A trans-synaptic nanocolumn aligns neurotransmitter release to receptors

In the paper

“The average estimated diameter of ~80 nm for RIM1/2 NCs was very close to the reported size of PSD-95 and AMPA receptor (AMPAR) NCs4–6.”

What the sources say

• Partly supported

  The Results section, “Scaffold molecules are organized in subsynaptic clusters” (page unavailable), reports a PSD-95 subcluster diameter of 83 ± 4 nm, close to the citing sentence’s ~80 nm. The Results section, “Subsynaptic scaffolding domains concentrate synaptic AMPARs” (page unavailable), reports AMPAR enrichment within those domains but does not give a separate AMPAR nanocluster diameter. This source therefore supports the PSD-95 size comparison, but not the stated AMPAR nanocluster size. (LLM, conf=0.84)

  cites [4] MacGillavry, H. D., Song, Y., Raghavachari, S. & Blanpied, T. A. Nanoscale scaffolding domains within the postsynaptic density concentrate synaptic AMPA receptors. Neuron 78, 615–622 (2013) sourceExperimental — accuracy not yet measured
• Partly supported

  The ‘Subsynaptic AMPAR clusters’ section reports AMPAR nanodomain axes near 80 nm, supporting that comparison. But ‘Nanoscale co-organization of PSD95 and AMPARs’ (Fig. 7E) reports PSD95 subdomain axes of 158.2 and 102.2 nm and explicitly describes the AMPAR nanodomains as smaller. The copy does not support treating both reported sizes as very close to 80 nm. (LLM, conf=0.85)

  cites [5] Nair, D. et al. Super-resolution imaging reveals that AMPA receptors inside synapses are dynamically organized in nanodomains regulated by PSD95. J. Neurosci. 33, 13204–13224 (2013) sourceExperimental — accuracy not yet measured
• Disputed

  The Results section (page unavailable) reports a mean diameter of about 200 nm for palmitoylated PSD-95 nanodomains, not a size very close to the citing sentence’s ~80 nm. It reports that AMPAR clusters associate with those nanodomains but gives no AMPAR-cluster diameter. (LLM, conf=0.86)

  Checked by a reasoning model — may be wrong.

  cites [6] Fukata, Y. et al. Local palmitoylation cycles define activity-regulated postsynaptic subdomains. J. Cell Biol. 202, 145–161 (2013) sourceExperimental — accuracy not yet measured

In the paper

“These presynaptic RIM nanoclusters closely aligned with concentrated postsynaptic receptors and scaffolding proteins4–6, suggesting a transsynaptic molecular “nanocolumn.””

What the sources say

• Partly supported

  The Results section reports that AMPA receptors are enriched in postsynaptic PSD-95 scaffold clusters. The Discussion proposes pre–post alignment as a possibility but also says these clusters may concentrate receptors toward the synapse’s center rather than specifically align them with release sites. It does not establish close alignment with presynaptic RIM nanoclusters. (LLM, conf=0.88)

  cites [4] MacGillavry, H. D., Song, Y., Raghavachari, S. & Blanpied, T. A. Nanoscale scaffolding domains within the postsynaptic density concentrate synaptic AMPA receptors. Neuron 78, 615–622 (2013) sourceExperimental — accuracy not yet measured
• Partly supported

  The Abstract reports concentrated postsynaptic AMPA-receptor nanodomains that are often, but not always, colocalized with PSD95 scaffold clusters. The Discussion only proposes a possible correlation with presynaptic release sites; it does not establish that presynaptic RIM nanoclusters closely align with those postsynaptic clusters. No page numbers are available in our copy. (LLM, conf=0.88)

  cites [5] Nair, D. et al. Super-resolution imaging reveals that AMPA receptors inside synapses are dynamically organized in nanodomains regulated by PSD95. J. Neurosci. 33, 13204–13224 (2013) sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section on subsynaptic nanodomains (Fig. 4F–H; page unavailable) shows postsynaptic PSD-95 nanodomains associated with AMPA receptors and apposed to presynaptic vGlut1 labeling. It does not identify presynaptic RIM nanoclusters or show that those clusters closely align with the postsynaptic proteins. (LLM, conf=0.86)

  cites [6] Fukata, Y. et al. Local palmitoylation cycles define activity-regulated postsynaptic subdomains. J. Cell Biol. 202, 145–161 (2013) sourceExperimental — accuracy not yet measured

In the paper

“as the PSD-95 NCs concentrate higher density of receptors7.”

