National Institute for Basic Biology

Research Support

NIBB CORE RESEARCH FACILITIESHeadYOSHIDA, Shosei

The NIBB Core Research Facilities support basic biologicalresearch conducted at NIBB. They consist of three facilities that develop and provide state-of-the-art technologies
aimed at increasing the understanding of biological functions
through the application of functional genomics, bioimaging,and bioinformatics. The NIBB Core Research Facilities also
act as an intellectual hub to promote collaboration among
NIBB researchers and other academic institutions.

FUNCTIONAL GENOMICS FACILITY

Professor

Representative Instruments
Genomics

The advent of next-generation sequencing (NGS) technologies is transforming modern biology thanks to ultra-highthroughput DNA sequencing. Utilizing HiSeq, NextSeq
and MiSeq (Illumina), Sequel (PacificBio Sciences), and
MinION and GridION (Oxford Nanopore Technologies), theFunctional Genomics Facility is committed to joint research
aimed at exploring new yet otherwise inaccessible fields inbasic biology. We have upgraded the Sequel instrument in
2021, which enabled a significant increase of the HiFi longread production.
During 2021, we carried out 53 NGS projects in collaboration with researchers from academic institutions throughout
the world. These projects cover a wide range of species(bacteria, animals, plants, and fungi) including both modeland non-model organisms, and various other applications
such as genomic re-sequencing, RNA-seq, single-cell
trnascriptome and ChIP-seq.

SHIGENOBU, Shuji

Technical Staff:

Technical Assistant:Admin Support Staff:

MORI, Tomoko
MAKINO, Yumiko
YAMAGUCHI, Katsushi
MORI, Syogo
ASAO, Hisayo
AKITA, Asaka
MATSUMOTO, Miwako
ICHIKAWA, Mariko

Figure 1. Next-generation sequencer

Proteomics

The Functional Genomics Facility is a division of the NIBBCore Research Facilities organized jointly by NIBB and
NIPS for the promotion of DNA and protein studies. The
facility maintains a wide array of core research equipment,
ranging from standard machinery (e.g. ultracentrifuges)
to cutting edge tools (e.g. next generation DNA sequencers), which amount to 90 instruments in total. The facility
is dedicated to fostering collaborations with researchers
both at NIBB and other academic institutions worldwide
through the provision of these tools as well as expertise. Ourcurrent focus is functional genomics. We also act as a bridge
between experimental biology and bioinformatics by providing close consultation and training.
In 2021, we still suffered from the effects of the COVID-19
pandemic that hampered research activities worldwide.
While we operated our facility placing the highest priority on
users’ safety, we provided remote support for the facilities’
users and online communication with collaborators to sustain
research projects. Such efforts resulted in 11 co-authoredpapers being published.

As is listed below, two types of mass spectrometers andtwo protein sequencers are used for proteome studies in ourfacility. In 2021, we analyzed approximately 600 samples
with mass spectrometers and protein sequencers.
- LC-MS (AB SCIEX TripleTOF 5600 system)- LC-MS (Thermo Fisher SCIENTIFIC Orbtrap Elite)
Protein sequencer (ABI Procise 494 HT; ABI Procise 492 cLC)

Figure 2. LC-MS/MS system

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National Institute for Basic Biology

Research Support

Other analytical instruments (excerpts)- Cell sorter (SONY SH800)- B ioimaging analyzer (BIO-RAD ChemiDoc XRS+ ;Fujifilm LAS 3000 mini; GE FLA9000)- Laser capture microdissection system (Thermo Fisher
Scientific Arcturus XT)- Real-time PCR machine (Thermo Fisher Scientific ABI
7500, QuantStudio 3)- Ultracentrifuge (Beckman XL-80XP etc.)-
M icroplate reader (PerkinElmer Nivo; Hitachi
SH-9000Lab)- Single-cell analysis system (Fluidigm C1, 10x Genomics
Chromium X)

Publication List on Cooperation:〔Original papers〕

T., Soyano, T., Liu, M., Mori, T., and Kawaguchi, M. (2022).
• Goto,Auxin methylation by IAMT1, duplicated in the legume lineage,

