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  National Bioresource Project for the Experimental Animal gNematode C. elegansh To Japanese >>
  Aim of the Project
Usefulness of Deletion mutants for the research using C. elegans
Research Management Committee
Address of the Core Facility
How to propose new target genes ( Progress status of mutant screening )
How to Receive Isolated Mutants ( Mutant DB )
Call for the Feedback
Technical Notes using Mutants from this Project
 
Aim of the Project
National Bioresource Project started in 2002 by the support of Ministry of Education, Culture, Science, Sports and Technology. The nematode C. elegans is among the organisms to be collected, stored and distributed. C. elegans is a good model organism suitable for research of life science. Genome and EST information have revealed almost all the genes on the chromosomes (Science 282, 2012-2018, 1998). The project is aimed to collect nematode bioresources available to researchers so that studies using the nematode are promoted. To this aim, research management committee advises the core facility (Tokyo Womenfs Medical University School of Medicine) how to work for the community. Most of the efforts would be paid to collect, store and distribute deletion mutants of C. elegans. Others are for example to collect information about the promoters and markers useful for C. elegans experiments.
Usefulness of Deletion mutants for the research using C. elegans
It is fruitful to isolate deletion mutants of the genes of interest, by the aid of gene structure information. Genetical and biochemical analyses of deletion mutants of the nematode would elucidate the molecular mechanisms underlying the various phenomena in the multicellular systems. Describing the phenotypes of mutants would contribute to understand how the gene works in the nematode. Once the phenotypes have been described, mutants can be used for general genetics; researchers may screen for mutants that enhance or suppress the phenotype. By this way, researcher can get insights into the possible other members which work on the same genetic pathway. When, researchers wish to isolate mutants showing subtle phenotype, deletion mutants would help statistical analyses to see the difference between wild-type and mutant animals. Expression patterns and structural similarity should be informative to make double mutations to see the function of redundant genes.
Researchers can conduct transgenic rescue experiments, once mutant phenotypes have bee described. Wild-type and mutant DNAs can be used to examine whether they are functional in vivo in the nematode and capable of rescuing the phenotypes. Functional transgenes with epitope tags may help to understand interaction among molecules in the mutant background. Transgenes with a domain swapped with others may reveal structure-function relationship of the molecule of interest. Extrachromosomal transgenes which rescue the mutant phenotypes would be useful for mosaic analyses, and eventually show where the product works.
Even if researchers cannot find any phenotypes, perhaps, biochemical analyses detecting the changes in protein expression by two-dimensional gel electropheoresis, or changes in RNA expression by microarray, may suggest the function of the molecule. Efforts by the researchers are expected to result in the further informative experiments in the future.
Research Management Committee
To optimize the project to work for the community, research management committee has been organized from Japanese C. elegans researchers. The committee advises the core facility in various aspects. Followings are the member as of April, 2012.
Yuich Iino (Chair, University of Tokyo)
Takeshi Ishihara (Kyushu University)
Shohei Mitani (Core Facility PI, Tokyo Womenfs Medical University)
Ikue Mori (Nagoya University)
Kazuya Nomura (Kyushu University)
Hitoshi Sawa (National Institute of Genetics)
Asako Sugimoto (Tohoku University)
Shin Takagi (Nagoya University)
Address of the Core Facility
When researchers wish to receive strains from the project, please send a form of MTA (Material Transfer Agreement) to the following address:
 
