Call for applications: 2024 Joint Usage and Joint Research Programs, Institute of Advanced
Medical Sciences, Tokushima University
9th January 2024
Tokushima University, also known as University of Tokushima, has a long history of advanced
medical sciences. Miyoshi muscular dystrophy and adjuvant disease were discovered here.
Immunoproteasomes, hepatocyte growth factor, and cathepsin L as well as many otherdisease-related human molecules have their home in our campus. In 1961, the medical schoolof Tokushima University founded three laboratories of enzyme research, which successfully
formed Institute for Enzyme Research in 1987. In 1998, Institute for Genome Research wasfounded to extend medical research to focus on genome functions. In 2010, Diabetes
Therapeutics and Research Center was formed to overcome the diabetes by creating platform
for the collaborations between clinical and basic researchers. In 2013, Fujii Memorial Instituteof Medical Sciences was founded in memory of Professor Setsuro Fujii, one of the founding
professors of original enzyme research laboratories. In 2016, the University has decided tomerge these four institutes to form the Institute of Advanced Medical Sciences, in order tofacilitate multi-disciplinal and trans-omic studies for advanced medical sciences.
Supported by the Joint Usage and Joint Research Programs of the MEXT, Japan, the Instituteof Advanced Medical Sciences, Tokushima University, calls for the applications for the joint
usage and/or joint research as follows. The proposed expenses should be used within the fiscal
year 2024 which begins on 1st April 2024 and ends on 31st March 2025.

(A)Joint Usage
State-of-art research facility of our institute is open for the support of the research in thefollowing 4 aspects. In principle, travel expenses will be supported (but if it is difficult to visit
our institute due to the situation of COVID-19, use for cancellation charges for flights, hotels
etc. and supplies expenses will be allowed). Up to 150,000 Japanese yens per successfulproposal per fiscal year will be supported for the following experiments.
A-1. Next-generation sequencing and microarray analyses (organized by Professor Seiichi
Oyadomari and Associate Professor Tetsuro Yoshimaru)
Next-generation sequencing analysis using NextSeq550 (illumina). Representative costs are
873,000 yens per sample for whole human genome sequencing. 216,000 yens (Mid) or１

546,000 yens (High) per run (2-12 samples) for whole human exon analysis (PE 75bp),
346,000 yens (Mid) or 873,000 yens (High) per run (3-12 samples) for whole human exon
analysis (PE 100-150bp). 216,000 yens (Mid) or 546,000 yens (High) per run (5-16 samples)for total human RNA-seq analysis (PE 75bp), 216,000 yens (Mid) or 289,000 yens (High) )per run (13-40 samples) for RNA-seq expression analysis (SR 50~75bp). 216,000 yens (Mid)or 289,000 yens (High) per run (8-26 samples) for ChIP-seq analysis of transcription factors(SR 50~75bp), 216,000 yens (Mid) or 546,000 yens (High) per run (3-10 samples) for ChIPseq analysis of histone modifications (PE 50~75bp), and 380,000 yens per slide (8 samples)for Agilent human microarray analysis (Each cost is estimated as present value (2020.11).
NextSeq

