where specified, the total number of brain slices used in the experiments.
Number of Cells Used
Where specified, the total number of cells used in the experiments.
Number (Mice/Slices Not Specified)
In some cases, experimenters only supply a number, without specifying whether
it refers to the number of mice, the number of slices or the number of cells.
In such cases, that number is reproduced here.
Mean Amplitude
The mean amplitude of the post-synaptic response following stimulation, measured
as a percentage of the baseline response. A baseline response corresponds to
100%. A figure significantly larger than 100% indicates that LTP has occurred;
a figure significantly smaller than 100% indicates that LTD has occurred. In
some cases these figures are not provided, in which case we provide a verbal
summary of the results, such as 'Robust LTP'.
Standard Error
The standard error of the mean amplitude, measured as a percentage of the baseline
response.
P-Value
Statistical measure of the significance of the difference between the wild-type
mean amplitude and the mutant mean amplitude. Where they are supplied, P-values
are given. When the paper does not supply them, we have provided a verbal statement
such as 'No Significant Difference'.
Paired-Pulse Facilitation (PPF) is a form of short-term synaptic plasticity.
Two neurones receive two pulses of stimulation in close succession (usually
in the tens of milliseconds). This leads to a short-term increase in the synaptic
strength; the post-synaptic response increases from its baseline level.
PPF Interstimulus Range (ms)
The time interval(s) between the two stimuli that were used to elicit PPF.
PPF Wild-Type Number
The number of wild-type mice/slices used in the PPF experiments.
PPF Mutant Number
The number of mutant mice/slices used in the PPF experiments.
Result
The result(s) of the PPF experiments, stated concisely.
NMDA/AMPA-related Tests Undertaken and Results
Any tests of NMDA and/or AMPA function were described here and their results
listed.
Depotentiation/Dedepression/Extra Information
Depotentiation is a reversal of LTP, produced by low-frequency stimulation of
the kind used to generate LTD. Dedepression, similarly, is a reversal of LTD,
produced by high-frequency stimulation of the kind used to generate LTP. Experiments
investigating either of these two phenomena, and any additional plasticity phenomena
not included elsewhere, are briefly described here.
