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13 results for “squamate brain”
Figs 1-6 in Minimizing the damage: a methodological proposal to remove the brains of anurans and squamates
Figs 1-6, Step-by-step dissection of an anuran brain: 1, specimen condition before the dissection; 2, cross-section cuts; 3, lifting the skin; 4, bones cut off surrounding the brain; 5, bones cut off straightly toward the nostrils; 6, eXposed brain. The red dots represent the points of insertion of the scissors. The arrows in figures 3 and 4 represent the direction of the movement. The arrow in figure 6 represents the medulla oblongata.
Figs 7-11 in Minimizing the damage: a methodological proposal to remove the brains of anurans and squamates
Figs 7-11, Step-by-step dissection of a snake brain: 7, sagittal cut from the upper edge of the rostral scale toward the occipital scales; 8, transversal cut from the posterior edge of the supraocular scale toward the other supraocular scale; 9, lifting the skin. The junction of the frontal bone with the parietal is highlighted, and the red dot represents the point of the insertion of the scissors; 10, bones cut off straightly toward following the sagittal/medial plane; 11, exposed brain. The arrow in figure 7 is pointing to the square bone. The arrow in figure 10 represents the direction of the movement. The arrow in figure 11 represents the medulla oblongata.
Figure 1 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 1</strong> <strong>Phylogeny and cerebellar diversity of squamates.</strong> <strong>a</strong> Phylogenetic tree of all snake and lizard species used in morphological and volumetric analyses, adapted from the most inclusive phylogenetic study available for extant squamates. The seven major locomotor modes for snakes (coloured squares) and/or lizards (coloured circles), as defined based on anatomical features, habitat use, and movement type, are indicated by the same colour code throughout the entire manuscript (see bottom left corner): limbless or limb-reduced burrower (red squares and circles); limbless or limb-reduced facultative burrower (purple squares and circles); limbless or limb-reduced multi-habitat using lateral undulation (orange squares and circles); limbless or limb-reduced multi-habitat using other movements (yellow squares); quadrupedal arboreal (dark blue circles); quadrupedal terrestrial (light blue circles); quadrupedal facultative bipedal/aerial (green circles). <strong>b</strong>–<strong>o</strong> 3D-volume rendering and high-resolution whole-brain segmentation of iodine-stained adult heads (<strong>b</strong>–<strong>h</strong>) highlighting the cerebellum structure (<strong>b</strong>–<strong>o</strong>, red colour) of selected representative squamates at indicated position in the phylogenetic tree: <em>Pantherophis guttatus</em> (<strong>b</strong>, <strong>i</strong>), <em>Epicrates cenchria</em> (<strong>c</strong>, <strong>j</strong>), <em>Pogona vitticeps</em> (<strong>d</strong>, <strong>k</strong>), <em>Draco volans</em> (<strong>e</strong>,<strong> l</strong>), <em>Bradypodion pumilum</em> (<strong>f</strong>, <strong>m</strong>), <em>Anguis fragilis</em> (<strong>g</strong>, <strong>n</strong>), <em>Melanoseps loveridgei</em> (<strong>h</strong>, <strong>o</strong>). High magnifications of 3D-rendered cerebella (<strong>i</strong>–<strong>o</strong>) are shown in pial surface (left panels) and lateral (right panels) views for each selected species. Scale bars: 1mm (<strong>b</strong>–<strong>h</strong>), 500 μm (<strong>i</strong>–<strong>o</strong>).</p>
Figure 8 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 8 Comparative transcriptomics of the squamate cerebellum.</strong> <strong>a</strong> Two-way hierarchical clustering heat map showing three clusters of genes (rows) that behave similarly (clusters 1 and 2) or differently (cluster 3) across ten selected squamate species (columns). Z-score colour intensities reflect scaled gene expression values, ranging from low (blue) to high (yellow), for 630 one-to-one orthologous genes identified in all species. <strong>b</strong> Pie charts showing the distribution of orthologous genes (in %) among all significantly enriched gene ontology terms for biological processes (hypergeometric test with a false discovery rate multiple-hypothesis correction, p-value < 0.01) in clusters identified in <strong>a</strong>. c Hierarchical clustering of pairwise Pearson’s correlation coefficients for 630 orthologous genes identified across all squamate species. Colour intensities of individual tiles in the heat map depict pairwise correlation coefficient values, ranging from low (blue) to high (yellow), between selected species with indicated locomotor mode (see colour code and symbols on the right). Numbers at nodes in the cluster dendrogram represent approximately unbiased p-values (in percentage) obtained by multiscale bootstrap resampling.</p> <p> </p> <p> </p> <p> </p>