What the sources say

• ?Could not verify

  The passages from “Membrane Proteins of Active Zones” discuss receptors concentrated in presynaptic active zones, not receptors concentrated by PSD-95 nanoclusters. Searches for “PSD-95 nanoclusters” and “PSD-95 postsynaptic density receptors clustering” found no passage in our copy addressing the claim. (LLM, conf=0.76)

  cites [7] Südhof, T. C. The presynaptic active zone. Neuron 75, 11–25 (2012) sourceExperimental — accuracy not yet measured

In the paper

“The alignment of pre and postsynaptic nanoscale subdomains4–6 suggests that even small synapses may be composed of dynamic functional modules28,29.”

What the sources say

• Supported

  The Discussion describes nanoscale postsynaptic scaffold domains whose reorganization can affect transmission, even without a change in receptor number. The Results report that these domains change over time in living synapses. This supports the cited suggestion of dynamic functional modules; the sentence cites other sources for pre- and postsynaptic alignment. (LLM, conf=0.88)

  cites [4] MacGillavry, H. D., Song, Y., Raghavachari, S. & Blanpied, T. A. Nanoscale scaffolding domains within the postsynaptic density concentrate synaptic AMPA receptors. Neuron 78, 615–622 (2013) source
• Partly supported

  The Discussion (page unavailable) describes dynamic AMPAR nanodomains that may act as functional units activated by single-vesicle release, supporting the proposed module concept. The cited paper does not specifically establish that this organization occurs in small synapses; the sentence’s alignment claim is attached to other citations. (LLM, conf=0.78)

  cites [5] Nair, D. et al. Super-resolution imaging reveals that AMPA receptors inside synapses are dynamically organized in nanodomains regulated by PSD95. J. Neurosci. 33, 13204–13224 (2013) sourceExperimental — accuracy not yet measured
• Supported

  The Results section ('Subsynaptic nanodomains of palmitoylated PSD-95 as building blocks of the PSD'; page unavailable) describes one to four nanodomains per spine and associates individual nanodomains with AMPA receptors. The Discussion (page unavailable) models these domains as building blocks that can be created through local palmitoylation, while the Results report activity-dependent remodeling. This supports the hedged suggestion of dynamic functional modules; the preceding claim about pre- and postsynaptic alignment is attached to other citations. (LLM, conf=0.86)

  cites [6] Fukata, Y. et al. Local palmitoylation cycles define activity-regulated postsynaptic subdomains. J. Cell Biol. 202, 145–161 (2013) source
• Supported

  The section ‘The unreliable single vesicle release site as a basic building block of synapses’ proposes functional release sites as units from which synapses are assembled. The Conclusions state that smaller synapses have a few such sites and describe how their calcium-channel coupling can change during maturation. This supports the hedged claim about small synapses comprising dynamic functional modules; the alignment claim is attached to other citations. (LLM, conf=0.88)

  cites [28] Tarr, T. B., Dittrich, M. & Meriney, S. D. Are unreliable release mechanisms conserved from NMJ to CNS? Trends Neurosci. 36, 14–22 (2013) source
• ?Not checked — no full text of the sourcecites [29] Lisman, J. & Raghavachari, S. A unified model of the presynaptic and postsynaptic changes during LTP at CA1 synapses. Sci. STKE 2006, re11 (2006) source

In the paper

“Nevertheless, sensitivity of PSD-95 NC size to latrunculin4 further suggests that the spine cytoskeleton is engaged at the “base” of the column.”

