310 results on '"Yuki Y"'
Search Results
2. Highly efficient multi-resonance thermally activated delayed fluorescence material toward a BT.2020 deep-blue emitter
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Junki Ochi, Yuki Yamasaki, Kojiro Tanaka, Yasuhiro Kondo, Kohei Isayama, Susumu Oda, Masakazu Kondo, and Takuji Hatakeyama
- Subjects
Science - Abstract
Abstract An ultrapure deep-blue multi-resonance-induced thermally activated delayed fluorescence material (DOB2-DABNA-A) is designed and synthesized. Benefiting from a fully resonating extended helical π-conjugated system, this compound has a small ΔE ST value of 3.6 meV and sufficient spin–orbit coupling to exhibit a high-rate constant for reverse intersystem crossing (k RISC = 1.1 × 106 s–1). Furthermore, an organic light-emitting diode employing DOB2-DABNA-A as an emitter is fabricated; it exhibits ultrapure deep-blue emission at 452 nm with a small full width at half maximum of 24 nm, corresponding to Commission Internationale de l’Éclairage (CIE) coordinates of (0.145, 0.049). The high k RISC value reduces the efficiency roll-off, resulting in a high external quantum efficiency (EQE) of 21.6% at 1000 cd m–2.
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- 2024
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3. Delivery of a BET protein degrader via a CEACAM6-targeted antibody–drug conjugate inhibits tumour growth in pancreatic cancer models
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Youya Nakazawa, Masayuki Miyano, Shuntaro Tsukamoto, Hiroyuki Kogai, Akihiko Yamamoto, Kentaro Iso, Satoshi Inoue, Yoshinobu Yamane, Yuki Yabe, Hirotatsu Umihara, Junichi Taguchi, Tsuyoshi Akagi, Atsumi Yamaguchi, Minaho Koga, Kohta Toshimitsu, Toshifumi Hirayama, Yohei Mukai, and Akihito Machinaga
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Science - Abstract
Abstract Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis of all cancers. To improve PDAC therapy, we establish screening systems based on organoid and co-culture technologies and find a payload of antibody–drug conjugate (ADC), a bromodomain and extra-terminal (BET) protein degrader named EBET. We select CEACAM6/CD66c as an ADC target and developed an antibody, #84.7, with minimal reactivity to CEACAM6-expressing normal cells. EBET-conjugated #84.7 (84-EBET) has lethal effects on various PDAC organoids and bystander efficacy on CEACAM6-negative PDAC cells and cancer-associated fibroblasts. In mouse studies, a single injection of 84-EBET induces marked tumor regression in various PDAC-patient-derived xenografts, with a decrease in the inflammatory phenotype of stromal cells and without significant body weight loss. Combination with standard chemotherapy or PD-1 antibody induces more profound and sustained regression without toxicity enhancement. Our preclinical evidence demonstrates potential efficacy by delivering BET protein degrader to PDAC and its microenvironment via CEACAM6-targeted ADC.
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- 2024
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4. Broadened quantum critical ground state in a disordered superconducting thin film
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Koichiro Ienaga, Yutaka Tamoto, Masahiro Yoda, Yuki Yoshimura, Takahiro Ishigami, and Satoshi Okuma
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Science - Abstract
Abstract A superconductor-insulator transition (SIT) in two dimensions is a prototypical quantum phase transition (QPT) with a clear quantum critical point (QCP) at zero temperature (T = 0). The SIT is induced by a field B and observed in disordered thin films. In some of weakly disordered or crystalline thin films, however, an anomalous metallic (AM) ground state emerges over a wide B range between the superconducting and insulating phases. It remains a fundamental open question how the QPT picture of the SIT is modified when the AM state appears. Here we present measurements of the Nernst effect N, which has great sensitivity to the fluctuations of the superconducting order parameter. From a thorough contour map of N in the B-T plane, we found a thermal-to-quantum crossover line of the superconducting fluctuations, a so-called ghost-temperature line associated with the QPT, as well as a ghost-field line associated with a thermal transition. The QCP is identified as a T = 0 intercept of the ghost-temperature line inside the AM state, which verifies that the AM state is a broadened critical state of the SIT.
