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Worm Breeder's Gazette,
1993]
It would be useful if worm labs had access to each other's strain lists. For instance, one lab may have put away in the freezer as uninteresting a mutation that is just what a second lab wants. Unfortunately, there have always been practical difficulties to sharing strain lists: they change frequently, and there is no common format. A new network program called Gopher (see contribution from Mike Cherry on previous page of this WBG issue, which discusses the use of Gopher in connection with accessing the ACEDB database) may be the solution to these problems. Gopher sends an inquiry over the Internet directly to the source, without the user having to know about any messy details. The reply is current, and comes back as text, so that format problems don't arise. Other kinds of information (e.g., pictures) can also be made available. To test the feasibility of Gopher for data sharing, we have set up Gopher service at the CGC (elegans.cbs.umn.edu; IP address 134.84.210.1) and the Avery lab (eatworms.swmed utexas.edu; IP address 129.112.11.21). By gopher to either of these addresses you can get the CGC bibliography, strain list, WBG subscriber directory, recent WBG tables of contents, Avery lab strain lists, pictures of mutants, manuscripts in press, and (thanks to Mike Cherry at Massachusetts General Hospital) access to ACEDB information. Gopher is available for Macintosh, IBM-PC, Unix, and Xwindows by anonymous ftp from boombox.micro.umn.edu (134.84.132.2). If you don't know how to get it, send e-mail to leon@eatworms.swmed.utexas.edu and we will try to help. Also, we would like to urge other labs to make data available by Gopher. If you do, send us e-mail so you can be included in the CGC menu. If you would like to make your strain lists available but don't know how, send e-mail and we'll see if we can help with that.
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Worm Breeder's Gazette,
1997]
Neuropeptides form the largest class of neuroactive substances, yet as a group their roles in nervous system function and development are still poorly understood. Only the FMRFamides and related neuropeptides (FaRPs) have been intensely studied in C. elegans. However, in Aplysia californica, over 40 neuropeptides have been identified and characterized. This suggests that many C. elegans neuropeptides have not yet been discovered. With the near completion of the C. elegans genome sequencing project, reverse genetic techniques can be applied to identify C. elegans neuropeptide genes. We are using FASTA and BLAST to search with previously identified neuropeptide sequences (stored in GENBANK) against the C. elegans genome sequence. We expect the products of neuropeptide genes to fit a prepropeptide model: they should contain a putative signal peptide region, followed by interrupted multiple repeats of the same or similar neuropeptide. Additionally, the predicted neuropeptides should be flanked by pairs of basic amino acids (KR, RR, KK, RK) or less frequently by monobasic residues (R or K) which are preferred sites of endoproteolytic cleavage. Potential C. elegans neuropeptide gene compatible with the prepropeptide model are then selected for molecular and genetic analysis. We are currently analyzing C. elegans genes encoding neuropeptides similar to Aplysia buccalin (C. elegans C01C4.1) and myomodulin (C. elegans T24D8.3, T24D8.4, T24D8.5 and T01B6.4). (See below.) Even though the predicted C. elegans neuropeptide sequences are not strikingly similar to the Aplysia neuropeptides, there is strong internal homology between neuropeptides within the same C. elegans genes. We are creating reporter constructs by fusing the promoter region of potential neuropeptide genes to the GFP gene using Fire laboratory vectors. We are injecting these reporter constructs to assess cellular expression patterns of these myomodulin-like and buccalin-like genes. We think that it is likely that the GENEFINDER predicted genes of T24D8.3, .4 and .5 are exons of a single gene. We will use RT-PCR to determine mRNA splicing patterns. Our long range goals include creating mutations in these genes and determining the function of these and other putative C. elegans neuropeptides. Identity is indicated with a colon, gaps with underlining. SLSMLRLG____ Aplysia Myomodulin A :MA:G:::LRPG T24D8.5 :MAYG:Q:FRPG # :IALG:S:FRPG :MAIG:A:MRPG T24D8.4 :IAIG:A:FRPG T24D8.3 N:LVG:Y:FRIG T01B6.4 DPNVDPYSYLPSVG Aplysia Buccalin _VNL::N:FRM:F: C01C4.1 ___M:ANAFRM:F: # ___M::NAFRM:F:
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Worm Breeder's Gazette,
2002]
The mitochondria play a critical role in the cellular energy supply and perform other essential roles in a variety of metabolic functions. The mitochondria electron transport respiratory chain (MRC) is typically composed of four multi-subunit enzymes (complexes I to IV) and the ATP synthase (complex V). Complex II is involved in both the tricarboxylic acid (TCA) cycle and the aerobic respiratory chains of mitochondria. It consists of 4 nuclear-encoded polypeptides: the flavoprotein (Fp/ SDHA), an iron-sulphur protein (Ip/ SDHB) and two integral membrane proteins (SDHC and SDHD). Clinically, complex II deficiency associated with SDHA gene mutations can result in myopathy, encephalopathy and isolated cardiomyopathy. Recently, the analysis of the susceptibility gene for familial paraganglioma syndrome revealed germ line mutations in the SDHB, SDHC and SDHD genes. Those genes are therefore considered to be tumor-suppressor genes. One can speculate that oxidative damage or ROS recycling dysfunction from impaired complex II could be important in explaining the damage to muscle and nerve cells. The molecular basis of such MRC enzyme deficiencies in humans remains largely unknown (1).