What the sources say

• Supported

  The Discussion reports that acute actin depolymerization with latrunculin A reduced the area of PSD-95 clusters. It also describes actin filaments contacting the PSD at its interior face, supporting the cited observation and the hedged inference about cytoskeletal engagement. The “base of the column” is the citing authors’ framing. (LLM, conf=0.90)

  cites [4] MacGillavry, H. D., Song, Y., Raghavachari, S. & Blanpied, T. A. Nanoscale scaffolding domains within the postsynaptic density concentrate synaptic AMPA receptors. Neuron 78, 615–622 (2013) source

In the paper

“For the synapse as a whole, the impact of presynaptic nanoscale organization and confined vesicle sites (Fig. 1, 2) will depend strongly on whether these RIM NCs align with postsynaptic receptor NCs4.”

What the sources say

• Partly supported

  The Results section (‘Clustered distribution shapes postsynaptic responses’; page not provided) reports simulated currents nearly twice as large when vesicles released glutamate over AMPA-receptor clusters rather than off-cluster. The Discussion identifies pre–post alignment as a way to maximize transmission, but does not establish that this effect depends on alignment of RIM nanoclusters specifically; it also reports an advantage for clustered receptors even with randomly distributed release sites. (LLM, conf=0.85)

  cites [4] MacGillavry, H. D., Song, Y., Raghavachari, S. & Blanpied, T. A. Nanoscale scaffolding domains within the postsynaptic density concentrate synaptic AMPA receptors. Neuron 78, 615–622 (2013) sourceExperimental — accuracy not yet measured

In the paper

“we compared them with spontaneous release in TTX (Fig. 2a–c), which most likely arises from single vesicle fusion13.”

What the sources say

• Supported

  In the Results section, the paper identifies spontaneous fusion events recorded in TTX. Its analysis estimates that 17% of events at 2 mM extracellular Ca²⁺ were multivesicular, supporting the claim that spontaneous release under those conditions most likely arises from single-vesicle fusion. The multivesicular fraction increased at higher Ca²⁺ concentrations. (LLM, conf=0.92)

  cites [13] Leitz, J. & Kavalali, E. T. Fast retrieval and autonomous regulation of single spontaneously recycling synaptic vesicles . eLife 3, e03658 (2014) source

In the paper

“evoked Pr was significantly positively correlated with Syn1a area, as reported previously50”

What the sources say

• ?Could not verify

  The Results section on modeling action potential-evoked release reports vesicular fusion probabilities for different channel-distribution models, but not a correlation with Syn1a area. Searches for “Syn1a,” synapsin area, and evoked release probability versus bouton area found no passage reporting the claimed correlation. Page numbers were unavailable in our copy. (LLM, conf=0.72)

  cites [50] Ermolyuk, Y. S. et al. Differential triggering of spontaneous glutamate release by P/Q-, N- and R-type Ca2+ channels. Nat. Neurosci. 16, 1754–1763 (2013) sourceExperimental — accuracy not yet measured

In the paper

“The extent of ga(r) over 1, i.e. r0 for ga(r0) =1, is related to the pattern size of the internal heterogeneity (Extended Data Figure 2b–c)39.”

What the sources say

• Supported

  In Results and Discussion, under “Pair correlation functions quantify heterogeneity,” the paper says the shape and range of a correlation function reveal the structure underlying heterogeneity. Its Figure 3 description gives a model for circular domains in which g(r) reaches 1 at the average circle radius, directly linking that crossing distance to pattern size. (LLM, conf=0.88)

  cites [39] Veatch, S. L. et al. Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting. PLoS One 7, e31457 (2012) source

In the paper

“we induced long-term potentiation via APV withdrawal and glycine stimulation19”

