2006/12/28
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Introduction to Resource Center No.13 |
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National BioResource Project "Pathogenic Microorganisms"
pathogenic fungi and actinomycetes
Core Facility: Research Center for Pathogenic Fungi
and Microbial Toxicoses, Chiba University
Yuzuru Mikami (Professor), Kazutaka Fukushima (Professor )
pathogenic bacteria
Sub-Facility:
Takeshi Honda (Professor, Research Institute for Microbial Diseases)
Chihiro Sasakawa (Professor, The Institute of Medical Science)
Takayuki Ezaki (Professor, Graduate School of Medicine, Gifu Univ.)
Yoshimi Benno (General Manager, RIKEN BioResource Center)
protozoa
Sub-Facility: Hiroji Kanbara (Professor, Institute of Tropical Medicine)
database
Sub-Facility: Hideaki Sugawara (Professor, Natl. Inst. Genet.)
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(1) Project Objective |
@Facilities that participate in the NBRP Pathogenic Microorganisms
contribute by developing systems aimed at consolidating the collection,
preservation, and distribution of pathogenic bacteria, actinomycetes, fungi,
and protozoa. They also develop databases, strengthen inter-facility
cooperation through online interaction, and contribute to worldwide research
in life science and infectious diseases by promoting the project with the aim
of preserving human health and ensuring a secure and healthy society.
Website of NBRP Pathogenic Microorganisms
http://wdcm.nig.ac.jp/byogen/
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(2) Characteristics of the Individual Institute Collections
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Research Center for Pathogenic Fungi and
Microbial Toxicoses, Chiba University
Core facility
This institute houses the largest collection of pathogenic fungi and
actinomycetes in Japan and is globally recognized for its top-class
standards. Almost 13,000 strains belonging to approximately 350 genera
of pathogenic fungi are preserved here. Highly pathogenic exogenous
fungi such as Coccidioides immitis (type 3 pathogen); imported fungal
pathogens such as Penicillium marneffei, Paracoccidioides brasiliensis,
and Histoplasma capsulatum; opportunistic and emerging fungal
pathogens such as Candida; and zoonotic fungal pathogens such as
Trichophyton mentagrophytes are exhaustively collected and preserved.
DNA resources of highly pathogenic fungi are also available. In addition,
1,600 strains belonging to approximately 30 genera, including standard
strains of pathogenic actinomycetes, are preserved. The genomic
sequences of all Nocardia species, including Nocardia farcinica, have
been elucidated for the first time in the world. Moreover, acid-fast
bacteria related to Rhodococcus and Gordonia are preserved, which
makes this collection unique in terms of quality and size.
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Institute of Tropical Medicine, Nagasaki University Sub- facility
This institute owns a globally unique collection of pathogenic
protozoa. The collection, preservation, and distribution of protozoa have
been conducted exclusively by ATCC, a US preservation facility.
Therefore, it is a valuable project even on a global scale. The distinctive
feature of this collection is that all the strains of preserved protozoa in
Japan have been included in it with the cooperation of affiliated institutes
throughout the country. In addition to enhancing the preservation of
conventional American trypanosomes, the institute collects and
distributes strains of visceral leishmania from Nepal and Entamoeba
histolytica and Blastocystis from Nepal and Indonesia by isolating the
organisms from both humans and monkeys. Researchers benefiting from
these resources have written interesting reports, and steady progress
has been made in line with the objective of this project.
RIKEN BioResource Center Sub- facility
This center conducts projects aimed at meeting the needs of the
research community and the society from the viewpoint of promoting
health and environmental preservation. It focuses mainly on the
nonclinical isolates of pathogenic microbes belonging to Biosafety Level
(BSL) 2. The center collects and preserves low-pathogenicity microbes
that are phylogenetically close to pathogenic microbes and distributes
preexisting and newly obtained BSL 2 strains in order to support
research on the identification and classification of pathogenic
microorganisms. In particular, the center promotes the preservation and
distribution of strains belonging to the genera Bacillus and Pseudomonas
whose records are annotated with advanced genetic, physiological, and
biochemical information.
Research Institute of Medical Sciences,The University of Tokyo Sub- facility
This institute conducts a service to distribute the following: (i) standard
bacteria used as positive controls in research, educational, and inspection
service environments; (ii) socially important pathogenic microbes; and (iii)
microbes used for training and research purposes in universities. Currently,
the institute preserves approximately 1,500 strains?a collection that
covers almost all the primary pathogenic bacteria such as Shigella;
pathogenic Escherichia coli, including enteropathogenic E. coli (EPEC)
and O157; nosocomial infectious bacteria such as opportunistic bacteria
and drug-resistant bacteria; intracellular parasitic bacteria such as atypical
acid-fast bacteria and obligate intracellular bacteria; zoonotic pathogenic
bacteria such as Brucella and Leptospire; emerging bacterial pathogens
such as Helicobacter pylori and Clostridium perfringens; pathogenic
bacteria causing disease outbreaks; and the internationally important
Orskovfs pathogenic E. coli. Furthermore, the center has implemented a
service for the collection of bacterial strains whose genomes have been
sequenced, which could be used as standards.
Research Institute for Microbial
Diseases, Osaka University Sub- facility
This institute owns an international collection of standard and
clinical isolates of primarily pathogenic E. coli, Vibrio, and other
enteropathogenic bacteria (8,515 strains included in the database).