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promotes root nodule development in Lotus japonicus. Proc. Natl.
Acad. Sci. U.S.A. 119. e2116549119. DOI: 10.1073/pnas.2116549119
Hasegawa, Y., Ueno, S., Wei, F.-J., Matsumoto, A., Uchiyama, K.,
Ujino-Ihara, T., Hakamata, T., Fujino, T., Kasahara, M., Bino Takahiro
and Yamaguchi, K., Shigenobu, S., Tsumura, Y., and Moriguchi, Y.
(2021). Identification and genetic diversity analysis of a male-sterile
gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don). Sci. Rep.
11, 1496. DOI: 10.1038/s41598-020-80688-1
Igawa-Ueda, K., Ikuta, T., Tame, A., Yamaguchi, K., Shigenobu, S.,
Hongo, Y., Takaki, Y., Fujikura, K., Maruyama, T., and Yoshida, T.
(2021). Symbiont Transmission onto the Cell Surface of Early Oocytes
in the Deep-sea Clam Phreagena okutanii. Zoolog. Sci. 38, 140–147.
DOI: 10.2108/zs200129
Ishida, S., Suzuki, H., Iwaki, A., Kawamura, S., Yamaoka, S., Kojima,M., Takebayashi, Y., Yamaguchi, K., Shigenobu, S., Sakakibara, H.,
Kohchi, T., and Nishihama, R. (2022). Diminished Auxin Signaling
Triggers Cellular Reprogramming by Inducing a Regeneration Factor in
the Liverwort Marchantia polymorpha. Plant Cell Physiol. 63, 384–400.
DOI: 10.1093/pcp/pcac004
Ishishita, S., Kitahara, S., Takahashi, M., Iwasaki, S., Tatsumoto, S.,
Hara, I., Kaneko, Y., Kinoshita, K., Yamaguchi, K., Harada, A., Ohmori,Y., Ohkawa, Y., Go, Y., Shigenobu, S., Matsuda, Y., and Suzuki, T.
(2022). Uterus-specific transcriptional regulation underlies eggshell
pigment production in Japanese quail. PLoS One 17, e0265008. DOI:
10.1371/journal.pone.0265008
Korgaonkar, A., Han, C., Lemire, A.L., Siwanowicz, I., Bennouna, D.,
Kopec, R.E., Andolfatto, P., Shigenobu, S., and Stern, D.L. (2021). A
novel family of secreted insect proteins linked to plant gall development.
Curr. Biol. 31, 1836-1849.e12. DOI: 10.1016/j.cub.2021.01.104
Maeda, T., Takahashi, S., Yoshida, T., Shimamura, S., Takaki, Y.,
Nagai, Y., Toyoda, A., Suzuki, Y., Arimoto, A., Ishii, H., Satoh, N.,
Nishiyama, T., Hasebe, M., Maruyama, T., Minagawa, J., Obokata, J.,
and Shigenobu, S. (2021). Chloroplast acquisition without the genetransfer in kleptoplastic sea slugs, Plakobranchus ocellatus. eLife 10,e60176. DOI: 10.7554/eLife.60176
Miyazaki, S., Fujiwara, K., Kai, K., Masuoka, Y., Gotoh, H., Niimi,
T., Hayashi, Y., Shigenobu, S., and Maekawa, K. (2021). Evolutionarytransition of doublesex regulation from sex-specific splicing to malespecific transcription in termites. Sci. Rep. 11, 15992. DOI: 10.1038/
s41598-021-95423-7
Okamoto, S., Kawasaki, A., Makino, Y., Ishida, T., and Sawa, S. (2022).
Long-distance translocation of CLAVATA3/ESR-related 2 peptide andits positive effect on roots sucrose status. Plant Physiol. 189, 2357–
2367. DOI: 10.1093/plphys/kiac227
Okamoto, S., Kawasaki, A., and Makino, Y. (2022). Characterization of
Oligopeptides in Solanum lycopersicum Xylem Exudates. Life 12. 592.
DOI: 10.3390/life12040592
Sato, K., Uehara, T., Holbein, J., Sasaki-Sekimoto, Y., Gan, P., Bino,

