&lt;title&gt;Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data&lt;/title&gt;

Verbeek, Fons J.; Broeder, Marjo J. den; Boon, Paul; Buitendijk, Bram; Doerry, Eckehard; Raaij, E. J. van; Živković, Danica

doi:10.1117/12.373465

Cited by 13 publications

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“…The atlas can be browsed with a number of applications that are made available through the internet (URL: bio-imaging.liacs.nl; Verbeek et al, 2000). The zebrafish ontology is the pivot in addressing the atlas of development.…”

Section: Computer Imaging Tools For Zebrafish Modelsmentioning

confidence: 99%

Section: Computer Imaging Tools For Zebrafish Modelsmentioning

confidence: 99%

“…A high-resolution image, composed of adjacent images, is acquired providing resolution at the cellular level . The anatomical structures in each section image are annotated with specialized software that produces 3D models (Verbeek et al, 2000;.For each stage, a 3D model is made available, consisting of the anatomical structures that can be distinguished at that particular stage. Standard staging conventions and anatomical nomenclatures are used.…”

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confidence: 99%

“…In order to be able to use these conventions in accessing other information systems, we have compiled it, enriched it and extended its granularity as an ontology (Belmamoune and Verbeek, 2007). The standard nomenclature is commonly referred to as the zebrafish ontology.The atlas can be browsed with a number of applications that are made available through the internet (URL: bio-imaging.liacs.nl; Verbeek et al, 2000). The zebrafish ontology is the pivot in addressing the atlas of development.…”

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confidence: 99%

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Zebrafish development and regeneration: new tools for biomedical research

Brittijn

Duivesteijn²,

Belmamoune³

et al. 2009

Int. J. Dev. Biol.

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146

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Basic research in pattern formation is concerned with the generation of phenotypes and tissues. It can therefore lead to new tools for medical research. These include phenotypic screening assays, applications in tissue engineering, as well as general advances in biomedical knowledge. Our aim here is to discuss this emerging field with special reference to tools based on zebrafish developmental biology. We describe phenotypic screening assays being developed in our own and other labs. Our assays involve: (i) systemic or local administration of a test compound or drug to zebrafish in vivo; (ii) the subsequent detection or "readout" of a defined phenotypic change. A positive readout may result from binding of the test compound to a molecular target involved in a developmental pathway. We present preliminary data on assays for compounds that modulate skeletal patterning, bone turnover, immune responses, inflammation and early-life stress. The assays use live zebrafish embryos and larvae as well as adult fish undergoing caudal fin regeneration. We describe proof-of-concept studies on the localised targeting of compounds into regeneration blastemas using microcarriers. Zebrafish are cheaper to maintain than rodents, produce large numbers of transparent eggs, and some zebrafish assays could be scaled-up into medium and high throughput screens. However, advances in automation and imaging are required. Zebrafish cannot replace mammalian models in the drug development pipeline. Nevertheless, they can provide a cost-effective bridge between cell-based assays and mammalian whole-organism models. KEY WORDS: Danio rerio, zebrafish, high-throughput screening, high-content screeningThis article is part of a special journal issue on "Pattern Formation". In this context, it seems appropriate to ask: 'what benefits to society can come from research into pattern formation?' The answer depends on how "pattern formation" is defined. For our purposes, it includes developmental mechanisms that generate Int. J. Dev. Biol. 53: 835-850 (2009) doi: 10.1387/ijdb.082615sb One is the field of human congenital malformations (the pres-836 S. A. Brittijn et al. ence at birth of anatomical abnormalities). Good examples are human malformations of fingers and toes, some cases of which are linked to mutations in the Hox family of developmental patterning genes (Akarsu et al., 1996;Goodman et al., 1997;Goodman, 2002). Teratology -the study of agents that cause congenital malformations -can be seen as applied pattern formation research. Tissue engineering, a medical research discipline that aims to create replacement tissues for patients who have suffered injury or surgical removal of tissues, is another area where knowledge of pattern formation can be applied. To date, the commonest approach to tissue engineering is to culture autologous cells on a synthetic template (Silva and Mooney, 2004). In the future, however, it may be possible to promote pattern formation by these cells so that they generate selforganised tissues or structures ...

