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102. 沖縄県の大学生における就業意識についての基礎的研究

Author

高良, 美樹, 金城, 亮, 廣瀬, 等, Takara, Miki, Kinjo, Akira, Hirose, Hitoshi, 高良, 美樹, 金城, 亮, 廣瀬, 等, Takara, Miki, Kinjo, Akira, and Hirose, Hitoshi

Abstract

本研究では、沖縄県の大学生における就業意識に関して、職業選択基準を中心に検討をおこなった。沖縄県内の2ヵ所の4年制大学に通う大学生449名（男子221名、女子224名、不明4名）を対象に調査を実施した。職業選択基準について尺度構成をおこなった後、各下位尺度得点について出身地（2；沖縄県内・県外）×性別（2）の要因計画に基づき分散分析をおこなった。その結果、県内出身学生が相対的に“地元志向”および“雇用条件”を重視する傾向が強いことが示された。また、女子学生が男子学生に比べ、“勤務制度”や“社会貢献”を重視していることが明らかになった。さらに、具体的な職業選択とそれを支えるイメージに関する内容分析、何のために働くかについての自己と他者間での認識の違いといった複合的な観点から大学生の就業意識についての探索的検討を試みた。

Published
2003

109. インターンシップの経験が大学生の就業意識に及ぼす効果 －職業レディネスおよび進路選択に対する自己効力感を中心として－

Author

高良, 美樹, 金城, 亮, Takara, Miki, Kinjo, Akira, 高良, 美樹, 金城, 亮, Takara, Miki, and Kinjo, Akira

Abstract

本研究では、職業レディネスおよび進路選択に対する自己効力感を指標として、インターンシップ（職場実習）の前後における大学生の就業意識の変化に焦点をあてた検討をおこなった。沖縄県内の3大学に通う文系の3年次学生398名（男子217名、女子181名）を対象に調査を実施した。職業レディネス21項目および進路選択に対する自己効力感30項目の各合計得点を従属変数として、インターンシップのタイプ（実務型・専門教育型・実習なし）×調査時期（実習前・後）の2要因混合計画による分散分析をおこなった結果、両得点ともに有意な効果は認められなかった。一方、インターンシップ経験に対する全般的満足度が高い群では、低い群に比べて事後調査における両得点が有意に高くなっており、インターンシップ・プログラムへの関与や満足が、職業レディネスや進路選択に対する自己効力感に促進的な影響を与えていることが示唆された。

Published
2001

116. リーダー行動と集団成績に関する情報がリーダー評定に与える効果

Author

Kinjo, Akira, Kurokawa, Masaru, and Sato, Seiichi

Abstract

The effects of informations about supervisory behavior and group productivity on evaluation of leaders were investigated. After read the description of the group productivity, leader's gender and supervisory behaviors of one specific group, 268 male and 139 female undergraduate students who were respectively assigned to one of 8 experimental conditions -- group productivity (High/Low) X leadership type (P/M) X leader's gender -- evaluated the leader's behavior using LBDQ, and also his/her personality and aptitude. Evaluations of leadership behavior were analyzed into initiating structure, consideration, and production emphasis. The results showed strong influences of productivity information on rating scores on the first two factors but production emphasis factor. As to these results, the implicit leadership theory was discussed.

Published
1991

128. Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner.

Author

Dasgupta, Bhaskar, Nakamura, Haruki, and Kinjo, Akira R.

Abstract

ABSTRACT To understand the dynamic aspects of multispecificity of ubiquitin, we studied nine ubiquitin-ligand (partner protein) complexes by normal mode analysis based on an elastic network model. The coupling between ubiquitin and ligand motions was analyzed by decomposing it into rigid-body (external) and vibrational (internal) motions of each subunit. We observed that in total the external motions in one of the subunits largely dominated the coupling. The combination of external motions of ubiquitin and the ligands showed general trends of rotations and translations. Moreover, we observed that the rotational motions of ubiquitin were correlated to the ligand orientations. We also identified ubiquitin atomic vibrations that differentiated the orientation of the ligand molecule. We observed that the extents of coupling were correlated to the shapes of the ligands, and this trend was more pronounced when the coupling involved vibrational motions of the ligand. In conclusion, an intricate interplay between internal and external motions of ubiquitin and the ligands help understand the dynamics of multispecificity, which is mostly guided by the shapes of the ligands and the complex. Proteins 2014; 82:77-89. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Published
2014
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130. PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

Author

Kinjo, Akira R., Reiko Yamashita, and Haruki Nakamura

Abstract

This article is a tutorial for PDBj Mine, a new database and its interface for Protein Data Bank Japan (PDBj). In PDBj Mine, data are loaded from files in the PDBMLplus format (an extension of PDBML, PDB's canonical XML format, enriched with annotations), which are then served for the user of PDBj via the worldwide web (WWW). We describe the basic design of the relational database (RDB) and web interfaces of PDBj Mine. The contents of PDBMLplus files are first broken into XPath entities, and these paths and data are indexed in the way that reflects the hierarchical structure of the XML files. The data for each XPath type are saved into the corresponding relational table that is named as the XPath itself. The generation of table definitions from the PDBMLplus XML schema is fully automated. For efficient search, frequently queried terms are compiled into a brief summary table. Casual users can perform simple keyword search, and 'Advanced Search' which can specify various conditions on the entries. More experienced users can query the database using SQL statements which can be constructed in a uniform manner. Thus, PDBj Mine achieves a combination of the flexibility of XML documents and the robustness of the RDB. [ABSTRACT FROM AUTHOR]

Published
2010
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131. Predicting absolute contact numbers of native protein structure from amino acid sequence.

Author

Kinjo, Akira R., Horimoto, Katsuhisa, and Nishikawa, Ken

Abstract

The contact number of an amino acid residue in a protein structure is defined by the number of Cβ atoms around the Cβ atom of the given residue, a quantity similar to, but different from, solvent accessible surface area. We present a method to predict the contact numbers of a protein from its amino acid sequence. The method is based on a simple linear regression scheme and predicts the absolute values of contact numbers. When single sequences are used for both parameter estimation and cross-validation, the present method predicts the contact numbers with a correlation coefficient of 0.555 on average. When multiple sequence alignments are used, the correlation increases to 0.627, which is a significant improvement over previous methods. In terms of discrete states prediction, the accuracies for 2-, 3-, and 10-state predictions are, respectively, 71.4%, 54.1%, and 18.9% with residue type-dependent unbiased thresholds, and 76.3%, 59.2%, and 21.8% with residue type-independent unbiased thresholds. The difference between accessible surface area and contact number from a prediction viewpoint and the application of contact number prediction to three-dimensional structure prediction are discussed. Proteins 2005. © 2004 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Published
2005
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132. Influence of the Model of Worker on Career Maturity of Junior College Students