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T., Yamaguchi, K., Ichihashi, Y., Maki, N., Shigenobu, S., Ohta, H.,
Franke, R.B., Siddique, S., Grundler, F.M.W., Suzuki, T., Kadota,
Y., and Shirasu, K. (2021). Transcriptomic Analysis of Resistant andSusceptible Responses in a New Model Root-Knot Nematode Infection
System Using Solanum torvum and Meloidogyne arenaria. Front. Plant
Sci. 12, 680151. DOI: 10.3389/fpls.2021.680151
Shigenobu, S., Hayashi, Y., Watanabe, D., Tokuda, G., Hojo, M.Y.,
Toga, K., Saiki, R., Yaguchi, H., Masuoka, Y., Suzuki, R., Suzuki, S.,
Kimura, M., Matsunami, M., Sugime, Y., Oguchi, K., Niimi, T., Gotoh,
H., Hojo, M.K., Miyazaki, S., Toyoda, A., Miura, T., and Maekawa,
K. (2022). Genomic and transcriptomic analyses of the subterranean
termite Reticulitermes speratus: Gene duplication facilitates social
evolution. Proc. Natl. Acad. Sci. U.S.A. 119, e2110361119. DOI:
10.1073/pnas.2110361119
Subhankar, B., Yamaguchi, K., Shigenobu, S., and Aoki, K. (2021).
Trans-species small RNAs move long distances in a parasitic
plant complex. Plant Biotechnol. 38, 187–196. DOI: 10.5511/
plantbiotechnology.21.0121a
Takeuchi, T., Matsubara, H., Minamitani, F., Satoh, Y., Tozawa, S.,
Moriyama, T., Maruyama, K., Suzuki, K.T., Shigenobu, S., Inoue, T.,
Tamura, K., Agata, K., and Hayashi, T. (2022). Newt Hoxa13 has an
essential and predominant role in digit formation during development
and regeneration. Development 149, dev200282. DOI: 10.1242/
dev.200282
Tominaga, T., Miura, C., Sumigawa, Y., Hirose, Y., Yamaguchi, K.,
Shigenobu, S., Mine, A., and Kaminaka, H. (2021). Conservation andDiversity in Gibberellin-Mediated Transcriptional Responses Among
Host Plants Forming Distinct Arbuscular Mycorrhizal Morphotypes.
Front. Plant Sci. 12, 795695. DOI: 10.3389/fpls.2021.795695
Yoshida, Y., Shaikhutdinov, N., Kozlova, O., Itoh, M., Tagami, M.,
Murata, M., Nishiyori-Sueki, H., Kojima-Ishiyama, M., Noma,
S., Cherkasov, A., Gazizova, G., Nasibullina, A., Deviatiiarov, R.,
Shagimardanova, E., Ryabova, A., Yamaguchi, K., Bino, T., Shigenobu,
S., Tokumoto, S., Miyata, Y., Cornette, R., Yamada, T.G., Funahashi,A., Tomita, M., Gusev, O., and Kikawada, T. (2022). High quality
genome assembly of the anhydrobiotic midge provides insights on asingle chromosome-based emergence of extreme desiccation tolerance.
NAR Genomics Bioinforma. 4, lqac029. DOI: 10.1093/nargab/lqac029〔Review article〕

T., Oguchi, K., Yamaguchi, H., Nakamura, M., Sato, D.,• Miura,Kobayashi, K., Kutsukake, N., Miura, K., Hayashi, Y., Hojo, M.,

Maekawa, K., Shigenobu, S., Kano, T., and Ishiguro, A. (2022).
Understanding of superorganisms: collective behavior, differentiationand social organization. Artif. Life Robot. 27, 204–212. DOI: 10.1007/
s10015-022-00754-x

SPECTROGRAPHY AND BIOIMAGING FACILITY

Specially Appointed Associate Professor

has been set up. The NIBB Collaborative Research Program
for the Use of the OLS supports about 10 projects every
year conducted by both visiting scientists, including foreign
researchers, as well as members of NIBB.

