Article Figures & Data
Figures
- Figure 1.
Spine reconstruction from confocal microscopy images. A, B, Apical (A) and basal (B) dendritic segments from intracellularly injected layer 3 pyramidal neurons from the human cingulate cortex. C, D, 3D reconstruction of each dendritic spine from the dendritic segment shown in A, B. Estimation of the spine volume values is shown by color codes (blue-white: 0–0.896 μm3). E, F, Surface meshes that were manually created for each individual spine. G–J, Higher magnification images of the dendritic segment shown in B. Spine lengths (that were measured in 3D) are also illustrated in H, J. K, Example of a typical spine showing a clear head and neck. White line shows neck length. L, Illustrates the corresponding surface mesh. White line shows neck diameter. Arrow indicates a spine not showing a clear head and neck. Dynamic scale bar (presented in L): 5 μm (A–F), 2 μm (G–J), and 0.6 μm (K, L).
- Figure 2.
Computational separation of spine heads and necks. A, Human apical spines, the same dendritic shaft that is presented in Figure 1A. B, Human basal spines, the same dendritic shaft that is presented in Figure 1B. Spine heads in green and spine necks in blue. The orange dots indicate the insertion point of the spine into the dendritic shaft.
- Figure 3.
Spine dataset classification. A, Complete spines, consisting of a single component that can be separated into the head and neck. B, Complete spines, consisting of a single component that could not be separated into the head and neck. C, Incomplete one component spines, detached from the dendritic shaft, containing mainly the head. D, Incomplete spines consisting of two components. E, Incomplete spines consisting of three components. The orange points indicate spine insertion on the dendritic shaft.
- Figure 4.
Spine neck repair of group C and group D spines. A, Incomplete spine mesh from group C. The orange dot indicates the base point, between the spine neck and the dendritic shaft. B, Repair of the neck by adding a cylinder between the base point and the closest vertex of the head. This cylinder is not the real neck; it was added just to enable measuring the neck length and separating the head and neck. C, Separation into head (green) and neck (blue). D, Incomplete spine mesh, consisting of two components (group D). E, Repair of the neck by adding a cylinder between the two components, resulted in a connected spine. F, Separation into head (green) and neck (blue). Scale bar: 200 nm. Extended Data Figure 4-1 shows the comparison between the morphologic parameters of only the complete spines (group A) and the complete and repaired spines (groups A, C, and D).
- Figure 5.
Human spines: morphologic parameter distributions. The distributions of the head volumes, neck lengths, and neck diameters of complete spines (group A). A–C, Comparison between basal and apical spines of the 40-year-old-individual. D–F, Comparison between basal and apical spines of the 85-year-old individual. G–I, Comparison between 40- and 85-year-old basal spines. J–L, Comparison between 40- and 85-year-old apical spines. Dashed vertical lines indicate the median values and the circles indicate the average. Apical 40 n = 430, basal 40 n = 1012, apical 85 n = 424, and basal 85 n = 670. Mann–Whitney U rank test, the asterisks indicate statistical significance; *p < 0.05, **p < 0.01, ***p < 0.001. Extended Data Figure 5-1 shows the distributions of the head volumes and neck lengths for the complete and repaired spines (groups A, C, and D). Extended Data Figure 5-2 shows the intraindividual analysis of the dendrites from the 40- and the 85-year-old humans.
- Figure 6.
Mouse spines: morphologic parameter distributions. The distributions of complete spines (group A). A–C, Head volume, neck length, and neck diameter distributions of basal (light gray, n = 163) and apical (dark gray, n = 88) spines. Dashed vertical lines indicate the median values and the circles indicate the average. p = 0.48, 0.23, 0.2; Mann–Whitney U rank test. Extended Data Figure 6-1 shows the results for the complete and repaired spines (groups A, C, and D).
- Figure 7.
Spine morphologic distributions of humans and mice. A–C, Head volume, neck length, and neck diameter distributions in human (green, n = 2536) and mouse (blue, n = 251) complete spines (group A). Mann–Whitney U rank test, ***p < 0.001. D–F, Correlation between spine head and neck morphologic variables. The correlation coefficients (Spearman) are indicated for each graph. The asterisks indicate statistical significance; **p < 0.01, ***p < 0.001. Two-sided p-value for a hypothesis test whose null hypothesis is that the slope is zero, using Wald test with t distribution of the test statistic. Extended Data Figure 7-1 shows the results for the complete and repaired spines (groups A, C, and D). Extended Data Figure 7-2 shows the correlation between head volume and neck length separately for different ages and dendrites.
- Figure 8.
Differences in morphologic parameters, including complete and repaired spines (groups A, C, and D). Apical and basal dendritic compartments of the 40- and the 85-year-old human individuals. Dendritic shaft and spine properties from previous work (gray font; Benavides-Piccione et al., 2013) and spine properties from the present work (black font).
Tables
- Table 1
Morphologic parameters values of human complete (group A) apical and basal spines from the 40- and 85-year-old individuals
Age Average ± STD Median Range Head volume (μm3) 40 Apical 0.3526 ± 0.25 0.2846 0.0274–1.6268 Basal 0.3426 ± 0.22 0.2978 0.0324–2.206 85 Apical 0.3816 ± 0.23 0.3331 0.0378–1.3154 Basal 0.4103 ± 0.25 0.3559 0.0189–1.538 Neck length (μm) 40 Apical 0.6739 ± 0.4 0.5664 0.1839–3.1336 Basal 0.7464 ± 0.46 0.6074 0.0353–2.9899 85 Apical 0.8025 ± 0.56 0.5976 0.1865–3.7792 Basal 0.7483 ± 0.47 0.5911 0.0818–4.0137 Neck diameter (nm) 40 Apical 339.9 ± 114.36 328.7 97.4–836.4 Basal 361.67 ± 122 346.32 113.5–868.4 85 Apical 340.08 ± 120 320.98 99.7–732.6 Basal 356.66 ± 124 340.62 100.9–811.8 Since neck diameters below the resolution limit (∼200 nm) cannot be visualized using LM, these values correspond to those spines that were completely visualized (60%). Extended Data Table 1-1 shows the morphologic parameters values for the complete and repaired spines (groups A, C, and D).
