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Identification and Functional Analysis of Stimuli-responsive Chemical Species during Enzyme Reaction

Planned Research

Project AreaStimuli-responsive Chemical Species for the Creation of Functional Molecules
Project/Area Number 24109017
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionOsaka University

Principal Investigator

Inoue Tsuyohi  大阪大学, 工学研究科, 教授 (20263204)

Co-Investigator(Kenkyū-buntansha) 中村 努  国立研究開発法人産業技術総合研究所, その他部局等, 研究員 (10357668)
松村 浩由  立命館大学, 生命科学部, 教授 (30324809)
Project Period (FY) 2012-06-28 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥84,240,000 (Direct Cost: ¥64,800,000、Indirect Cost: ¥19,440,000)
Fiscal Year 2016: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2015: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2014: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2013: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2012: ¥46,800,000 (Direct Cost: ¥36,000,000、Indirect Cost: ¥10,800,000)
Keywordsチオレドキシンペルオキシダーゼ / 還元反応 / 酵素反応 / 反応中間体 / Ⅹ 線構造解析 / 中性子線解析 / Ⅹ線自由電子レーザー / SACLA / Ⅹ線構造解析 / 蛋白質 / X線 / ペルオキシレドキシン / スーパーオキシドディスムターゼ / 反応機構解明 / 中性子線構造解析
Outline of Final Research Achievements

Peroxiredoxin (Prx) has a Cys residue at its active site and shows the enzyme activity via S-OH intermediate containing hypervalent sulfur in the process of reducing hydrogen peroxide to water. For uncovering the presence of H atoms on the S atom by neutron analysis, we tried to obtain large crystals of Prx (ApPrx, PhPrx, TkPrx) derived from three types of hyperthermophilic archaea. None of them diffracted up to 3.0A resolution, and the presence of H atom on the S atom was not proved to date. However, the similar structure of S-OH intermediate existed in PhPrx, demonstrating the generality of the S-OH intermediate.

On the other hand, X-ray free electron laser is superior as a method to investigate stimuli-responsive chemical species. We have acquired a knowledge on structural change accompanying reduction upon X-ray irradiation was obtained from the completely oxidized form of nitrite reductase (NIR).

Report

(6 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (39 results)

All 2017 2016 2015 2014 2013 2012 Other

All Journal Article (25 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 25 results,  Open Access: 13 results,  Acknowledgement Compliant: 2 results) Presentation (11 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results) Remarks (3 results)

  • [Journal Article] A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea2017

    • Author(s)
      T. Kono, S. Mehrotra, C. Endo, N. Kizu, M. Matsuda, H. Kimura, E. Mizohata, T. Inoue, T. Hasunuma, A. Yokota, H. Matsumura, H. Ashida
    • Journal Title

      Nature Commun.

      Volume: 8 Issue: 1 Pages: 14007-14007

    • DOI

      10.1038/ncomms14007

    • NAID

      120005947453

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Protein crystallization with paper2016

    • Author(s)
      Miki Matsuoka, Keisuke Kakinouchi, Hiroaki Adachi, Mihoko Maruyama, Shigeru Sugiyama, Satoshi Sano, Hiroshi Y. Yoshikawa, Yoshinori Takahashi, Masashi Yoshimura, Hiroyoshi Matsumura, Satoshi Murakami, Tsuyoshi Inoue, Yusuke Mori and Kazufumi Takano
    • Journal Title

      Jpn. J. Appl. Phys.,

      Volume: 55 Pages: 050302-050302

    • NAID

      210000146451

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography.2016

    • Author(s)
      Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E.
    • Journal Title

      J. Biochem

      Volume: 未定 Issue: 5 Pages: 527-538

    • DOI

      10.1093/jb/mvv133

    • NAID

      40020833586

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A crystallization technique for obtaining large protein crystals with increased mechanical stability using agarose gel combined with a stirring technique2016

    • Author(s)
      M. Maruyama, Y. Hayashi, H. Y. Yoshikawa, S. Okada, H. Koizumi, M. Tachibana, S. Sugiyama, H. Adachi, H. Matsumura, T. Inoue, K. Takano, S. Murakami, M. Yoshimura, Y. Mori
    • Journal Title

      J. Crystal Growth

      Volume: 452 Pages: 172-178

    • DOI

      10.1016/j.jcrysgro.2015.11.008

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Promotion of protein crystal growth by actively switching crystal growth mode via femtosecond laser ablation2016

    • Author(s)
      Y. Tominaga, M. Maruyama, M. Yoshimura, H. Koizumi, M. Tachibana, S. Sugiyama, H. Adachi, K. Tsukamoto, H. Matsumura, K. Takano, S. Murakami, T. Inoue, H. Y. Yoshikawa, Y. Mori
    • Journal Title

      Nature Photonics

      Volume: 10 Issue: 11 Pages: 723-726

    • DOI

      10.1038/nphoton.2016.202

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES.2016

    • Author(s)
      Kado Y1, Mizohata E2, Nagatoishi S3, Iijima M4, Shinoda K4, Miyafusa T3, Nakayama T2, Yoshizumi T2, Sugiyama A4, Kawamura T4, Lee YH4, Matsumura H2, Doi H4, Fujitani H4, Kodama T4, Shibasaki Y4, Tsumoto K5, Inoue T6.
    • Journal Title

      J Biol Chem.