Author

Hirose, Hitoshi, Takara, Miki, Kinjo, Akira, and Hirose, Makiko

Abstract

働く人のモデルの有無が短期大学生の進路に及ぼす影響を明らかにするため、保育士、幼稚園教諭を目指す学科に所属する短期大学２年生を調査対象者として検討した。その結果、１）半数近くの学生が入学前後で働く人のモデルをもち、働く人との間柄は「教師」、職業は「保育士」が多い、２）大学入学前に働く人のモデルが存在した場合、より専門志向の理由で入学し、大学進学理由では「教師」に影響を受けた学生が多い、３）大学入学後に働く人のモデルが存在した場合、自分自身のみならず、社会にも目を向けた仕事をする理由であり、その理由の形成では「父親」に影響を受けた学生が多い、４）卒業後の進路（進路目標の決定状況→過去一年間の準備・活動の有無→現状)では、入学前後で働く人のモデルが存在する場合、「準備・活動」に積極的な影響があった。ただし、準備・活動の具体的な内容は、比較的初期の準備・活動に留まっており、そのことから実際の就職の内定には結びついていないとも考えられた。５）入学前後で働く人のモデルが存在する場合、職業レディネスが高く、卒業後の進路を考慮して大学・学科を選択しており、また、大学・学科の講義・演習科目の内容が役立ったと評価していた。, 紀要論文

