Worms

General information about C. elegans.

C. elegans genomics.

Microarrays

SAGE

Promoter microarray for chromatin IP

Expression patterns

RNAi

The C. elegans Gene Knockout Project Deletion strains for 1800 genes and counting. Gary Moulder,Project Manager, Gary-Moulder@mail.omrf.ouhsc.edu

Protein-Protein interactions Interactome. Vidal lab project to find protein-protein interactions by yeast two-hybrid method. 436 interactions found.

Protein Structures Structural Genomics of Caenorhabditis elegans. 3D structure of 5 genes.

Genomic expression libraries

ESTs Yuji Kohara, National Institute of Genetics, Japan. Order from: ykohara@lab.nig.ac.jp

Genomic clones Specific cosmids or YACs of genomic DNA can be requested from Alan Coulson at the Sanger Centre (alan@sanger.ac.uk).

Worm strains Caenorhabditis Genetics Center. Strains available on request.

Bioinformatic resources

Genomic sequence

Worm resource link collections

Publications, Literature

C. elegans technology

Proc Natl Acad Sci U S A 1997 Nov 25;94(24):13128-33

Genetically targeted cell disruption in Caenorhabditis elegans.

Harbinder S, Tavernarakis N, Herndon LA, Kinnell M, Xu SQ, Fire A, Driscoll M

Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Center for Advanced Biotechnology and Medicine, Piscataway 08855, USA.

The elimination of identified cells is a powerful tool for investigating development and system function. Here we report on genetically mediated cell disruption effected by the toxic Caenorhabditis elegans mec-4(d) allele. We found that ectopic expression of mec-4(d) in the nematode causes dysfunction of a wide range of nerve, muscle, and hypodermal cells. mec-4(d)-mediated toxicity is dependent on the activity of a second gene, mec-6, rendering cell disruption conditionally dependent on genetic background. We describe a set of mec-4(d) vectors that facilitate construction of cell-specific disruption reagents and note that genetic cell disruption can be used for functional analyses of specific neurons or neuronal classes, for confirmation of neuronal circuitry, for generation of nematode populations lacking defined classes of functional cells, and for genetic screens. We suggest that mec-4(d) and/or related genes may be effective general tools for cell inactivation that could be used toward similar purposes in higher organisms.

J Exp Zool 1993 Jul 1;266(3):227-33

Targeted single-cell induction of gene products in Caenorhabditis elegans: a new tool for developmental studies.

Stringham EG, Candido EP

Department of Biochemistry, U.B.C., Vancouver, Canada.

Heat shock promoters have been employed to achieve tightly regulated expression of transformed genes in a wide variety of model systems including tissue culture cells, bacteria, yeast, Drosophila, and more recently Caenorhabditis elegans. Here we investigate the feasibility of using a laser microbeam to induce a sub-lethal heat shock response in individual cells of C. elegans. We demonstrate that in transgenic strains carrying heat shock promoter-lacZ fusions, single cell expression of beta-galactosidase in a variety of cell types of endodermal, mesodermal, or ectodermal origin can be achieved after pulsing with a laser. A tissue-general, inducible promoter can therefore be converted into one of single cell specificity which can be induced rapidly at any point in development, offering unique opportunities to study cell-cell interactions in C. elegans. This technique defines a new approach to generate mosaic animals and may be adaptable to other organisms or tissues.

Proc Natl Acad Sci U S A 1993 May 15;90(10):4359-63

Alteration of Caenorhabditis elegans gene expression by targeted transformation.

Broverman S, MacMorris M, Blumenthal T

Department of Biology, Indiana University, Bloomington 47405.

We have produced strains carrying a synthetic fusion of parts of two vitellogenin genes, vit-2 and vit-6, integrated into the Caenorhabditis elegans genome. In most of the 63 transformant strains, the plasmid sequences are integrated at random locations in the genome. However, in two strains the transgene integrated by homologous recombination into the endogenous vit-2 gene. In both cases the reciprocal exchange between the chromosome and the injected circular plasmid containing a promoter deletion led to switching of the plasmid-borne promoter and the endogenous promoter, with a reduction in vit-2 expression. Thus in nematodes, transforming DNA can integrate by homologous recombination to result in partial inactivation of the chromosomal locus. The simplicity of the event and its reasonably high frequency suggest that gene targeting by homologous recombination should be considered as a method for directed inactivation of C. elegans genes.

