BioResource Now ! Vol.7 No.7

BioResource Now !
Issue Number 7
Introduction toResource Center
No.37Ongoing
Column No. 59

July 2011

Taro Nakamura (Graduate School of Science, Osaka City University)・
Yoshinobu Kaneko (Graduate School of Engineering, Osaka University)

Yeast Genetic Resource Center (YGRC) Supports Researchin Yeast : The Ultimate Model Organism
P1 - 2
Google’s Image Searching ServiceP2

Introduction to Resource Center〈No.37〉

Yeast Genetic Resource Center (YGRC)
Supports Research in Yeast : The Ultimate Model Organism
1. Yeast : The ultimate model organism
Yeast has a long relationship with humans
as one of the most practical microorganisms
and an extremely useful model organism forresearch. Among the more than 1000 yeast
species existing in nature, fission yeast(Schizosaccharomyces pombe) and budding
yeast (Saccharomyces cerevisiae) (Fig. 1) arefrequently used in life science research. A
variety of convenient experimental methods,
including recombinant DNA technology, hasbeen developed for use of these yeasts inresearch. Many biological mechanisms, suchas the cell cycle, intracellular protein transport,
and autophagy, have been elucidated throughresearch in yeast. Yeast was also among theearliest eukaryotes to have its genome
completely sequenced. Full-fledged databases
based on genome information are available,
and various post-genome studies are being
actively conducted on yeast. There are a large
number of researchers studying yeasts, andmany academic societies and study groups
have been organized primarily by yeast
researchers. In this respect, yeast can beconsidered the ultimate model organism in life
sciences research.

Fig. 1: Differential interference images offission yeast (left) and budding yeast (right)

2. YGRC is acknowledged as a worldleading yeast resource center
Despite the usefulness of yeast in research,
institutions that provide yeast resources havenot been fully developed. Along with theinitiation of the National BioResource Project(NBRP), the Yeast Genetic Resource Center(YGRC) launched operations in 2002 with highexpectations of the yeast research communities. Division of labor was achieved such thatS. pombe and S. cerevisiae are maintained by
Osaka City University and Osaka University,respectively. The scale of operations has been
expanding year by year, and in the past fewyears, resources have been distributed inapproximately 2000 cases per year. In 2010,
approximately 60% of these resources were
distributed overseas, to a total of 24 countries(Fig. 2). Fission yeast resources from YGRC
are acknowledged as the best in the world, bothin term of quality and quantity. YGRC’ s resources of budding yeast are also considered tobe world class, and include many highly original
resources developed by Japanese researchers.

Taro Nakamura, Professor

Graduate School of Science, Osaka City University

Yoshinobu Kaneko, Associate Professor

Graduate School of Engineering, Osaka University

YGRC is thus globally recognized as a topyeast resource center. Here, we describe therecently acquired remarkable yeastresources.
件Europe(ca.25%）

YGRC

North America（ca.25%)

Asia and Oceania(ca.10％)Fig. 2: Destinations of yeast resources
distributed from YGRC in the fiscal year 2010

3. YGRC maintains the source strainof S. pombe
Almost all the S. pombe laboratory strainsused worldwide have been derived from asingle strain, the Leupold strain, which wasisolated by Dr. Urs Leupold, a geneticist at theUniversity of Bern in Switzerland. The Leupoldstrain and other strains developed by Leupoldthat had been preserved at the University ofBern were deposited at YGRC in the fiscal year
2010. Possession of the source strain of S.
pombe strains used worldwide signifies thestatus of YGRC as a world-class yeast
resource center. We also preserve the source
strains of other popular yeast strains and thestrain S288C, which was used for the first
genome-sequencing project.