133. Contributory presentations/posters

Author

Manoj, N., Srinivas, V., Surolia, A., Vijayan, M., Suguna, K., Ravishankar, R., Suguna, K., Surolia, A., Vijayan, M., Schwarzenbacher, R., Zeth, K., Diederichs, Kostner, G., Gries, A., Laggner, P., Prassl, R., Madhusudan, Akamine, Pearl, Xuong, Nguyen-huu, Taylor, Susan, Sagar, M., Ravishankar, R., Saikrishnan, K., Roy, S., Purnapatre, K., Handa, P., Varshney, U., Vijayan, M., Biswal, B., Sukumar, N., Vijayan, M., Rao, J., Johnson, A., Pattabhi, Vasantha, Krishna, S., Sastri, Mira, Savithri, H., Murthy, M., Pillai, Bindu, Kannan, Hosur, M., Kumar, Mukesh, Patwardhan, Swati, Kannan, K., Hosur, M., Padmanabhaa, B., Sasaki-Sugio, S., Nukaga, M., Matsuzaki, T., Karthikevan, S., Sharma, S., Sharma, A., Paramasivam, M., Kumar, P., Khan, J., Yadav, S., Srinivasan, A., Singh, T., Gourinath, S., Alam, Neelima, Srintvasan, A., Singh, T., Chandra, Vikas, Kaur, Punit, Betzel, Ch., Singh, T., Ghosh, S., Bera, A., Bhattacharya, S., Chakraborty, S., Pal, A., Mukhopadhyay, B., Dey, I., Haldar, U., Baneriee, Asok, Sevcik, Jozef, Solovicova, Adriana, Sekar, K., Sundaralingam, M., Betzel, Ch., Genov, N., Singh, T., Liang, Dong-cai, Jiang, Tao, Zhang, Ji-ping, Chang, Wen-rui, Jahnke, Wolfgang, Blommers, Marcel, Panchal, S., Hosur, R., Pillay, Bindu, Hosur, M., Mathur, Puniti, Srivatsun, S., Joshi, Ratan, Jaganathan, N., Chauhan, V., Atreya, H., Sahu, S., Chary, K., Govil, Girjesh, Adjadj, Elisabeth, Quinjou, Éric, Izadi-Pruneyre, Nadia, Blouquit, Yves, Mispelter, Joël, Heyd, Bernadette, Lerat, Guilhem, Milnard, Philippe, Desmadreil, Michel, Lin, Y., Rao, B., Raghunathan, Vidva, Chau, Mei, Rao, B., Pesais, Prashant, Srivastava, Sudha, Coutinho, Evans, Saran, Anil, Sapico, Leizl, Gesme, Jayson, Lijima, Herbert, Paxton, Raymond, Srikrishnan, Thamarapu, Grace, C., Nagenagowda, G., Lynn, A., Cowsik, Sudha, Sahu, Sarata, Chauhan, S., Bhattacharya, A., Chary, K., Govil, G., Kumar, Anil, Pellecchia, Maurizio, Zuiderweg, Erik, Kawano, Keiichi, Aizawa, Tomoyasu, Fujitani, Naoki, Hayakawa, Yoichi, Ohnishi, Atsushi, Ohkubo, Tadayasu, Kumaki, Yasuhiro, Hikichi, Kunio, Nitta, Katsutoshi, Rani Parvathy, V., Chary, K., Kini, R., Govil, G., Koshiba, Takumi, Kobashigawa, Yoshihiro, Yao, Min, Demura, Makoto, Nakagawa, Astushi, Tanaka, Isao, Kuwajima, Kunihiro, Nitta, Katsutoshi, Linge, Jens, Donoghue, Seán, Nilges, Michael, Chakshusmathi, G., Ratnaparkhi, Girish, Madhu, P., Varadarajan, R., Tetreau, C., Tourbez, M., Lavalette, D., Manno, M., Biagio, P., Martorana, V., Emanuele, A., Vaiana, S., Bulone, D., Palma-Vittorelli, M., Palma, M., Trivedi, V., Cheng, S., Chien, W., Yang, S., Francis, S., Chang, D., Batra, Renn, Geeves, Michael, Manstein, Dietmar, Trvlska, Joanna, Grochowski, Pawel, Geller, Maciej, Ginalski, K., Grochowski, P., Lesyng, B., Lavalette, P., Tetreau, C., Tourbez, M., Blouquit, Y., Roccatano, D., Amadei, A., Nola, A., Berendsen, H., Ho, Bosco, Curmi, P., Berry, H., Lairez, D., Pauthe, E., Pelta, J., Kothekar, V., Sahi, Shakti, Srinivasan, M., Singh, Anil, Madhusudnan, Kartha, Nandel, Fateh, Kaur, Harpreet, Nandel, Fateh, Singh, Balwinder, Jain, D., Feenstra, K., Berendsen, Herman, Tama, F., Sanejouand, Y., Go, N., Sharma, Deepak, Sharma, Sunita, Pasha, Santosh, Brahmachari, Samir, Viiavaraghavan, R., Makker, Jyoti, Dey, Sharmisllia, Kumar, S., Singh, T., Lakshmikanth, G., Krishnamoorthy, G., Mazhul, V., Zaitseva, E., Kierdaszuk, Borys, Widengren, J., Terry, B., Mets, Ü., Rigler, R., Swaminathan, R., Thamotharan, S., Yathindra, N., Shibata, Y., Chosrowjan, H., Mataga, N., Morisima, I., Chakraharty, Tania, Xiao, Ming, Cooke, Roger, Selvin, Paul, Branca, C., Faraone, A., Magazù, S., Maisano, G., Migliardo, P., Villari, V., Behere, Digambar, Deva, M., Brunori, M., Cutruzzolà, F., Gibson, Q., Savino, C., Travaglini-Allocatelli, C., Vallone, B., Prasad, Swati, Mazumdar, Shyamalava, Mitra, Samaresh, Soto, P., Fayad, R., Sukovataya, I., Tyulkova, N., Mamedov, Sh., Aktas, B., Canturk, M., Aksakal, B., Yilgin, R., Bogutska, K., Miroshnichenko, N., Chacko, S., DiSanto, M., Hypolite, J., Zheng, Y-M., Wein, A., Wojciechowski, M., Grycuk, T., Antosiewicz, J., Lesyng, B., Ceruso, Marc, Nola, Alfredo, Bandvopadhvay, Subhasis, Chatterjee, Bishnu, Choudhury, Devapriva, Thompson, Andrew, Stojanoff, Vivian, Pinkner, Jerome, Hultgren, Scott, Khight, Stefan, Flatters, Delphine, Goodfellow, Julia, Takazawatt, Fumi, Kanehisa, Minoru, Sasai, Masaki, Nakamura, Hironori, Sasai, Masaki, Han, Wang, Zheng, Yuan, Xin, Wang, Min, Pan, Bhakuni, Vlnod, Kulkarni, Sangeeta, Ahmad, Atta, Prakash, Koodathingal, Prajapati, Shashi, Surin, Alexey, Matsumoto, Tomoharu, Yang, Li, Nakagawa, Yuki, Kimura, Kazumoto, Amemiya, Yoshiyuki, Semisotnov, Gennady, Kihara, Hiroshi, Tayyab, Saad, Muzammil, Salman, Kumar, Yogesh, Kulkarni, Sangeeta, Prajapati, Shashi, Prakash, Koodathingal, Ahmad, Atta, Bhakuni, Vinod, Sundd, Monica, Kundu, Suman, Jagannadham, M., Kundu, Suman, Sundd, Monica, Jagannadham, Medicherla, Chandani, Bina, Dhar, Ruby, Sinha, Lalankumar, Warrier, Deepti, Mehrotra, Sonam, Khandelwal, Purnima, Seth, Subhendu, Hosur, R., Sasidhar, Y., Prabha, C., Gidwani, Arun, Ahmad, Atta, Kulkarni, Sangeeta, Madhusudan, K., Bhakuni, Vinod, Kinjo, Akira, Nishikawa, Ken, Chakravarty, Suvobrata, Varadarajan, Raghavan, Noyelle, K., Haezebrouck, P., Joniau, M., Dael, H., Dash, Sheffali, Jha, Indra, Bhat, Rajiv, Mohanty, Prasanna, Bandyopadhyay, A., Sonawat, H., Rao, Ch., Datta, Siddhartha, Rajaraman, K., Raman, B., Ramakrishna, T., Rao, Ch., Pande, A., Pande, J., Betts, S., Asherie, N., Ogun, O., King, J., Benedek, G., Sokolova, I., Tyulkova, N., Kalacheva, G., Sonoyama, Masashi, Yokoyama, Yasunori, Taira, Kunihiro, Mitaku, Shigeki, Nakazawal, Chicko, Sasakil, Takanori, Mukai, Yuri, Kamo, Naoki, Sonoyama, Masashi, Mitaku, Shigeki, Dalal, Seema, Regan, Lynne, Mukai, Yuri, Kamo, Naoki, Mituku, Shigeki, Roychoudhury, Mihir, Kumar, Devesh, Lőrinczv, Dénes, Könczöl, Franciska, Farkas, László, Belagyi, Joseph, Schick, Christoph, Thomson, Christy, Ananthanarayanan, Vettai, Alirzayeva, E., Baba-Zade, S., Gromiha, M., Oobatake, M., Kono, H., An, J., Uedaira, H., Sarai, A., Takano, Kazufumi, Yamagata, Yuriko, Yutani, Katsuhide, Jas, Gouri, Muñoz, Victor, Hofrichter, James, Eaton, William, Penoyar, Jonathan, Srikrishnan, Thamarapu, Lo