Alpha shapes: Determining 3D shape complexity across morphologically diverse structures

Background. Following recent advances in bioimaging, high-resolution 3D models of biological structures are now generated rapidly and at low-cost. To utilise this data to address evolutionary and ecological questions, an array of tools has been developed to conduct 3D shape analysis and quantify topographic complexity. Here we focus particularly on shape techniques applied to irregular-shaped objects lacking clear homologous landmarks, and propose the new ‘alpha-shapes’ method for quantifying 3D shape complexity. Methods. We apply alpha-shapes to quantify shape complexity in the mammalian baculum as an example of a morphologically disparate structure. Micro- computed-tomography (μCT) scans of bacula were conducted. Bacula were binarised and converted into point clouds. Following application of a scaling factor to account for absolute differences in size, a suite of alpha-shapes was fitted to each specimen. An alpha shape is a formed from a subcomplex of the Delaunay triangulation of a given set of points, and ranges in refinement from a very coarse mesh (approximating convex hulls) to a very fine fit. ‘Optimal’ alpha was defined as the degree of refinement necessary in order for alpha-shape volume to equal CT voxel volume, and was taken as a metric of overall shape ‘complexity’. Results Our results show that alpha-shapes can be used to quantify interspecific variation in shape ‘complexity’ within biological structures of disparate geometry. The ‘stepped’ nature of alpha curves is informative with regards to the contribution of specific morphological features to overall shape ‘complexity’. Alpha-shapes agrees with other measures of topographic complexity (dissection index, Dirichlet normal energy) in identifying ursid bacula as having low shape complexity. However, alpha-shapes estimates mustelid bacula as possessing the highest topographic complexity, contrasting with other shape metrics. 3D fractal dimension is found to be an inappropriate metric of complexity when applied to bacula. Conclusions. The alpha-shapes methodology can be used to calculate ‘optimal’ alpha refinement as a proxy for shape ‘complexity’ without identifying landmarks. The implementation of alpha-shapes is straightforward, and is automated to process large datasets quickly. Beyond genital shape, we consider the alpha-shapes technique to hold considerable promise for new applications across evolutionary, ecological and palaeoecological disciplines

Integrative roles of transforming growth factor-α in the cytoprotection mechanisms of gastric mucosal injury

<p>Abstract</p> <p>Background</p> <p>Transforming growth factor α (TGFα) protects against gastric mucosal injury and facilitates wound healing. However, its overexpression is known to induce hypertrophic gastropathy resembling Menetrier's disease in transgenic (TG) mice on an FVB background, as one of the authors reported previously. We studied another TGFα-expressing mouse line on a CD1 background, whose gastric mucosa appears normal. Since this TG mouse had a strong resistance to ethanol-induced gastric injury, we considered the long-term effect of TGFα on several gastric protection mechanisms.</p> <p>Methods</p> <p>TGFα-expressing transgenic (TG) mouse lines bearing human TGFα cDNA under the control of the mouse metallothionein gene I promoter were generated on a CD1 mouse background, and analyzed their ethanol injury-resistant phenotypes produced by TGFα.</p> <p>Results</p> <p>In the TG mucosa, blood flow was well maintained after ethanol injury. Further, neural and inducible types of NO synthases were consistently and widely expressed in the TG mucosa, compared with the limited distribution of neural type NO synthase in the luminal pit region of the wild-type (WT) mucosa. COX-2 and its upstream transcription factor NfkB were constitutively elevated in the TG mucosa even before ethanol administration, whereas they were induced in the same region of the WT mucosa only after ethanol injury. Two anti-apoptotic proteins, HSP70 and Bcl-2, were upregulated in the TG mucosa even before ethanol administration, while they were not expressed in the WT mucosa before the injury. Furthermore, pro-caspase 3 activation was inhibited in the TG mucosa, while it was converted to the active form in the WT mucosa following ethanol administration.</p> <p>Conclusion</p> <p>We conclude that TGFα maintains the gastric mucosal defense against gastric injury by integrating other cytoprotective mechanisms.</p