- A monthly newsletter which supports information integration -

BioResource Newsletter  Vol.2 No.10

 Information on
    Resource-related Events:


 Introduction to
    Resource Center No. 11:

EGenetic Resources for E. coli and
  its Plasmid Vector




  Hironori Niki, Professor,
  Microbial Genetics Laboratory

Ongoing Column No.18:

ENotification of Updates on Weblog Sites



Download the PDF version of this newsletter at

Bioresources information is available at the following URLs

NBRP http://www.nbrp.jp/index.jsp
SHIGEN  http://www.shigen.nig.ac.jp/
WGR http://www.shigen.nig.ac.jp/wgr/
JGR http://www.shigen.nig.ac.jp/wgr/jgr/jgrUrlList.jsp

Information on Resource-related Events

"Molecular Biology Society of Japan: Forum 2006h
      December 6 - 8, 2006 at Nagoya Congress Center
      NBRP Panel Exhibition : http://www.aeplan.co.jp/mbsj2006forum/

      Detailed information is available at   http://www.nbrp.jp/index.jsp


Introduction to Resource Center No.12

 Genetic Resources for Escherichia coli and its Plasmid Vector

      Hironori Niki, Professor, Microbial Genetics Laboratory
      Genetic Strains Research Center, National Institute of Genetics


yPzThe Escherichia coli genetic resource project has been in operation for 30 years.

   The National Institute of Genetics (NIG) founded the Microbial Genetics Laboratory in 1976 to conduct the property development and preservation project for E. coli, Bacillus subtilis, and Salmonella spp. and phages and plasmids that infect these microorganisms. The preservation and provision projects undertaken for approximately 15,000 mutant strains have received wide appreciation from researchers worldwide. In 1997, the laboratory was redesignated as the current Microbial Genetics Laboratory, Genetic Strains Research Center. Since July 2002, it has continued to expand its activities as the core institute for E. coli research under the National BioResource Project (NBRP). Currently, 30 years since the redesignation, carefully selected genetic resources of over 23,000 E. coli strains are available. The development and maintenance of the laboratory to date can be largely attributed to the endeavors of Dr. Akiko Nishimura, who has been involved in the project from the outset. Her contributions are much appreciated not only by researchers dealing with E. coli but also by numerous other researchers who have benefited from the available resources. Even after Dr. Nishimura retired in March 2005, the project continues to date. Starting from this fiscal year, the cloning vector collection project conducted by Dr. Seiichi Yasuda has been included under the NBRP E. coli project upon his retirement. Thus, the E. coli project is developing further, and its contribution to other research activities is increasing.


(A brochure with a list of the preserved and provided strains was published in 1994)

yQzAbundant resources are preserved and available.

   All the published resources provided here are nonpathogenic strains derived from E. coli K12 strains. Thus, any of these strains can be used in recombinant DNA experiments. In addition, most of these strains are nonrecombinant. The resources are broadly categorized into the following three groups.

 Mutant E. coli Strain Resources
 Cloned Genetic Resources

 Cloning Vector and Host Resources

   The mutant E. coli strain resources include mutant strains constructed by numerous researchers in the past for genes related to metabolism, DNA replication, or protein synthesis. In addition, an exhaustive list of gene-knockout mutant strains that were systematically constructed after the E. coli genome was sequenced has been included under these resources. The following three types of gene-knockout mutant strains are available.

NBRP E. coli

NBRP E. coli

Transposon-insertion mutant strains: These comprise gene-knockout strains that are constructed by transposon insertion into their genome and continue to grow after the insertion. A total of 6,492 strains in which transposon insertion sites were confirmed by genomic sequencing are available.
Extensive chromosome-deletion mutant strains: These comprise mutant strains in which wide regions of the E. coli chromosome are deleted. A total of 124 strains are available, including mutant strains lacking 1.4 Mbp, which corresponds to 29.7% of their original chromosome length.
KEIO collection:This includes strains in which a gene is knocked out and replaced by a kanamycin-resistance gene. A total of 3,840 E. coli mutant strains that are able to grow despite the replacement are available.
   The cloned genetic resources comprise the following two exhaustive clone libraries of plasmid vectors with different properties.
ASKA clones: This library comprises genetic resources for individual genes cloned by using high-copy-number vectors; these are expressed as His-tagged gene products.
Mobile Plasmid Clones: This library comprises individual genes cloned by using low-copy-number vectors; the plasmids used in this case can be transferred to target cells by merely mixing them with the cells because the plasmids contain mob gene which enables the plasmids to transfer from F+ to F- by F-mediated conjunction.
   Finally, the cloning vector and host resources include 465 cloning vectors and 83 host E. coli strains. The vectors are available only for use with E. coli. With regard to the vectors, in addition to information pertaining to their lineage and selective markers, plasmid maps can also be referenced. This information is also available in a brochure, which can be ordered from the website for cloning vectors.