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Section: Computer Imaging Tools For Zebrafish Modelsmentioning

confidence: 99%

Section: Computer Imaging Tools For Zebrafish Modelsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Zebrafish development and regeneration: new tools for biomedical research

Brittijn

Duivesteijn²,

Belmamoune³

et al. 2009

Int. J. Dev. Biol.

Self Cite

146

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“…In the atlas, each 3D model is the result of 3D reconstruction of section images in which each anatomical structure is delineated by a contour; a.k.a. the graphical annotation and each anatomical domain is associated with an anatomical name representing the semantic annotation [16,17,18].…”

Section: Introductionmentioning

confidence: 99%

Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

Belmamoune

Verbeek

2008

Journal of Integrative Bioinformatics

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SummaryThe Gene Expression Management System (GEMS) is a database system for patterns of gene expression. These patterns result from systematic whole-mount fluorescent in situ hybridization studies on zebrafish embryos. GEMS is an integrative platform that addresses one of the important challenges of developmental biology: how to integrate genetic data that underpin morphological changes during embryogenesis. Our motivation to build this system was by the need to be able to organize and compare multiple patterns of gene expression at tissue level. Integration with other developmental and biomolecular databases will further support our understanding of development. The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS. The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term. These terms are extracted from a formal anatomical ontology, i.e. the Developmental Anatomy Ontology of Zebrafish (DAOZ). In the GEMS, anatomical terms from this ontology together with terms from the Gene Ontology (GO) are also used to annotate patterns of gene expression and in this manner providing mechanisms for integration and retrieval . The annotations are the glue for integration of patterns of gene expression in GEMS as well as in other biomolecular databases. At the one hand, zebrafish anatomy terminology allows gene expression data within GEMS to be integrated with phenotypical data in the 3D atlas of zebrafish development. At the other hand, GO terms extend GEMS expression patterns integration to a wide range of bioinformatics resources.

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A three‐dimensional atlas of pituitary gland development in the zebrafish

Chapman

Sawitzke

Campbell

et al. 2005

J of Comparative Neurology

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The pituitary gland is unique to Chordates, with significant variation within this group, offering an excellent opportunity to increase insight into phylogenetic relationships within this phylum. The structure of the pituitary in adult Teleosts (class: Osteichthyes) is quite different from that in other chordates and is also variable among members of the class. Therefore, a complete description of the structure and development of the pituitary in members of this class is a critical component to our overall understanding of this gland. An obvious teleost model organism is the zebrafish, Danio rerio, as a significant amount of work has been done on the molecular control of pituitary development in this fish. However, very little work has been published on the morphological development of the pituitary in the zebrafish; the present study aims to fill this void. The pituitary develops from cells on the rostrodorsal portion of the head and reaches its final position, ventral to the hypothalamus, as the cephalic flexure occurs and the jaws and mouth form. The pituitary placode is juxtaposed to cells that will form the olfactory vesicles, the stomodeum, and the hatching gland. The volume of the pituitary is greatest at 24 hours post fertilization (hpf). From 24 to 120 hpf, the pituitary decreases in height and width as it undergoes convergent extension, increasing in length with the axis. The adenohypophysis is a morphologically distinct structure by 24 hpf, whereas the neurohypophysis remains indistinct until 72 hpf. The findings of this study correlate well with the available molecular data.

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<title>Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data</title>

Cited by 13 publications

References 0 publications

Zebrafish development and regeneration: new tools for biomedical research

Zebrafish development and regeneration: new tools for biomedical research

Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

A three‐dimensional atlas of pituitary gland development in the zebrafish

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