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The correct wiring of neuronal circuits depends on outgrowth and guidance of neuronal processes during development. In the past two decades, great progress has been made in understanding the molecular basis of axon outgrowth and guidance. Genetic analysis in Caenorhabditis elegans has played a key role in elucidating conserved pathways regulating axon guidance, including Netrin signaling, the slit Slit/Robo pathway, Wnt signaling, and others. Axon guidance factors were first identified by screens for mutations affecting animal behavior, and by direct visual screens for axon guidance defects. Genetic analysis of these pathways has revealed the complex and combinatorial nature of guidance cues, and has delineated how cues guide growth cones via receptor activity and cytoskeletal rearrangement. Several axon guidance pathways also affect directed migrations of non-neuronal cells in C. elegans, with implications for normal and pathological cell migrations in situations such as tumor metastasis. The small number of neurons and highly stereotyped axonal architecture of the C. elegans nervous system allow analysis of axon guidance at the level of single identified axons, and permit in vivo tests of prevailing models of axon guidance. C. elegans axons also have a robust capacity to undergo regenerative regrowth after precise laser injury (axotomy). Although such axon regrowth shares some similarities with developmental axon outgrowth, screens for regrowth mutants have revealed regeneration-specific pathways and factors that were not identified in developmental screens. Several areas remain poorly understood, including how major axon tracts are formed in the embryo, and the function of axon regeneration in the natural environment.

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.03.004 Byline: Ralf Schnabel (a), Marcus Bischoff (a), Arend Hintze (a), Anja-Kristina Schulz (a), Andreas Hejnol (a), Hans Meinhardt (b), Harald Hutter (c) Keywords: Cell migration; Cell guidance; Pattern formation; 4D microscopy; Bioinformatics Abstract: 4D microscopic observations of Caenorhabditis elegans development show that the nematode uses an unprecedented strategy for development. The embryo achieves pattern formation by sorting cells, through far-ranging movements, into coherent regions before morphogenesis is initiated. This sorting of cells is coupled to their particular fate. If cell identity is altered by experiment, cells are rerouted to positions appropriate to their new fates even across the whole embryo. This cell behavior defines a new mechanism of pattern formation, a mechanism that is also found in other animals. We call this new mechanism 'cell focusing'. When the fate of cells is changed, they move to new positions which also affect the shape of the body. Thus, this process is also important for morphogenesis. Author Affiliation: (a) Technische Universitat Braunschweig Carolo Wilhelmina, Institut fur Genetik, Spielmann Str. 7, D-38106 Braunschweig, Germany (b) MPI fur Entwicklungsbiologie, Spemannstr. 35, D-72076 Tubingen, Germany (c) Simon Fraser University, Department of Biological Sciences, Burnaby BC, Canada V5A 1S6 Article History: Received 2 September 2005; Revised 23 February 2006; Accepted 7 March 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.02.042 Byline: Christina Schmid, Valentin Schwarz, Harald Hutter Keywords: Development; Neuron; Axon guidance; Ventral cord; Transcription factor; ETS-box Abstract: Neurons send out axons and dendrites over large distances into target areas where they eventually form synapses with selected target cells. Axonal navigation is controlled by a variety of extracellular signals and neurons express receptors only for that subset of signals they need to navigate to their own target area. How the expression of axon guidance receptors is regulated is not understood. In genetic screens for mutants with axon guidance defects, we identified an ETS-domain transcription factor, AST-1, specifically required for axon navigation in certain classes of interneurons. In addition, ast-1 has a role in the differentiation of the ventral cord pioneer neuron AVG. Outside the nervous system, ast-1 is essential for morphogenesis of the pharynx. Ast-1 is transiently expressed in several classes of neurons (including AVG) during neuronal differentiation with a peak expression during late stages of neuronal differentiation and axon outgrowth. Ast-1 genetically interacts with other transcription factors controlling neuronal differentiation like lin-11 and zag-1 as well as components of the netrin pathway suggesting that ast-1 might control the expression of components of the netrin signal transduction machinery. Author Affiliation: Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany Article History: Received 27 September 2005; Revised 16 December 2005; Accepted 6 February 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.05.025 Byline: Harald Hutter (a), Irene Wacker (a), Christina Schmid (a), Edward M. Hedgecock (b) Keywords: Development; neuron; Axon guidance; Pioneer; Asymmetry; Ventral cord; ast-genes Abstract: The ventral cord in C. elegans is the major longitudinal axon tract containing essential components of the motor circuit. In genetic screens using transgenic animals expressing neuron specific GFP reporters, we identified twelve genes required for the correct outgrowth of interneuron axons of the motor circuit. In mutant animals, axons fail to navigate correctly towards the ventral cord or fail to fasciculate correctly within the ventral cord. Several of those mutants define previously uncharacterised genes. Two of the genes, ast-4 and ast-7, are involved in the generation of left-right asymmetry of the two ventral cord axon tracts. Three other genes specifically affect pioneer-follower relationships between early and late outgrowing axons, controlling either differentiation of a pioneer neuron (lin-11) or the ability of axons to follow a pioneer (ast-2, unc-130). Navigation of the ventral cord pioneer neuron AVG itself is defective in ast-4, ast-6 and unc-130 mutants. Correlation of these defects with navigation defects in different classes of follower axons revealed a true pioneer role for AVG in the guidance of interneurons in the ventral cord. Taken together, these genes provide a basis to address different aspects of axon navigation within the ventral cord of C. elegans. Author Affiliation: (a) Max-Planck-Institut fur medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany (b) John Hopkins University, Department of Biology, 3400 North Charles Street, 21218 Baltimore, MD 21218, USA Article History: Received 9 March 2005; Revised 3 May 2005; Accepted 18 May 2005

