Algorithms to automatically quantify the geometric similarity of anatomical surfaces

We describe new approaches for distances between pairs of 2-dimensional surfaces (embedded in 3-dimensional space) that use local structures and global information contained in inter-structure geometric relationships. We present algorithms to automatically determine these distances as well as geometric correspondences. This is motivated by the aspiration of students of natural science to understand the continuity of form that unites the diversity of life. At present, scientists using physical traits to study evolutionary relationships among living and extinct animals analyze data extracted from carefully defined anatomical correspondence points (landmarks). Identifying and recording these landmarks is time consuming and can be done accurately only by trained morphologists. This renders these studies inaccessible to non-morphologists, and causes phenomics to lag behind genomics in elucidating evolutionary patterns. Unlike other algorithms presented for morphological correspondences our approach does not require any preliminary marking of special features or landmarks by the user. It also differs from other seminal work in computational geometry in that our algorithms are polynomial in nature and thus faster, making pairwise comparisons feasible for significantly larger numbers of digitized surfaces. We illustrate our approach using three datasets representing teeth and different bones of primates and humans, and show that it leads to highly accurate results.Comment: Changes with respect to v1, v2: an Erratum was added, correcting the references for one of the three datasets. Note that the datasets and code for this paper can be obtained from the Data Conservancy (see Download column on v1, v2

The Origin And Loss Of Periodic Patterning In The Turtle Shell

The origin of the turtle shell over 200 million years ago greatly modified the amniote body plan, and the morphological plasticity of the shell has promoted the adaptive radiation of turtles. The shell, comprising a dorsal carapace and a ventral plastron, is a layered structure formed by basal endochondral axial skeletal elements (ribs, vertebrae) and plates of bone, which are overlain by keratinous ectodermal scutes. Studies of turtle development have mostly focused on the bones of the shell; however, the genetic regulation of the epidermal scutes has not been investigated. Here, we show that scutes develop from an array of patterned placodes and that these placodes are absent from a soft-shelled turtle in which scutes were lost secondarily. Experimentally inhibiting Shh, Bmp or Fgf signaling results in the disruption of the placodal pattern. Finally, a computational model is used to show how two coupled reaction-diffusion systems reproduce both natural and abnormal variation in turtle scutes. Taken together, these placodal signaling centers are likely to represent developmental modules that are responsible for the evolution of scutes in turtles, and the regulation of these centers has allowed for the diversification of the turtle shell

Modeling enamel matrix secretion in mammalian teeth

The most mineralized tissue of the mammalian body is tooth enamel. Especially in species with thick enamel, three-dimensional (3D) tomography data has shown that the distribution of enamel varies across the occlusal surface of the tooth crown. Differences in enamel thickness among species and within the tooth crown have been used to examine taxonomic affiliations, life history, and functional properties of teeth. Before becoming fully mineralized, enamel matrix is secreted on the top of a dentine template, and it remains to be explored how matrix thickness is spatially regulated. To provide a predictive framework to examine enamel distribution, we introduce a computational model of enamel matrix secretion that maps the dentine topography to the enamel surface topography. Starting from empirical enamel-dentine junctions, enamel matrix deposition is modeled as a diffusion-limited free boundary problem. Using laboratory microCT and synchrotron tomographic data of pig molars that have markedly different dentine and enamel surface topographies, we show how diffusion-limited matrix deposition accounts for both the process of matrix secretion and the final enamel distribution. Simulations reveal how concave and convex dentine features have distinct effects on enamel surface, thereby explaining why the enamel surface is not a straightforward extrapolation of the dentine template. Human and orangutan molar simulations show that even subtle variation in dentine topography can be mapped to the enamel surface features. Mechanistic models of extracellular matrix deposition can be used to predict occlusal morphologies of teeth. Author summary Teeth of most mammals are covered by a layer of highly mineralized enamel that cannot be replaced or repaired. The enamel layer is not uniform over the underlying dentine, and spatial regulation of enamel formation is critical for making a functional tooth. To explore which kind of mechanisms could underlie the complex patterns of enamel distribution, we present a computational model. Starting from tomography-imaged teeth from which enamel has been digitally removed, enamel is restored on dentine surfaces by simulating diffusion-limited secretion of enamel matrix. Our simulations show how the combination of subtle features of dentine and diffusion-limited secretion of the enamel matrix can substantially increase the complexity of the enamel surface. We propose that the strength of the diffusion-limited process is a key factor in determining enamel distribution among mammalian species.Peer reviewe