4. Genome-wide resources of ﬁssion
yeastsYGRC maintains a wide range of fission
yeast resources but here we introduce
genome-wide resources. The green
fluorescent protein (GFP)-fusion protein
library was deposited by the Hiraoka
Laboratory at Osaka University. In thislibrary, the GFP gene was fused with 1,000
out of approximately 5,000 open reading
frames (ORFs) in the fission yeast genome
to localize each protein (1). This collection
can be used not only to localize proteins but

also to screen proteins located in specificintracellular structures. This series of strains is
one of the most popular fission yeast
resources. In addition, insert fragments fromapproximately 60,000 clones in the fission
yeast genome library (2) and those of about
22,000 clones in the full-length cDNA librarywere sequenced under the genome information
consolidation program in fiscal years 2005 and2006 in cooperation with the Kohara Laboratory
at the National Institute of Genetics.

Insert fragments from the genome library
cover more than 95% of the whole genomeof fission yeast. These draft sequences wereregistered in international databases. Inaddition, these clones were also registeredin Genome Viewer (the genome database ofNBRP Yeast) described later.

5. Popular or recommended resources
for budding yeast
The top 10 list of budding yeast resources
distributed in the fiscal year 2010 was
dominated by plasmids and strains of yeast
harboring the auxin-inducible degron (AID)
system (3), which was developed for researching gene functions by inducing thedegradation of specific proteins in budding
yeast using auxin, a plant hormone. Twohundred and fifty-seven clones wereshipped domestically and internationally to
12 countries. These resources will
hopefully facilitate interesting research
results in a few years.
We also preserve genomic DNA clones
of budding yeast, which were genome
fragments of the S288C strain partiallydigested using Sau3AI and cloned into
YEp51B plasmids (4). Currently, 363 clones
Strain These clones are also
have been released.
registered in the Genome Viewer (seesection 6). We plan to slowly continue toincrease the number of clones. Many typesof cloned genes deposited by researchers
are also available. Since these clones arefound online on the Genome Viewer, pleasesearch to find your gene of interest. In July,
we released the gTOW6000 resource(http://tenure5.vbl.okayama-u.ac.jp/~hmlab/
gTOW6000/); it comprises approximately
5,800 clones of yeast strains harboring
pTOWug2-836 plasmid vectors (YEp-type)linked with each PCR-amplified gene.
Rank

NBRP Code

Strain or DNA# Times
Distributed

1123

BYP6739
BYP6740DNADNA

3535

BYP6744

DNA234

BYP6743

DNA225

BYP6742

DNA156

BY25598

Strain147

BY25602

Strain137

BYP6741

DNA139BY25594

Strain1110

BY25576

Strain

10Table 1: List of top 10 budding yeast resources
distributed in the fiscal year 2010.
To the next page

BioResource Now ! Vol.7 No.7

6. Genome Viewer :Database for surveying the yeastgenome by using Google Maps
Information on all the yeast strains andDNA resources provided by NBRP are available in Genome Viewer, powered by Google
Maps (Fig. 3). In Genome Viewer, each genein fission yeast and budding yeast has a linkthat connects to the GeneDB of the Wellcome
Trust Sanger Institute in the UK and the
Saccharomyces Genome Database (SGD) ofStanford University in the US, respectively;thus, gene information is easily available. On
finding an interesting resource, the user canjump to the order page simply by clicking on
the link and can request distribution byinputting the destination information. Paymentis generally made by credit card, but otherpayment methods can also be selected. Thus,
yeast resources can be ordered in a manner
similar to online shopping. After an order isplaced, the resources are usually delivered
within a week. This ordering system wasdeveloped in cooperation with the NBRP
Information Center.