What the sources say

• Partly supported

  The Experimental Procedures section (page unavailable) describes inducing LTP by perfusing hippocampal neurons with glycine-containing, magnesium-free solution. The paper lists APV as a reagent and reports that APV blocks chemLTP-induced SynGAP dispersion, but our copy does not describe APV withdrawal as part of the induction method. (LLM, conf=0.88)

  cites [19] Araki, Y., Zeng, M., Zhang, M. & Huganir, R. L. Rapid dispersion of SynGAP from synaptic spines triggers AMPA receptor insertion and spine enlargement during LTP. Neuron 85, 173–189 (2015) sourceExperimental — accuracy not yet measured

In the paper

“Central to this approach is the relationship between channel opening probability and its distance from a release site, determined previously by stochastic modeling approaches3,16,47: (6)Po(r)=0.42e-r/88nm”

What the sources say

• Supported

  The Figure 7C caption in the Implications of RLD section gives an exponential fit for the average opening probability of individual AMPA receptors as radial distance from the release site increases. It states the same equation as the citing sentence. (LLM, conf=0.95)

  cites [3] Franks, K. M., Stevens, C. F. & Sejnowski, T. J. Independent sources of quantal variability at single glutamatergic synapses. J. Neurosci. 23, 3186–3195 (2003) source
• ?Not checked — no full text of the sourcecites [16] Raghavachari, S. & Lisman, J. E. Properties of quantal transmission at CA1 synapses. J. Neurophysiol. 92, 2456–2467 (2004) source
• Partly supported

  The Results report simulations in which receptor distance from the release site affects AMPA-mediated responses, and the Discussion says response amplitude increases with proximity. But our copy does not give an opening-probability equation or the claimed 0.42 coefficient and 88-nm decay length; its 42% figure is a comparison of EPSC amplitudes, not an opening probability. (LLM, conf=0.86)

  cites [47] Xie, X., Liaw, J.-S., Baudry, M. & Berger, T. W. Novel expression mechanism for synaptic potentiation: alignment of presynaptic release site and postsynaptic receptor. Proc. Natl Acad. Sci. USA 94, 6983–6988 (1997) sourceExperimental — accuracy not yet measured

In the paper

“The average estimated diameter of ~80 nm for RIM1/2 NCs was very close to the reported size of PSD-95 and AMPA receptor (AMPAR) NCs4–6.”

In the paper

“Using localization microscopy, we report here that key proteins mediating vesicle priming and fusion are mutually co-enriched within nanometer-scaled subregions of the presynaptic active zone.”

In the paper

“The measured ACF showed significant nonuniformity compared to random ensembles (Fig. 1d).”

In the paper

“The distribution of RIM1/2 within the AZ, measured as 3D local density, was distinctively nonuniform with notable high-density peaks, which we characterized as nanoclusters (NCs, Fig. 1c, e).”

In the paper

“Remarkably, NMDA receptor activation triggered distinct phases of plasticity in which postsynaptic reorganization was followed by transsynaptic nanoscale realignment.”

In the paper

“However, following the 25-minute recovery, the enrichment index of RIM1/2 with respect to PSD-95 NCs increased with a corresponding increase in the percentage of enriched PSD-95 NCs (Fig. 4g–h).”

In the paper

“Following this stimulus, postsynaptic nanostructure was markedly disrupted in the generally opposite manner, with the synaptic cluster volume of PSD-95 and the number, volume, and protein density of PSD-95 NCs all reduced (Figs. 4d–f, Suppl. Table 3).”

In the paper

“Randomizing NC positions and out-of-NC molecules (keeping localizations within NC borders intact) abolished the PCF to chance level, while randomizing just the out-of-NC molecules only modestly reduced the PCF, indicating that the precise positioning of the NCs themselves dominate the overall correlation of protein distributions (Fig. 3c–d).”

In the paper

“These changes were prevented by co-application of the NMDAR antagonist APV (Fig 4a–c, Extended Data Fig. 10m).”

In the paper

“Similar results were found when we studied NMDA-induced changes on RIM1/2 and GluA2/3 alignment (Extended Data Fig. 10a–h).”