      Volume: 291 Issue: 5 Pages: 2319-2330

    • DOI

      10.1074/jbc.m115.656009

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.2016

    • Author(s)
      Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy ME, Inoue T, Iwata S, Mizohata E.
    • Journal Title

      PNAS

      Volume: 113 Issue: 11 Pages: 2828-2933

    • DOI

      10.1073/pnas.1517770113

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Insights into unknown foreign ligand in copper nitrite reductase2015

    • Author(s)
      Yohta Fukuda, Tse Ka Man, Yuji Kado, Eiichi Mizohata, Hiroyoshi Matsumura, Tsuyoshi Inoue
    • Journal Title

      Biochem. Biophys. Res. Commun.,

      Volume: 464(2) Issue: 2 Pages: 622-628

    • DOI

      10.1016/j.bbrc.2015.07.025

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant.2015

    • Author(s)
      Kawato T, Mizohata E, Shimizu Y, Meshizuka T, Yamamoto T, Takasu N, Matsuoka M, Matsumura H, Kodama T, Kanai M, Doi H, Inoue T, Sugiyama A
    • Journal Title

      Biosci Biotechnol Biochem.

      Volume: 79 Issue: 4 Pages: 640-642

    • DOI

      10.1080/09168451.2014.991692

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Grease matrix as a versatile carrier of proteins for serial crystallography.2015

    • Author(s)
      Sugahara, M.; Mizohata, E.; Nango, E.; Suzuki, M.; Tanaka, T.; Masuda, T.; Tanaka, R.; Shimamura, T.; Tanaka, Y.; Suno, C.; Ihara, K.; Pan, D.; Kakinouchi, K.; Sugiyama, S.; Murata, M.; Inoue, T.; Tono, K.; Song, C.; Park, J.; Kameshima, T.; Hatsui, T.; Joti, Y.; Yabashi, M.; Iwata, S
    • Journal Title

      Nature Methods,

      Volume: 12 Pages: 61-63

    • NAID

      120005682565

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure-based design of a streptavidin mutant specific for an artificial biotin analogue.2015

    • Author(s)
      Kawato, T.; Mizohata, E.; Shimizu, Y.; Meshizuka, T.; Yamamoto, T. Takasu, N.; Matsuoka, M.; Matsumura, H.; Kodama, T.; Kanai, M.; Doi, H.; Inoue, T.; Sugiyama, A.
    • Journal Title

      J. of Biochemistry

      Volume: 1 Issue: 6 Pages: 1-9

    • DOI

      10.1093/jb/mvv004

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystal structure of streptavidin mutant with low immunogenicity.2015

    • Author(s)
      Kawato T, Mizohata E, Meshizuka T, Doi H, Kawamura T, Matsumura H, Yumura K, Tsumoto K, Kodama T, Inoue T & Sugiyama A.
    • Journal Title

      J Biosci Bioeng.

      Volume: 119(6) Issue: 6 Pages: 642-647

    • DOI

      10.1016/j.jbiosc.2014.10.025

    • NAID

      110009970751

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.2014

    • Author(s)
      Nakayama, T.; Mizohata, E.; Yamashita, T.; Nagatoishi, S.; Nakakido, M.; Iwanari, H.; Mochizuki, Y.; Kado, Y.; Yokota, Y.; Satoh, R.; Tsumoto, K.; Fujitani, H.; Kodama, T.; Hamakubo, T.; Inoue T
    • Journal Title

      Protein Science,

      Volume: 24 Pages: 328-340

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural insights into the function of a thermostable copper-containing nitrite reductase2014

    • Author(s)
      Y Fukuda, et al.
    • Journal Title

      The Journal of Biochemistry

      Volume: 155 Issue: 2 Pages: 123-135

    • DOI

      10.1093/jb/mvt107

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Jumonji/Arid1b (Jarid1b) protein modulates human esophageal cancer cell growth.2013

    • Author(s)
      Kano, Y., Konno, M., Ohta, K., Haraguchi, N., Nishikawa, S., Kagawa, Y., Hamabe, A., Hasegawa, S., Ogawa, H., Fukusumi, T., Noguchi, Y., Ozaki, M., Kudo, T., Sakai, D., Satoh, T., Ishii, M., Mizohata, E., Inoue, T., Mori, M., Doki, Y., Ishii, H.
    • Journal Title

      Mol.Clin. Oncol.

