Developmental bioinformatics: linking genetic data to virtual embryos.
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This paper discusses current efforts to produce databases of gene expression for the major model embryos used in developmental biology. The efforts to build these resources were motivated by the need for immediate internet access to all types of research data, and the production of these databases is a major and new challenge for bioinformatics. Thus far bioinformatics has mainly been concerned with textually oriented resources and data, much of it concerned with gene and protein sequences. Because the genetic basis of developmental biology is integrated with developmental anatomy, these databases require the use of images to link molecular data with spatial information. In order to standardise database formats, digital atlases of some model systems are being produced that include integrated anatomical descriptions and these are being linked to appropriate genetic data. Integrating such image-based, searchable data into databases makes new demands on the field of bioinformatics and we consider here the imaging modalities that are used to obtain information and we discuss in particular the production of 3D images from serial sections. Next, we consider how to integrate textual and spatial descriptions of gene expression and the key tool needed to make this possible, i.e. anatomical nomenclature. A short review of internet resources on developmental biology is also given and future prospects for the development of these databases are discussed. (+info)
Developmental biology and the redirection or replacement of cells.
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The aim of developmental biology is to understand how an egg converts itself into a complete organism through the processes of cell differentiation, morphogenesis and size regulation. The principles that have emerged over recent decades include the constancy of the genome in nearly all cells of an individual, the existence of stem cells in many organs and the overwhelming importance of signalling between cells for the determination of their fate. These and other characteristics of development are discussed here in relation to the prospect of achieving cell and tissue correction or replacement with the help of nuclear transplantation and signalling factors. Nuclear transplantation offers a one-step procedure for generating multipotent embryo cells from the cells of an adult tissue such as skin. It should be possible to proliferate the resulting cells as can be done for mouse embryonic stem cells. Embryo cells can be made to differentiate in many directions by exposing them to various agents or to different concentrations of a single factor such as the transforming growth factor beta class signalling molecule activin. The possibility of a cancerous condition being acquired during these experimental manipulations can be guarded against by transfecting cells with a conditional suicide gene. Thus it may be possible to generate replacement cells or tissues from an adult human for transplantation back to the original donor, without the disadvantage of any genetic incompatibility. (+info)
The Cambrian "explosion": slow-fuse or megatonnage?
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Clearly, the fossil record from the Cambrian period is an invaluable tool for deciphering animal evolution. Less clear, however, is how to integrate the paleontological information with molecular phylogeny and developmental biology data. Equally challenging is answering why the Cambrian period provided such a rich interval for the redeployment of genes that led to more complex body plans. (+info)
Embracing complexity: organicism for the 21st century.
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Organicism (materialistic holism) has provided the philosophical underpinnings for embryology since the time of Kant. It had influenced the founders of developmental mechanics, and the importance of organicism to embryology was explicitly recognized by such figures as O. Hertwig, H. Spemann, R. Harrison, A. M. Dalq, J. Needham, and C. H. Waddington. Many of the principles of organicism remain in contemporary developmental biology, but they are rarely defined as such. A combination of genetic reductionism and the adoption of holism by unscientific communities has led to the devaluation of organicism as a fruitful heuristic for research. This essay attempts to define organicism, provide a brief history of its importance to experimental embryology, outline some sociologically based reasons for its decline, and document its value in contemporary developmental biology. Based on principles or organicism, developmental biology should become a science of emerging complexity. However, this does mean that some of us will have to learn calculus. (+info)
Comparative genetics: a third model nematode species.
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Recent studies have introduced Oscheius sp. CEW1 as a third nematode species accessible to genetic analysis, joining the better known Caenorhabditis elegans and Pristionchus pacificus. A group of vulva-defective mutants in Oscheius has been identified, with defects not seen in C. elegans. (+info)
Introducing the Spemann-Mangold organizer: experiments and insights that generated a key concept in developmental biology.
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The "organizer paper", published by Hans Spemann and Hilde Mangold in 1924, initiated a new epoch in developmental biology. Also it marked the climax of Spemann's life-long research which began at the end of the nineteenth century. This introduction retraces some of the steps by which Spemann arrived at the organizer concept: The problem of amphibian lens induction including the so-called lens controversy, the early constriction experiments creating double headed malformations, and the homeo- and heteroplastic transplantations during gastrula stages of the newt. Furthermore this paper will--based on historical documents--repudiate some objections raised to the contribution of Spemann and Hilde Mangold to the discovery and interpretation of the organizer effect. (+info)
Developmental biology of amphibians after Hans Spemann in Germany.
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After the Hans Spemann and Hilde Mangold discovery of the importance of the dorsal blastopore lip for axis formation in the early embryo (Nobelprize for Spemann, 1935), the scientific community tried in a goldrush-like manner to find the inducing factors responsible for the programming of early embyronic determination and differentiation. The slow progress towards a solution of this problem caused a fading of interest on behalf of most laboratories. This article describes the activities of a few laboratories in Finland, Japan and Germany, which continued their studies despite tremendous experimental difficulties. Finally only Heinz Tiedemann's group in Berlin was the first which could isolate a mesoderm/endoderm inducing factor in highly purified form, the so-called vegetalizing factor, now known as activin. Furthermore this article describes the identification of neuralizing factors like Chordin, Cerberus and Dickkopf in the zone of the Spemann-Mangold organizer. The finding that BMP-4 acts as an antagonist to these factors located on the dorsal side led to a new understanding of the mechanisms of action of inducing (neuralizing) factors and early embryonic pattern formation. Moreover, the observations that closely related genes and their products were also found in Drosophila, Zebrafish, Mice and Human were the basis for new concepts of evolutionary mechanisms (dorsal/ventral and anterior/posterior polarity or conserved processes in eye-development of all 7 animal phyla). (+info)
Spemann's heritage in Finnish developmental biology.
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The Finnish school of developmental biology can be considered a direct descendant of Spemann's school as both the original technology and the fundamental problems were introduced into Finland by Gunnar Ekman (1883-1937) who had worked for extended periods in Germany. After his early death, the work was continued by Sulo Toivonen (1909-1995), and until 1968 the group explored the mechanisms of primary induction and the subsequent segregation of the central nervous system. The extensive investigations led to the formulation of the "double-gradient" hypothesis and ultimately to its experimental vindication. (+info)