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Jonathan B L Bard

Publications and source records attributed to Jonathan B L Bard.

10 recordsLinked to original sources
PubMed2005

Anatomics: the intersection of anatomy and bioinformatics.

Computational resources are now using the tissue names of the major model organisms so that tissue-associated data can be archived in and retrieved from databases on the basis of developing and adult anatomy. For this to be done, the set of tissues in that organism (its anatome) has to be organized in a way that is computer-comprehensible. Indeed, such formalization is a necessary part of what is becoming known as systems biology, in which explanations of high-level biological phenomena are not only sought in terms of lower-level events, but are articulated within a computational framework. Lists of tissue names alone, however, turn out to be inadequate for this formalization because tissue organization is essentially hierarchical and thus cannot easily be put into tables, the natural format of relational databases. The solution now adopted is to organize the anatomy of each organism as a hierarchy of tissue names and linking relationships (e.g. the tibia is PART OF the leg, the tibia IS-A bone) within what are known as ontologies. In these, a unique ID is assigned to each tissue and this can be used within, for example, gene-expression databases to link data to tissue organization, and also used to query other data sources (interoperability), while inferences about the anatomy can be made within the ontology on the basis of the relationships. There are now about 15 such anatomical ontologies, many of which are linked to organism databases; these ontologies are now publicly available at the Open Biological Ontologies website (http://obo.sourceforge.net) from where they can be freely downloaded and viewed using standard tools. This review considers how anatomy is formalized within ontologies, together with the problems that have had to be solved for this to be done. It is suggested that the appropriate term for the analysis, computer formulation and use of the anatome is anatomics.

Adult↗
PubMed2004

Pathbase: a database of mutant mouse pathology.

Pathbase is a database that stores images of the abnormal histology associated with spontaneous and induced mutations of both embryonic and adult mice including those produced by transgenesis, targeted mutagenesis and chemical mutagenesis. Images of normal mouse histology and strain-dependent background lesions are also available. The database and the images are publicly accessible (http://www.pathbase.net) and linked by anatomical site, gene and other identifiers to relevant databases; there are also facilities for public comment and record annotation. The database is structured around a novel ontology of mouse disorders (MPATH) and provides high-resolution downloadable images of normal and diseased tissues that are searchable through orthogonal ontologies for pathology, developmental stage, anatomy and gene attributes (GO terms), together with controlled vocabularies for type of genetic manipulation or mutation, genotype and free text annotation for mouse strain and additional attributes. The database is actively curated and data records assessed by pathologists in the Pathbase Consortium before publication. The database interface is designed to have optimal browser and platform compatibility and to interact directly with other web-based mouse genetic resources.

Animals↗
PubMed2004

Pathbase: a new reference resource and database for laboratory mouse pathology.

Pathbase (http://www.pathbase.net) is a web accessible database of histopathological images of laboratory mice, developed as a resource for the coding and archiving of data derived from the analysis of mutant or genetically engineered mice and their background strains. The metadata for the images, which allows retrieval and interoperability with other databases, is derived from a series of orthogonal ontologies and controlled vocabularies. One of these controlled vocabularies, MPATH, was developed by the Pathbase Consortium as a formal description of the content of mouse histopathological images. The database currently has over 1000 images on-line with 2000 more under curation and presents a paradigm for the development of future databases dedicated to aspects of experimental biology.

Animals↗
PubMed2003

The growth and morphogenesis of the early mouse mandible: a quantitative analysis.

Three-dimensional reconstruction and BrdU incorporation have been used to quantify the development and growth of the mouse mandible and to analyse its relationship to Meckel's cartilage and the molar teeth. The mandible anlage is first histologically detectable at E13.5 as paired plates of osteoid tissue within condensed mesenchyme (approximately 0.9 mm long and approximately 0.36 mm deep) that are lateral to the two arms of Meckel's cartilage. Over the next 3 days, each plate lengthens to approximately 3.6 mm, and extends medially at its superior and inferior edges, folding over to enclose the alveolar nerve and Meckel's cartilage and producing additional processes that form the molar tooth sockets (E15.5). At around E15.5, the first molar tooth socket forms from two processes that extend from the medial and distal parts of the mandible to surround the tooth. By E16.5, this process is complete in the distal region where Meckel's cartilage is beginning to degenerate. Mandible ossification begins at E14 with proliferation restricted to the outer surface. BrdU incorporation rates are particularly high at the proximal and distal ends where lengthening occurs, and at the superior and inferior edges as they extend medially to surround Meckel's cartilage. Incorporation rates slow at the distal ends of each mandible at E16.5 as they approach each other at the symphysis. The results indicate that the mandible mainly grows at its periphery, and the pattern of mandibular growth and morphogenesis suggests that these processes are mainly directed and constrained by paracrine signalling from Meckel's cartilage and the tooth buds.