ORFs of the genome databasecDNA clones
Corresponding strains

Genomic DNA clones

Fig. 3: Genome Viewer１）Strains for genetics research(ca. 20,000 strains)２）Plasmid DNA clones (ca. 4,500 clones)
３）Vector plasmids for cloning４）DNA libraries (4 types)５）Genome library clones and full-length
cDNA clone sets with sequenced insert
fragments (ca. 62,000 clones in total)
References
１. Hayashi, A et.al., Genes Cells
14: 217-225 (2009)
２. Nakamura, T et al., Mol. Biol. Cell
12:3955-3972 (2001)
３. Nishimura, K., et al., Nat. Methods
6:917-922 (2009)
４. Akada, R. et al., Mol. Gen. Genet.
254:267-274 (1997)

7. Pursuit of further enhancement of
YGRC as a permanent resource center

The motto of the NBRP
Yeast project is to establish “aresource center for researchers
by researchers.” Through YGRC,
we continue to strengthen ourclose relationship with yeast
research communities and aimto further develop the available Website for YGRC
http://yeast.lab.nig.ac.jp/resources.
nig/index_en.html

Ongoing Column [No. 59]

Google ʼ s Image Searching Service2

Have you ever thought that it would be useful to search for images
similar to an image of your interest?
Although this service was initiated last year on smartphones,
searchable image targets were limited. However, this function has
been available in Google Images since June 2011. Using this searchengine, unlimited targets can be searched, and the function can bereadily used on personal computers.

Reﬁning search results

Similar images

Upload an image for searching①

Open the image search page by clicking on “Images” (Fig. 1, ①)
on the Google search page.
Next, click on the camera icon (Fig. 1, ②) on the right corner ofthe search box, and select “Upload an image” (Fig. 2) to upload
an image that can be used for the search.

②

Fig. 4:
Results of image
search refinement③

Fig. 3: Refining image search results
On the image refinement page, select “Size” (Fig. 3, ①); “Color”(Fig. 3, ②); and “Type (face, photo, clip art, and line drawing)”(Fig. 3, ③) to refine your results. Since the color of the flower inthis example is yellow, select yellow and refine the search results.
Thus, only similar images will be selected (Fig. 4).

Images

② Click on
the camera icon
① Click on“Images”

Increasing search accuracy by using keywords
Okinawa

Fig. 1: Google Images Website
http://www.google.co.jp/imghp?hl=en&tab=wiUploading an image

10min.

Images similar to the uploaded images are displayed on thesearch result page on the basis of Google’ s independentalgorithm. If no image interests you, click on “Visually similarimages” to refine the targets of the image search.

This useful service is introduced in this issue.
1

Resources provided by
Yeast Genetic Resource Center (YGRC)

Overall chromosome image

Image＋Keywords
search accuracy↑

In order to search images using both an image and keywords, firstupload an image. When the thumbnail of your image appears
inside the search box, you can input a keyword such as “Okinawa”
and click the search button. By doing this, images matching boththe source image and the keyword can be searched.

Image usedfor the search

Upload an image

Guidelines for searching images

Users should avoid uploading any copyrighted images. Images arehandled according to the log data of Google’ s privacy policy（http://www.google.com/intl/en/privacy/privacy-policy.html) .

Fig. 2: Image uploading screen（Tohru Watanabe）

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

Reprinting and reduplication of any content of this newsletter is prohibited.
All the contents are protected by the Japanese copyright law and international
regulations.

Download the PDF version of this newsletter at
http://www.shigen.nig.ac.jp/shigen/news/

BioResource Information

Editor's Note(NBRP) www.nbrp.jp/(SHIGEN) www.shigen.nig.ac.jp/(WGR) www.shigen.nig.ac.jp/wgr/(JGR) www.shigen.nig.ac.jp/wgr/jgr/jgrUrlList.jsp

NBRP projects are now in the 2nd term of the ﬁnal ﬁscal year, and we areamazed by the achievements of each resource institution. We believe thatthrough the released information, NBRP Yeast has brought improvements
among other resource centers in aspects such as the consolidation ofcollections, preservation, and distribution systems of resources;
publication of information; and feedback for achievements. The
enthusiasm of project members and the cooperation of researcher
communities will be the key to further success. (Y.Y.)“translated by ASL translation service”

BioResource Now !
Issue Number 7 July 20112