2006/4/29
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Introduction to Resource Center No. 8 |
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Recent Trends at the Drosophila Genetic Resource Center
Masatoshi YAMAMOTO,
Director of Drosophila Genetic Resource Center,
Kyoto Institute of Technology
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Genetic Resource Center
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(1) Website Renewal |
This website was launched immediately after
the Drosophila Genetic Resource Center was established as a facility in the Kyoto Institute of Technology by
the order of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in 1999 and has been
regularly updated since then. In April this year, the website was renewed. Consequently, the "What's New"
articles can be posted more rapidly and conveniently than before.
At the lower left corner of the homepage, there is a link to a website called "Flystock".
This website contains an integrative database that lists the Drosophila strains maintained at the primary institute
(Drosophila Genetic Resource Center, Kyoto Institute of Technology) and the secondary institutes (National Institute
of Genetics, Ehime University, and Kyorin University), which promote the National BioResource Project (NBRP) "Drosophila".
This database enables the search of Drosophila strains that are preserved at the major institutes in the country as well
as receive orders for strains. Although this database currently does not cover all the maintained strains, a new, more
efficient and powerful Drosophila database is under construction and will be launched soon.
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Flystock DB
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(2) The Advantages of Actively Accepting Deposited Strains |
The endeavor of this center and its collaborative institutes came to
fruition due to NBRP. The Drosophila Genetic Resource Center has developed into a center with the biggest number of maintained
strains (in fiscal year 2005) in the world, and we rank second only to the Bloomington Drosophila Stock Center at
Indiana University in the United States with respect to the number of provided strains.
Many deposited strains that have been developed by domestic researchers are unique and useful,
and most importantly, featuring excellent characteristics of the respective strains. In order to develop and expand
as a genetic resource center on a global scale, genetic resources should be of high quality. In this regard,
we deeply appreciate the support and consideration of the domestic researchers.
"The Drosophila Genetic Resource Center is an incubator for your lab." This statement is used to
introduce our undertakings in supporting researches and to clearly convey the objectives of this center. Our objective
is to efficiently maintain the flow of providing strains to promote researches and facilitating the deposit of those
research achievements back to the center so that it would contribute to other researches.
In order to ensure that generated or developed strains obtained as research achievements are used
efficiently as genetic resources, we should actively welcome researchers to deposit strains. Our undertakings include
requesting strain deposition and receiving the deposited strains as well as releasing and providing the deposited strains.
We plan to release information on the deposited Drosophila strains together with other related
information such as journal articles which describe the development of the strains (on DGRC or Flystock). When searching
for strains, the search result from the strain database will include literature references and allow users to order the strains.
The user will then have sufficient information regarding the depositor's literature when requesting for the strains and therefore,
when a research achievement is published as a journal article, the depositor's literature citations will increase.
Thus, we are employing a method that would benefit the strain depositor by increasing the citation count of the literature.
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(3) Completion of the Gakudo Hall and the Memorial International Symposium |
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As mentioned on the Drosophila Genetic Resource Center (http://www.dgrc.kit.ac.jp/jp/nbrp/topics/000049.html)
website and on the public information website of NBRP, the Gakudo Hall was built on the Saga campus of the Kyoto Institute of Technology with contributions from
Nippon Shinyaku Co., Ltd., and the completion ceremony was conducted on March 6, 2006. The description of the ceremony is available on the universityfs website.
ihttp://www.kit.ac.jp/01/topics/2005/gakudou/ gakudou060315.htmlj
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The view of the Gakudo Hall from the mulberry field located southward. |
Gakudo Hall is named after gGakudo Yojin (Hints on learning Buddhism),h which was taught by Dogen Zenji,
in hopes that the hall will develop into a venue for international interaction where researchers who seek scientific facts can genuinely discuss their work and pursue
their duties and social responsibilities. It is known that the propagation of Buddhism in Japan was initiated at Mt. Hiei; therefore, the Buddhist priest of the highest order,
Ryusho Kobayashi, a retired executive of Enryakuji at Mt. Hiei, was asked to write the name on the name plate. He graciously accepted our request. His powerful spirit belies
his age of 78 years. We would like to reiterate our appreciation to him. We can well understand the feeling of tension that he must have experienced in accepting our request
because writing on a cypress board allows no room for mistakes, as opposed to writing on paper.
As inferred from the name, gGakudo Hall,h the then CEO of Nippon Shinyaku and the anonymous benefactors disliked the idea of naming the hall after the company.
However, we wish to express our gratitude for their donation and therefore have considered using a logo that represents gNippon Shinyakufs 14 selected herbsh (Yaku so juyon sen).