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- 2024
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5. Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants
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Tomokazu Tamura, Jumpei Ito, Keiya Uriu, Jiri Zahradnik, Izumi Kida, Yuki Anraku, Hesham Nasser, Maya Shofa, Yoshitaka Oda, Spyros Lytras, Naganori Nao, Yukari Itakura, Sayaka Deguchi, Rigel Suzuki, Lei Wang, MST Monira Begum, Shunsuke Kita, Hisano Yajima, Jiei Sasaki, Kaori Sasaki-Tabata, Ryo Shimizu, Masumi Tsuda, Yusuke Kosugi, Shigeru Fujita, Lin Pan, Daniel Sauter, Kumiko Yoshimatsu, Saori Suzuki, Hiroyuki Asakura, Mami Nagashima, Kenji Sadamasu, Kazuhisa Yoshimura, Yuki Yamamoto, Tetsuharu Nagamoto, Gideon Schreiber, Katsumi Maenaka, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Takao Hashiguchi, Terumasa Ikeda, Takasuke Fukuhara, Akatsuki Saito, Shinya Tanaka, Keita Matsuno, Kazuo Takayama, and Kei Sato
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Science - Abstract
Abstract In late 2022, SARS-CoV-2 Omicron subvariants have become highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged through the recombination of two cocirculating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022. XBB.1 is the variant most profoundly resistant to BA.2/5 breakthrough infection sera to date and is more fusogenic than BA.2.75. The recombination breakpoint is located in the receptor-binding domain of spike, and each region of the recombinant spike confers immune evasion and increases fusogenicity. We further provide the structural basis for the interaction between XBB.1 spike and human ACE2. Finally, the intrinsic pathogenicity of XBB.1 in male hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provides evidence suggesting that XBB is the first observed SARS-CoV-2 variant to increase its fitness through recombination rather than substitutions.
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- 2023
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6. Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant
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Jumpei Ito, Rigel Suzuki, Keiya Uriu, Yukari Itakura, Jiri Zahradnik, Kanako Terakado Kimura, Sayaka Deguchi, Lei Wang, Spyros Lytras, Tomokazu Tamura, Izumi Kida, Hesham Nasser, Maya Shofa, Mst Monira Begum, Masumi Tsuda, Yoshitaka Oda, Tateki Suzuki, Jiei Sasaki, Kaori Sasaki-Tabata, Shigeru Fujita, Kumiko Yoshimatsu, Hayato Ito, Naganori Nao, Hiroyuki Asakura, Mami Nagashima, Kenji Sadamasu, Kazuhisa Yoshimura, Yuki Yamamoto, Tetsuharu Nagamoto, Jin Kuramochi, Gideon Schreiber, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Akatsuki Saito, Keita Matsuno, Kazuo Takayama, Takao Hashiguchi, Shinya Tanaka, Takasuke Fukuhara, Terumasa Ikeda, and Kei Sato
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Science - Abstract
Abstract In late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.
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- 2023
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7. The 3′ Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies
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Hidefumi Suzuki, Ryota Abe, Miho Shimada, Tomonori Hirose, Hiroko Hirose, Keisuke Noguchi, Yoko Ike, Nanami Yasui, Kazuki Furugori, Yuki Yamaguchi, Atsushi Toyoda, Yutaka Suzuki, Tatsuro Yamamoto, Noriko Saitoh, Shigeo Sato, Chieri Tomomori-Sato, Ronald C. Conaway, Joan W. Conaway, and Hidehisa Takahashi
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Science - Abstract
Transcription termination is generally accompanied by the 3′-end processing of transcripts. Here the authors demonstrate a role for Mediator in transcript end site proximal pausing of replication-dependent histone genes.
