- A monthly newsletter which supports information integration -

BioResource Newsletter  Vol.1  No.8

 Information on
    Resource-related Events :


 Introduction to Resource
    Database No. 1 :

 Resource Database of Deletion
 Mutants of Nematode

 Information Technology
    (Special Edition) :




No.8 2005/08/30  

Download the PDF version here

Other bioresources are available at the following URL:
NBRP (http://www.nbrp.jp/index.jsp)
SHIGEN (http://www.shigen.nig.ac.jp/index.htm)
WGR (http://shigen.lab.nig.ac.jp/wgr/)
JGR (http://shigen.lab.nig.ac.jp/wgr/jgr/jgrUrlList.jsp)

hot news Information on Resource-related Events

 Title: NBRP "Cell" Symposium

Schedule: September 29

Venue: National Museum of Emerging Science and Innovation


 Title: "Japanese Monkey" Project in the Forth Year
- Results and Future Studies

Schedule: September 30

Venue: The International Conference Hall, Tokyo Chamber of
Commerce and Industry building


 Title: "Technical Training for the Analysis of Intestinal
Flora by the Terminal RFLP Method"

Schedule: Beginning of November to Beginning of December

Venue: Japan Collection of Microorganisms Building, Wako Institute
of the Institute of Physical and Chemical Research (Wako, Saitama)


 Title: "Technical Training for the Transformation and
Preservation of Plant Cultured Cells"

Schedule: November 7 - 9

Venue: BioResource Building, Tsukuba Institute of the Institute
of Physical and Chemical Research (Tsukuba, Ibaraki )


 Title: International Symposium on Standardization of
Genetic Resources of Oryzias latipes

Schedule: November 14 - 15

Venue: The Noyori Memorial Conference Hall, Nagoya University

 Introduction to Resource Database No. 1

Resource Database of Deletion Mutants of Nematode
1. Contents of the Service

   This month, we are going to introduce the database of deletion mutants of nematodes resources. The resources of this database are preserved and provided by Dr. Shohei Mitani of Tokyo Womenfs Medical University; this university is the center for the National BioResource Project (NBRP) for nematode. This database is constructed by Dr. Mitani in collaboration with us, the Information Center. As of August 2005, information on 1600 mutants is disclosed from the following site:


Fig. 1: A screenshot of the National BioResource Project C. elegans website

Fig. 1: A screenshot of the National BioResource Project "C. elegans" website

   Nematode C. elegans is handled differently from other NBRP resources, as described in the following.

   The norm would be to collect and prepare information on resources before releasing it. However, in the case of nematode deletion mutants, the order-received production system is adopted in which preparation starts after a request is received from a user. This is possible because culture pools of nematodes with random deletion mutations, which cover almost all the genes, have already been prepared. Since the nematode is cryopreserved and its genome sequencing is already completed, gene identification by PCR is possible. This screening system is due to the excellent effort of Dr. Mitani. The National BioResource Project website for "C. elegans" (Fig. 1) provides information regarding the following aspects: (1) How to request a new screening; (2) Progress status of mutant screening; (3) How to receive isolated mutants; (4) Mutant DB; etc.

2. Progress Status of Mutant Screening

   The "progress status of mutant screening" web page (Fig. 2), is necessary to manage the order-received production system. As shown in Fig. 2, progress is indicated in four stages, namely, "Received (yellow)"; "In progress (red)"; "Difficult, may take longer (blue)"; and "Completed (green)."

   When a new screening is requested, you can check whether or not other researchers have already requested for the same gene on this site; this is to avoid duplication of requests.

Fig. 2: Progress state
Fig. 2: Progress state

3: System for Cooperation with Overseas Databases

   A list of isolated mutants is shown in Fig. 3 . When the "Allele" of the target gene is clicked, detailed information on the mutant (Fig. 4) is displayed including the following details: (1) Allele; (2) Gene name, cosmid; (3) link to WormBase; (4) Phenotype; (5) Mutation site; (6) Chromosome; (7) Putative gene structure; (8) Map position; (9) Balancer; (10) Map position of balancer; (11) Sequence of primers; (12) Distributed lab; etc. Searching by item is also possible.

Fig 3: A list of isolated mutants
Fig 3: A list of
isolated mutants

Fig. 4: Detailed information on the mutant
Fig. 4: Detailed information on the mutant

   This database is linked from WormBase in three parts which is the Variation report (Fig. 5-1), Gene Summary (Fig. 5-2), and Sequence Summary (Fig. 5-3). In the description item shown in the Variation report, there is a link to the NBRP-C.elegans website.

    Although the database was just released in 2003, research results have already been obtained by using its resources. Henceforth, I would really like to disclose the journal articles published by using these mutants. (Y. Y.)

Fig. 5-1: Variation report in WormBase

Fig. 5-2
Fig. 5-2: Gene Summary

Fig. 5-3: Sequence Summary

 Information Technology (Special Edition)

"Although this has been frequently talked about, we would like to discuss the security topic again."

  @When you access the Internet from a personal computer in a university or research institution, it is most likely that the computer will use the name of the organization to connect to the Internet.

   Therefore, if someone hacked into your personal computer and used it to attack other computers (i.e., disclose personal information of other people), the attacked computer will point its finger to your organization as its attacker. That can cause very serious problems. In order to avoid such problems, the following countermeasures should be implemented at the very least .

1. Automatically update Windows security patch (correction program)

   The newest virus tries to attack the defects of the most recent security patch. Continuous usage of the latest patch is important.

2. Use antivirus software and automatically update it. The latest version of the antivirus software should be used.

    Never use old versions of antivirus software. Also, the virus definition files should be automatically updated to the most recent version.

   If the above countermeasures are applied, minimum security can be achieved. Finally, people familiar with such countermeasures should access the following URL. (N. K.)

( http://itpro.nikkeibp.co.jp/free/ITPro/NEWS/20050819/166505/ )

Ongoing column "About Search Engines" will appear in the next issue.

Editor's note: The National BioResource Project celebrated its third anniversary on July 1st and has entered its fourth year. Although the target of 100% information disclosure has barely been achieved and there are still many incomplete databases, the nematode database has been stably managed since an early stage because of the order-received production system. Dr. Mitani tries his best to achieve "one paper for one mutant". It is my honor to be able to introduce him and the database in my article. (Y. Y.)

Contact: Yata 1111, Mishima, Shizuoka 411-8640, JAPAN
Center for Genetic Resources Information, National Institute of Genetics
Tel: 055-981-6885 (Yamazaki)

(translated by ASL translation service and proofread by Sharoh Yip)