In the paper

“Isolated non-synaptic small groups of localizations showed a weaker ACF that was significant over a much smaller distance (Fig. 1d).”

In the paper

“Randomizing NC positions and out-of-NC molecules (keeping localizations within NC borders intact) abolished the PCF to chance level, while randomizing just the out-of-NC molecules only modestly reduced the PCF, indicating that the precise positioning of the NCs themselves dominate the overall correlation of protein distributions (Fig. 3c–d).”

In the paper

“NCs of each protein were more likely to be located near the center of synapses than near the edge (Fig. 1f, Extended Data Fig. 2i).”

In the paper

“Conversely, considering all individual RIM1 localizations, the distance from the nearest pHuse localization decreased as a function of RIM1 δ1 (Fig. 2k).”

In the paper

“We found 44.4 ± 3.0 % of PSD-95 NCs to be enriched (Extended Data Fig. 7b), and these NCs were opposed to RIM1/2 molecule densities that were 2.0 ± 0.1 times the average RIM1/2 synaptic cluster density (Fig. 3f).”

In the paper

“Similar to PSD-95, GluA2 was significantly enriched relative to RIM1/2 NCs, decaying e-fold per 66.9 ± 15.4 nm.”

In the paper

“the measured distribution with transsynaptic alignment gained 21.8 ± 0.5% in synaptic strength compared to a uniform distribution of AZ and PSD proteins (Extended Data Fig. 8), suggesting this synaptic architecture facilitates higher single vesicle response potency.”

In the paper

“and RIM1/2 was correspondingly enriched with respect to Shank NCs (Extended Data Fig. 9b).”

In the paper

“Notably, we found that transsynaptic molecular alignment may extend deeper into the postsynaptic cell, as postsynaptic scaffold molecules farther from the plasma membrane also colocalized with PSD-95 NCs (Extended Data Fig. 9a,c), and RIM1/2 was correspondingly enriched with respect to Shank NCs (Extended Data Fig. 9b).”

In the paper

“We found 44.4 ± 3.0 % of PSD-95 NCs to be enriched (Extended Data Fig. 7b), and these NCs were opposed to RIM1/2 molecule densities that were 2.0 ± 0.1 times the average RIM1/2 synaptic cluster density (Fig. 3f).”

In the paper

“A similar PSD-95 protein enrichment profile was found relative to the centers of RIM1/2 NCs (Fig. 3e).”

In the paper

“The frequency of action potential (AP)-independent spontaneous release events observed in TTX detected with vGpH was similar to the frequency of NMDA receptor (NMDAR)-dependent postsynaptic Ca2+ transients measured separately using the Ca2+ sensor GCaMP6f (Extended Data Fig. 5a).”

In the paper

“Furthermore, within individual boutons, RIM1 molecules within 40 nm of a pHuse location had significantly higher δ1 than those further away (Fig. 2j).”

In the paper

“Comparisons between these three proteins suggested that Munc13 had a wider distribution than RIM1/2 across the AZ and the distribution of Bassoon was closer to uniform throughout the synapse (Fig. 1g–i, Extended Data Fig. 2f–n).”

In the paper

“Single electrical field stimuli evoked vesicle fusion (Fig. 2a–b, Extended Data Fig. 4a) with a release probability (Pr) of 0.11 ± 0.01 per bouton, comparable to previous measurements, which was also sensitive to extracellular Ca2+ (Extended Data Fig. 4b–d), as expected.”

In the paper

“RIM1/2 staining revealed no change in synaptic cluster size or intensity at any point.”

In the paper

“The measured AZ-PSD distributions showed a significantly elevated PCF compared to simulated AZ-PSD distributions with either distribution fully randomized (Fig. 3b).”

In the paper

“This enrichment was again principally dependent on the relative positioning of NCs within synaptic clusters (Fig. 3e).”