KAMEI, Yasuhiro

Technical Staff:
Visiting Undergraduate:
Technical Assistant:

KONDO, Maki
TANIGUCHI-SAIDA, Misako
YOSHIKAWA, Ryusei
ICHIKAWA, Chiaki
ASAO, Momoko
NAKAGAWA, Mami
AOYAMA, Chie

Figure 1. An example of an experiment using the Large Spectrograph. In
this photo, various color rays (monochromatic light from right side andreflected by mirrors) are irradiated simultaneously onto samples stored incooling chambers.

The Spectrography and Bioimaging Facility assists bothcollaborative and core research by managing and maintaining research tools that use Light. The facility, under theguidance of Dr. Kamei, also provides technical support
through the management of technical staff assisting in theadvancement of collaborative and core research projects,
as well as academic support to researchers (please refer tothe Collaborative Research Group Research Enhancement
Strategy Office section for more information). Among theequipment available are advanced biological microscopes,
and the Okazaki Large Spectrograph for photobiology. The
Okazaki Large Spectrograph is the world’s largest wide
spectrum exposure mechanism, and is capable of producing a range of wavelengths from 250 nm (ultraviolet) to
1,000 nm (infrared) along its 10-meter focal curve, thus
allowing exposure to strong monochromatic light. The facility’s microscopes, which include cutting edge devices suchas confocal and multi-photon excitation microscopes, are an
indispensable part of core and collaborative projects conducted by both internal and external researchers.

Microscopes

This facility also provides bioimaging machinery (Figure2), such as wide-field microscopes (Olympus IX-81 and
BX-63), confocal microscopes (Leica TCS-SP8, Nikon
A1R, Nikon A1Rsi and Yokogawa CSU-X1 with EM-CCD/
CMOS cameras), multi-photon microscopes (Olympus
FV1000-MP, FV1200-MPs, Leica TCS-SP8 MPs) and otheradvanced laser microscopes boasting specialized, cuttingedge technology (Light-sheet Microscope and Infrared LaserEvoked Gene Operator microscope: IR-LEGO), which canbe utilized by researchers within NIBB, as well as collaborative guest researchers. Starting from 2016, we have commenced two new types of Collaborative Research Programs.
One is a new category within the NIBB Collaborative
Research for Integrative Bioimaging program using machinery and bioimage processing/analysis techniques, and theother is the Advanced Bioimaging Support Program (ABiS)
which operates under the framework of the Grant-in-Aid for
Scientific Research on Innovative Areas.

Standard Instruments:
Okazaki Large Spectrograph (OLS)

The spectrograph runs on a 30 kW Xenon arc lamp andprojects a wavelength spectrum ranging from 250 nm (ultraviolet) to 1,000 nm (infrared) onto its 10 m focal curve withan intensity of monochromatic light at each wavelength morethan twice as great as that of the corresponding monochromatic component of tropical sunlight at noon (Watanabe etal., Photochem. Photobiol. 36, 491-498, 1982). The spectrograph is dedicated to action spectroscopical studies ofvarious light-controlled biological processes.
In addition to the other action spectroscopical studies concerning various regulatory and damaging effects of light onliving organisms, research involving both biological andartificial organic molecules have been conducted since it

Figure 2. Multi-color confocal microscope image of muscle in a transgenic medaka larva. Each muscle cell expressed randomly various color
variants of fluorescent protein, such as Cerulean, GFP, YFP and dsRed.
The transgenic line was provided by NBRP Medaka.