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- 2022
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8. National identity predicts public health support during a global pandemic
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Jay J. Van Bavel, Aleksandra Cichocka, Valerio Capraro, Hallgeir Sjåstad, John B. Nezlek, Tomislav Pavlović, Mark Alfano, Michele J. Gelfand, Flavio Azevedo, Michèle D. Birtel, Aleksandra Cislak, Patricia L. Lockwood, Robert Malcolm Ross, Koen Abts, Elena Agadullina, John Jamir Benzon Aruta, Sahba Nomvula Besharati, Alexander Bor, Becky L. Choma, Charles David Crabtree, William A. Cunningham, Koustav De, Waqas Ejaz, Christian T. Elbaek, Andrej Findor, Daniel Flichtentrei, Renata Franc, Biljana Gjoneska, June Gruber, Estrella Gualda, Yusaku Horiuchi, Toan Luu Duc Huynh, Augustin Ibanez, Mostak Ahamed Imran, Jacob Israelashvili, Katarzyna Jasko, Jaroslaw Kantorowicz, Elena Kantorowicz-Reznichenko, André Krouwel, Michael Laakasuo, Claus Lamm, Caroline Leygue, Ming-Jen Lin, Mohammad Sabbir Mansoor, Antoine Marie, Lewend Mayiwar, Honorata Mazepus, Cillian McHugh, John Paul Minda, Panagiotis Mitkidis, Andreas Olsson, Tobias Otterbring, Dominic J. Packer, Anat Perry, Michael Bang Petersen, Arathy Puthillam, Julián C. Riaño-Moreno, Tobias Rothmund, Hernando Santamaría-García, Petra C. Schmid, Drozdstoy Stoyanov, Shruti Tewari, Bojan Todosijević, Manos Tsakiris, Hans H. Tung, Radu G. Umbreș, Edmunds Vanags, Madalina Vlasceanu, Andrew Vonasch, Meltem Yucel, Yucheng Zhang, Mohcine Abad, Eli Adler, Narin Akrawi, Hamza Alaoui Mdarhri, Hanane Amara, David M. Amodio, Benedict G. Antazo, Matthew Apps, F. Ceren Ay, Mouhamadou Hady Ba, Sergio Barbosa, Brock Bastian, Anton Berg, Maria P. Bernal-Zárate, Michael Bernstein, Michał Białek, Ennio Bilancini, Natalia Bogatyreva, Leonardo Boncinelli, Jonathan E. Booth, Sylvie Borau, Ondrej Buchel, C. Daryl Cameron, Chrissie F. Carvalho, Tatiana Celadin, Chiara Cerami, Hom Nath Chalise, Xiaojun Cheng, Luca Cian, Kate Cockcroft, Jane Conway, Mateo Andres Córdoba-Delgado, Chiara Crespi, Marie Crouzevialle, Jo Cutler, Marzena Cypryańska, Justyna Dabrowska, Michael A. Daniels, Victoria H. Davis, Pamala N. Dayley, Sylvain Delouvee, Ognjan Denkovski, Guillaume Dezecache, Nathan A. Dhaliwal, Alelie B. Diato, Roberto Di Paolo, Marianna Drosinou, Uwe Dulleck, Jānis Ekmanis, Arhan S. Ertan, Tom W. Etienne, Hapsa Hossain Farhana, Fahima Farkhari, Harry Farmer, Ali Fenwick, Kristijan Fidanovski, Terry Flew, Shona Fraser, Raymond Boadi Frempong, Jonathan A. Fugelsang, Jessica Gale, E. Begoña Garcia-Navarro, Prasad Garladinne, Oussama Ghajjou, Theofilos Gkinopoulos, Kurt Gray, Siobhán M. Griffin, Bjarki Gronfeldt, Mert Gümren, Ranju Lama Gurung, Eran Halperin, Elizabeth Harris, Volo Herzon, Matej Hruška, Guanxiong Huang, Matthias F. C. Hudecek, Ozan Isler, Simon Jangard, Frederik J. Jørgensen, Frank Kachanoff, John Kahn, Apsara Katuwal Dangol, Oleksandra Keudel, Lina Koppel, Mika Koverola, Emily Kubin, Anton Kunnari, Yordan Kutiyski, Oscar Laguna, Josh Leota, Eva Lermer, Jonathan Levy, Neil Levy, Chunyun Li, Elizabeth U. Long, Chiara Longoni, Marina Maglić, Darragh McCashin, Alexander L. Metcalf, Igor Mikloušić, Soulaimane El Mimouni, Asako Miura, Juliana Molina-Paredes, César Monroy-Fonseca, Elena Morales-Marente, David Moreau, Rafał Muda, Annalisa Myer, Kyle Nash, Tarik Nesh-Nash, Jonas P. Nitschke, Matthew