- Table 2
Morphologic parameters of apical (n = 88) and basal (n = 163) spines from complete mouse spines (group A)
Average ± STD Median Range Head volume (μm3) Apical 0.1875 ± 0.14 0.1441 0.0151–0.9041 Basal 0.1832 ± 0.13 0.1468 0.0161–0.7097 Neck length (μm) Apical 0.5627 ± 0.33 0.4994 0.0195–2.4059 Basal 0.5467 ± 0.31 0.463 0.2074–2.2687 Neck diameter (nm) Apical 295.86 ± 116 288.06 92.41–640.53 Basal 278.55 ± 102 267.1 88.61–676.45 Since neck diameters below the resolution limit (∼200 nm) cannot be visualized using LM, these values correspond to those spines that were completely visualized (60%). Extended Data Table 2-1 shows the morphologic parameters values for the complete and repaired spines (groups A, C, and D).
Extended Data Figure 4-1
The repair process extends necks without changing head sizes. Head volume and neck length distributions of the complete spines (group A, continuous lines) and including the repaired spines (groups A, C, and D, dashed lines). A, B, Basal spines of the 40-year-old individual, n = 1359, 1012. C, D, Apical spines of the 40-year-old individual, n = 925, 430. E, F, Basal spines of the 85-year-old individual, n = 949, 670. G, H, Apical spines of the 85-year-old individual, n = 623, 424. Vertical lines indicate the median values. Mann–Whitney U rank test, the asterisks indicate statistical significance; ***p < 0.001. Download Figure 4-1, EPS file.
Extended Data Figure 5-1
Human spines morphological parameter distributions in the complete and repaired spines (groups A, C, and D). The distributions of the head volumes and neck lengths. A, B, Comparison between basal and apical spines of the 40-year-old individual. C, D, Comparison between basal and apical spines of the 85-year-old individual. E, F, Comparison between 40- and 85-year-old spines in the basal spines. G, H, Comparison between 40- and 85-year-old spines in the apical spines. Dashed lines indicate the median values and the circles indicate the average. Apical 40 n = 925, basal 40 n = 1,359, apical 85 n = 623, and basal 85 n = 949. Mann–Whitney U rank test, the asterisks indicate statistical significance; **p < 0.01, ***p < 0.001. Download Figure 5-1, EPS file.
Extended Data Figure 5-2
Intraindividual analysis of the dendrites from the 40- and 85-year-old humans. Tukey’s pairwise multiple comparison test for the head volume, neck length, and neck diameter in apical and basal dendrites; complete spines (group A). Red squares indicate that the two varieties are significantly different (p < 0.05). Download Figure 5-2, TIF file.
Extended Data Table 1-1
The head volume and neck length values of the apical and basal spines from the 40- and 85-year-old individuals of the complete and repaired spines (groups A, C, and D) Download Table 1-1, DOCX file.
Extended Data Table 2-1
The head volume and neck length values of the apical (n = 153) and basal (n = 290) spines from mice of the complete and repaired spines (groups A, C, and D) Download Table 2-1, DOCX file.
Extended Data Figure 6-1
Mouse spines morphological parameter distributions in complete and repaired spines (groups A, C, and D). A, B, Head volume and neck length distributions of basal (light gray, n = 290) and apical (dark gray, n = 153) dendritic spines. The parameters were calculated only for the complete spines (group A). Dashed lines indicate the median values and the circles indicate the average; p = 0.17, 0.23; Mann–Whitney U rank test. Download Figure 6-1, EPS file.
Extended Data Figure 7-1
Comparing spine morphological distributions of humans and mice. A–C, Head volume, neck length, and neck diameter distributions in human (green, n = 2536) and mouse (blue, n = 251) complete spines (group A) in a linear scale. D, E, Head volume and neck length distributions in human (green, n = 3856) and mouse (blue, n = 443) complete and repaired spines (groups A, C, and D). F, Correlation between spine head volume and neck length. The correlation coefficients (Spearman) are indicated. Two-sided p-value for a hypothesis test whose null hypothesis is that the slope is zero, using Wald test with t distribution of the test statistic. G, H, Spine volume and spine length distributions in humans (n = 3856, green) and mice (n = 443, blue). The thin dashed lines indicate the distribution of the all spines (groups A, B, C, and D), including those that are unseparated into head and neck, in humans (n = 7044) and mice (n = 1536). I, The sphericity of the spine head in humans and mice (p = 0.077). Mann–Whitney U rank test, the asterisks indicate statistical significance; ***p < 0.001. Download Figure 7-1, EPS file.
Extended Data Figure 7-2
Spine morphological distributions of different age and dendrites of humans. Correlation between spine head volume and neck length of the complete and repaired spines (groups A, C, and D). A, 40-year-old apical dendrite. B, 85-year-old apical dendrite. C, 40-year-old basal dendrite. D, 85-year-old basal dendrite. The correlation coefficients (Spearman) are indicated. The asterisks indicate statistical significance; ***p < 0.001. Two-sided p-value for a hypothesis test whose null hypothesis is that the slope is zero, using Wald test with t distribution of the test statistic. Download Figure 7-2, EPS file.
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