Further information is available on the NBRP E. coli website.
Please make use of these resources for your research considering the property of each resource.


(Information posted on the website for cloning vectors)

yRzResources are available for basic research worldwide.

   The E. coli-related resources introduced here are widely available for basic science research worldwide. Although, as described later, availing of certain resources requires the permission of the institute that deposited that particular resource (developers), other resources are immediately provided on request. After confirming the receipt of the E. coli strains provided, users are expected to fill out the material transfer agreement (MTA) documents and mail them back to the NIG. Further, it is mandatory that the MTA be signed or sealed. The term gcenter presidenth on the document refers to the academic dean in the case of undergraduate or graduate schools and the director in the case of research institutes. An official in charge of intellectual property rights, if present, is expected to sign and seal the documents. Currently, resources are provided free of cost since the center is aided by the NBRP project; the users generally bear only the shipping cost, and the resources are shipped and paid for on arrival.


   @Of the resources available, availing of the KEIO collection and ASKA clones requires preliminary permission from the depositor?the Nara Institute of Science and Technology (NAIST)?to protect its intellectual property rights. The request for these resources is accepted on the website, and the mail confirming acceptance, deposit agreement form, and MTA are mailed. The completed and signed deposit agreement form and the MTA should be mailed to an officer in charge of intellectual property rights at the NAIST and NIG, respectively. The requested resources are provided on submission of these two documents. We request user cooperation although the process is slightly complicated and time-consuming. A confirmation system for tracking the request status is being consolidated on the website, with the aid of Dr. Yamazaki at the Information Center, to enable users to check the status of their deposit agreement form and MTA after making a resource request.

ASKA request

y 4 zPlease cite NBRP E. coli if our resources prove fruitful for your research.

   NBRP E. coli aims to function as a resource center meeting the highest level of international standards. Our task is to provide resources to researchers who need them. Thus, if our project contributes to your research, we consider our activities rewarded. We would, therefore, be very grateful if National BioResource Project (NIG, Japan): E.coli or NBRP (NIG, Japan) : E.coli received mention in the acknowledgements section of published
articles or research presentations.

Information Technology Vol.18

 "Notification of Updateson Weblog Sites"     google

   As of September 2006, the number of active users who post an article on a weblog site at least once a month exceeded 1.7 million (*). Thus, some readers of this newsletter may be transmitting information via weblog sites. Most weblog sites provide an gRSS fieldh that records information updated on the sites; however, does anyone really make use of this feature? Presently, updated information on a site can be immediately reflected in the search results of search engines such as Ask.jp, Google, or Yahoo! by notifying them using the RSS.
   For instance, in the case of Ask.jp, the address of the PING (update acceptance) server (http://ping.ask.jp/xmlrpc.m) is displayed. Most weblog services contain PING transmitting functions, and the updated information can be reflected in the Ask.jp search results within 5 min by notifying the PING server of the updates.

Ask jp


"Fig. Google"

"Fig. Yahoo!"

   @Similarly, Google provides a service by which it can be notified of updates on weblog sites either manually or via API. Manual notification can be done by visiting the website http://blogsearch.google.co.jp/ping, typing the address of the concerned weblog site or the field address, and clicking the "Submit Blog" button. Subsequently, Google will display the information on the update of the weblog in searches conducted worldwide.
   Finally, Yahoo! provides a service called "Site Explorer" (http://siteexplorer.search.yahoo.com/).Since this service is provided by Yahoo! US, it requires a Yahoo! US ID. First, the concerned weblog address should be entered. Next, a specified file should be uploaded for Yahoo! to confirm whether the account owner is an authorized administrator of the site. Subsequently, the field address should be typed and the "Add Feed" button should be clicked on to complete the process.
   These are useful services for weblog users hopeful of their weblogs becoming known to as many users as possible.

   * Reference URLF   https://www.google.com/webmasters/sitemaps/

iGaku Kimuraj

Editor's Note: FThe E. coli resource project was handed over to the enthusiastic Dr. Niki by Dr. Akiko Nishimura who previously headed it. Since the provision of an exhaustive collection of genome-wide mutant strains was initiated, the number of resources provided has increased dramatically, and it brings squeals of delight to downstairs of my office. I appreciate the contribution of the introductory article. The E. coli resource database together with the Profiling of E. coli Chromosome (PEC) database, another database that mainly contains essential gene information, is used by numerous researchers worldwide. (Y.Y.)

Contact Address:
1111 Yata, Mishima-shi, Shizuoka 411-8540, Japan
Center for Genetic Resource Information, National Institute of Genetics
Tel: 055-981-6885 (Yamazaki)@
E-mail BRnews@chanko.lab.nig.ac.jp

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