Cell or stage restricted worm promoters

Promoter Description of promoter Expressed in... References
dpy-7   hypodermal cell 9121480
col-19 235 bp segment of col-19 5' sequences adult-specific expression in hypodermal cells 7671811
mec-3 Two blocks of sequence that are each sufficient to generate the cellular pattern of mec-3 transcription. In certain lineages, mec-3 is transcribed in neurons that are anterior daughters of cells containing UNC-86. 8798157
tmy-1 660 to 800 bp upstream of the initial methionine codon Expressed in the body wall muscles, vulva, anus muscles and male tail muscles 7666414
cpr-1 5' flanking region Expressed exclusively in gut cells of all developmental stages except the embryo. 7666414
pgp-1   Gut promoter.  

C. elegans promoter studies

Dev Dyn 1993 Feb;196(2):124-32

Molecular markers of differentiation in Caenorhabditis elegans obtained by promoter trapping.

Young JM, Hope IA

Department of Pure and Applied Biology, University of Leeds, United Kingdom.

Differentiation of specific cell types during animal development can be detected by monitoring expression of appropriate genes. For this study, six different beta-galactosidase expression patterns which can be used as differentiation markers in the nematode Caenorhabditis elegans are described. An earlier promoter trap screen identified pools of recombinant plasmids which gave patterns of beta-galactosidase expression when used to transform C. elegans. Each recombinant plasmid contained a random fragment of C. elegans genomic DNA fused upstream of a promoterless lacZ gene. Six of these pools were chosen, and individual pattern-producing plasmids within these pools were identified. The expression patterns have been characterized more thoroughly than in the original screen, thereby providing molecular markers for differentiation of several cell types. Many of the expression patterns involve more than one cell type. The genomic origin of the inserts of active plasmids were determined through localization on the physical genome map.

Mol Gen Genet 1998 Nov;260(2-3):300-8

Promoter trapping identifies real genes in C. elegans.

Hope IA, Arnold JM, McCarroll D, Jun G, Krupa AP, Herbert R

School of Biology, The University of Leeds, UK. i.a.hope@leeds.ac.uk

Promoter trapping involved screening uncharacterized fragments of C. elegans genomic DNA for C. elegans promoter activity. By sequencing the ends of these DNA fragments and locating their genomic origin using the available genome sequence data, promoter trapping has now been shown to identify real promoters of real genes, exactly as anticipated. Developmental expression patterns have thereby been linked to gene sequence, allowing further inferences on gene function to be drawn. Some expression patterns generated by promoter trapping include subcellular details. Localization to the surface of particular cells or even particular aspects of the cell surface was found to be consistent with the genes, now associated with these patterns, encoding membrane-spanning proteins. Data on gene expression patterns are easier to generate and characterize than mutant phenotypes and may provide the best means of interpreting the large quantity of sequence data currently being generated in genome projects.

Gene 1990 Sep 14;93(2):189-98

A modular set of lacZ fusion vectors for studying gene expression in Caenorhabditis elegans.

Fire A, Harrison SW, Dixon D

Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210.

We describe a series of plasmid vectors which contain modular features particularly useful for studying gene expression in eukaryotic systems. The vectors contain the Escherichia coli beta-galactosidase (beta Gal)-encoding region (the lacZ gene) flanked by unique polylinker segments on the 5' and 3' ends, and several combinations of a variety of modules: a selectable marker (an amber suppressor tRNA), a translational initiation region, a synthetic intron segment, the early polyadenylation signal from SV40, and 3' regions from two nematode genes. A segment encoding the nuclear localization peptide from the SV40 T antigen is incorporated into many of the constructs, leading to beta Gal accumulation in nuclei, which can facilitate identification of producing cells in complex tissues. To make functional beta Gal fusions to secreted proteins, we constructed plasmids with an alternate module encoding a synthetic transmembrane domain upstream from lacZ. This domain is designed to stop transfer of secreted proteins across the membrane during secretion, allowing the beta Gal domain of the fusion polypeptide to remain in the cytoplasm and thus function in enzymatic assays. We have used the vectors to analyze expression of several genes in the nematode Caenorhabditis elegans, and have demonstrated in these studies that lacZ can be expressed in a wide variety of different tissues and cell types. These vectors should be useful in studying gene expression both in C. elegans and in other experimental systems.