Coregulator DIN-1 and DAF-12 is shown interacting physically and genetically to instruct organismal fates. It is proposed that the DIN-1S/DAF-12 complex serves as a molecular switch that implements slow life history alternatives in response to diminished hormonal signals.

Mutations in the unc-39 gene of C. elegans lead to migration and differentiation defects in a subset of mesodermal and ectodermal cells, including muscles and neurons. Defects include mesodermal specification and differentiation as well a neuronal migration and axon pathfinding defects. Molecular analysis revealed that unc-39 corresponds to the previously named gene ceh-35 and that the UNC-39 protein belongs to the Six4/5 family of homeodomain transcription factors and is similar to human Six5, a protein implicated in the pathogenesis of type I myotonic dystrophy (DM1). We show that human Six5 and UNC-39 are functional homologs, suggesting that further characterization of the C. elegans unc-39 gene might provide insight into the etiology of DM1. Keywords: C. elegans; unc-39; Myotonic dystrophy

Caenorhabditis elegans is renowned for its invariant embryogenesis. This pattern of development is in apparent contrast to other organisms from Drosophila to higher vertebrates. With the aid of a 4D microscope system (multifocal, time-lapse video recording system) which permits the extensive documentation and analysis of cell divisions, cell positions, and migrations in single embryos we have analyzed normal embryogenesis of C. elegans. The instrumentation reveals a naturally occurring variability in cell division timing, cell positioning, and cell-cell contacts which could not have been detected by the direct observation used earlier (Sulston et al., 1983, Dev. Biol. 100, 64-119). Embryos are very flexible and produce an essentially invariant premorphogenetic stage from variable earlier stages. An analysis of the distribution of the descendants of the early founder blastomeres at the premorphogenetic stage shows that these establish discrete regions in the embryo, a process involving a considerable amount of cell movement, which again varies in different embryos. Only cell fate assignment remains invariant. However, as shown earlier, this is not due to an autonomous invariant specification of cell fates but due to the fact that cell-cell interactions occur very early when the topology of blastomeres in the embryo is still sufficiently precise to ensure reproducible patterns of inductions. A new concept that founder blastomeres produce embryonic regions in the embryo can explain the striking complexity of the lineage per se and also the complicated asymmetric lineage patterns by which the bilateral symmetry of the embryo is established. Many cells, including bilateral homologs, were apparently chosen for a specific fate solely by their position in the embryo, irrespectively of the lineage descent by which the cells are created. We postulate that the production of regions by cell-cell interactions is the pivotal principle guiding the embryogenesis of C. elegans and that the embryogenesis of the worm follows the same basic principles as embryogenesis in other organisms.