S. Nurse, Yohsuke Ohtsubo, Victoria Oldemburgo de Mello, Cathal O’Madagain, Michal Onderco, M. Soledad Palacios-Galvez, Jussi Palomäki, Yafeng Pan, Zsófia Papp, Philip Pärnamets, Mariola Paruzel-Czachura, Zoran Pavlović, César Payán-Gómez, Silva Perander, Michael Mark Pitman, Rajib Prasad, Joanna Pyrkosz-Pacyna, Steve Rathje, Ali Raza, Gabriel G. Rêgo, Kasey Rhee, Claire E. Robertson, Iván Rodríguez-Pascual, Teemu Saikkonen, Octavio Salvador-Ginez, Waldir M. Sampaio, Gaia C. Santi, Natalia Santiago-Tovar, David Savage, Julian A. Scheffer, Philipp Schönegger, David T. Schultner, Enid M. Schutte, Andy Scott, Madhavi Sharma, Pujan Sharma, Ahmed Skali, David Stadelmann, Clara Alexandra Stafford, Dragan Stanojević, Anna Stefaniak, Anni Sternisko, Augustin Stoica, Kristina K. Stoyanova, Brent Strickland, Jukka Sundvall, Jeffrey P. Thomas, Gustav Tinghög, Benno Torgler, Iris J. Traast, Raffaele Tucciarelli, Michael Tyrala, Nick D. Ungson, Mete S. Uysal, Paul A. M. Van Lange, Jan-Willem van Prooijen, Dirk van Rooy, Daniel Västfjäll, Peter Verkoeijen, Joana B. Vieira, Christian von Sikorski, Alexander Cameron Walker, Jennifer Watermeyer, Erik Wetter, Ashley Whillans, Robin Willardt, Michael J. A. Wohl, Adrian Dominik Wójcik, Kaidi Wu, Yuki Yamada, Onurcan Yilmaz, Kumar Yogeeswaran, Carolin-Theresa Ziemer, Rolf A. Zwaan, and Paulo S. Boggio
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Science - Abstract
Understanding collective behaviour is an important aspect of managing the pandemic response. Here the authors show in a large global study that participants that reported identifying more strongly with their nation reported greater engagement in public health behaviours and support for public health policies in the context of the pandemic.
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- 2022
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9. Tau activates microglia via the PQBP1-cGAS-STING pathway to promote brain inflammation
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Meihua Jin, Hiroki Shiwaku, Hikari Tanaka, Takayuki Obita, Sakurako Ohuchi, Yuki Yoshioka, Xiaocen Jin, Kanoh Kondo, Kyota Fujita, Hidenori Homma, Kazuyuki Nakajima, Mineyuki Mizuguchi, and Hitoshi Okazawa
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Science - Abstract
Brain inflammation generally accelerates neurodegeneration but the mechanisms of this are not fully characterised. Here the authors show that PQBP1 in microglia is important for sensing extrinsic Tau 3 R/4 R proteins and triggers an innate immune response through cGAS and STING resulting in cognitive impairment.
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- 2021
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10. FoxG1 regulates the formation of cortical GABAergic circuit during an early postnatal critical period resulting in autism spectrum disorder-like phenotypes
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Goichi Miyoshi, Yoshifumi Ueta, Akiyo Natsubori, Kou Hiraga, Hironobu Osaki, Yuki Yagasaki, Yusuke Kishi, Yuchio Yanagawa, Gord Fishell, Robert P. Machold, and Mariko Miyata
- Subjects
Science - Abstract
Cortical excitatory/inhibitory (E/I) imbalance is a feature of autism spectrum disorder (ASD). Here, the authors show that FoxG1 regulates the formation of cortical GABAergic circuits affecting social behaviour during a specific postnatal time window in mouse models of ASD.