The effect of amoxicillin on dental enamel development in vivo

The exposure to amoxicillin has been associated with molar incisor hypomineralization. This study aimed to determine if amoxicillin disturbs the enamel mineralization in in vivo experiments. Fifteen pregnant rats were randomly assigned into three groups to received daily phosphatase-buffered saline or amoxicillin as either 100 or 500 mg/kg. Mice received treatment from day 13 of pregnancy to day 40 postnatal. After birth, the offsprings from each litter continued to receive the same treatment according to their respective group. Calcium (Ca) and phosphorus (P) content in the dental hard tissues were analyzed from 60 upper first molars and 60 upper incisors by the complexometric titration method and colorimetric analysis using a spectrophotometer at 680 nm, respectively. Lower incisors were analyzed by X-ray microtomography, it was measured the electron density of lingual and buccal enamel, and the enamel and dentin thickness. Differences in Ca and P content and electron density among the groups were analyzed by one-way ANOVA. There was no significant difference on enamel electron density and thickness among the groups (p > 0.05). However, in incisors, the higher dose of amoxicillin decreased markedly the electron density in some rats. There were no statistically significant differences in Ca (p = 0.180) or P content (p = 0.054), although the higher dose of amoxicillin could affect the enamel in some animals. The amoxicillin did not significantly alter the enamel mineralization and thickness in rats. © 2020Peer reviewe

Early Holocene fauna from a new subfossil site: A first assessment from Christmas River, south central Madagascar