550

Systemenablesarrayscanningfor

Infinium

methylation

EPIC,

HumanKaryomap and CytoSNP Chip. Please contact us for single cell analysis using
Chromium Single Cell Controller from 10X Genomics. Analysis of human samples requires
approval from each institution committee regarding human genome and gene analysis
research ethics. CLC genomics workbench (Qiagen）is available in each analysis.
Please contact Associate Professor Yoshimaru for details (tmaru@genome.tokushima-u.ac.jp).
Human sample analyses require the prior approval from appropriate intramural committee ofthe applicant’s affiliated organization.
A-2. Proteome analysis (organized by Professor Hidetaka Kosako and Assistant Professor
Harunori Yoshikawa)
Proteome analysis using high resolution mass spectrometers (Orbitrap Fusion and Q Exactive
Plus, Thermo Fisher Scientific). Proteome Discoverer, BioPharma Finder, Mascot, andScaffold can be used for data analysis. Representative costs are 15,000 yen per sample foridentification and quantitation of proteins from electrophoresed gel fragments orimmunoprecipitates, 20,000 to 30,000 yen per sample for identification and quantitation of
PTMs such as phosphorylation and ubiquitination of proteins, 15,000 to 30,000 yen per
sample for global identification and quantitation (by TMT labeling, PRM, and LFQ) of
proteins and PTM sites in complex samples such as cell lysates. Please contact Professor
Kosako for details (kosako@tokushima-u.ac.jp). Human sample analysis requires the priorapproval from appropriate intramural committee.
uHPLC analysis using Vanquish Duo uHPLC system (Thermo Fisher Scientific), especiallyseparation of native and large protein complexes (i.e. polysomes and ribosomes) by Size
Exclusion Chromatography. Costs are 10,000 yen per 10 samples (depending on themeasurement conditions). Please contact Assistant Professor Yoshikawa for details２(yoshikawa.harunori@tokushima-u.ac.jp).
A-3. Genome editing of laboratory mice or cultured cells (organized by Professor Tatsuya
Takemoto and Associate Professor Shun Sawatsubashi)
Generation of genetically modified mice by an improved zygote electroporation technology ofCRISPR/Cas9-mediated genome editing. Costs are 700,000-800,000 yen for generating agene-disrupted mouse or a point mutant mouse, 1,000,000-1,200,000 yen for generating along-DNA knock-in mouse (e.g. an EGFP knock-in reporter mouse). Costs for mouse
breeding and shipping are also required. Please contact Professor Takemoto for details(takemoto.tatsuya@tokushima-u.ac.jp)
Generation of genome-edited cultured cells using the CRISPR/Cas9 system, including geneknock-out cells and reporter knock-in cells by the VIKING method (Sci Rep.8,593,2018).
Costs are 150,000-400,000 yen for generating genome-edited cultured cells. If necessary,
we can also establish cell lines from single cells, sort cells using a fluorescent reporter, andanalyze genome sequences. A separate fee is required for these procedures. Please contact
Associate Professor Sawatsubashi for details (shun-sawa2@tokushima-u.ac.jp)
A-4. Genome editing of cells (organized by Professor Seiichi Oyadomari)Generation of genome-wide knockout cells with a pooled lentiviral sgRNA library using
CRISPR/Cas9 technology for high-throughput functional genomic screening. Costs are
400,000 yen for generating genome-wide knockout human or mouse cells. Costs for nextgeneration sequencing and shipping are also required. Please contact Professor Oyadomari
for details (oyadomar@tokushima-u.ac.jp)
A-5. Biomolecular size measurement and interaction analysis (organized by ProfessorTomohide Saio)
Biomolecular size measurement using the SEC-MALS system (Wyatt DAWN HELEOS II 8+).
The size of protein homo/hetero oligomers after gel filtration is measured by multi-angle lightscattering. NMR (Bruker Avance III 500 MHz) is used for structural characterization andinteraction analysis of biomolecules and peptides. The total number of the projects is limited
to 5 per year. Costs for SEC-MALS are 7,000-15,000 yen/sample depending on the numberof measurement conditions. Costs for NMR measurements are 12,000-80,000 yen/sample
depending on the type of measurement, but the amount varies depending on the sample andmeasurement. Please contact Professor Saio for details (saio@tokushima-u.ac.jp).

