Overview of FEED, the feeding experiments end-user database

Jaw Elevator Muscle Coordination during Rhythmic Mastication in Primates: Are Triplets Units of Motor Control?

The activity of mammal jaw elevator muscles during chewing has often been described using the concept of the triplet motor pattern, in which triplet I (balancing side superficial masseter and medial pterygoid; working side posterior temporalis) is consistently activated before triplet II (working side superficial masseter and medial pterygoid; balancing side posterior temporalis), and each triplet of muscles is recruited and modulated as a unit. Here, new measures of unison, synchrony, and coordination are used to determine whether in 5 primate species (Propithecus verreauxi, Eulemur fulvus, Papio anubis, Macaca fuscata,and Pan troglodytes)muscles in the same triplet are active more in unison, are more synchronized, and are more highly coordinated than muscles in different triplets. Results show that triplet I muscle pairs are active more in unison than other muscle pairs in Eulemur, Macaca, and Papio,buttriplet muscle pairs are mostly not more tightly synchronized than non-triplet pairs. Triplet muscles are more coordinated during triplet pattern cycles than non-triplet cycles, while non-triplet muscle pairs are more coordinated during non-triplet cycles than triplet cycles. These results suggest that the central nervous system alters patterns of coordination between cycles, recruiting triplet muscles as a coordinated unit during triplet cycles but employing a different pattern of muscle coordination during non-triplet cycles. The triplet motor pattern may simplify modulation of rhythmic mastication by being one possible unit of coordination that can be recruited on a cycle-to-cycle basis.

Evaluating the triplet hypothesis during rhythmic mastication in primates

Mammalian mastication involves precise jaw movements including transverse movement of the mandible during the power stroke. Jaw elevation and transverse movement are driven by asymmetrical jaw elevator muscle activity, which is thought to include a phylogenetically primitive and conserved triplet motor pattern consisting of: triplet I (balancing side: superficial masseter and medial pterygoid; working side: posterior temporalis), which reaches onset, peak and offset first; and triplet II (working side: superficial masseter and medial pterygoid; balancing side: posterior temporalis), which is active second. Although the presence of a triplet motor pattern has been confirmed in several primate species, the prevalence of this motor pattern - i.e. the proportion of masticatory cycles that display it - has not been evaluated in primates. The present study quantifies the presence and prevalence of the triplet motor pattern in five different primate species, Eulemur fulvus, Propithecus verreauxi, Papio anubis, Macacafuscata and Pan troglodytes, using mean onset, peak and offset time relative to working superficial masseter. In all five of the species studied, the mean triplet motor pattern was observed at peak muscle activation, and in four out of the five species the triplet motor pattern occurred more frequently than expected at random at peak muscle activation and offset. Non-triplet motor patterns were observed in varying proportions at different time points in the masticatory cycle, suggesting that the presence or absence of the triplet motor pattern is not a binomial trait. Instead, the primate masticatory motor pattern is malleable within individual cycles, within individual animals and therefore within species.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

Background

In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required.

Development and Testing of the Ontology

Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar.

Results and Significance

Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

Finding our way through phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

BACKGROUND

Elucidating 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.

RESULTS

Previously, 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.

CONCLUSIONS

The 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/

A preliminary analysis of correlations between chewing motor patterns and mandibular morphology across mammals

The establishment of a publicly-accessible repository of physiological data on feeding in mammals, the Feeding Experiments End-user Database (FEED), along with improvements in reconstruction of mammalian phylogeny, significantly improves our ability to address long-standing questions about the evolution of mammalian feeding. In this study, we use comparative phylogenetic methods to examine correlations between jaw robusticity and both the relative recruitment and the relative time of peak activity for the superficial masseter, deep masseter, and temporalis muscles across 19 mammalian species from six orders. We find little evidence for a relationship between jaw robusticity and electromyographic (EMG) activity for either the superficial masseter or temporalis muscles across mammals. We hypothesize that future analyses may identify significant associations between these physiological and morphological variables within subgroups of mammals that share similar diets, feeding behaviors, and/or phylogenetic histories. Alternatively, the relative peak recruitment and timing of the balancing-side (i.e., non-chewing-side) deep masseter muscle (BDM) is significantly negatively correlated with the relative area of the mandibular symphysis across our mammalian sample. This relationship exists despite BDM activity being associated with different loading regimes in the symphyses of primates compared to ungulates, suggesting a basic association between magnitude of symphyseal loads and symphyseal area among these mammals. Because our sample primarily represents mammals that use significant transverse movements during chewing, future research should address whether the correlations between BDM activity and symphyseal morphology characterize all mammals or should be restricted to this "transverse chewing" group. Finally, the significant correlations observed in this study suggest that physiological parameters are an integrated and evolving component of feeding across mammals.