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Worm Breeder's Gazette,
1990]
The Internet is an international computer network. It is much faster and more reliable than Bitnet and provides facilities for connecting to and running remote machines (Telnet), transferring very large files (FTP) and remotely querying other machines (finger) as well as for standard electronic mail. An Internet connection will be required to remotely access the electronic worm community library being developed by Bruce Schatz at the University of Arizona ( schatz@cs.arizona.edu). The Internet is physically based on the NSFnet and the many regional high-speed backbone networks in the U.S.; it is typically based on the national network (such as JANET in the U. K.) in other countries. Internet communication within the U.S. is essentially real-time; international Internet communication typically takes only a few minutes. As most academic institutions are already on the Internet, getting an Internet connection to your laboratory will be straightforward in most cases. Internet is very easy to use. For example: mail cfields@nmsu.edu will send me electronic mail. Similarly: telnet haywire.nmsu.edu will connect your computer - and hence your terminal - to our machine haywire at NMSU, allowing you to logon and run programs remotely, while: ftp haywire.nmsu.edu will connect your computer to haywire and allow you to transfer very large - many megabtye - files. The latter two functions often do not work internationally due to mismatches in communication protocols (they require the TCP/IP network standard), but sending international email is as easy as sending email within a single country. One of the following will probably work for getting an Internet
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[
Worm Breeder's Gazette,
1996]
The B- and T-cell based adaptive immunity is thought to be found only in vertebrates. In contrast, several systems categorized in innate immunity (e.g. the defense by phagocytes, superoxides, and antibacterial proteins etc) have been reported in many species of animals, both vertebrates and invertebrates. It might be worthwhile if we can study the innate immunity of nematodes, because of the utility of C. elegans. Previously, we reported that at least three humoral defense activities (antibacterial, bacteriolytic, and agglutinating) were detected in the body fluid of the parasitic nematode Ascaris suum (1). The substantial nature of these activities was suggested to be proteins/peptides, because all of them were lost by trypsin digestion. One of them, ASABF (Ascaris suum antibacterial factor) is a heat-stable antibacterial protein with molecular mass of 7 kDa. Recently, we purified ASABF, and its amino acid sequence was determined. Eight Cys residues which might contribute to intramolecular disulfide bonds were found in this sequence. MPsrch data base searches revealed weak sequence identity between ASABF and insect/arthropod defensins (IADs), the antibacterial proteins which contain 6 Cys residues (2). Jumbling test supported that this similarity was significant. All of them were positively charged proteins. In addition, Gram-positive bacteria were much more sensitive to ASABF (IC50=0.6 microgram/ml, against Staphylococcus aureus) than Gram-negative bacteria (IC50=50 microgram/ml, against Esherichia coli), and this antibacterial spectrum is similar to IADs. However, ASABF consisted of over 60 residues, whereas IADs consisted of only 30-40 residues. The positions of Cys residues in the sequence of IADs were highly conserved, and they are essential to the antibacterial activity. In contrast, an additional Cys of ASABF was found at the internal position of conserved array of Cys residues. ASABF, therefore, is not a typical IAD, although ASABF might be evolutionally related to IADs. Many antibacterial proteins have been isolated from various insect sources. Their gene regulation mechanisms have been explored in Drosophila and other insects. Interestingly, similar regulatory factors which originally found in vertebrates (e.g. NFkappaB) was also essential in insects. Its relationship to factors involved in embryonic pattern formation has been discussed (Dif and dorsal)(3, 4). What will be found in the ASABF genes? The sequencing of cDNAs and genes of ASABF, and the search for its homologues in C.elegans are currently proceeding. (1) Kato, Y. (1995) Zool. Sci. 12, 225-230. (2) Boman, H.G. (1995) Annu. Rev. Immunol. 13, 61-92. (3) Ip, Y.T. et al. (1993) Cell 75, 753-763. (4) Hoffmann, J.A. (1995) J. Cell. Biochem. 21A, 188 (an abstract for Keystone symposia 1995)