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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.
[
2000]
There is growing interest in the use of bioindicators to assess metal toxicity in soil. The current ASTM Standard Guide for Conducting Laboratory Soil Toxicity Test with the lumbricid earthworm Eisenia fetida (E 1676-97) uses a common earthworm. The nematode Caenorhabditis elegans is a natural soil inhabitant with many characteristics that make an ideal alternate test organism. It has been used to assess metal toxicity in aquatic media, agar plates and in soil. Work is currently underway on the design of a C. elegans procedure for metals in soil. The objective of this study was to determine differences in LC50S between the chloride salt and the nitrate salt forms of cadmium, copper, lead, nickel, and zinc, in three types of soil: Cecil, Tifton, and ASTM artificial soil. Results indicated that the toxicological effect of the metallic salt varies and is dependent on the particular metal. For Cd and Pb the nitrate form is more toxic while Cu and Ni are more toxic in the chloride form. The composition of the soil also effected toxicity, with the metal being the least toxic in ASTM soil and more toxic in the Tifton soil. This strongly correlated with organic matter and clay content of the soil. It is important to determine the effects of carrier salt form and soil composition on metal toxicity, not only in order to standardize the protocol for C. elegans soil toxicity testing, but also in establishing acceptable exposure concentrations in the soil.