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- 2021
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11. The role of Mediator and Little Elongation Complex in transcription termination
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Hidehisa Takahashi, Amol Ranjan, Shiyuan Chen, Hidefumi Suzuki, Mio Shibata, Tomonori Hirose, Hiroko Hirose, Kazunori Sasaki, Ryota Abe, Kai Chen, Yanfeng He, Ying Zhang, Ichigaku Takigawa, Tadasuke Tsukiyama, Masashi Watanabe, Satoshi Fujii, Midori Iida, Junichi Yamamoto, Yuki Yamaguchi, Yutaka Suzuki, Masaki Matsumoto, Keiichi I. Nakayama, Michael P. Washburn, Anita Saraf, Laurence Florens, Shigeo Sato, Chieri Tomomori-Sato, Ronald C. Conaway, Joan W. Conaway, and Shigetsugu Hatakeyama
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Science - Abstract
Mediator subunit MED26 was shown to help recruit Super Elongation Complex (SEC) or Little Elongation Complex (LEC) to control the expression of certain genes. Here, the authors provide evidence that MED26 recruits LEC to regulate transcription termination of non-polyadenylated genes, including snRNA and replication-dependent histone (RDH) genes at Cajal bodies.
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- 2020
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12. Author Correction: National identity predicts public health support during a global pandemic
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Jay J. Van Bavel, Aleksandra Cichocka, Valerio Capraro, Hallgeir Sjåstad, John B. Nezlek, Tomislav Pavlović, Mark Alfano, Michele J. Gelfand, Flavio Azevedo, Michèle D. Birtel, Aleksandra Cislak, Patricia L. Lockwood, Robert Malcolm Ross, Koen Abts, Elena Agadullina, John Jamir Benzon Aruta, Sahba Nomvula Besharati, Alexander Bor, Becky L. Choma, Charles David Crabtree, William A. Cunningham, Koustav De, Waqas Ejaz, Christian T. Elbaek, Andrej Findor, Daniel Flichtentrei, Renata Franc, Biljana Gjoneska, June Gruber, Estrella Gualda, Yusaku Horiuchi, Toan Luu Duc Huynh, Agustin Ibanez, Mostak Ahamed Imran, Jacob Israelashvili, Katarzyna Jasko, Jaroslaw Kantorowicz, Elena Kantorowicz-Reznichenko, André Krouwel, Michael Laakasuo, Claus Lamm, Caroline Leygue, Ming-Jen Lin, Mohammad Sabbir Mansoor, Antoine Marie, Lewend Mayiwar, Honorata Mazepus, Cillian McHugh, John Paul Minda, Panagiotis Mitkidis, Andreas Olsson, Tobias Otterbring, Dominic J. Packer, Anat Perry, Michael Bang Petersen, Arathy Puthillam, Julián C. Riaño-Moreno, Tobias Rothmund, Hernando Santamaría-García, Petra C. Schmid, Drozdstoy Stoyanov, Shruti Tewari, Bojan Todosijević, Manos Tsakiris, Hans H. Tung, Radu G. Umbreș, Edmunds Vanags, Madalina Vlasceanu, Andrew Vonasch, Meltem Yucel, Yucheng Zhang, Mohcine Abad, Eli Adler, Narin Akrawi, Hamza Alaoui Mdarhri, Hanane Amara, David M. Amodio, Benedict G. Antazo, Matthew Apps, F. Ceren Ay, Mouhamadou Hady Ba, Sergio Barbosa, Brock Bastian, Anton Berg, Maria P. Bernal-Zárate, Michael Bernstein, Michał Białek, Ennio Bilancini, Natalia Bogatyreva, Leonardo Boncinelli, Jonathan E. Booth, Sylvie Borau, Ondrej Buchel, C. Daryl Cameron, Chrissie F. Carvalho, Tatiana Celadin, Chiara Cerami, Hom Nath Chalise, Xiaojun Cheng, Luca Cian, Kate Cockcroft, Jane Conway, Mateo Andres Córdoba-Delgado, Chiara Crespi, Marie Crouzevialle, Jo Cutler, Marzena Cypryańska, Justyna Dabrowska, Michael A. Daniels, Victoria