We report on faunal remains recovered during recent explorations at ‘Christmas River’, the only subfossil locality known from Madagascar’s south central plateau. Recovered remains of several extinct taxa date to approximately 10,000 14C years before present (BP), including crocodiles, tortoises, the elephant bird Aepyornis, the carnivoran Cryptoprocta spelea, the lemurs Archaeolemur majori, Pachylemur insignis, and Megaladapis edwardsi, and abundant remains of the dwarf hippopotamus, Hippopotamus lemerlei. The presence of southern - limited, forest - dependent species at Christmas River supports the hypothesis that forest once extended, perhaps discontinuously, across the central highlands towards the west. One theory is that sites in the north central highlands, which are higher in elevation, maintained more mesic conditions during Plio - Quaternary climate shifts than those of the lower elevation sites of the south central highlands. Thus, elevation above sea level may have acted as a filter that limited species dispersal across the island in the past. Such a scenario would explain the distinction between more humid, higher elevation, northern highland subfossil communities versus more arid, lower elevation, southern subfossil communities. Continued exploration at Christmas River thus provides a remarkable opportunity for deciphering ecological changes that have taken place in south central Madagascar during the Holocene.RÉSUMÉMadagascar est reconnue comme l’une des régions les plus sensibles du monde en ce qui concerne les menaces pesant sur sa biodiversité, et cela à cause de niveaux d’endémisme inégalés, d’une diversité variée et d’un impact humain important sur l’environnement. Suite à la colonisation par l’Homme il y a plus de 2000 ans, des extinctions de masse de la faune et un important recul forestier ont eu lieu en laissant des marques sur les écosystèmes modernes qui sont dans un état de bouleversement écologique. Certaines plantes endémiques, par exemple, ont perdu d’importantes espèces mutualistes, des animaux ont été obligés d’exploiter d’autres ressources ou habiter des endroits auxquels ils sont mal adaptés. La diversité des plantes et des animaux a diminué, est menacée ou a même complètement disparue de certaines routes de dissémination. Bien que l’Homme soit largement incriminé dans son rôle de déclencheur de ces extinctions massives, les transformations anthropiques qui ont contribué au changement du climat sont controversées. Les hautes - terres de Madagascar sont actuellement dominées par des zones herbeuses étendues qui agissent comme des barrières empêchant les mouvements de la faune de part et d’autre de l’île. Nous suggérons qu’une forêt humide plus ou moins continue devait s’étendre sur les hautes-terres. Des informations paléoécologiques des hautes - terres du Centre sud sontènécessaires pour évaluer cette hypothèse afin de démêler la contribution relative des facteurs climatiques et anthropiques dans les changements paléoécologiques de la région. Cependant, les stations de subfossiles étaient jusqu’alors inconnues dans cette région. Nous présentons ici les résultats de recherches réalisées sur les restes fauniques découverts au cours de fouilles récentes à Christmas River, la seule station de subfossiles connue des hautes - terres du Centre sud de Madagascar. Des restes de plusieurs espèces datant approximativement de 10,000 14C B.P. ont été identifiés dont des restes appartenant à des espèces de crocodile, de tortue, de l’Aepyornis, du carnivore Cryptoprocta spelea, des lémuriens Archaeolemur majori, Pachylemur insignis et Megaladapis edwardsi ainsi que de nombreux restes de l’hippopotame nain Hippopotamus lemerlei. La présence à Christmas River d’espèces sylvicoles endémiques du Sud appuie l’hypothèse de l’existence d’une forêt, certainement discontinue, mais qui s’étendait sur les hautes - terres centrales en se poursuivant vers l’ouest. Une théorie a proposé que les sites septentrionaux des hautes - terres centrales, à des altitudes plus élevées, maintenaient des conditions plus humides au cours des changements du Plio - quaternaire que les sites méridionaux de ces hautes - terres centrales. Ainsi, dans le passé, l’altitude a du agir comme un filtre qui empêchait la dispersion des espèces d’un endroit à l’autre de l’île. Un tel scénario expliquerait la distinction entre les communautés subfossiles du nord des hautes - terres qui étaient plus humides à haute altitude et les communautés subfossiles du sud aride à basse altitude. La poursuite de l’exploration à Christmas River constitue une occasion unique pour décoder les changements écologiques qui sont intervenus dans le Sud de cette région centrale de Madagascar au cours de l’Holocène

Development and regeneration of the crushing dentition of skates (Rajidae)

Sharks and rays (elasmobranchs) have the remarkable capacity to continuously regenerate their teeth. The polyphyodont system is considered the ancestral condition of the gnathostome dentition. Despite this shared regenerative ability, sharks and rays exhibit dramatic interspecific variation in their tooth morphology. Ray (batoidea) teeth typically constitute crushing pads of flattened teeth, whereas shark teeth are pointed, multi-cuspid units. Although recent research has addressed the molecular development of the shark dentition, little is known about that of the ray. Furthermore, how dental diversity within the elasmobranch lineage is achieved remains unknown. Here, we examine dental development and regeneration in two Batoid species: the thornback skate (Raja clavata) and the little skate (Leucoraja erinacea). Using in situ hybridization and immunohistochemistry, we examine the expression of a core gnathostome dental gene set during early development of the skate dentition and compare it to development in the shark. Elasmobranch tooth development is highly conserved, with sox2 likely playing an important role in the initiation and regeneration of teeth. Alterations to conserved genes expressed in an enamel knot-like signalling centre may explain the morphological diversity of elasmobranch teeth, thereby enabling sharks and rays to occupy diverse dietary and ecological niches