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National Institute for Basic Biology

Research Support

The light-sheet microscope was developed by Dr. Ernst
Stelzer’s group at the European Molecular Biology
Laboratory (EMBL). This microscope can realize high-speed
z-axis scanning in deeper tissues by illuminating specimensfrom the side with a light sheet (more information is given in
the report submitted by Dr. Shigenori Nonaka’s Laboratory
for Spatiotemporal Regulations). Subsequently, Dr. Nonaka
has conducted and supported roughly 10 Collaborative
Research Program projects for Integrative Bioimaging. The
IR-LEGO, developed by Drs. Shunsuke Yuba and Yasuhiro
Kamei at the National Institute of Advanced Industrial
Science and Technology (AIST), can induce a target gene ofinterest by heating a single target cell in vivo with a high efficiency irradiating infrared laser. This microscope technology
can be applied to thermal biology through local heating (thedetails of this are provided in the next section). IR-LEGO
was also used for about 10 Collaborative Research projects,
including applications aimed at both animals and plants.

Workshop, Symposium and Training course

In 2021, we held the 9 th biological image processing
training course in cooperation with Drs. Kagayaki Kato,
Shigenori Nonaka, Yasuhiro Kamei, Takashi Murata andHiroshi Koyama. The course was held in an online meeting
format due to the COVID-19 pandemic. We have also
started a new course “Optical Microscopy Principle Training
Course” cooperation with Drs. Joe Sakamoto, Yasuhiro
Kamei, Atsushi Taniguchi, Shigenori Nonaka in NIBB andMotosuke Tsutsumi and Kohei Otomo in ExCELLS. In thiscourse, participants learned microscopy principles thoroughlectures and built bright-field and fluorescent microscopes bythemselves using optical devices, such as lenses, filters, lightsources and cameras (Figure 3). We additionally hold sometraining courses and seminars related to microscopy andimage analysis, including their technologies and applications.

Figure 3. A scene from the 1st Optical Microscopy Principle Training
Course. The participants built up a basic microscope by themselves using
optical devices.

Publication List on Cooperation〔Original papers (Selected)〕S., Mochida, K., Fujimoto, S., Mokodongan, D.F., Sumarto,• Ansai,
B.K.A., Masengi, K.W.A., Hadiaty, R.K., Nagano, A.J., Toyoda, A.,•96

Naruse, K., Yamahira, K., and Kitano, J. (2021). Genome editing
reveals fitness effects of a gene for sexual dichromatism in Sulawesianfishes. Nat. Commun. 12. 1350. DOI: 10.1038/s41467-021-21697-0
Beppu, K., Tsutsumi, R., Ansai, S., Ochiai, N., Terakawa, M., Mori, M.,
Kuroda, M., Horikawa, K., Tomoi, T., Sakamoto, J., Kamei, Y., Naruse,
K., and Sakaue, H. (2022). Development of a screening system for

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agents that modulate taste receptor expression with the CRISPR-Cas9
system in medaka. Biochem. Biophys. Res. Commun. 601, 65–72. DOI:
10.1016/j.bbrc.2022.02.082
Goto, T., Soyano, T., Liu, M., Mori, T., and Kawaguchi, M. (2022).
Auxin methylation by IAMT1, duplicated in the legume lineage,
promotes root nodule development in Lotus japonicus. Proc. Natl.
Acad. Sci. U.S.A. 119, e2116549119. DOI: 10.1073/pnas.2116549119
Kaneko, E., Sato, H., and Fukamachi, S. (2021). Validation of the threechamber strategy for studying mate choice in medaka. PLoS One 16,
e0259741. DOI: 10.1371/journal.pone.0259741
Kinoshita, N., Yamamoto, T.S., Yasue, N., Takagi, C., Fujimori,T., and Ueno, N. (2022). Article Force-dependent remodeling ofcytoplasmic ZO-1 condensates contributes to cell-cell adhesion throughenhancing tight junctions. iSCIENCE 25, 103846. DOI: 10.1016/j.
isci.2022.103846
Matsuo, M., Kamei, Y., and Fukamachi, S. (2021). Behavioural redlight sensitivity in fish according to the optomotor response. R. Soc.
Open Sci. 8, 210415. DOI: 10.1098/rsos.210415
Mohri, T., and Kyozuka, K. (2022). Starfish oocytes of A. pectinifera
reveal marked differences in sperm-induced electrical and intracellular
calcium changes during oocyte maturation and at fertilization. Mol.
Reprod. Dev. 89, 3–22. DOI: 10.1002/mrd.23544
Tokanai, K., Kamei, Y., and Minokawa, T. (2021). An easy andrapid staining method for confocal microscopic observation andreconstruction of three-dimensional images of echinoderm larvae andjuveniles. Dev. Growth Differ. 63, 478–487. DOI: 10.1111/dgd.12758
Wu, D., Arakawa, H., Fujita, A., Hashimoto, H., Hibi, M., Naruse, K.,
Kamei, Y., Sato, C., and Kitajima, K. (2021). A point-mutation in the
C- domain of CMP-sialic acid synthetase leads to lethality of medaka
due to protein insolubility. Sci. Rep. 11, 23211. DOI: 10.1038/s41598021-01715-3
Zeng, C.-W., Kamei, Y., Shigenobu, S., Sheu, J.-C., and Tsai, H.-J.
(2021). Injury-induced Cavl-expressing cells at lesion rostral side playmajor roles in spinal cord regeneration. Open Biol. 11, 200304. DOI:
10.1098/rsob.200304〔Research activity by Yasuhiro Kamei〕
Specially Appointed Associate Professor Yasuhiro Kamei is the principal
investigator of Laboratory for Biothermology. For details, please refer tothe laboratory page.