H. Davis, Pamala N. Dayley, Sylvain Delouvee, Ognjan Denkovski, Guillaume Dezecache, Nathan A. Dhaliwal, Alelie B. Diato, Roberto Di Paolo, Marianna Drosinou, Uwe Dulleck, Jānis Ekmanis, Arhan S. Ertan, Tom W. Etienne, Hapsa Hossain Farhana, Fahima Farkhari, Harry Farmer, Ali Fenwick, Kristijan Fidanovski, Terry Flew, Shona Fraser, Raymond Boadi Frempong, Jonathan A. Fugelsang, Jessica Gale, E. Begoña Garcia-Navarro, Prasad Garladinne, Oussama Ghajjou, Theofilos Gkinopoulos, Kurt Gray, Siobhán M. Griffin, Bjarki Gronfeldt, Mert Gümren, Ranju Lama Gurung, Eran Halperin, Elizabeth Harris, Volo Herzon, Matej Hruška, Guanxiong Huang, Matthias F. C. Hudecek, Ozan Isler, Simon Jangard, Frederik J. Jørgensen, Frank Kachanoff, John Kahn, Apsara Katuwal Dangol, Oleksandra Keudel, Lina Koppel, Mika Koverola, Emily Kubin, Anton Kunnari, Yordan Kutiyski, Oscar Laguna, Josh Leota, Eva Lermer, Jonathan Levy, Neil Levy, Chunyun Li, Elizabeth U. Long, Chiara Longoni, Marina Maglić, Darragh McCashin, Alexander L. Metcalf, Igor Mikloušić, Soulaimane El Mimouni, Asako Miura, Juliana Molina-Paredes, César Monroy-Fonseca, Elena Morales-Marente, David Moreau, Rafał Muda, Annalisa Myer, Kyle Nash, Tarik Nesh-Nash, Jonas P. Nitschke, Matthew S. Nurse, Yohsuke Ohtsubo, Victoria Oldemburgo de Mello, Cathal O’Madagain, Michal Onderco, M. Soledad Palacios-Galvez, Jussi Palomäki, Yafeng Pan, Zsófia Papp, Philip Pärnamets, Mariola Paruzel-Czachura, Zoran Pavlović, César Payán-Gómez, Silva Perander, Michael Mark Pitman, Rajib Prasad, Joanna Pyrkosz-Pacyna, Steve Rathje, Ali Raza, Gabriel G. Rêgo, Kasey Rhee, Claire E. Robertson, Iván Rodríguez-Pascual, Teemu Saikkonen, Octavio Salvador-Ginez, Waldir M. Sampaio, Gaia C. Santi, Natalia Santiago-Tovar, David Savage, Julian A. Scheffer, Philipp Schönegger, David T. Schultner, Enid M. Schutte, Andy Scott, Madhavi Sharma, Pujan Sharma, Ahmed Skali, David Stadelmann, Clara Alexandra Stafford, Dragan Stanojević, Anna Stefaniak, Anni Sternisko, Augustin Stoica, Kristina K. Stoyanova, Brent Strickland, Jukka Sundvall, Jeffrey P. Thomas, Gustav Tinghög, Benno Torgler, Iris J. Traast, Raffaele Tucciarelli, Michael Tyrala, Nick D. Ungson, Mete S. Uysal, Paul A. M. Van Lange, Jan-Willem van Prooijen, Dirk van Rooy, Daniel Västfjäll, Peter Verkoeijen, Joana B. Vieira, Christian von Sikorski, Alexander Cameron Walker, Jennifer Watermeyer, Erik Wetter, Ashley Whillans, Robin Willardt, Michael J. A. Wohl, Adrian Dominik Wójcik, Kaidi Wu, Yuki Yamada, Onurcan Yilmaz, Kumar Yogeeswaran, Carolin-Theresa Ziemer, Rolf A. Zwaan, and Paulo S. Boggio
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Science - Published
- 2022
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13. Nanocomposite electrodes for high current density over 3 A cm−2 in solid oxide electrolysis cells
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Hiroyuki Shimada, Toshiaki Yamaguchi, Haruo Kishimoto, Hirofumi Sumi, Yuki Yamaguchi, Katsuhiro Nomura, and Yoshinobu Fujishiro
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Science - Abstract
High-temperature solid oxide electrolysis cells are a promising technology for energy conversion, but higher current density is needed to increase efficiency. Here the authors design nanocomposite electrodes to improve electronic and ionic conductivity to achieve a high current density.
