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[
WormBook,
2006]
Transposons are discrete segments of DNA capable of moving through the genome of their host via an RNA intermediate in the case of class I retrotransposon or via a "cut-and-paste" mechanism for class II DNA transposons. Since transposons take advantage of their host''s cellular machinery to proliferate in the genome and enter new hosts, transposable elements can be viewed as parasitic or "selfish DNA". However, transposons may have been beneficial for their hosts as genome evolution drivers, thus providing an example of molecular mutualism. Interactions between transposon and C. elegans research were undoubtedly mutualistic, leading to the advent of needed genomic tools to drive C. elegans research while providing insights into the transposition field. Tc1, the first C. elegans transposon to be identified, turned out to be the founding member of a widespread family of mobile elements: the Tc1/ mariner superfamily. The investigation into transposition regulation in C. elegans has uncovered an unforeseen link between transposition, genome surveillance and RNA interference. Conversely, transposons were utilized soon after their identification to inactivate and clone genes, providing some of the first molecular identities of C. elegans genes. Recent results suggest that transposons might provide a means to engineer site-directed mutations into the C. elegans genome. This article describes the different transposons present in the C. elegans genome with a specific emphasis on the ones that proved to be mobile under laboratory conditions. Mechanisms and control of transposition are discussed briefly. Some tools based on the use of transposons for C. elegans research are presented at the end of this review.
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Genome Res,
1995]
Caenorhabditis elegans, a free-living nematode worm, has proved a particularly useful model organism for studying the anatomy, behavior, genetics, and development of a metazoan. It also has one of the smallest genomes of the higher eukaryotes (100 Mb distributed over six chromosomes), making it an ideal candidate for detailed molecular analysis. The C. elegans genome project began over 10 years ago and is a collaberative effort between two laboratories (St. Louis, MO, USA and Cambridge, UK), with the ultimate aim of mapping and sequencing the whole of the 100-Mb genome. The consortium has now completed the sequence of approximately one-fifth of the genome and plans to have sequenced more than half the genome before the end
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Biochim Biophys Acta,
2014]
As biological force-sensing systems mechanosensitive (MS) ion channels present the best example of coupling molecular dynamics of membrane proteins to the mechanics of the surrounding cell membrane. In animal cells MS channels have over the past two decades been very much in focus of mechanotransduction research. In recent years this helped to raise awareness of basic and medical researchers about the role that abnormal MS channels may play in the pathophysiology of diseases, such as cardiac hypertrophy, atrial fibrillation, muscular dystrophy or polycystic kidney disease. To date a large number of MS channels from organisms of diverse phylogenetic origins have been identified at the molecular level; however, the structure of only few of them has been determined. Although their function has extensively been studied in a great variety of cells and tissues by different experimental approaches it is, with exception of bacterial MS channels, very little known about how these channels sense mechanical force and which cellular components may contribute to their function. By focusing on MS channels found in animal cells this article discusses the ways in which the connections between cytoskeleton and ion channels may contribute to mechanosensory transduction in these cells. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Herve.
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[
Methods Cell Biol,
1995]
The clone-based physical map of the 100-Mb Caenorhabditis elegans genome has evolved over a number of years. Although the detection of clone overlaps and construction of the map have of necessity been carried out centrally, it has been essentially a community project. Without the provision of cloned markers and relevant map information by the C. elegans community as a whole, the map would lack the genetic anchor points and coherent structure that make it a viable entity. Currently, the map consists of 13 mapped contigs totaling in excess of 95 Mb and 2 significant unmapped contigs totaling 1.3 Mb. Telomeric clones are not yet in place. The map carries 600 physically mapped loci, of which 262 have genetic map data. With one exception, the physical extents of the remaining gaps are not known. The exception is the remaining gap on linkage group (LG) II. This has been shown to be bridged by a 225-kb Sse83871 fragment. Because the clones constituting the map are a central resource, there is essentially no necessity for individuals to construct cosmid and yeast artificial chromosome (YAC) libraries. Consequently, such protocols are not included here. Similarly, protocols for clone fingerprinting, which forms the basis of the determination of cosmid overlaps and the mapping of clones received from outside sources and has to be a centralized operation, and YAC linkage are not give here. What follows is essentially a "user's guide" to the physical map. Details of map construction are given where required for interpretation of the map as distributed. The physical mapping has been a collaboration between the MRC Laboratory of Molecular Biology, Cambridge, United Kingdom (now at The Sanger Centre, Cambridge, UK) and Washington University School of Medicine, St. Louis, Missouri. Inquiries regarding map interpretation, information, and materials should be addressed to alan@sanger.ac.uk or rw@nematode.wustl.edu.
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[
Methods Cell Biol,
1995]
ACeDB (A Caenorhabditis elegans Data Base) is a data management and display system that contains a wide range of genomic and other information about C. elegans. This chapter provides an overview of ACeDB for the C. elegans user, focusing in particular on the Macintosh version Macace. Previous reviews of AceDB include those of Thierry-Mieg and Durbin (1992) and Durbin and Thierry-Mieg (1994), which describe the general properties of the whole system, and that by Dunham et al. (1994), which discussed the use of AceDB for physical map data collection and assembly. ACeDB was developed by Jean Thierry-Mieg and Richard Durbin primarily for the C. elegans project, when the genomic sequencing project was just beginning in 1990. The original aim was to create a single database that integrated the genetic and physical maps with both genomic sequence data and the literature references. The forerunner of ACeDB was the program CONTIG9 (Sulston et al., 1988), which was developed to maintain and edit the physical map. CONTIG9 served researchers around the world by providing critical on-line access to the current physical map as it was being constructed (Coulson et al., 1986). This policy of immediate access allowed members of the worm community to see the same data as the people making the map, and proved very successful in maximizing use of the map. The same approach was adopted as a template for ACeDB. These two principles, developing a comprehensive database for all types of genomic and related data and providing public access to the data in the same form as used by the data-collecting laboratories, have continued to underlie developments of ACeDB. Over the last 5 years, a wide range of genome projects relating to other organisms have taken the ACeDB program and used it to develop databases for their own data. ACeDB has been used both in public projects designed to redistribute public data in a coordinated fashion and laboratory-based projects for collecting new data. Others, such as the C. elegans ACeDB, have used the database for both purposes. The reason it has been possible to adapt ACeDB so widely is that its flexible data structure allows new types of objects and new types of information about these objects to be added easily. This chapter describes (1) how to obtain ACeDB and documentation for it, (2) how to access and use the information in ACeDB, and (3) how to use ACeDB as a laboratory-based data managing system. Some of what we discuss is specific to the nematode database, but other information applies to the basic computer software program and, hence, to any database using the ACeDB program.