Various enteropathogenic bacteria that have been isolated during
outbreaks in the country or from overseas travelers are preserved,
and abundant information, for example, the properties of each
strain and pathogenic agent, is available. The institute is
enthusiastically involved in the preservation and distribution of
genomically sequenced strains of E. coli (EHEC O157:H7), Vibrio
parahaemolyticus (KX-V 237), and Streptococcus pyrogenes(SSI-1) and the inclusion of patented strains and newly reported
strains in its collection. In addition, the institute also serves as a
reference center.
Graduate School of Medicine,
Gifu University Sub- facility
This institute holds the nationfs largest collection of standard
pathogenic bacterial strains (more than 20,000); this includes
approximately 80% of all bacterial strains that are pathogenic to
humans. The collection mainly includes strains of asporogenic
anaerobic bacteria and aerobic nonfermentative gram-negative and
gram-positive bacteria; aerobic microbes that are pathogenic to
humans, animals, and plants; and many standard bacterial strains.
The institute preserves 10 of 35 bacterial species (580 strains)
belonging to BSL 3, almost all of the roughly 320 species belonging
to BSL 2 (approximately 9,000 strains), and nearly 600 species
belonging to BSL 1 (9,000 strains).
National Institute of Genetics Sub- facility
This institute is in charge of developing a database for the
Pathogenic Microorganisms project with the objective of preserving
and distributing microbial strains. Furthermore, this institute has
published detailed data on bacterial toxins and released several
animations which educate students and the general public about
the O157 strain, Trichophyton, and malarial parasite.
Armadillo, a carrier of bacteria that cause
paracccidioidmycosis and the
morphology of the causative fungus(Paracoccidioides brasiliensis)
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(3) Gallery |
The gallery contains regularly updated information and images of
pathogenic fungi and actinomycetes and is available free of cost for
use in research and education.
http://www.pf.chiba-u.ac.jp/
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(4) Promoting the Project |
In order to disseminate information among researchers affiliated to
projects on pathogenic microorganisms, two symposiums?the 13th
conference of the Japan Society for Culture Collections and the 9th
International Symposium of the Research Center for Pathogenic Fungi
and Microbial Toxicoses at Chiba University?were organized and well
received in the fiscal year 2006. |
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NBRP poster exhibition was conducted at
the 9th International Symposium of the
Research Center for Pathogenic Fungi and
Microbial Toxicoses at Chiba University |
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(5) Future Expansion |
We will continue our endeavor of augmenting the collection of
strains with known genome sequences, exogenous pathogenic
microbial strains, and bacterial strains for epidemiological studies;
establishment of a genetic library; accumulation of genetic information;
development of a diagnostic method for gene identification by culture
and nonculture systems; and promotion of public education. |
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Information Technology Vol.20 |
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A text mining system for searching journal articles "Textpresso"
I talked about the CMap system in the August issue. In this issue, I
will introduce Textpresso which is also provided by the Generic Model
Organism Database (GMOD). Textpresso is a text mining system to
search journal articles which was developed by Hans-Michael Muller,
Eimear Kenny, and Paul Sternberg, creators of WormBase. Currently,
7,877 full-text articles and 22,180 abstracts are searchable in WormBase.
http://www.textpresso.org/index_oldsystem.html i*j
Furthermore, other groups in GMOD have also implemented Textpresso
and the Textpresso website has links to sections on Drosophila and yeasts.
Textpresso allows you to search with general keywords just like a
Google search. In addition to that, Textpresso also allows you to select
ontology phrases from a pull-down menu
and search for articles which contain the
selected ontology phrase because the
journal articles have been preliminarily
mined according to categories referred to
as "Textpresso Ontology".The current Textpresso Ontology
includes biological entities (Allele, Cell or
Cell Group, Gene, Cellular Component,
Phenotype, Molecular Function, etc.) and
relationships between the entities (Action,
Association, Biological Process, Effect,
Pathway, etc.). Among them, Cellular
Component, Molecular Function, and
Biological Process use data from Gene Ontology (GO) Consortium.
@@ For example, when you want to search for genes related to daf-16 ,
type daf-16 into the textbox as shown in ‡@, select [association] and
[gene] from the pull-down menus and click on search. The list of journal
articles retrieved will be displayed as shown in ‡A.
The Select buttons ‡B in image ‡A links to View Match VM , journals OT ,
PubMed RA and can be outputted in the Endnote (EN) format. Upon
clicking the VM link, sentences in the selected articles are displayed
with the related keywords displayed in color.
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Image ‡C shows the result of the search conducted in ‡@.
Sentences with the keyword daf-16 or "complex" and "binding" which
was associated with the term [association], or terms such as genes, sod-3, def-2
which was associated with the term [gene], were
retrieved and displayed in each result.
The method of searching by text mining as introduced in this example
is considered extremely useful for searching through massive amount of
information. We are developing a database for rice (Oryzabase) and are
considering Textpresso as one of the methods for article searching.
(*jThe current version of Textpresso available at WormBase is a newer
version than the one provided as an open-source.
(Rie Tsuchiya)
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Editor's Note: The final BioResource Now! newsletter in 2006 was
contributed by Prof. Mikami, who is in charge of resources on pathogenic
microorganisms. The research on pathogenic microbes is a cornerstone to
support peace and security, and Japan is at the forefront in this field. We
recommend that our readers visit the web gallery of the Research Center for
Pathogenic Fungi and Microbial Toxicoses, Chiba University. In December, the
NCBI released dbGaP-a database of diseases. Currently, approximately
3,000 data regarding ophthalmic diseases and Parkinson's disease are
recorded in the database, and the published information is extremely useful to
not only researchers but also the general public. We hope that the information
will also be made available in Japanese. We wish all our readers a happy new
year. (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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