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- 2019
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14. Spin current generation in organic antiferromagnets
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Makoto Naka, Satoru Hayami, Hiroaki Kusunose, Yuki Yanagi, Yukitoshi Motome, and Hitoshi Seo
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Science - Abstract
Spin current generation in organic materials is hindered by the light elements in the molecules. Here the authors predict a class of organic antiferromagnets with checker-plate type molecular arrangements can be spin current generator under thermal gradient or an electric field, even without spin-orbit coupling.
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- 2019
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15. Non-trivial surface states of samarium hexaboride at the (111) surface
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Yoshiyuki Ohtsubo, Yuki Yamashita, Kenta Hagiwara, Shin-ichiro Ideta, Kiyohisa Tanaka, Ryu Yukawa, Koji Horiba, Hiroshi Kumigashira, Koji Miyamoto, Taichi Okuda, Wataru Hirano, Fumitoshi Iga, and Shin-ichi Kimura
- Subjects
Science - Abstract
Samarium hexaboride has unusual electronic properties that have been suggested to arise from topological effects. Here the authors present spin-resolved ARPES measurements of the (111) surface and observe surface states that may give insight into the bulk topological properties.
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- 2019
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16. HLA-DP84Gly constitutively presents endogenous peptides generated by the class I antigen processing pathway
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Yuki Yamashita, Mark Anczurowski, Munehide Nakatsugawa, Makito Tanaka, Yuki Kagoya, Ankit Sinha, Kenji Chamoto, Toshiki Ochi, Tingxi Guo, Kayoko Saso, Marcus O. Butler, Mark D. Minden, Thomas Kislinger, and Naoto Hirano
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Science - Abstract
MHC class I and II molecules generally present endogenous and exogenous peptides, respectively, through distinct mechanisms. Here, the authors show that the class II molecule HLA-DP84Glyuses both class I and II mechanisms to constitutively present peptides.
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- 2017
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17. Light-induced unfolding and refolding of supramolecular polymer nanofibres
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Bimalendu Adhikari, Yuki Yamada, Mitsuaki Yamauchi, Kengo Wakita, Xu Lin, Keisuke Aratsu, Tomonori Ohba, Takashi Karatsu, Martin J. Hollamby, Nobutaka Shimizu, Hideaki Takagi, Rie Haruki, Shin-ichi Adachi, and Shiki Yagai
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Science - Abstract
Dynamically controlling the conformations of 1D elongated supramolecular polymers can induce functions comparable to protein folding/unfolding. Here the authors show light-induced conformational changes of azobenzene-based supramolecular polymers from helically coiled to extended/randomly coiled conformations.
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- 2017
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18. Rewiring of jasmonate and phytochrome B signalling uncouples plant growth-defense tradeoffs
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Marcelo L. Campos, Yuki Yoshida, Ian T. Major, Dalton de Oliveira Ferreira, Sarathi M. Weraduwage, John E. Froehlich, Brendan F. Johnson, David M. Kramer, Georg Jander, Thomas D. Sharkey, and Gregg A. Howe
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Science - Abstract
Plant immune responses are often associated with reduced growth. Here, the authors show that combining mutations in transcriptional repressors of the defense and light perception pathways can confer both robust growth and strong herbivore defense, demonstrating that growth-defense tradeoffs can be uncoupled.
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- 2016
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19. Superconcentrated electrolytes for a high-voltage lithium-ion battery
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Jianhui Wang, Yuki Yamada, Keitaro Sodeyama, Ching Hua Chiang, Yoshitaka Tateyama, and Atsuo Yamada
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Science - Abstract
Electrode degradation due to metal-ion dissolution in conventional electrolyte hampers the performance of 5 V-class lithium ion batteries. Here, the authors employ a high concentration electrolyte to inhibit metal-ion dissolution and realize a stable high voltage LiNi0.5Mn1.5O4/graphite battery.