      Volume: 1 Issue: 4 Pages: 753-757

    • DOI

      10.3892/mco.2013.127

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fabrication of poly(γ-glutamic acid) monolith by thermally induced phase separation and its application2013

    • Author(s)
      S. B. Park, T Fujimoto, E Mizohata, T Inoue, M.- H. Sung, and H. Uyama
    • Journal Title

      J. Microbiol. Biotechnol. 23

      Volume: 23 Pages: 942-952

    • DOI

      10.1016/j.polymdegradstab.2013.11.019

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of peroxiredoxin from anaerobic hyperthermophilic archaeon Pyrococcus horikoshii2013

    • Author(s)
      T. Nakamura*, A. Mori, M. Niiyama, H. Matsumura, C. Tokuyama, J. Morita, K. Uegaki and T. Inoue
    • Journal Title

      Acta. Cryst.

      Volume: F69 Issue: 7 Pages: 719-722

    • DOI

      10.1107/s1744309113014036

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Expression, purification, crystallization and preliminary crystallographic analysis of spermidine acetyltransferase from Escherichia coli.2013

    • Author(s)
      Niiyama, M. et al.
    • Journal Title

      Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.

      Volume: 69 Issue: 8 Pages: 884-887

    • DOI

      10.1107/s1744309113017132

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus2013

    • Author(s)
      J. Fujita, Y. Miyazaki, M. Hirose, C. Nagao, E. Mizohata, Y. Matsumoto, K. Mizuguchi, T. Inoue, and H. Matsumura
    • Journal Title

      Acta. Cryst.

      Volume: F69 Issue: 8 Pages: 895-898

    • DOI

      10.1107/s1744309113017727

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells2013

    • Author(s)
      T. Yoshimaru, M. Komatsu, T. Matsuo, Y.-A. Chen, Y. Murakami, K. Mizuguchi, E. Mizohata, T. Inoue, M. Akiyama, R. Yamaguchi, S. Imoto, S. Miyano, Y. Miyoshi, M. Sasa, Y. Nakamura, and T. Katagiri
    • Journal Title

      Nature Communications

      Volume: 4 Issue: 1 Pages: 2433-2433

    • DOI

      10.1038/ncomms3443

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Construction and characterization of functional anti-epiregulin humanized monoclonal antibodies2013

    • Author(s)
      Y.-H. Lee, M. Iijima, Y. Kado, T. Inoue, A. Sugiyama, H. Doi, Y. Shibasaki, T. Kodama
    • Journal Title

      Biochem. Biophys. Res. Commun

      Volume: 441 Issue: 4 Pages: 1011-1017

    • DOI

      10.1016/j.bbrc.2013.11.014

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid2013

    • Author(s)
      M. Hirose, S. Sugiyama, M. Niiyama, D. Matsuoka, T. Hara, E. Mizohata, S. Murakami, T. Inoue, S. Matsuoka, and M. Murata
    • Journal Title

      10.1107/S0909049513021298

      Volume: 20 Pages: 923-928

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] C(sp3)-H Bond Hydroxylation Catalyzed by Myoglobin Reconstituted with Manganese Porphycene2013

    • Author(s)
      Koji Oohora, Yushi Kihira, Eiichi Mizohata, Tsuyoshi Inoue, Takashi Hayashi
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 135 Issue: 46 Pages: 17282-17285

    • DOI

      10.1021/ja409404k

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Crystal structure of rice Rubisco and implications for activation2012

    • Author(s)
      Hiroyoshi Matsumura
    • Journal Title

      J. Mol. Biol.,

      Volume: 422(1) Issue: 1 Pages: 75-86

    • DOI

      10.1016/j.jmb.2012.05.014

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spatially precise, soft microseeding of single protein crystalsby femtosecond laser ablation2012

    • Author(s)
      Hiroshi Yoshikawa
    • Journal Title

      Cryst. Growth Des.,

      Volume: 12(9) Issue: 9 Pages: 4334-4339

    • DOI

      10.1021/cg300018t

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] The molecular design of a mutant streptavidin with high specificity for only an artificial biotin derivative2017

    • Author(s)
      Tsuyoshi Inoue, Tatsuya Kawato, Eiichi Mizohata, Yohei Shimizu, Tomohiro Meshizuka, Tomohiro Yamamoto, Noriaki Takasu, Masahiro Matsuoka, Tatsuhiko Kodama, Motomu Kanai, Hirofumi Doi, Akira Sugiyama
    • Organizer
      11th Pure and Applied Chemistry International Conference 2017 (PACCON 2017)
    • Place of Presentation
      CENTRA GOVERNMENT COMPLEX HOTEL & CONVENTION CENTRE CHAENG WATTHANA, Bangkok
    • Year and Date
      2017-02-02
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structural Bioinorganic Chemistry of Copper Enzymes2016