The parameters necessary to the formation of the body wall muscle in the nematode Caenorhabditis elegans includes the cell autonomous expression of perlecan, a component of the extracellular matrix. A polyclonal antibody first detected perlecan at the comma stage of muscle development, wherein, muscle cells exhibited morphological flexibility to be able to compensate for missing cells and alterations in tissue composition, and to form a functional quadrant.

Abstract Background Almost half of the Caenorhabditis elegans genome encodes proteins with either a signal peptide or a transmembrane domain. Therefore a substantial fraction of the proteins are localized to membranes, reside in the secretory pathway or are secreted. While these proteins are of interest to a variety of different researchers ranging from developmental biologists to immunologists, most of secreted proteins have not been functionally characterized so far. Results We grouped proteins containing a signal peptide or a transmembrane domain using various criteria including evolutionary origin, common domain organization and functional categories. We found that putative secreted proteins are enriched for small proteins and nematode-specific proteins. Many secreted proteins are predominantly expressed in specific life stages or in one of the two sexes suggesting stage- or sex-specific functions. More than a third of the putative secreted proteins are upregulated upon exposure to pathogens, indicating that a substantial fraction may have a role in immune response. Slightly more than half of the transmembrane proteins can be grouped into broad functional categories based on sequence similarity to proteins with known function. By far the largest groups are channels and transporters, various classes of enzymes and putative receptors with signaling function. Conclusion Our analysis provides an overview of all putative secreted and transmembrane proteins in C. elegans. This can serve as a basis for selecting groups of proteins for large-scale functional analysis using reverse genetic approaches.

Abstract Background The majority of the genes even in well-studied multi-cellular model organisms have not been functionally characterized yet. Mining the numerous genome wide data sets related to protein function to retrieve potential candidate genes for a particular biological process remains a challenge. Description GExplore has been developed to provide a user-friendly database interface for data mining at the gene expression/protein function level to help in hypothesis development and experiment design. It supports combinatorial searches for proteins with certain domains, tissue- or developmental stage-specific expression patterns, and mutant phenotypes. GExplore operates on a stand-alone database and has fast response times, which is essential for exploratory searches. The interface is not only user-friendly, but also modular so that it accommodates additional data sets in the future. Conclusion GExplore is an online database for quick mining of data related to gene and protein function, providing a multi-gene display of data sets related to the domain composition of proteins as well as expression and phenotype data. GExplore is publicly available at: http://genome.sfu.ca/gexplore/

Abstract Background Cell adhesion molecules of the immunoglobulin superfamily (IgCAMs) form one of the largest and most diverse families of adhesion molecules and receptors in the nervous system. Many members of this family mediate contact and communication among neurons during development. The Caenorhabditis elegans genome contains a comparatively small number of IgCAMs, most of which are evolutionarily conserved and found across all animal phyla. Only some of these have been functionally characterized so far. Results We systematically analyzed previously uncharacterized IgCAMs in C. elegans. Green fluorescent protein reporter constructs of 12 IgCAMs revealed that expression generally is not confined to a single tissue and that all tissues express at least one of the IgCAMs. Most IgCAMs were expressed in neurons. Within the nervous system significant overlap in expression was found in central components of the motor circuit, in particular the command interneurons, ventral cord motoneurons as well as motoneurons innervating head muscles. Sensory neurons are underrepresented among the cells expressing these IgCAMs. We isolated mutations for eight of the genes showing neuronal expression. Phenotypic analysis of single mutants revealed limited neuronal defects, in particular axon navigation defects in some of the mutants. Systematic genetic interaction studies uncovered two cases of functional overlap among three and four genes, respectively. A strain combining mutations in all eight genes is viable and shows no additional defects in the neurons that were analyzed, suggesting that genetic interactions among those genes are limited. Conclusion Genetic interactions involving multiple IgCAMs affecting axon outgrowth demonstrate functional overlap among IgCAMs during nervous system development.