Verde, Philip, Kardos, J., Bódi, Á., Venekei, I., Závodszky, P., Gráf, L., Szilágyi, András, Závodszky, Péter, Allan, R., Walshaw, J., Woolfson, D., Funahashi, Jun, Takano, Kazufumi, Yamagata, Yuriko, Yutani, Katsuhide, Gupta, Savan, Mazumdar, Shyamalava, Di Nola, A., Mangoni, M., Roccatano, P., Ramachandraiah, Gosu, Chandra, Nagasuma, Kothekar, V., Srinivasan, M., Sahi, Shakti, Chakraborty, S., Bhattacharya, S., Bera, A., Ghosh, S., Pal, A., Haldar, U., Mukhopadhyay, B., Baneriee, Asok, Ciani, Barbara, Woolfson, Derek, Nair, Usha, Kaur, Kanwal, Salunke, Dinakar, Swaminathan, Chittoor, Surolia, Avadhesha, Rigler, R., Pramanik, A., Jonasson, P., Kratz, G., Jansson, O., Nygren, P., Ståhl, S., Ekberg, K., Johansson, B., Uhlén, S., Uhlén, M., Jörnvall, H., Wahren, J., Welfle, Karin, Misselwitz, Rolf, Höhne, Wolfgang, Welfle, Heinz, Mazhul, V., Zaitseva, E., Mitskevich, L., Fedurkina, N., Kurganov, B., Jarori, Gotam, Maity, Haripada, Guharay, J., Sengupta, B., Sengupta, P., Sridevi, K., Kasturi, S., Gupta, S., Agarwal, Gunjan, Kwong, Suzanne, Briehl, Robin, Ismailova, O., N, Tyulkova, Hariharan, C., Pines, D., Pines, E., Zamai, M., Cohen-Luria, R., Yayon, A., Parola, A., Padya, M., Spooner, G., Woolfeon, D., Bakshi, Panchan, Sharma, Deepak, Sharma, Sunita, Bharadwaj, D., Pasha, Santosh, Sharma, U., Srivastava, N., Barthwal, R., Jagannathan, N., Matsuda, Keiko, Nishioka, Takaaki, Go, Nobuhiro, Aita, T., Urata, S., Husimi, Y., Majumder, Mainak, Chatterjee, Bishnu, Abrescia, Nicola, Malinina, Lucy, Subirana, Juan, Aymami, Juan, Eritxa, Ramón, Coll, Miquel, Premraj, B., Yathindra, N., Thenmalarchelvi, R., Yathindra, N., Kumar, P., Gautham, N., Kan, Lou, Ming-Hou, Lin, Shwu-Bin, Sana, Tapas, Roy, Kanal, Bruant, N., Flatters, D., Lavery, R., Genest, D., Rons, Remo, Sklenar, Heinz, Lavery, Richard, Kundu, Sudip, Bhattacharyya, Dhananjay, Bandyopadhyay, Debashree, Thakur, Ashoke, Majumdar, Rabi, Barceló, F., Portugal, J., Ramanathan, Sunita, Chary, K., Rao, B., Gliosli, Mahua, Kumar, N., Varshney, Umesh, Chary, K., Pataskar, Shashank, Brahmachari, Samir, Sarojini, R., Selvasekarapandian, S., Kolandaivel, P., Sukumar, S., Selvasekarapandian, S., Sarojini, R., Kolmdaivel, P., Sukumar, S., Sarojini, R., Selvasekarapandian, S., Kolandaivel, P., Sukumar, S., Selvasekarapandian, S., Sarojini, R., Kolandaivel, P., Sukumar, S., Maiti, Motilal, Sen, Anjana, Das, Suman, Terra, Elisa, Suraci, Chiara, Diviacco, Silvia, Quadrifoglio, Franco, Xodo, Luigi, Bandyopadhyay, Debashree, Bhattacharyya, Dhananjay, Kundu, Sudip, Thakur, Ashoke, Das, Suman, Ray, Arghya, Maiti, Motilal, Karthikeyan, G., Chary, Kandala, Rao, Basuthkar, Mujeeb, Anwer, James, Thomas, Kasyanenko, N., Haya, E., Bogdanov, A., Zanina, A., Bugs, M., Cornélio, M., Srikrishnan, Thamarapu, Tolstorukov, M., Sanval, Nitish, Tiwari, S., Tiwari, S., Sanyal, Nitish, Choudhury, Mihir, Kumar, Devesh, Sanyal, Nitish, Patel, P., Bhavesh, Neel, Hosur, R., Gabrielian, Anna, Wennmalm, Stefan, Edman, Lars, Rigler, Rudolf, Constantinescu, B., Radu, L., Radulcscu, I., Gazdaru, D., Wärmländer, Sebastian, Leijon, Mikael, Aoki, Setsuyuki, Kondo, Takao, Ishiura, Masahiro, Pashinskaya, V., Kosevich, M., Shelkovsky, V., Blagoy, Yu., Wang, Ji-hua, Malathi, R., Chandrasekhar, K., Premraj, B., Patel, P., Kandimalla, E., Agrawal, S., Hosur, R., Yathindra, N., Rastogi, V., Palafox, M., Singh, Chatar, Beniaminov, A., Bondarenko, S., Zdobnov, E., Minyat, E., Ulyanov, N., Ivanov, V., Singh, J., Sonawane, Kailas, Grosjean, Henri, Tewari, Ravindra, Sonavane, Uddhavesh, Morin, Annie, Grosjean, Henri, Tewari, Ravindra, Doherty, Elizabeth, Doudna, Jennifer, Tochio, H., Sato, S., Matsuo, H., Shirakawa, M., Kyogoku, Y., Javaram, B., Dixit, Surjit, Shukla, Piyush, Kalra, Parul, Das, Achintya, McConnell, Kevin, Beveridge, David, Sawyer, W., Chan, R., Eccelston, J., Yan, Yuling, Davidson, B., Ray, Arghya, Tuite, Eimer, Norden, Bengt, Nielsen, Peter, Takahashi, Masayuki, Ghosh, Anirban, Bansal, Manju, Christ, Frauke, Thole, Hubert, Wende, Wolfgang, Pingoud, Alfred, Pingoud, Vera, Luthra, Pratibha, Chandra, Ramesh, Sen, Ranjan, King, Rodney, Weisberg, Robert, Larsen, Olaf, Berends, Jos, Heus, Hans, Hilbers, Cornelis, Stokkum, Ivo, Gobets, Bas, Grondelle, Rienk, Amerongen, Herbert, Sngrvan, HE., Babayan, Yu., Khudaverdian, N., Kono, H., Gromiha, M., Pichierri, F., Aida, M., Prabakaran, P., Sayano, K., An, J., Uedaira, H., Sarai, A., Serva, Saulius, Merkienė, Eglė, Vilkaitis, Giedrius, Weinhold, Elmar, Klimašauskas, Saulius, Marsich, Eleonora, Bandiera, Antonella, Xodo, Luigi, Manzini, Giorgio, Potikyan, G., Arakelyan, V., Babayan, Yu., Ninaber, Alex, Goodfellow, Julia, Ito, Yoichiro, Ohta, Shigeru, Husimi, Yuzuru, Usukura, J., Tagami, H., Aiba, H., Suarez, Mougli, Nunes, Elia, Keszenman, Deborah, Candreva, E., Nunes, Elia, Thyberg, Per, Földes-Papp, Zeno, Rigler, Rudolf, Joshi, Amita, Rao, Basuthkar, Singh, Dinesh, Rajeswari, M., Ira, Krishnamoorthy, G., Pregetter, M., Prassl, R., Schwarzenbacher, R., Amenitsch, H., Chapman, J., Laggner, P., Pandev, B., Mishra, K., Pohl, E., Sun, J., Agapov, I., Tonevitsky, A., Pohl, P., Dennison, S., Guharay, J., Sengupta, P., Gorbeako, G., Dynbko, T., Pappavee, N., Mishra, A., Manuel, Prieto, Rodrigo, Almeida, Luis, Loura, Gendel, L., Przestalski, S., Kuczera, J., Kleszczyńska, H., Kral, T., Chernitsky, E., Senkovich, O., Rosin, V., Allakhverdieva, Y., Papageorgiou, G., Gasanov, R., Apetrei, Calin, Savopol, Tudor, Balea, Marius, Cucu, D., Mihailescu, D., Ramanathan, K., Bačić, Goran, Sajot, Nicolas, Garnier, Norbert, Crouzy, Serge, Genest, Monique, Várkonyi, Z., Zsiros, O., Farkas, T., Combos, Z., Cribier, Sophie, Fraceto, I., Schreier, S., Spisni, A., Paula, F., Sevšek, F., Gomišček, G., Arrigler, V., Svetina, S., Žekš, B., Nomura, Fumimasa, Nagata, Miki, Takiguchi, Kingo, Hotani, Hirokazu, Panicker, Lata, Parvathanathan, P., Ishino, A., Saitoh, A., Hotani, H., Takiguchi, K., Afonin, S., Takahashi, A., Nakato, Y., Takizawa, T., Marathe, Dipti, Mishra, K., Jørgensen, Kent, Rawat, Satinder, Nair, Usha, Rukmini, R., Chattopadhyay, Amitabha, Šentiurc, M., Štrancar, J., Stolič, Z., Filipin, K., Pečar, S., Chattopadhyay, Amitabha, Biswas, S., Rukmini, R., Sana, Satyen, Samanta, Anunay, Kinoshita, Koji, Yamazaki, Masahito, Ohba, Tetsuhiko, Kiuchi, Tai, Yoshitoshi, Kamakura, Goto, Akira, Kumeta, Takaaki, Ohki, Kazuo, Sugar, I., Thompson, T., Thompson, K., Biltonen, R., Suezaki, Y., Ichinose, H., Takiguchi, K., Hotani, H., Akivama, M., Matuoka, S., Tsuchihashi, K., Gasa, S., Mattjus, P., Molotkovsky, J., Pike, H., Brown, R., Arora, Ashish, Kleinschmidt, Jörg, Tamm, Lukas, Luneva, O., Gendel, L., Kruglyakova, K., Fedin, V., Kuptsoya, O., Borst, J., Visser, N., Visser, A., Dyubko, T., Ogihara, Toshihiko, Mishima, Kiyoshi, Shvaleva, A., Radenović, N., Minić, P., Jeremić, M., Radenović, Č., Aripov, T., Tadjibaeva, E., Vagina, O., Zamaraeva, M., Salakhutdinov, B., Cole, A., Poppofl, M., Naylor, C., Titball, R., Basak, A., Eaton, J., Naylor, C., Justin, N., Moss, D., Titball, R., Basak, A., Nomura, F., Nagata, M., Ishjkawa, S., Takiguchi, K., Takahashi, S., Hotani, H., Obuchi, Kaoru, Staudegger, Erich, Kriechbaum, Manfred, Lehrer, Robert, Waring, Alan, Lohner, Karl, Gangl, Susanne, Mayer, Bernd, Köhler, Gottfried, Shobini, J., Mishra, A., Guttenberg, Z., Lortz, B., Hu, B., Sackmann, E., Kozlova, N., Lukyanenko, L., Antonovich, A., Slobozhanina, E., Chernitsky, E., Krylov, Andrey, Antonenko, Yuri, Kotova, Elena, Yaroslavov, Alexander, Ghosh, Subhendu, Bera, Amal, Das, Sudipto, Urbánková, Eva, Jelokhani-Niaraki, Masood, Freeman, Karl, Jezek, Petr, Usmanov, P., Ongarbaev, A., Tonkikh, A., Pohl, Peter, Saparov, Sapar, Harikumar, P., Reeves, J., Rao, S., Sikdar, S., Ghatpande, A., Rao, S., Sikdar, S., Corsso, C., Campos de Carvalho, A., Varanda, W., ElHamel, C., Dé, E., Saint, N., Molle, G., Varshney, Anurae, Mathew, M., Loots, E., Isacoff, E., Kasai, Michiki, Yamaguchi, Naohiro, Ghosh, Paramita, Ghosh, Subhendu, Tigyi, Joseph, Tigyi, Gabor, Liliom, Karoly, Miledi, Ricardo, Djurisic, Maja, Andjus, Pavle, Shrivastava, Indira, Sansom, M., Barrias, C., Oliveira, P., Mauricio, A., Rebelo da Costa, A., Lopes, I., Barrias, C., Fedorovich, S., Chubanov, V., Sholukh, M., Konev, S., Fedirko, N., Manko, V., Klevets, M., Shvinka, N., Prabhananda, B., Kombrabail, Mamata, Aravamudhan, S., Venegas-Cotero, Berenice, Blake, Ivan, Zhang, Zhi-hong, Hu, Xiao-jian, Zhou, Han-qing, Cheng, Wei-ying, Feng, Hang-fang, Dubitsky, L., Vovkanvch, L., Zalyvsky, I., Savio-Galimberti, E., Bonazzola, P., Ponce-Homos, J., Parisi, Mario, Capurro, Claudia, Toriano, Roxana, Ready, Laxma, Jones, Larry, Thomas, David, Tashmukhamedov, B., Sagdullaev, B., Usmanov, P., Mauricio, A., Heitzmann, D., Warth, R., Bleich, M., Greger, R., Ferreira, K., Ferreira, H., Zagoory, Orna, Alfahel, Essa, Parola, Abraham, Priel, Zvi, Hama-Inaba, H., Wang, R., Choi, K., Nakajima, T., Haginoya, K., Mori, M., Ohyama, H., Yukawa, O., Hayata, I., Joshi, Nanda, Kannurpatti, Sridhar, Joshi, Preeti, Sinha, Mau, Shen, Xun, Hu, Tianhui, Bei, Ling, Knetsch, Menno, Schäfers, Nicole, Manstein, Dietmar, Sandblom, John, Galvanovskis, Juris, Pologea-Moraru, Roxana, Kovacs, Eugenia, Savopol, Tudor, Dinu, Alexandra, Sanghvi, S., Mishra, K., Jazbinšek, V., Thiel, G., Müller, W., Wübeller, G., Tronteli, Z., Fajmut, Leš, Marhl, Marko, Brumen, Milan, Volotovski, I., Sokolovski, S., Knight, M., Vasil’ev, Alexei, Chalyi, Alexander, Sharma, P., Steinbach, P., Sharma, M., Amin, N., Barchir, J., Albers, R., Pant, H., Balasubramanyam, M., Condrescu, M., Reeves, J., Gardner, J., Monajembashi, Shamci, Pilarczyk, Gotz, Greulich, K., Kovacs, Eugenia, El-Refaei, F., Talaat, M., El-Awadi, A., Ali, F., Tahradník, Ivan, Pavelková, Jana, Zahradniková, Alexandra, Zhorov, Boris, Ananthanaravanan, Vettai, Michailov, M., Neu, E., Seidenbusch, W., Gornik, E., Martin, D., Welscher, U., Weiss, D., Pattnaik, B., Jellali, A., Forster, V., Hicks, D., Sahel, J., Dreyfus, H., Picaud, S., Wang, Hong-Wei, Sui, Sen-fang, Luther, Pradeep, Barry, John, Morris, Ed, Squire, John, Sundari, C., Balasubramanian, D., Veluraia, K., Christlet, T., Suresh, M., Berry, H., Pelta, J., Lairez, D., Laretta-Garde, V., Krilov, Dubravka, Stojanović, Nataša, Herak, Janko, Jasuja, Ravi, Ivanova, Maria, Mirchev, Rossen, Ferrone, Frank, Stopar, David, Spruijt, Ruud, Wolfs, Cor, Hemminga, Marcus, Arcovito, G., Spirito, M., Sui, Sen-fang, Wang, Hong-Wei, Agrawal, Rajendra, Heagle, Amy, Penczek, Pawel, Grassucci, Robert, Frank, Joachim, Sharma, Manjuli, Jeyakumar, Loice, Fleischer, Sidney, Wagenknecht, Terence, Knupp, Carlo, Munro, Peter, Luther, Pradeep, Ezra, Eric, Squire, John, Ichihara, Koji, Kitazawa, Hidefumi, Iguchi, Yusuke, Hotani, Hirokazu, Itoh, Tomohiko, Pifat, Greta, Kveder, Marina, Pečar, Slavko, Schara, Milan, Nair, Deepak, Singh, Kavita, Rao, Kanury, Salunke, Dinakar, Kaur, Kanwaljeet, Jain, Deepti, Sundaravadivel, B., Goel, Manisha, Salunke, D., Kovalenko, E., Semenkova, G., Cherenkevich, S., Lakshmanan, T., Sriram, D., Srinivasan, S., Loganathan, D., Ramalingam, T., Lebrón, J., Bjorkman, P., Singh, A., Gayatri, T., Jain, Deepti, Kaur, Kanwaljeet, Sundaravadivel, B., Salunke, Dinakar, Caffarena, Ernesto, Grigera, J., Bisch, Paulo, Kiessling, V., Fromherz, P., Rao, K., Gaikwad, S., Khan, M., Suresh, C., Kaliannan, P., Gromiha, M., Elanthiraiyan, M., Chadha, K., Payne, J., Ambrus, J., Nair, M., Nair, Madhavan, Mahajan, S., Chadha, K., Hewitt, R., Schwartz, S., Bourguignon, J., Faure, M., Cohen-Addad, C., Neuburger, M., Ober, R., Sieker, L., Macherel, D., Douce, R., Gurumurthy, D., Velmurugan, S., Lobo, Z., Srivastava, Sudha, Phadke, Ratna, Govil, Girjesh, Desai, Prashant, Coutinho, Evans, Guseinova, I., Suleimanov, S., Zulfugarov, I., Novruzova, S., Aliev, J., Ismayilov, M., Savchenko, T., Alieva, D., Ilík, Petr, Kouřil, Roman, Bartošková, Hana, Nauš, Jan, Gaikwad, Jvoti, Thomas, Sarah, Vidyasagar, P., Garab, G., Simidjiev, I., Rajagopal, S., Várkonyi, Zs., Stoylova, S., Cseh, Z., Papp, E., Mustárdy, L., Holzenburg, A., Bruder, R., Genick, U., Woo, T., Millar, D., Gerwert, K., Getzoff, E., Jávorfí, Tamás, Garab, Győző, Naqvi, K., Kalimullah, Md., Gaikwad, Jyoti, Thomas, Sarah, Semwal, Manoj, Vidyasagar, P., Kouril, Roman, Ilik, Petr, Naus, Man, Pomozi, István, Horváth, Gábor, Wehner, Rüdiger, Bernard, Gary, Damjanović, Ana, Ritz, Thorsten, Schulten, Klaus, Jushuo, Wang, Jixiu, Shan, Yandao, Gong, Tingyun, Kuang, Nanming, Zhao, Freiberg, Arvi, Timpmann, Kõu, Ruus, Rein, Woodbury, Neal, Nemtseva, E., Kudryasheva, N., Sizykh, A., Shikhov, V., Nesterenko, T., Tikhomirov, A., Forti, Giorgio, Finazzi, Giovanni, Furia, Alberto, Barbagallo, Romina, Forti, Giorgio, Iskenderova, S., Agalarov, R., Gasanov, R., Osamu, Miyashita, Nobuhiro, G., Soni, R., Ramrakhiani, M., Yagi, Hiromasa, Tozawa, Kacko, Sekino, Nobuaki, Iwabuchi, Tomoyuki, Yoshida, Masasuke, Akutsu, Hideo, Avetisyan, A., Kaulen, A., Skulachev, V., Feniouk, B., Breyton, Cécile, Kühlbrandt, Werner, Assarsson, Maria, Gräslund, Astrid, Zsiros, O., Horváth, G., Mustárdy, L., Libisch, B., Gombos, Z., Budagovskaya, N., Kudryasheva, N., Harada, Erisa, Fukuoka, Yuki, Ohmura, Tomoaki, Fukunishi, Arima, Kawai, Gota, Watanabe, Kimitsuna, Akutsu, Hideo, Derganc, Jure, Božič, Bojan, Svetina, Saša, Žekš, Boštjan, Hoh, J., Li, Z., Rossmanith, G., Beer, E., Treijtel, B., Frederix, P., Blangè, T., Hénon, S., Galtet, F., Laurent, V., Planus, E., Isabey, D., Rath, L., Dash, P., Raval, M., Ramakrishnan, C., Balaram, R., Randic, Milan, Basak, Subhash, Vracko, Marjan, Nandy, Ashesh, Amic, Dragan, Beslo, Drago, Nikolic, Sonja, Trinajstic, Nenad, Walahaw, J., Woolfson, D., Lensink, Marc, Berendsen, Herman, Reddy, Boojala, Shindylov, Ilya, Bourne, Philip, Donnamaria, M., Xammar Oro, J., Grigera, J., Neagu, Monica, Neagu, Adrian, Praprotnik, Matej, Janežič, Dušanka, Mark, Pekka, Nilsson, Lennart, Martorana, V., Bulone, D., Fata, L., Manno, M., Biagio, P., Dardenne, Laurent, Werneck, Araken, Neto, Marçal, Bisch, Paulo, Kannan, N., Vishveshwara, S., Christlet, T., Veluraja, K., Grunwald, Gregory, Balaban, Alexandra, Basak, Kanika, Gute, Brian, Mills, Denise, Opitz, David, Balasubramanian, Krishnan, Mihalas, G., Lungeanu, Diana, Macovievici, G., Gruia, Raluca, Neagu, Monica, Cortez-Maghelly, C., Dalcin, B., Passos, E., Blesic, S., Ljubisavljevic, M., Milosevic, S., Stratimirovic, D., Bachhawat, Nandita, Mande, Shekhar, Ghosh, S., Nandy, A., Saito, Ayumu, Nishigaki, Koichi, Nishigaki, Koichi, Naimuddin, Mohammed, Mitaku, Shigeki, Hirokawa, Takatsugu, Ono, Mitsuo, Takaesu, Hirotomo, El Gohary, M., Ahmed, Abdalla, Eissa, A., Nakashima, Hiroshi, Nishikawa, Ken, Neagu, Monica, Neagu, Adrian, Raghava, G., Kurgalvuk, N., Goryn, O., Gerstman, Bernard, Gritsenko, E., Remmel, N., Maznyak, O., Kratasyuk, V., Esimbekova, E., Kratasyuk, V., Tchitchkan, D., Koulchitsky, S., Tikhonov, A., German, A., Pesotskaya, Y., Pashkevich, S., Pletnev, S., Kulchitsky, V., Duvvuri, Umamaheswar, Charagundla, Sridhar, Rizi, Rahim, Leigh, John, Reddy, Ravinder, Kumar, Mahesh, Coshic, O., Julka, P., Rath, O., Jagannathan, NR., Iliescu, Karina, Sajin, Maria, Moisoi, Nicolcta, Petcu, Ileana, Kuzmenko, A., Morozova, R., Nikolenko, I., Donchenko, G., Rahman, M., Ahmed, M., Naimuddin, Mohammed, Watanabe, Takehiro, Nishigaki, Koichi, Rubin, Y., Gilboa, H., Sharony, R., Ammar, R., Uretzky, G., Khubchandani, M., Mallick, H., Kumar, V., Jagannathan, N., Borthakur, Arijitt, Shapiro, Erik, Begum, M., Degaonkar, Mahaveer, Govindasamy, S., Dimitrov, Ivan, Kumosani, T., Bild, W., Stefanescu, I., Titescu, G., Iliescu, R., Lupusoru, C., Nastasa, V., Haulica, I., Khetawat, Gopal, Faraday, N., Nealen, M., Noga, S., Bray, P., Ananieva, T., Lycholat, E., Pashinskaya, V., Kosevich, MV., Stepanyan, S., Lycholat, E., Ananieva, T., Antonyuk, S., Khachatryan, R., Arakelian, H., Kumar, A., Ayrapetyan, S., Mkheyan, V., Agadjanyan, S., Khachatryan, A., Rajan, S., Kabaleeswaran, V., Malathi, R., Gopalakrishnan, Geetha, Govindachari, T., Ramrakhiani, Meera, Lowe, Phillip, Badley, Andrew, Cullen, David, Hermel, H., Schmahl, W., Möhwald, H., Singh, Anil, Majumdar, Nirmalya, Das, Joydip, Madhusudnan, Kartha, Dér, András, Kelemen, Loránd, Oroszi, László, Hámori, András, Ramsden, Jeremy, Ormos, Pál, Savitri, D., Mitra, Chanchal, Yanagida, Toshio, Esaki, Seiji, Kimura, Yuji, Nishida, Tomoyuki, Sowa, Yosiyuki, Radu, M., Koltover, V., Estrin, Ya., Kasumova, L., Bubnov, V., Laukhina, E., Dotta, Rajiv, Degaonkar, M., Raghunathan, P., Jayasundar, Rama, Jagannathan, N., Novák, Pavel, Marko, Milan, Zahradník, Ivan, Hirata, Hiroaki, Miyata, Hidetake, Ohki, Kazuo, Balaji, J., Sengupta, P., Maiti, S., Gonsalves, M., Barker, A., Macpherson, J., O’Hare, D., Winlove, C., Unwin, P., Sengupta, P., Phillip, R., Banerjee, S., Kumar, G., Maiti, S., Nagayaka, K., Danev, R., Sugitani, S., Murata, K., Gősch, Michael, Blom, H., Thyberg, P., Földes-Papp, Z., Björk, G., Holm, J., Heino, T., Rigler, Rudolf, Yokochi, Masashi, Inagaki, Fuyuhiko, Kusunoki, Masami, Matthews, E., Pines, J., Chukova, Yu., Koltover, Vitaly, Bansal, Geetanjali, Singh, Uma, Bansal, M., Nakata, Kotoko, Nakano, Tastuya, Kaminuma, Tsuguchika, Kang, B., Singh, U., Kirn, Bonn, Potocnik, Neja, Stare, Vito, Shukla, Latal, Natarajan, V., Devasagayam, T., Sastry, M., Kesavan, P., Sayfutdinov, R., Adamovich, V., Rogozin, D., Degermendzhy, A., Khetrapal, C., Ramanathan, K., Gowda, G., Ghimire, Kedar, Masaru, Ishida, Fujita, H., Ishiwata, S., Kishimoto, Y., Kawahara, S., Suzuki, M., Mori, H., Mishina, M., Kirino, Y., Ohshima, H., Dukhin, A., Shilov, V., Goetz, P., Sengupta, B., Guharay, J., Sengupta, P., and Mishra, R.