In the paper

“By fitting the photon number distributions of evoked and spontaneous events, we estimated that ~72–82% of evoked events arose from single-vesicle fusion (Fig. 2c).”

In the paper

“Indeed, near pHuse sites, the average RIM1 δ1 was significantly greater than chance (Fig. 2i).”

In the paper

“3D-STORM imaging of RIM1/2, PSD-95, and GKAP1 at the same synapses further confirmed their mutual co-enrichment (Extended Data Fig. 9d–f).”

In the paper

“RIM1/2 localization densities within a 60 nm radius were significantly higher than the synaptic cluster average, decaying e-fold per 43.2 ± 12.1 nm away from the peak.”

In the paper

“Unlike PSD-95, RIM1/2 distributions were not affected immediately following the stimulus (Fig. 4d–f).”

In the paper

“In contrast, presynaptic nanostructure underwent a strikingly different pattern of reorganization that was detectable only in relation to PSD-95 NCs.”

In the paper

“We likewise found quantitatively similar number, characteristics, and alignment of pre- and postsynaptic NCs in acute hippocampal slices from adult rats (Extended Data Fig. 7f–h).”

In the paper

“Comparisons between these three proteins suggested that Munc13 had a wider distribution than RIM1/2 across the AZ and the distribution of Bassoon was closer to uniform throughout the synapse (Fig. 1g–i, Extended Data Fig. 2f–n).”

In the paper

“These tests suggest that there is no significant difference between these two antibodies.”

In the paper

“Mean distance from pHuse localizations as a function of local density measured by 5 × NND (Raw data R = 0.23***, n = 26/13).”

In the paper

“Enrichment of RIM1/2 to Shank NCs, n = 80 NCs from 32 synapses, scale 200 nm.”

In the paper

“Nevertheless, we find that they are still significantly smaller than the large majority of the nanoclusters we detected.”

In the paper

“spontaneous event frequency showed no relationship with Syn1a area (e, linear fit, evoked R = 0.30**, spontaneous R = 0.12, n.s.)”

In the paper

“Plasticity within nanocolumns”

In the paper

“Cumulative distributions of fusion areas for spontaneous and evoked release (K–S test, D = 0.23*)”

In the paper

“The percentage of PSD-95 NCs that were enriched with GKAP1, RIM1/2 or both with color-coded randomizations. *p<0.05, **p<0.01, ANOVA on ranks with pairwise comparison procedures (Dunn’s method), n = 32 NCs from 17 synapses in 7 different cultures.”

In the paper

“There was no difference between PSD-95 clusters with different labeling methods”

In the paper

“Proportion of pHuse localizations within 40 nm of a RIM1 localization as a function of RIM1 local density measured by 5 × NND (R = 0.35***).”

In the paper

“RIM1-mEos3.1 PALM identifies NCs”

In the paper

“The nanobodies showed a significant smaller size than antibodies.”

In the paper

“Enrichment profile between RIM1/2 and PSD-95 in tissue slices (28 synapses from 7 sections, 4 animals). *p<0.05 between measured and randomized synapses, two way ANOVA with pairwise comparison procedures (Dunn’s method).”

In the paper

“the r(0) for isolated localization groups were significantly less than r(0) for PSD-95 clusters.”

In the paper

“We found no significant difference between evoked area with and without excluding these events (Extended Data Fig. 5d).”

In the paper

“The two types of localizations groups showed similar variation in all dimensions.”

In the paper

“Enrichment of Homer1 with PSD-95 NCs, n = 118 NCs from 48 synapses, scale 100 nm.”

In the paper

“pHuse reveals differences between evoked and spontaneous fusion site areas”

In the paper

“This mixture probability defined the lower estimate (72%) for the percentage of single stimulus evoked fusion arising from single vesicles.”

In the paper

“Pooled data from 15 sets of simulations showing that the radius where g(r) first crosses 1 reasonably estimates the average NC diameters.”