Figure 7 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 7</strong> <strong>Variability in the arrangement of Purkinje cells (PCs) in the squamate cerebellum.</strong> <strong>a</strong>, <strong>b</strong> Representative light-sheet microscopy imaging of cleared whole-cerebella showing the 3D distribution and arrangement of calbindin 1 (CALB1)-immunolabelled PCs in two representative species with different locomotor modes (see colour code and symbols in top left corner): <em>Pogona vitticeps </em>(<strong>a</strong>) and <em>Boaedon fuliginosus</em> (<strong>b</strong>). The boxed areas in the coronal 3Drendered cerebellar views (top panels) are shown at higher magnifications in coronal (left) and sagittal (right) views in the lower panels. <strong>c</strong>, Violin plot showing the quantitative distribution of CALB1-immunolabelled PCs in the cerebellar cortex of selected squamate species with similar or different locomotor modes (colour code and symbols as above). Due to intra- and interspecies heterogeneity in molecular layer (ML) thickness, the position of individual cells (n = 250–750 per species) was calculated as the distance (in %) from the granule cell layer (GCL) to the outer border (pial surface) of the ML, and error bars represent the standard deviation. Four major positioning patterns containing three or four squamate species and reflecting the increased scattering of PCs (from I to IV) were identified based on Kruskal-Wallis statistics. Immunohistochemistry with CALB1 marker (red staining) on sagittal sections of the cerebellar cortex in selected representative species are shown at low and high magnifications (insets) for each pattern: <em>Pogona vitticeps</em> (I), <em>Eryx colubrinus</em> (II), <em>Pseudopus apodus</em> (III), <em>Dasypeltis gansi</em> (IV). Scale bars: 30 μm (<strong>a</strong>, <strong>b</strong>), 100 μm (<strong>c</strong>).</p> <p> </p> <p> </p>
Figure 6 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 6 Cerebellar size variation in squamates with different locomotor behaviours.</strong> <strong>a</strong> Scatter plot showing the correlation of cerebellum relative to wholebrain volume (in mm3) for selected representative squamate species (see colour code and symbols in bottom right corner). The coloured lines and shadings represent the phylogenetic generalized least squares (PGLS) regression lines and 95% confidence intervals for each locomotor mode, respectively. <strong>b</strong> Ridgeline plot showing the distribution of the cerebellum-to-whole-brain volume ratios (in percentage) for each indicated limbless or limbreduced (top panels) or quadrupedal (bottom) locomotor mode. Colour gradient, ranging from yellow to blue, reflects the tail distribution probability.</p>
Supplementary Figure 1 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Supplementary Fig. 1:</strong> <strong>Definition of 3D anatomical landmarks.</strong> <strong>a</strong>, Position of 3D anatomical landmarks on the whole brain of the lizard <em>Agama agama</em> in dorsal (top left panel), ventral (top right), and lateral (bottom) views. <strong>b</strong>, Position of 3D anatomical landmarks on the isolated cerebellum of <em>Agama agama</em> in pial surface (left panel) and lateral (right) views. <strong>c</strong>, Schematic representation of the whole-brain of <em>Agama agama</em> highlighting the five major regions used for landmarking. <strong>d</strong>, Table showing the definition of 3D anatomical landmarks with associated number (see <strong>a</strong>, <strong>b</strong>) and brain region (see <strong>c</strong>).</p>
Supplementary Figure 2 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Supplementary Fig. 2: Phylomorphospace and landmark-free geometric morphometric methods.</strong> <strong>a</strong>, <strong>b</strong>, Plots of 2D phylomorphospace (with species names indicated) showing the cerebellar (<strong>a</strong>) and whole-brain (<strong>b</strong>) shape distribution of snakes (coloured squares) and lizards (coloured circles) with different locomotor modes (see colour code in <strong>a</strong>). Numbers in brackets indicate the percentage of variance explained by each of the PC axes, and 68% confidence ellipses are shown for each locomotor mode. Asterisks in (<strong>a</strong>) mark individuals belonging to the Scincidae family. <strong>c</strong>, <strong>d</strong>, Plots of 3D morphospace obtained using landmark-free ShapeWorks (<strong>c</strong>) and GPSA (<strong>d</strong>) methods, showing the cerebellar (<strong>c</strong>) and whole-brain (<strong>d</strong>) shape distribution of snakes (coloured cubes) and lizards (coloured spheres) with different locomotor modes (see colour code in <strong>a</strong>). Numbers in brackets indicate the percentage of variance explained by each of the PC axes. The PC2 axis in (<strong>d</strong>) was inverted for better comparison with landmark-based geometric morphometric methods.</p> <p> </p> <p> </p>