Nippon Shinyaku Co., Ltd. declared that they have grown and developed because of the benefits offered by plants, and they selected 14 primary herbs to represent their company
on their 80th foundation anniversary. As a token of our appreciation to Nippon Shinyaku, representative herbs were selected from these 14 herbs, and denoted on the room identification
plates, adding colors to the insipid name plates. The herb designs were provided by the Institute for Botanical Research at Yamashina, Nippon Shinyaku Co., Ltd. |
Ribbon cutting at the completion ceremony of the Gakudo Hall.Kazuto Hatsuyama, President, Nippon Shinyaku, Co., Ltd. (center); Mr. Shigeru Kure, Director of Genome Research, Life Science Division, Ministry of Education, Culture, Sports, Science &Technology (MEXT) (right of the center); Yoshimichi Ejima, President of the Kyoto Institute of Technology (left of the center)
The Buddhist priest of the highest order, Ryusho Kobayashi (left), stands at the entrance in front of the stele on which "Toei Joubutsu"
was engraved to have the honor of seeing the Konpon Chudo. February 24, 2006. |
A tablecloth with the designs of the 14 selected herbs on it, and the room identification plates placed in Gakudo Hall; these were manufactured for the 80th foundation anniversary of Nippon Shinyaku Co., Ltd. |
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The 1st International Seminar at the Gakudo Hall |
Three prominent Drosophila researchers were invited for the memorable international seminar.
The first researcher to be invited was Distinguished Professor emeritus Thomas Kaufman from the Bloomington Stock Center at the Indiana University
in the United States. It is practically the worldfs largest strain center and provides Drosophila strains which are trusted and utilized by all researchers.
The Drosophila Genetic Resource Center and the Bloomington Stock Center mutually hold important strains and conduct discussions on future administrative
plans as international strain centers. Thomas Kaufman is a prominent researcher of the homeobox genes in embryology, and he is currently conducting a
research on the evolution of insects.
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The second researcher to be invited was Professor Asa Rasumuson-Lestander. Prior to the approbation of the Drosophila Genetic Resource Center by MEXT in 1999, Umea University in Sweden faced difficulties in acquiring research funds from the EU and the stock center that had maintained numerous strains with chromosome aberrations was closed. In Japan, the public hearing of MEXT was still going on and the future prospects had not been envisioned yet. However, since the loss of the strains at Umea University would have been a substantial loss, I asked Professor Asa to somehow
retain the strains for another year and promised to accept all the strains in Kyoto later. |
In addition to organizing the center within the budget, I had to
make considerable efforts to obtain the certificate for the building and the facility of the center. Meanwhile, Professor Asa was maintaining the strains by
utilizing her personal research fund. We were desperate to hold on to the strains; however, it is wonderful to reminisce about how we have developed a strong
mutual trust in each other. The sustenance of our relationship can be credited to Professor emeritus Mel Green who played an important role in solidifying our
mutual trust. Professor Mel and I have been discussing the necessity of having a strain center since 1990 and it was his consideration that facilitated the
formation of a personnel foundation for accumulating information on the strain center from Umea University and Indiana University; this initiative enabled
drafting of important documents for public hearing at MEXT. |
The third researcher to be invited was Professor emeritus Dan Lindsley, the author of"The Bible",
which is a must-have for Drosophila researchers. Together with "The Mutants of Drosophila melanogaster" by Bridges, "Genetic Variations of Drosophila
melanogaster" and "The Genome of Drosophila melanogaster" are known as "The Red Book" or "The Bible". Later, these books were digitized, and they
became the basis for the construction of the current FlyBase. Currently, Professor Dan Lindsley is 80 years old. He had to return to his country
immediately after the international symposium because he did not have an assistant who could observe the flies in his ongoing experiment; thus, he
returned to continue and supervise his experiment.
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The southern side of the huge training room in the Gakudo Hall has glass windows, and the room has a high ceiling.
During the symposium, the room was bright with a pleasant atmosphere, and the symposium received an enthusiastic response. |
(4) Program for Genetic Resource Education and Development |
The goals of NBRP are maintaining genetic resource and controlling their quality, and also establishing a system to supply reliable strains
whenever they are required. When such a system is established, it is common for researchers who are in a hurry to begin their study to utilize
the strains obtained from the resource center immediately without inspecting them. However, this is a precarious situation, and a fundamental
feature of biology, which is that organisms continuously undergo mutation, may be forgotten. The consolidation of the genetic resources tends
to reduce the number of human resources with detailed knowledge of genetic resources. Due to the competitive environment in the scientific
research community, which has recently been in question, the priority is to accomplish results by utilizing any useful tool as soon as possible.
Naturally, maintenance and control of high-quality genetic resources should be expected. However, researchers should recognize the fact that
organisms do change and inspect research materials before using them for experiments. If the researchers provide feedback on the state of the
resource that they received, that would aid the maintenance of strains at a higher quality.
Under such circumstances, the Graduate School of Science and Technology at the Kyoto Institute of Technology
have collaborated with the Graduate School of Agriculture at the University of Miyazaki since 2006 to initiate the gProgram for Genetic Resource
Education and Developmenth to develop a model curriculum for training skilled professionals.
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Kyoto Institute of Technology and University of Miyazaki are the primary institutes of NBRP
for Drosophila and Lotus japonicus, respectively; these are experimental animal and plant models with distinctive small-sized features. With the
objective of producing skilled engineers, lectures on biological resources, biodiversity and environment and their related regulations that aim
to cover fundamental topics necessary for the handling of extensive organism species are incorporated into the curriculum. Seminars on animal
genetic resource are conducted at the Kyoto Institute of Technology while seminars on plant genetic resource in University of Miyazaki.