C. elegans crosses/staging of cultures.

To set up crosses such that the worms are infertile: Use fer-15(b26). fer-15(b26) homozygotes are infertile. Roughly 1 offspring per 100 adults remains.

Use fer-15(b26);spe-9. Even more sterile.

Treat the worms with 50 uM FUdR

Aging articles from the Worm Breeder's Gazette.

Subject: longevity in C. elegans 2

Date: 1997/08/24

Author: Vladimir V. Bakaev

Posting History

>From The Worm Breeder's Gazette, 1995, v. 14, No. 1, p. 103.

THE EFFECT OF LOW TEMPERATURES DURING EARLY DEVELOPMENT ON LONGEVITY AND FECUNDITY IN THE NEMATODE C. elegans

Vladimir V. Bakaev, box 45, Novosibirsk, 630107, USSR

The purpose of the present experiment is to investigate, how low temperatures in the early stages of development can influence fecundity, length of prereproductive peri- od, length of reproductive period, length of postrepro- ductive period and mean life span in the nematode C. ele- gans (Bristol, N2, wild type). To microtitre wells were added 0,75 ml of liquid medium with E. coli (OP 50) and 3 adult nematodes. Animals were kept during 12 hours in the room temperature, then adult nematodes were discarded and wells were stored in different temperatures during 2 days, then they were transferred in room temperature. New- ly appeared worms were transferred in next wells, every well contains a single nematode. In every following day these worms were transferred in next wells. All the ex- periments were done in the darkness. Results are given in mean+/-S.E. 

                    Tempe- Number            Length of                Mean
                    rature  of     	     			      life
                    ï½C    progeny    prerepro- reproduc- postrep-    span
                                      ductive  tive      roductive    days    n
                                      period    period    period
                                      days      days      days

                    21,3  79,8+/-5,4  2,2+/-0,1 8,3+/-0,4 12,8+/-1,1 24,4+/-1,1 26
                    9,0  77,0+/-5,5  3,3+/-0,1 7,7+/-0,6 11,1+/-1,3 22,8+/-1,5 25
                    6,3  67,8+/-3,4  3,8+/-0,1 7,0+/-0,4 11,7+/-1,5 23,2+/-1,5 23
                    2,0  68,5+/-5,0  4,3+/-0,2 7,1+/-0,4  8,6+/-1,2 21,1+/-1,1 20
Then, lowering of ambient temperatures during early deve- lopment of nematode C. elegans resulted in decreasing of progeny. There is a decrease in the mean life span as tem- perature during larval development decreased, as well as the length of reproductive and the length of postreproduc- tive periods. Then, the length of prereproductive period is increased by diminishing of the temperature of early development. These results demonstrate, that the higher is the temperature, the earlier nematodes started reproduc- tion. These results do not support the widely accepted point of view, that lowering of temperature increases life span of different animals. There exist optimal life conditions for species, in which life span of this species is maximal. But the problem arises: what must we do in order to obtain the marked increase of longevity and, probably, immortali- ty? Undoubtedly, it appeared reasonable to seek a new un- usual experimental approaches. Acknowledgment: The author wishes to express his thanks to CGC for providing C. elegans and E. coli.
Subject: longevity in C. elegans

Date: 1997/08/19

Author: Vladimir V. Bakaev

Posting History

>From The Worm Breeder's Gazette, 1995, v. 14, No. 1, p. 102.