Figure 5 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 5 Cerebellar shape variation in squamates with different locomotor behaviours.</strong> <strong>a</strong> 3D plot of principal component (PC) scores showing shape distribution of isolated cerebella from snakes (coloured cubes) and lizards (coloured spheres) with different locomotor modes (see colour code and symbols in bottom left corner). Numbers in brackets indicate the percentage of variance explained by each of the PC axes, and 68% confidence ellipses are shown for each locomotor mode. The 3D-rendered cerebella corresponding to extreme (indicated by coloured solid arrows, with species names) or representative (coloured dashed arrows, with species names) lizard and snake species in both positive and negative directions along the first two PCs are shown in pial (left) and lateral (right) views. <strong>b</strong> Warped surfaces of cerebellum representing the reconstructed mean shape configuration for each indicated limbless or limb-reduced (left panels) or quadrupedal (right) locomotion mode are shown in pial surface (top row) and lateral views (bottom). Colour gradient, ranging from blue to yellow, reflects the relative Procrustes distance (in μm) of shape changes from the overall mean shape for the entire dataset.</p>
Figure 4 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 4</strong> <strong>Morphological variation of major brain subdivisions in squamates with different locomotor behaviours.</strong> <strong>a</strong>–<strong>e</strong> 2D plots of principal component (PC) scores showing the diencephalon (<strong>a</strong>), cerebellum (<strong>b</strong>), telencephalon (<strong>c</strong>), medulla oblongata (<strong>d</strong>) and mesencephalon (<strong>e</strong>) shape distribution of snakes (coloured squares) and lizards (coloured circles) with different locomotor modes (see colour code in bottom right corner). Numbers in brackets indicate the percentage of variance explained by each of the PC axes, and 68% confidence ellipses are shown for each locomotor mode. 2D wireframes illustrate shape changes associated with the first two PCs for each brain subdivision in top and lateral (<strong>a</strong>, <strong>c</strong>, <strong>d</strong>), pial surface and lateral (<strong>b</strong>), or front and lateral (<strong>e</strong>) views.</p>
Figure 3 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 3</strong> <strong>Whole-brain shape variation in squamates with different locomotor behaviours.</strong> 3D plot of principal component (PC) scores showing the whole-brain shape distribution of snakes (coloured cubes) and lizards (coloured spheres) with different locomotor modes (see colour code and symbols in bottom left corner). Numbers in brackets indicate the percentage of variance explained by each of the PC axes, and 68% confidence ellipses are shown for each locomotor mode. The 3D-rendered whole-brains corresponding to extreme (indicated by coloured solid arrows, with species names) or representative (coloured dashed arrows, with species names) lizard and snake species in both positive and negative directions along the first two PCs are shown in dorsal (top) and lateral (bottom) views.</p>
Figure 2 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 2<strong> </strong>Comparative anatomy of whole-brain and cerebellar cortex.</strong> <strong>a</strong> Direct comparison of dissected (top panels) and 3D reconstructed (bottom) Pogona vitticeps brain in lateral (left panels) and dorsal (right) views. <strong>b</strong>, <strong>c</strong> Single and merged immunostainings for ZIC1/2/3 granule cell marker (green) and DAPI (blue) on sagittal sections of <em>Anolis carolinensis</em> (<strong>b</strong>) and<em> Epicrates cenchria</em> (<strong>c</strong>)<strong> </strong>cerebellar cortex. White dashed lines highlight both the cerebellum profile and part of optic tectum in contact with the cerebellum to illustrate their spatial relationships in the two species. Crossed white arrows point towards rostral (R), caudal (C), dorsal (D) and ventral (V) directions. Pial and ventricular cerebellar surfaces are indicated on their respective side. GCL, granule cell layer; ML, molecular layer; IV, fourth ventricle. Scale bars: 1mm (<strong>a</strong>), 100 μm<strong> </strong>(<strong>b</strong>,<strong> </strong><strong>c</strong>).</p>
Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization
GEO Series GSE139570. Pogona vitticeps; Trioceros jacksonii; Dasypeltis gansi; Chrysopelea ornata; Pantherophis guttatus; Pseudopus apodus; Python regius; Basiliscus vittatus; Mochlus fernandi; Eryx colubrinus. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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International Brain Laboratory public data
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OpenNeuro
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