Mosaic Convergence of Rodent Dentitions

BACKGROUND:Understanding mechanisms responsible for changes in tooth morphology in the course of evolution is an area of investigation common to both paleontology and developmental biology. Detailed analyses of molar tooth crown shape have shown frequent homoplasia in mammalian evolution, which requires accurate investigation of the evolutionary pathways provided by the fossil record. The necessity of preservation of an effective occlusion has been hypothesized to functionally constrain crown morphological changes and to also facilitate convergent evolution. The Muroidea superfamily constitutes a relevant model for the study of molar crown diversification because it encompasses one third of the extant mammalian biodiversity. METHODOLOGY/PRINCIPAL FINDINGS:Combined microwear and 3D-topographic analyses performed on fossil and extant muroid molars allow for a first quantification of the relationships between changes in crown morphology and functionality of occlusion. Based on an abundant fossil record and on a well resolved phylogeny, our results show that the most derived functional condition associates longitudinal chewing and non interlocking of cusps. This condition has been reached at least 7 times within muroids via two main types of evolutionary pathways each respecting functional continuity. In the first type, the flattening of tooth crown which induces the removal of cusp interlocking occurs before the rotation of the chewing movement. In the second type however, flattening is subsequent to rotation of the chewing movement which can be associated with certain changes in cusp morphology. CONCLUSION/SIGNIFICANCE:The reverse orders of the changes involved in these different pathways reveal a mosaic evolution of mammalian dentition in which direction of chewing and crown shape seem to be partly decoupled. Either can change in respect to strong functional constraints affecting occlusion which thereby limit the number of the possible pathways. Because convergent pathways imply distinct ontogenetic trajectories, new Evo/Devo comparative studies on cusp morphogenesis are necessary

Loss of heterozygosity at 18q21 is indicative of recurrence and therefore poor prognosis in a subset of colorectal cancers

Adjuvant therapies are increasingly used in colorectal cancers for the prevention of recurrence. These therapies have side-effects and should, thus, be used only if really beneficial. However, the development of recurrence cannot be predicted reliably at the moment of diagnosis, and targeting of adjuvant therapies is thus based only on the primary stage of the cancer. Loss of heterozygosity (LOH) in the long arm of chromosome 18 is suggested to be related to poor survival and possibly to the development of metastases. We studied the value of LOH at 18q21 as a marker of colorectal cancer prognosis, association with clinicopathological variables, tumour recurrence and survival of the patients. Of the 255 patients studied, 195 were informative as regards LOH status when analysed in primary colorectal cancer specimens using the polymerase chain reaction (PCR) and fragment analysis. LOH at 18q21 was significantly associated with the development of recurrence (P= 0.01) and indicated poor survival in patients of Dukes' classes B and C, in which most recurrences (82%) occurred. An increased rate of tumour recurrence is the reason for poor survival among patients with LOH at 18q21 in primary cancer. These patients are a possible target group for recurrence-preventing adjuvant therapies. © 1999 Cancer Research Campaig

Evolutionary Patterns in the Dentition of Duplicidentata (Mammalia) and a Novel Trend in the Molarization of Premolars

The cusp homology of Lagomorpha has long been problematic largely because their teeth are highly derived relative to their more typically tribosphenic ancestors. Within this context, the lagomorph central cusp has been particularly difficult to homologize with other tribosphenic cusps; authors have previously considered it the paracone, protocone, metacone, amphicone, or an entirely new cusp.Here we present newly described fossil duplicidentates (Lagomorpha and Mimotonidae) in the context of a well-constrained phylogeny to establish a nomenclatural system for cusps based on the tribosphenic pattern. We show that the central cusp of lagomorphs is homologous with the metaconule of other mammals. We also show that the buccal acquisition of a second cusp on the premolars (molarization) within duplicidentates is atypical with respect to other mammalian lineages; within the earliest lagomorphs, a second buccal cusp is added mesially to an isolated buccal cusp.The distal shift of the ‘ancestral’ paracone within early duplicidentates amounts to the changing of a paracone into a metacone in these lineages. For this reason, we support a strictly topological approach to cusp names, and suggest a discontinuity in nomenclature to capture the complexity of the interplay between evolutionary history and the developmental process that have produced cusp patterns in duplicidentates

Reply to: Revisiting life history and morphological proxies for early mammaliaform metabolic rates

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