THE EFFECT OF INTERMITTENT TEMPERATURE ON LONGEVITY AND FECUNDITY OF C. ELEGANS

Vladimir V. Bakaev, box 45, Novosibirsk, 630107, USSR

It is well known that low temperatures can prolong longevity of different animals. In this study the experimental worms were mantained in liquid medium with E. coli in +21oC during the day (8 - 12 hrs) and in +4oC during the night, in dark- ness. One control group was mantained in +21oC and other control group was mantained in +4oC constantly. The obtained results are presented in the following table. 

                                Control group    Experimental  Control group
                                  (+21oC)          group          (+4oC)
                                  Mean+/-S.D.    Mean+/-S.D.  Mean+/-S.D.

                    Mean longe-  19,86+/-1,63    22,96+/-1,57  38,3+/-2,72
                    vity (days)    (n = 22)        (n = 24)      (n = 22)

                    Maximal lon-
                    gevity (days)      34              35            50

                    Minimal lon-
                    gevity (days)      6              10            5

                    Mean        76,91+/-4,54    54,33+/-3,32  4,54+/-2,07
                    fecundity      (n = 22)        (n = 24)      (n = 22)

                    Maximal          118              95            46
                    fecundity

                    Minimal
                    fecundity          33              25            0
It can be concluded that such intermittent temperature is not able to prolong the life-span of C. elegans significantly, in comparison with constant cold, as well as fecundity. Acknowledgment: The author wishes to express his thanks to CGC for providing C. elegans (wild line) and E. coli OP50.
Subject:

ATP and longevity in C. elegans Date: 1998/03/15

Author: daemon

Posting History

>From The Worm Breeder's Gazette, 1998, v. 15, No. 2, p. 56.

AN ATTEMPT TO SLOW AGING IN C. elegans. 7. NO EFFECT OF SODIUM ADENOSINETRIPHOSPHATE

Vladimir V. Bakaev, box 45, Novosibirsk, 630107, USSR

The purpose of this study was to investigate the effect of different concentrations of sodium adenosinetriphosphate in water solutions on nematode life span. In this experiment sodium adenosinetriphosphate was used in following diluti- ons: 1:10(3), 1:10(4), 1:10(5), 1:10(6) and 1:10(7). Three adult animals (3 - 5 days old) were kept in microtitre wells containing 0,75 ml of liquid medium (with E. coli and witho- ut sodium adenosinetriphosphate) during 4 hours, then they were discarded and newborn larvae were transferred in next wells (with sodium adenosinetriphosphate in any concentrati- on) every day (one worm in one well). This investigation was carried out in temperature +21oC and in the darkness. The obtained results are presented in the following table. 

                    Concentration of  		Longevity (days)      n
		    sodium     
                    adenosinetriphosphate  mean+/-S.E. maximal  
                    Control        
		    1:10(2) 		 12  20,8+/-1,7  	      27    	 	                      	    	             
                    1:10(3)        	 12  	  5,6+/-0,2  	      6    	 	                      	   
		    1:10(4)        	 12  	  6,1+/-0,2  	      8    	 	           
		    1:10(5)        	 12  	  10,7+/-1,2  	      20   

		    1:10(6)        	 12  	 20,7+/-1,3  	      27

		    1:10(7)   		 12  	  20,9+/-1.8  	      26
The nematodes in concentration of sodium adenosinetriphosp- hate 1:10(3) were unable to have progeny, then, the concent- rations 1:10(3) and 1:10(4) were toxic. The concentration 1:10(5) was slightly toxic (the differences between longevi- ties in concentrations 1:10(3), 1:10(4), 1:10(5) and in control were statistically significant, P < 0,001 in all these cases). The longevities in concentrations 1:10(6) and 1:10(7) and in control were similar (the differences between longevities in concentrations 1:10(6) and 1:10(7) and in control were statistically not significant, P > 0,05 in all these cases).

Conclusion: If the water solution of sodium adenosinetrip- hosphate was applied to C. elegans during the whole life span in above described conditions, it was not able to pro- long the life span of these animals.

Acknowledgment: The author wishes to express his thanks to CGC for providing C. elegans (Bristol, N2) and E. coli OP50.