[
Worm Breeder's Gazette,
1990]
A number of improvements have been made in the gm automated DNA sequence analysis system: (1) The ratio of AT-containing to CG-containing dinucleotides has been added as a test for introns. This works better than AT frequency alone in C. elegans.(2) A branch site consensus sequence or an enhanced dinucleotide ratio can be required as an additional test on introns. (3) Predicted amino-acid sequence files are generated in a format appropriate for input to the Dana-Farber motif-identification program plsearch. (4) A graphic interface based on X-windows, version 11 is available as an option. (5) The complete analysis algorithm is significantly faster than the previous version. (6) A greedy model evaluation algorithm is available as an option. This algorithm generates the longest, non-overlapping models that cover a sequence and is much faster than the complete analysis algorithm. The program has been tested on Sun3, Sun4 and VAX machines running Unix (Ultrix on the VAX). Results for a series of tests run on a Sun 4/60 are shown in the table. [See Figure 1] gm can be run remotely on our machine, using the Internet. To do this, telnet to haywire.nmsu.edu, and logon as gm_guest with password gmuser. Read the README file for information on running gm. We are also distributing gm as C source code to nonprofit laboratories, either via anonymous ftp to haywire.nmsu.edu, or on tape. If you would like to receive gm on tape, send a 1/4' cartridge or 1/2' reel tape to: Chris Fields, Box 30001/3CRL, New Mexico State University, Las Cruces, New Mexico 88003-0001, USA; Telephone (505) 646-2848.
[
Worm Breeder's Gazette,
1994]
Telomeres confer stability to the chromosome ends by protecting them from degradation and illegitimate recombination and might contribute to the spatial organization of the chromosomes in the nucleus. Furthermore, they affect the expression of telomeric proximal genes and might be involved in the mechanism of somatic cell aging (for review see Biessmann and Mason, 1992, Advances in Genetics 30, 185-249). The protecting telomeric extremities of the chromosomes are maintained by special enzymes, the telomerases, which add repeats of the telomeric sequence after each round of replication (for review see Blackburn, 1992, Ann. Rev. Biochem. 61, 113-129). Telomerases are ribonucleoproteins, acting as RNA dependent DNA polymerases, which contain their own RNA template as an integral part of the enzyme, unlike the conventional reverse transcriptases. The RNA component of telomerases from several Ciliates species has been identified and cloned, but all attempts to clone the gene(s) for the protein component(s) from any system have failed so far. We assume that new telomere formation during the process of chromatin diminution in A. Iumbricoides requires a strong telomerase activity to resynthetize several kilobases of telomeric sequences in somatic cells (for review see Tobler et al., 1992, TIG 8, 427-432). In vitro extracts from eliminating developmental stages might thus be well suited for the isolation of the telomerase protein (or other factors) and for the cloning of the corresponding genes. Therefore, extracts from 4-8 cell stages were established and their quality was assessed by the ability to transcribe 5S rRNA genes (pol III) and SL RNA genes (pol II). Faithful in vitro extracts were tested for telomerase activity; our preliminary results revealed a possible nonprocessive and RNAse sensitive telomerase activity, capable of adding specific nucleotide sequences to the oligonucleotide primer (TTAGGC)(4). Currently, these data are being confirmed and extended. In a parallel approach, we will try to identify the C. elegans telomerase gene genetically.