Published
1999
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Author

Kurokawa, Masaru, Sakata, Kiriko, Shinohara, Shinobu, Kinjo, Akira, Kurokawa, Masaru, Sakata, Kiriko, Shinohara, Shinobu, and Kinjo, Akira

Abstract

This study examined sex effects in like-dislike rating of male and female behaviors or traits. Additionally, the effect of rater's attitude toward women was examined. Five hundred and four male and four hundred and sixty female subjects (include 411 undergraduates) rated each 33 items which described a man/woman whose behavior/trait was masculine, feminine, or neutral. In relation to certain items, there were sex differences both of raters and rated persons. For example, the decisive man was more liked than the woman, who has same character. However, the male hard drinker was liked slightly more than the female hard drinker by male raters but not by female raters. The interactions of target person's sex and rater's sex was obtained on certain items related to the leadership behavior. Men more liked the 'bossy (Oyabun-hada)' male but not so 'bossy' female. Women liked the 'bossy' female at the same degree to the male. The effect of rater's attitude toward women was rather slight.

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Author

Kinjo, Akira, Kurokawa, Masaru, Sato, Seiichi, Kinjo, Akira, Kurokawa, Masaru, and Sato, Seiichi

Abstract

The effects of informations about supervisory behavior and group productivity on evaluation of leaders were investigated. After read the description of the group productivity, leader's gender and supervisory behaviors of one specific group, 268 male and 139 female undergraduate students who were respectively assigned to one of 8 experimental conditions -- group productivity (High/Low) X leadership type (P/M) X leader's gender -- evaluated the leader's behavior using LBDQ, and also his/her personality and aptitude. Evaluations of leadership behavior were analyzed into initiating structure, consideration, and production emphasis. The results showed strong influences of productivity information on rating scores on the first two factors but production emphasis factor. As to these results, the implicit leadership theory was discussed.

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Author

Kinjo, Akira, Kurokawa, Masaru, Kinjo, Akira, and Kurokawa, Masaru

Abstract

This study investigated the effects of the "Orientation Camp" upon the freshmen's adjustments and satisfactions to their new college-lives. Two-hundred and sixty-seven freshmen who participated in the camp and 148 freshmen who didn't participate in it were administered questionnaires two or three times. Their scores of adjustment and satisfaction to their new lives were examined by 2 X 2 X 2 (participant/not participant of the camp, the choice order of Hiroshima University, the first/not the first and before/after the Camp) ANOVA. The scores of adjustment and satisfaction after the camp decreased as compared with before the camp. However, the scores of adjustment of the freshmen who participated the camp and whose choices were the first were higher than the scores of the other groups both before and after the camp. The scores of satisfaction of the freshmen who didn't participate and whose choices were the first decreased markedly. The results suggest that the Orientation Camp was effective only for the freshmen who willingly entered Hiroshima University to adjust to their new college-lives but not for those who reluctantly entered.

137. Recoverable one-dimensional encoding of three-dimensional protein structures

Author

Kinjo, Akira R. and Nishikawa, Ken

Abstract

Summary: One-dimensional (1D) structures of proteins such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it is still not clear whether a given set of 1D structures contains sufficient information for recovering the underlying 3D structure. Here we show that the 3D structure of a protein can be recovered from a set of three types of 1D structures, namely, secondary structure, contact number and residue-wise contact order which is introduced here for the first time. Using simulated annealing molecular dynamics simulations, the structures satisfying the given native 1D structural restraints were sought for 16 proteins of various structural classes and of sizes ranging from 56 to 146 residues. By selecting the structures best satisfying the restraints, all the proteins showed a coordinate RMS deviation of <4 Å from the native structure, and, for most of them, the deviation was even <2 Å. The present result opens a new possibility to protein structure prediction and our understanding of the sequence–structure relationship. Contact: akinjo@genes.nig.ac.jp

Published
2005
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138. Plasticity-led and mutation-led evolutions are different modes of the same developmental gene regulatory network.

