Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.

BackgroundElucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent ‘natural’ phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.ResultsPreviously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.ConclusionsThe newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies.The ontology release files associated with the ontology merge described in this manuscript are available at: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/Current ontology release files are available always available at: http://purl.obolibrary.org/obo/uberon/releases/

Vertebrate teeth are attached to jaws by a variety of mechanisms, including acrodont, pleurodont, and thecodont modes of attachment. Recent studies have suggested that various modes of attachment exist within each sub-category. Especially squamates feature a broad diversity of modes of attachment. Here we have investigated tooth attachment tissues in the late cretaceous mosasaur Clidastes and compared mosasaur tooth attachment with modes of attachment found in other extant reptiles. Using histologic analysis of ultrathin ground sections, four distinct mineralized tissues that anchor mosasaur teeth to the jaw were identified: (i) an acellular cementum layer at the interface between root and cellular cementum, (ii) a massive cone consisting of trabecular cellular cementum, (iii) the mineralized periodontal ligament containing mineralized Sharpey's fibers, and (iv) the interdental ridges connecting adjacent teeth. The complex, multilayered attachment apparatus in mosasaurs was compared with attachment tissues in extant reptiles, including Iguana and Caiman. Based on our comparative analysis we postulate the presence of a quadruple-layer tissue architecture underlying reptilian tooth attachment, comprised of acellular cementum, cellular cementum, mineralized periodontal ligament, and interdental ridge (alveolar bone). We propose that the mineralization status of the periodontal ligament is a dynamic feature in vertebrate evolution subject to functional adaptation.

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1. Intracellular recordings were made in the somata of dorsal root ganglion cells in the L7 or S1 DRG in cats anesthetized with alpha-chloralose. The properties of the action potentials (amplitude, duration, peak rate of rise), duration of afterhyperpolarization (AHP), magnitude of inward rectification, and axonal conduction velocity were measured. The adequate stimulus was determined, and the extent to which these properties are correlated was investigated. 2. All cells with receptive fields could be classified as mechanoreceptors. Most cells with A-beta-axons (greater than 36 m/s) could be activated by gentle mechanical stimulation but a small minority with conduction velocity in the low end of the A-beta-range were nociceptors. Cells with A-delta-axons (2-36 m/s) innervated either the very sensitive Down hair follicles (D-hairs) or high-threshold mechanoreceptors (HTMRs). In addition a group of A-delta-fibers was found for which no receptive field could be described. Their spikes, AHPs, and membrane properties were indistinguishable from those of cells supplying HTMRs (see below) and they were lumped together with A-delta-HTMRs. 3. A-beta-neurons exhibited smaller, briefer spikes than A-delta-neurons, even those supplying D-hairs. Peak rate of rise (dV/dt)max and inward rectification were significantly larger in A-beta-cells than in A-delta s, whereas AHP duration and input resistance were smaller. However, the values of these parameters in cells of a given conduction velocity range were generally associated with receptor type. 4. A-delta-HTMRs exhibited spikes of greater amplitude and duration, longer AHP duration, and smaller inward rectification than D-hairs. The long duration of these spikes was due largely to a prominent hump on their descending limb. Input resistance was similar in both groups of cells. 5. A-beta-HTMRs differed from A-beta-cells innervating low threshold receptors in the same general way that A-delta-HTMRs differed from D-hairs. However, A-beta-LTMRs supplying different receptor types (e.g., slowly adapting type I, Pacinian corpuscles, etc.) exhibited no correlation between receptor type and electrophysiology of the soma. 6. These differences in spike parameters occur at the level of the membrane rather than in the degree of somal invasion because the largest amplitude spikes also exhibited the slowest time course (i.e., in HTMRs). Systematic variation in AHP duration and inward rectification also suggest differences in the proportions of ionic channel types among these cells.(ABSTRACT TRUNCATED AT 400 WORDS)