DATA INTEGRATION AND ANALYSIS FACILITY

Associate Professor

UCHIYAMA, Ikuo

Technical Staff:
Technical Assistant:

NISHIDE, Hiroyo
NAKAMURA, Takanori
SUGIURA, Hiroki
KOTANI, KeikoThe Data Integration and Analysis Facility supports
research activities based on large-scale biological data
analysis, such as genomic sequence, expression data, andimaging data analysis. To achieve this, the facility maintains
high-performance computers with large-capacity storage
systems. It accordingly supports the development of data
analysis pipelines and database construction based on thesesystems, and also sets up websites to distribute data worldwide as well as providing basic technical support. In addition
to computational analysis, the Data Integration and Analysis
Facility supports NIBB’s information infrastructure, themaintenance of the institute’s network systems and provides
computer/network consultation for institute members.

PowerEdge R620, 720TB). All subsystems are connected via
a high-speed InfiniBand network, so that large amounts ofdata can be efficiently processed. Some personal computersand color printers are also available for use. On this system,
we provide various biological databases and data retrieval/analysis programs, and support large-scale data analysis anddatabase construction for institute members and collaborative
researchers. We have provided support in the construction
and maintenance of published databases of various modeland non-model organisms in particular. These include XDB(Xenopus laevis), PHYSCObase (Physcomitrella patens),
iNewt (Pleurodales waltl), The Plant Organelles Database,
MBGD (microbial genomes), DB-HABs (harmful algal
blooms), and ChaetoBase (Chaetoceros gracilis).
The facility also provides network communication services.
Most of the PCs in each laboratory, as well as all of theabove-mentioned service machines, are connected by alocal area network, which is linked to the high-performance
backbone ORION network connecting the three research
institutes in Okazaki. Many local services, including
sequence analysis, file sharing, and printer services, areprovided through this network. We also maintain a public
World Wide Web server that hosts the NIBB home page(https://www.nibb.ac.jp/en).

Research activity by Ikuo Uchiyama

Associate Professor Ikuo Uchiyama is the principal investigator of the Laboratory of Genome Informatics. For moredetails, please refer to the laboratory page.

Representative Instruments

Our main computer system is the Biological Information
Analysis System (BIAS) (Figure 1), which consists of ahigh-performance cluster system (HPE Apollo r2800, 20
nodes/800 cores, 192 GB memory/node), a shared memory
parallel computer (HPE ProLiant DL560, 72 cores, 3TB
memory; HP ProLiant DL980 G7, 80 cores, 4TB memory),a high-throughput storage system (DDN SFA7700X,
1.52PB+880TB), and a large capacity storage system (DELL

Figure 1. Biological Information Analysis System

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