National Bioresource Project for the nematode
c/o Dr. Shohei Mitani, Department of Physiology, Tokyo Womenfs Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan.
E-mail: mitani1@research.twmu.ac.jp
How to propose new target genes
(1) A researcher (including student) can ask goneh new target gene per person to be screened for mutant. Please fill in the names of the gene, proposer, laboratory, Institute, principal investigator.
(2) Screening for new mutants of target genes would be processed in an order as requested. However, how long to isolate a mutant depends on the gene structure and the order of isolation may be changed. Researchers can see the status of each target gene by the gProgress state pageh.
(3) Placing new target genes and asking for the already isolated mutants will be treated independently. We will not announce the isolation of proposed mutants to each proposer. Proposers should be careful with the status of the target genes by themselves, and send the MTA to receive the alleles.
How to Receive Isolated Mutants  Flow of application  ]
(1) Mutants are available to researchers irrespectively of whether he or she has proposed the target genes. Because we handle so many mutants that we will not advise the mutant recipients how to analyze each mutant. Please consider carefully the aim and methods of the experiment by yourselves before requesting the strains.
(2) Strains are at present restricted for academic use only. Also, it should be noted that the mutants should not be used for patent application. Principal investigators should fill in an MTA (MATERIAL TRANSFER AGREEMENT) for each strain and send it to the core facility via the post office or equivalents. Please do not send an MTA by FAX. However, scanned PDF files attached with an e-mail are acceptable. The core facility will start the processes for shipping when it receives the MTA filled correctly.
(3) We may ship the same mutant strain to more than one laboratory. (The first receiver cannot limit other researchers.)
(4) When we ship a mutant strain, we describes the name of the Principal Investigator and date on the database.
(5) One laboratory can receive mutants of up to 10 alleles as gin-analysis-stateh.
(6) Please pay the handling and shipping fee with a credit card.
(7) When researchers finish the analysis and inform that to the core facility, we will exclude the allele from gin-analysis-stateh. Then, researchers can receive other alleles in a total of more than 10. When we receive the information from researchers, we post, on the database, the brief information as well as the name of Principal Investigator who provides the information. We also recommend researchers to send the same information to WormBase. Please append your publication information through each mutant description page.
Followings are examples of phenotype description. If you do not find any phenotype, it should be noted that the information may be useful for other researchers to design new experiments.
 
  Ex1)
    gFertile. Normal locomotion. Abnormal chemotaxis against XX.h
  Ex2)
    gLarval lethal (L2-L3 stage). Chemotaxis assay could not be performed.h
  Ex3)
    gHealthy. Fertile. chemotaxis assay (whatever assay you did) normal against X, Y and Z.h
Call for the Feedback
(1) Please send reprints of publication to the core facility laboratory to help us support the research community. It will also help us to add the citation to the database.
(2) If you are aware of any problem about mutants from this project, please let us know. The helpful information includes mistakes about deletion sites, rearrangement of the target gene, changes in the annotation of the gene. These will affect analysis using the strain and be informative for the community.
Technical Notes using Mutants from this Project
(1) The core facility laboratory use the random mutagenesis method with TMP/UV combined with gene-specific primer sets (Gengyo-Ando & Mitani, 2000). We find genomic rearrangement in a small fraction among deletion mutants obtained from our mutagenesis protocol. We have found so far such rearrangements, only in the mutants with deletion longer than 500 bp. When rearrangements occur sometimes wild-type genes are still present besides deleted genes of interest, resulting in gnon-reduction-of-functionh state. We routinely examine the absence of such wild-type sequences using primer located in the deleted region if the mutant is ghomozygous viableh and has deletion longer than 500 bp. However, if the mutant is not homozygous viable, such a test is harder, and we do not perform the test. Please examine by yourself, for example, that the lethal phenotype is caused by side mutation not relevant to the gene of interest. We recommend you to rescue the mutant by a transgenene of the wild-type DNA fragment. Moreover, extrachromosomal DNA which rescues the lethal mutation is useful for experiments, because rescuing DNA is lost at a rate during transmission to the progeny allowing the phenotype analysis.
(2) On the database, we include mutants whose deletion sites are not expected to truncate a protein product according to the gene prediction. Please examine newest information about the gene structure before you use the mutants. Sometimes, deletion in promoter or intron may be useful to examine the change in expression. Also it should be noted that weak alleles are valuable if null mutations are lethal.