    • Author(s)
      Yohta Fukuda, Eiichi Mizohata, Tsuyoshi Inoue
    • Organizer
      The 4th International Symposium for Young Chemists on Stimuli-Responsive Chemical Species for the Creation of Functional Molecules
    • Place of Presentation
      大阪大学吹田キャンパス 工学研究科 サントリーメモリアルホール(大阪府・吹田市)
    • Year and Date
      2016-12-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 中性子用大型良質タンパク質結晶育成を目指して2016

    • Author(s)
      安達宏昭、岡田詩乃、杉山成、丸山美帆子、高野和文、吉川洋史、村上聡、松村浩由、井上豪、森勇介
    • Organizer
      日本結晶学会平成28年度年会
    • Place of Presentation
      茨城県立県民文化センター(茨城県・水戸市)
    • Year and Date
      2016-11-17
    • Related Report
      2016 Annual Research Report
  • [Presentation] SACLA が解明した銅含有亜硝酸還元酵素の常温無損傷構造2016

    • Author(s)
      溝端 栄一
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県・福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] エピレギュリン-抗体複合体構造解析に基づく分子認識機構の解明2016

    • Author(s)
      門 祐示、溝端 栄一、長門石 曉、 飯嶋 真理子、篠田 恵子、宮房 孝光、 中山 泰亮、吉住 拓真、杉山 暁、 川村 猛、Lee Yougn-Hun、松村 浩由 、土居 洋文、児玉 龍彦、柴崎 芳一、津本 浩平、井上 豪
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県・福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] 親和性向上を目的とした抗ROBO1 scFv の変異体解析2016

    • Author(s)
      由井 杏奈、工藤 翔太、秋葉 宏樹、中木戸 誠、長門石 曉、井上 豪、浜窪 隆雄、津本 浩平
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県・福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Growth of High-Quality and Large Protein Crystals for Neutron Crystallography2013

    • Author(s)
      Hiroyoshi Matsumura
    • Organizer
      感応性化学種が拓く新物質科学 第1回国際シンポジウム
    • Place of Presentation
      メルパルク広島
    • Year and Date
      2013-03-26
    • Related Report
      2012 Annual Research Report
  • [Presentation] Hypervalent Intermediate Observed during Oxidation of Peroxiredoxin from an Aerobic Hyperthermophilic Archaeon Aeropyrum pernix K12013

    • Author(s)
      Tsuyoshi Inoue
    • Organizer
      感応性化学種が拓く新物質科学 第1回国際シンポジウム
    • Place of Presentation
      メルパルク広島
    • Year and Date
      2013-03-26
    • Related Report
      2012 Annual Research Report
  • [Presentation] Crystal structure of Archaeal Peroxiredoxin from an Anaerobic Hyperthermophilic Archaeon Pyrococcus horikoshii2013

    • Author(s)
      Tsutomu Nakamura
    • Organizer
      感応性化学種が拓く新物質科学 第1回国際シンポジウム
    • Place of Presentation
      メルパルク広島
    • Year and Date
      2013-03-26
    • Related Report
      2012 Annual Research Report
  • [Presentation] 嫌気性古細菌由来ペルオキシレドキシンの結晶化と構造解析2013

    • Author(s)
      中村 努
    • Organizer
      第12 回 産総研・産技連LS-BT 合同研究発表会
    • Place of Presentation
      産総研つくばセンター
    • Year and Date
      2013-02-05
    • Related Report
      2012 Annual Research Report
  • [Presentation] 生体酵素系に生成する感応性化学種の同定と機能解明2012

    • Author(s)
      井上 豪
    • Organizer
      感応性化学種が拓く新物質科学 第1回公開シンポジウム
    • Place of Presentation
      京都大学・宇治おうばくプラザ・きはだホール
    • Related Report
      2012 Annual Research Report
  • [Remarks] 井上豪Home Page

    • URL

      http://www.chem.eng.osaka-u.ac.jp/~inoue-tken/ja/staffs/inoue/index.html

    • Related Report
      2012 Annual Research Report
  • [Remarks] Hiroyoshi Matsumura (松村 浩由) Homepage

    • URL

      http://www.chem.eng.osaka-u.ac.jp/~inoue-tken/ja/staffs/matsumura/

    • Related Report
      2012 Annual Research Report
  • [Remarks] 中村努Home Page

    • URL

      http://unit.aist.go.jp/hri/group/bmd-rg/member/nakamura.htm

    • Related Report
      2012 Annual Research Report

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Published: 2012-11-27   Modified: 2019-07-29  

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