Author

Ng ETH and Kinjo AR

Subjects
Mutation genetics, Phenotype, Gene Regulatory Networks genetics, Biological Evolution
Abstract

The standard theory of evolution proposes that mutations cause heritable variations, which are naturally selected, leading to evolution. However, this mutation-led evolution (MLE) is being questioned by an alternative theory called plasticity-led evolution (PLE). PLE suggests that an environmental change induces adaptive phenotypes, which are later genetically accommodated. According to PLE, developmental systems should be able to respond to environmental changes adaptively. However, developmental systems are known to be robust against environmental and mutational perturbations. Thus, we expect a transition from a robust state to a plastic one. To test this hypothesis, we constructed a gene regulatory network (GRN) model that integrates developmental processes, hierarchical regulation, and environmental cues. We then simulated its evolution over different magnitudes of environmental changes. Our findings indicate that this GRN model exhibits PLE under large environmental changes and MLE under small environmental changes. Furthermore, we observed that the GRN model is susceptible to environmental or genetic fluctuations under large environmental changes but is robust under small environmental changes. This indicates a breakdown of robustness due to large environmental changes. Before the breakdown of robustness, the distribution of phenotypes is biased and aligned to the environmental changes, which would facilitate rapid adaptation should a large environmental change occur. These observations suggest that the evolutionary transition from mutation-led to plasticity-led evolution is due to a developmental transition from robust to susceptible regimes over increasing magnitudes of environmental change. Thus, the GRN model can reconcile these conflicting theories of evolution., Competing Interests: The authors declare there are no competing interests., (©2024 Ng and Kinjo.)

Published
2024
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139. Plasticity-led evolution as an intrinsic property of developmental gene regulatory networks.

Author

Ng ETH and Kinjo AR

Subjects
Gene Regulatory Networks, Phenotype, Mutation, Adaptation, Physiological genetics, Biological Evolution
Abstract

The modern evolutionary synthesis seemingly fails to explain how a population can survive a large environmental change: the pre-existence of heritable variants adapted to the novel environment is too opportunistic, whereas the search for new adaptive mutations after the environmental change is so slow that the population may go extinct. Plasticity-led evolution, the initial environmental induction of a novel adaptive phenotype followed by genetic accommodation, has been proposed to solve this problem. However, the mechanism enabling plasticity-led evolution remains unclear. Here, we present computational models that exhibit behaviors compatible with plasticity-led evolution by extending the Wagner model of gene regulatory networks. The models show adaptive plastic response and the uncovering of cryptic mutations under large environmental changes, followed by genetic accommodation. Moreover, these behaviors are consistently observed over distinct novel environments. We further show that environmental cues, developmental processes, and hierarchical regulation cooperatively amplify the above behaviors and accelerate evolution. These observations suggest plasticity-led evolution is a universal property of complex developmental systems independent of particular mutations., (© 2023. The Author(s).)

Published
2023
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140. Mechanism of evolution by genetic assimilation : Equivalence and independence of genetic mutation and epigenetic modulation in phenotypic expression.

Author

Nishikawa K and Kinjo AR

Abstract

Conrad H. Waddington discovered the phenomenon of genetic assimilation through a series of experiments on fruit flies. In those experiments, artificially exerted environmental stress induced plastic phenotypic changes in the fruit flies, but after some generations, the same phenotypic variant started to appear without the environmental stress. Both the initial state (where the phenotypic changes were environmentally induced and plastic) and the final state (where the phenotypic changes were genetically fixed and constitutive) are experimental facts. However, it remains unclear how the environmentally induced phenotypic change in the first generation becomes genetically fixed in the central process of genetic assimilation itself. We have argued that the key to understanding the mechanism of genetic assimilation lies in epigenetics, and proposed the "cooperative model" in which the evolutionary process depends on both genetic and epigenetic factors. Evolutionary simulations based on the cooperative model reproduced the process of genetic assimilation. Detailed analysis of the trajectories has revealed genetic assimilation is a process in which epigenetically induced phenotypic changes are incrementally and statistically replaced with multiple minor genetic mutations through natural selection. In this scenario, epigenetic and genetic changes may be considered as mutually independent but equivalent in terms of their effects on phenotypic changes. This finding rejects the common (and confused) hypothesis that epigenetically induced phenotypic changes depend on genetic mutations. Furthermore, we argue that transgenerational epigenetic inheritance is not required for evolution by genetic assimilation.

Published
2018
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141. A new look at an old view of denaturant induced protein unfolding.

Author

Hall D, Kinjo AR, and Goto Y

Subjects
Models, Molecular, Protein Conformation drug effects, Protein Denaturation drug effects, Protein Unfolding drug effects, Proteins chemistry
Abstract

We re-examine a site-binding approach independently proposed by Schellman (Schellman, J.A. (1958) Compt. rend. Lab. Carlsberg Ser. Chim. 30, 439-449) and Aune and Tanford (Aune, K.C. and Tanford, D. (1969) Biochemistry, 8, 4586-4590) for explicitly including the denaturant concentration within the protein unfolding equilibrium. We extend and formalize the approach through development of a multi-dimensional analytical model in which the folding reaction coordinate is defined by the number of denaturant molecules bound to sites located on either the initially folded, or unfolded, states of the protein. We use the developed method to re-examine the mechanistic determinants underlying the sigmoidal shape of the unfolding transition. A natural feature of our method is that it presents a landscape picture of the denaturant induced protein unfolding reaction., (Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.)

Published
2018
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142. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.

Author

Kinjo AR, Bekker GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, and Nakamura H

Subjects
Japan, Models, Molecular, Protein Conformation, Structure-Activity Relationship, User-Computer Interface, Web Browser, Databases, Protein, Software
Abstract

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2017
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143. A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions.

Author

Kinjo AR

Abstract

The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences. The model parameters for short-range and long-range interactions were determined by a self-consistent condition and by a Gaussian approximation, respectively. Using this model with and without long-range interactions, I analyzed the globin and V-set domains by increasing the "temperature" and by "mutating" a site. The correlations between residue conservation and various measures of the system's stability indicate that the long-range interactions make the conservation pattern more specific to the structure, and increasingly stabilize better conserved residues.

Published
2016
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144. Liquid-theory analogy of direct-coupling analysis of multiple-sequence alignment and its implications for protein structure prediction.

Author

Kinjo AR

Abstract

The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract "direct" correlations between distant sites that are latent in "indirect" correlations observed in a protein multiple-sequence alignment. I show that the direct correlation can be obtained by using a formulation analogous to the Ornstein-Zernike integral equation in liquid theory. This formulation intuitively illustrates how the indirect or apparent correlation arises from an infinite series of direct correlations, and provides interesting insights into protein structure prediction.

Published
2015
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145. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Author

Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, and Takagi T

Abstract

Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research., Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization., Conclusion: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

Published
2013
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146. Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Author

Kinjo AR and Nakamura H

Subjects
Computational Biology methods, Databases, Protein, Internet, Nucleic Acids metabolism, Protein Binding, Protein Folding, Software, Amino Acid Motifs, Ligands, Nucleic Acids chemistry, Nucleotide Motifs, Protein Interaction Domains and Motifs, Proteins chemistry
Abstract

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

Published
2013
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147. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

Author

Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, and Takagi T

Abstract

Background: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009., Results: Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs., Conclusions: Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

Published
2011
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148. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Author

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, and Takagi T

Abstract

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

Published
2010
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