In the paper

“Changes in PSD-95 NC area induced by NMDA and blocked by APV (n = 28 and 21, respectively). **p<0.01, n.s. = not significant, paired t-test.”

In the paper

“Note that similar to the results from the RIM1/2-PSD-95 analyses, only those RIM1/2 NCs that were enriched with GluR2/3 (dark red) were increased in volume.”

In the paper

“This architecture thus suggests a simple organizational principle of CNS synapses to maintain and modulate synaptic efficiency.”

In the paper

“Thus, we propose that the nanoarchitecture of the active zone directs action potential evoked vesicle fusion to occur preferentially at sites directly opposing postsynaptic receptor-scaffold ensembles.”

In the paper

“indicating that the precise positioning of the NCs themselves dominate the overall correlation of protein distributions (Fig. 3c–d).”

In the paper

“Because the delayed presynaptic modification was specific to aligned NCs, it may be that nanocolumns point to an alignment-specific, retrograde presynaptic compensation following postsynaptic depression (Fig. 4j), potentially relating to previous reports of presynaptic homeostatic plasticity22.”

What the sources say

• ?Not checked — no full text of the sourcecites [22] Davis, G. W. & Müller, M. Homeostatic control of presynaptic neurotransmitter release. Annu. Rev. Physiol. 77, 251–270 (2015) source

In the paper

“Together, these observations revealed a complex and heterogeneous molecular architecture within single synapses, typified by dense assemblies of fusion-associated proteins nearer the center.”

In the paper

“The graded protein densities involved suggest this may not be a clearly delineated structural element.”

In the paper

“Thus, this detailed metric for assessing nanoscale alignment revealed strong co-enrichment of these key proteins along narrow, transcellular columns.”

In the paper

“Thus, nanodistribution of RIM predicts the local probability of evoked fusion.”

In the paper

“Altogether, these results revealed an axially oriented molecular ensemble spanning the cleft within the bounds of the synapse, evoking the concept of a transsynaptic “nanocolumn” enriched with key proteins that regulate synaptic transmission (Extended Data Fig. 9g).”

In the paper

“Similar distribution and NC properties were found using a different antibody targeted toward a separate epitope in RIM1 (Extended Data Fig. 2d).”

In the paper

“vGpH, which increases in green fluorescence intensity upon vesicle fusion12.”

What the sources say

• ?Not checked — no full text of the sourcecites [12] Balaji, J. & Ryan, T. A. Single-vesicle imaging reveals that synaptic vesicle exocytosis and endocytosis are coupled by a single stochastic mode. Proc. Natl Acad. Sci. USA 104, 20576–20581 (2007) source

In the paper

“This suggests that pHuse area may be a better approximate for AZ area and the functional parameters of a synapse than bouton area.”

In the paper

“The difference between the size of the isolated localizations groups and PSD-95 clusters calculated by autocorrelation also argues against the possibility that the nanoclusters we detected were due to repetitive switching of one or a few fluorophores.”

In the paper

“Overall, these results demonstrated that the NCs we detected in our study were unlikely due to artifacts of antibody binding and labeling.”

In the paper

“Preferential release in nanocolumns can increase synaptic strength”

In the paper

“Since all the transsynaptic analyses were well controlled by randomizing simulations, this contamination is not able to produce false positives for transsynaptic alignment analyses.”

In the paper

“These results demonstrate that the NCs we detected in our study were not due to aggregation of multiple secondary antibodies to the primary antibodies.”

In the paper

“Since the number of localizations in one NC was typically small, using convex hull or alpha shape would greatly under-estimate the NC volume due to the border effect.”

In the paper

“Consequently, they may have prevented detection of small or weakly enriched NCs.”

In the paper

“These criteria were chosen based on a conservative strategy such that no NCs were identified in simulations of randomly distributed synaptic clusters with different densities.”

In the paper

“On the contrary, it may attenuate the significance of the differences in transsynaptic analyses based on NCs, including cross-correlation, protein enrichment and the fraction of enriched NCs.”