Students move around the concerned universities to attend the seminars.
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Curator is a person in charge of important preserved materials and research resources at a museum, art gallery, or a research institute and
denotes a skilled professional such as the director or a responsible museum attendant. |
page top |
Maintained Resources |
DGRC (Kyoto Institute of Technology) |
14492 strains |
Basic strains |
4001 strains |
NP Lines (Gal4 enhancer trap) |
1973 strains |
GS Lines (Gene Search System) |
4572 strains |
Protein Trap Lines |
369 strains |
LA Gene-induce (with y+ marker) |
938 strains |
Others |
2639 strains |
NIG-Fly (Nataional Institute of Genetics) |
5633 strains |
NP Lines (Gal4 enhancer trap) |
2715 strains |
RNAi strains |
2037 strains |
RNAi strains |
881 strains |
EHIME-Fly (Ehime University) |
488 strains |
Wild type Drosophila from Japan |
53 species
412 strains |
KYORIN-Fly (Kyorin University) |
459 strains |
Wild-type strains
Drosophila melanogaster species group
Drosophila ananassae species subgroup
Subgenus Drosophila
Genus Chymomyza
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255 strains |
Mutant strains
Drosophila ananassae species subgroup
Drosophila auraria complex
Drosophila hydei
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204 strains |
ifrom Flystockj |
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Information Technology: Vol. 13 |
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"Bioinformatics in 10 minutes"
"Sequence Manipulation using Cygwin (Windows)"
In the previous issue, I have demonstrated the use of a terminal window on Mac OS X
which might not have been useful to Windows users. In this issue, I will explain the use of a terminal
or a UNIX-like environment on Windows. Cygwin enables us to experience UNIX or LINUX on Windows machines.
1. Download the installer
(setup.exe) from http://www.cygwin.com/ and double-click on the icon.
After that, click as instructed to complete the installation. (The installation process takes some time.
For detailed descriptions of the installation procedure, please type the keyword cygwin on search engines
such as Google, and refer to the numerous websites that contain detailed descriptions.)
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2. Once the installation is complete,
double-click the gCygwinh icon (a shortcut) that appears on the desktop to initiate it. A black screen will be displayed. |
3. Type the following on the black screen and press Enter.
$mkdir test |
4. Type the following on the black screen and press Enter.
$ls
Then, the word typed in step 3, "test", along with some other words will be displayed. Here, the words displayed indicate
a file or a folder. The previous command "mkdir test" will create a folder named "test".
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5. Type the following on the black screen and press Enter.
$cd test
The command "cd" is a command to move to another directory, and in this case, it implies moving into the
"test" folder. Now, you are located in the "test". folder. The question that arises is where is this "test" folder located?
Go to My Computer -> Local Disc (C:) -> Documents and Settings -> "your user name" and check if the folder, "test", has been created.
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6.
Next, as indicated in the title of this bioinformatics section, let us try to manipulate a base sequence. Open the "test" folder and right-click on New -> Text Document to create a new text document. Once the file is created, change the file name to "sequence".
In the "sequence" file, copy an arbitrary base sequence (in one byte Roman characters) (no line feed or space should be added). Now the file is ready for use.
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8. Finally, let us excise a part of the base sequence (5th to 10th letter). Type the following on the black screen and press Enter. The 5th to 10th letters will be shown.
$cut -c 5-10 sequence.txt |
In the previous and current series, we have tried working in a UNIX- or LINUX-like environment. Currently, UNIX or LINUX is used frequently in bioinformatics. In addition, it is considered that the researchers currently working on wet experiments (conducting experiments using actual biological
materials) will require knowledge of the dry experiments (conducting experiments or data processing using computers). It would be great if these series sparked interest in UNIX or LINUX and encourage readers to explore the field of bioinformatics.
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Editor's Note: Drosophila is possibly one of the biological resources
that have been used for the longest time. The individual size of Drosophila is small, the generation time
is short (approximately two weeks), and breeding is relatively easy; thus, Drosophila are particularly
appropriate for hybridization experiments that are necessary in genetics. In genetics, knowledge gained
using Drosophila led to the development of molecular biology, neural biology, and developmental biology.
Another factor that supports the Drosophila research community is that the community has created a research
environment wherein researchers can easily obtain the necessary resources. The Kyoto Institute of Technology
is a part of this community, and it plays an important role as a representative institute in Japan.
Another characteristic of Drosophila research in the 21st century is its contribution
in bioinformatics. The database for Drosophila, namely, Flybase is a famous integrative database of model
organisms known to all biologists. Recently, the activites in bioontology that enables the utilization of
interspecies information have progressed. Drosophila, as the forefront life science, will continue to fly
into the future. I would like to sincerely thank Dr. Yamamoto for contributing in spite of his busy schedule. (Y. Y.)
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Contact: Yata 1111, Mishima, Shizuoka 411-8540, Japan
Center for Genetic Resources 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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