Animals↗
PubMed2003

An ontology of human developmental anatomy.

Human developmental anatomy has been organized as structured lists of the major constituent tissues present during each of Carnegie stages 1-20 (E1-E50, approximately 8500 anatomically defined tissue items). For each of these stages, the tissues have been organized as a hierarchy in which an individual tissue is catalogued as part of a larger tissue. Such a formal representation of knowledge is known as an ontology and this anatomical ontology can be used in databases to store, organize and search for data associated with the tissues present at each developmental stage. The anatomical data for compiling these hierarchies comes from the literature, from observations on embryos in the Patten Collection (Ann Arbor, MI, USA) and from comparisons with mouse tissues at similar stages of development. The ontology is available in three versions. The first gives hierarchies of the named tissues present at each Carnegie stage (http://www.ana.ed.ac.uk/anatomy/database/humat/) and is intended to help analyse both normal and abnormal human embryos; it carries hyperlinked notes on some ambiguities in the literature that have been clarified through analysing sectioned material. The second contains many additional subsidiary tissue domains and is intended for handling tissue-associated data (e.g. gene-expression) in a database. This version is available at the humat site and at http://genex.hgu.mrc.ac.uk/Resources/intro.html/), and has been designed to be interoperable with the ontology for mouse developmental anatomy, also available at the genex site. The third gives the second version in GO ontology syntax (with standard IDs for each tissue) and can be downloaded from both the genex and the Open Biological Ontology sites (http://obo.sourceforge.net/).

Databases, Factual↗
PubMed2003

EMAP and EMAGE: a framework for understanding spatially organized data.

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.

Animals↗
PubMed2002

Growth and death in the developing mammalian kidney: signals, receptors and conversations.

Because the kidney (metanephros) starts to function before completing development, its patterning and morphogenesis need to be closely integrated with its growth. This is achieved by blast cells at the kidney periphery generating new nephrons that link up to the extending collecting-duct arborisation, while earlier-formed and more internal nephrons are maturing and beginning to filter serum. This pattern of development requires that cell division and apoptosis be co-ordinated in the various kidney compartments (collecting-ducts, blast cells, metanephric mesenchyme, nephrons and vascular system). The underlying regulatory networks for cell proliferation are beginning to be unravelled, mainly through expression studies, mutation analysis and experimentation in vitro. This article summarises current knowledge of kidney growth and apoptosis, and analyses some of the 80 or so ligand-receptor pairings that seem to sustain development and growth. It also points to some unanswered questions, the most intriguing being what role does apoptosis play during normal kidney development?

Animals↗
PubMed2002

Apoptosis in the cortex of the developing mouse kidney.

Published levels of apoptosis in developing rat kidney (approximately 2.5%) seem large for a tissue with no obvious need for continual cell death. This paper examines the levels and patterns of apoptosis and mitosis in the cortical region of the developing metanephros of the mouse, the standard mammalian model embryo. Using confocal microscopy on specimens stained with propidium iodide to highlight nuclear morphology, optical sections of wholemount kidneys to a depth of approximately 50 microm were analysed and mitotic, apoptotic and interphase nuclei counted in the various compartments. Of the approximately 200 000 cells examined over E11.5-16.5, 2-3% were mitotic, confirming observations based on cryosections; the mitotic index peaked at E14.5, dropping to approximately 0.5% by P14. The mean apoptotic index during this period was 0.28%; this figure from wholemounts was approximately 10% of that earlier reported in cryosectioned rat kidneys. One possible explanation for the difference is that cryosectioning turns out to create small nuclear fragments that can stain strongly with propidium. Such fragments are not seen in wholemounts and do not stain with TUNEL. Wholemount mouse E11.5 tails and E16.5 lungs were also analysed and both their mitotic and their apoptotic indexes were similar to those in wholemount developing kidneys. These results show that the level of apoptosis in wholemount embryonic mouse kidney cortex is far less than previously reported in cryosectioned rat embryonic kidneys, and typical of that in other mouse embryonic tissues whose development seems not to require apoptosis.

Animals↗
PubMed2002

Using bioinformatics to identify kidney genes.

Online knowledge of genes involved in mouse kidney development is available from the literature (PubMed) and text-based (Kidney Development and Mouse Gene Expression-GXD) databases. Further information is in gene databases of other organisms having tissues homologous to the metanephros (e.g. Drosophila Malpighian tubules; tools are available for identifying mouse homologues of non-mouse genes) and from tissues homologous to those in the developing kidney (e.g. mesothelium that, like nephrons, arises from a mesenchyme to epithelial transition). Future databases will also include graphical data, and this knowledge will provide a further level of insight. These databases and tools are discussed here.

Animals↗