2006/10/31
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Information on Resource-related Events |
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Introduction to Resource Center No.12 |
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Genetic Resources for Escherichia coli and its Plasmid Vector
Hironori Niki, Professor, Microbial Genetics Laboratory
Genetic Strains Research Center, National Institute of Genetics |
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yPzThe Escherichia coli genetic resource project has been
in operation for 30 years.
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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.
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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.
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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
http://shigen.lab.nig.ac.jp/ecoli/strain/ |
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.
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(Information posted on the website for cloning vectors) |
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yRzResources are available for basic research worldwide.
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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. |
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@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.
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y 4 zPlease cite NBRP E. coli if our resources prove
fruitful for your research.
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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. |
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Information Technology Vol.18 |
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"Notification of Updateson Weblog Sites"
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!"
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@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. |
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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) |
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