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(B)Joint Research
The Institute welcomes the proposal for collaborative joint research with the following
laboratories. In principle, up to 300,000 Japanese yens per proposal per fiscal year will besupported to a successful research proposal.
Multiple applications from one laboratory will be accepted if the research themes are different.
B-1. Division of Protein Expression
B-2. Professor Yasuo Shinohara, yshinoha@genome.tokushima-u.ac.jp
B-2. Division of Cell Signaling
B-3. Professor Hidetaka Kosako, kosako@tokushima-u.ac.jp
B-3. Division of Embryology
B-4. Professor Tatsuya Takemoto, takemoto.tatsuya@tokushima-u.ac.jp
B-4. Division of Molecular Biology
B-5. Professor Seiichi Oyadomari, oyadomar@genome.tokushima-u.ac.jp
B-5. Division of Molecular Neurobiology
B-6. Professor Suehiro Sakaguchi, sakaguchi@tokushima-u.ac.jp
B-6. Division of Molecular Medicine
B-7. Professor Yoshiyuki Minegishi, yminegishi@genome.tokushima-u.ac.jp
B-7. Division of Pathology and Metabolome Research for Host Defense
B-8. Professor Hiroshi Kido, kido@tokushima-u.ac.jp
B-8. Division of Diabetes Therapeutics and Research
B-9. Professor Munehide Matsuhisa, matuhisa@tokushima-u.ac.jp
B-9. Division of Molecular Life Science
B-10. Professor Tomohide Saio, saio@tokushima-u.ac.jp
B-10. Division of Experimental Immunology
B-14. Professor Izumi Ohigashi, ohigashi@genome.tokushima-u.ac.jp
B-11. Division of Pathogenetic Signaling
B-10. Professor Kiyohito Mizutani, kiyohito_mizutani@tokushima-u.ac.jp
B-12. Division of Biomechanics and Signaling
B-10. Associate Professor Hajime Fukui, fhajime@tokushima-u.ac.jp
B-13. Division of Molecular CytoMorphology
B-10. Associate Professor Yoshiyuki Fukuda, fukuday@tokushima-u.ac.jp
B-14. Division of Gene Regulation
B-10. Associate Professor Hotaka Kobayashi, kobayashi.hotaka@tokushima-u.ac.jp
B-15. Department of Immunology and Parasitology
B-11. Professor Koji Yasutomo, yasutomo@tokushima-u.ac.jp
４B-16. Department of Oral Molecular Pathology
B-12. Professor Naozumi Ishimaru, ishimaru.n@tokushima-u.ac.jp
B-17. Department of Pharmaceutical SciencesB-13. Professor Kosuke Namba, namba@tokushima-u.ac.jp
In the case you cannot visit our Institute due to the pandemic of COVID-19, we encourage
the joint research and joint usage activities without your visiting. Please consult closelywith our Institute’s researchers and conduct your projects.

Eligibility
A researcher affiliated with a university or a public research institute, or a researcher approvedby the Director of our Institute. The approval from the affiliated organization is required. The
Institute of Advanced Medical Sciences does not discriminate on the basis of nationality, race,religion, disability, gender, marital status, sexual orientation, age, or any other illegal or unfair
basis.

Application
Please convert the complete application that contains the following items to a single PDF
document within two pages, and send as an e-mail attachment to <kyodo@tokushimau.ac.jp> with the subject line: “Application for Joint Usage Joint Research Programs”.
Application deadline is 26th February 2024.
-Personal information: Full name, Degree(s), Title, Organization, Mailing address, Phone
number, E-mail address, and Country of citizenship-Three names of your references-Representative research records, chiefly within the last five years-Proposed research: Title, Aspect (choose one from Joint Usage A1-A5 and Joint Research
B1-B17, Contact researcher at out Institute, Research aims, Methods, Necessities, Outcomes,
Budget, and Research duration

ScheduleDeadline of the application is 26th February 2024. Successful applicants will be notified
before the end of March 2024. Approved joint usage and/or joint research should beperformed between 1st April 2024 and 31st March 2025.
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Selection and Notification of Selection
As for joint research, we will select research topics related to "chronic inflammation" aspriority research topics.
Applicants will be notified of the decision and the amount of research expenses by the end ofMarch after deliberation by the committee, which includes academic experts outside ouruniversity.
If your application is accepted, please report it to your institution.

Obligations
Successfully selected applicants must send us a brief report of their research activities andfindings within two pages. The report should include the publication of the papers and thepresentations at scientific meetings. A single PDF document that contains the report has tobe sent to us via e-mail by 31st March 2025.
When the selected applicant is reporting the findings out of the Joint Usage and Joint
Research Programs in an academic paper, she/he must state clearly in that paper that theresearch was carried out under the support of The Joint Usage and Joint Research Programs,
the Institute of Advanced Medical Sciences, Tokushima University. A copy of that paper must
be sent to us.
The leader or a member of the project will be requested to make a presentation at the Joint Usage andJoint Research Programs Conference.

Handling of Intellectual Property Rights
In principle, the degree of contribution of each researcher and his/her institution to theinvention will be taken into consideration, and the attribution of the invention will bedetermined through consultation.

Export Security Control
Procedures based on Security Export Control Regulations of Tokushima University may berequired when providing research equipment, samples, technical guidance, etc. to overseas
countries or conducting joint research with overseas researchers.

６Contact
Administration OfficeInstitute of Advanced Medical Sciences, Tokushima University 3-18-15 Kuramoto,Tokushima 770-8503, Japan
Telephone: +81-88-633-9420
E-mail: kyodo@tokushima-u.ac.jp

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