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- 2016
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20. Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance
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Yasuaki Kabe, Takanori Nakane, Ikko Koike, Tatsuya Yamamoto, Yuki Sugiura, Erisa Harada, Kenji Sugase, Tatsuro Shimamura, Mitsuyo Ohmura, Kazumi Muraoka, Ayumi Yamamoto, Takeshi Uchida, So Iwata, Yuki Yamaguchi, Elena Krayukhina, Masanori Noda, Hiroshi Handa, Koichiro Ishimori, Susumu Uchiyama, Takuya Kobayashi, and Makoto Suematsu
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Science - Abstract
PGRMC1 binds to EGFR and cytochromes P450, and is known to be involved in cancer proliferation and in drug resistance. Here, the authors determine the structure of the cytosolic domain of PGRMC1, which forms a dimer via haem–haem stacking, and propose how this interaction could be involved in its function.
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- 2016
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21. Modeling NK-cell lymphoma in mice reveals its cell-of-origin and microenvironmental changes and identifies therapeutic targets.
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Koya J, Tanigawa T, Mizuno K, Kim H, Ito Y, Yuasa M, Yamaguchi K, Kogure Y, Saito Y, Shingaki S, Tabata M, Murakami K, Chiba K, Okada A, Shiraishi Y, Marouf A, Liévin R, Chaubard S, Jaccard A, Hermine O, de Leval L, Tournilhac O, Damaj G, Gaulard P, Couronné L, Yasui T, Nakashima K, Miyoshi H, Ohshima K, and Kataoka K
- Subjects
- Animals, Mice, Humans, Mice, Knockout, Disease Models, Animal, Interferon-gamma metabolism, Receptors, CXCR6 metabolism, Receptors, CXCR6 genetics, Chemokine CXCL16 metabolism, Chemokine CXCL16 genetics, Herpesvirus 4, Human, Gene Expression Regulation, Neoplastic, Signal Transduction, Salivary Glands pathology, Salivary Glands metabolism, Myeloid Cells metabolism, Cell Line, Tumor, Mice, Inbred C57BL, Killer Cells, Natural immunology, Killer Cells, Natural metabolism, Tumor Microenvironment immunology, Lymphoma, Extranodal NK-T-Cell genetics, Lymphoma, Extranodal NK-T-Cell metabolism, Lymphoma, Extranodal NK-T-Cell virology, Lymphoma, Extranodal NK-T-Cell pathology, Proto-Oncogene Proteins c-myc metabolism, Proto-Oncogene Proteins c-myc genetics, Tumor Suppressor Protein p53 metabolism, Tumor Suppressor Protein p53 genetics
- Abstract
Extranodal NK/T-cell lymphoma (ENKTCL) is an Epstein-Barr virus (EBV)-related neoplasm preferentially involving the upper aerodigestive tract. Here we show that NK-cell-specific Trp53 disruption in mice leads to the development of NK-cell lymphomas after long latency, which involve not only the hematopoietic system but also the salivary glands. Before tumor onset, Trp53 knockout causes extensive gene expression changes, resulting in immature NK-cell expansion, exclusively in the salivary glands. Both human and murine NK-cell lymphomas express tissue-resident markers, suggesting tissue-resident NK cells as their cell-of-origin. Murine NK-cell lymphomas show recurrent Myc amplifications and upregulation of MYC target gene signatures. EBV-encoded latent membrane protein 1 expression accelerates NK-cell lymphomagenesis and causes diverse microenvironmental changes, particularly myeloid propagation, through interferon-γ signaling. In turn, myeloid cells support tumor cells via CXCL16-CXCR6 signaling and its inhibition is effective against NK-cell tumors in vivo. Remarkably, KLRG1-expressing cells expand in the tumor and are capable of repopulating tumors in secondary recipients. Furthermore, targeting KLRG1 alone or combined with MYC inhibition using an eIF4 inhibitor is effective against NK-cell tumors. Therefore, our observations provide insights into the pathogenesis and highlight potential therapeutic targets, including CXCL16, KLRG1, and MYC, in ENKTCL, which can help improve its diagnostic and therapeutic strategies., (© 2024. The Author(s).)
- Published
- 2024
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22. The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons.
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Taniue K, Sugawara A, Zeng C, Han H, Gao X, Shimoura Y, Ozeki AN, Onoguchi-Mizutani R, Seki M, Suzuki Y, Hamada M, and Akimitsu N
- Subjects
- Humans, HeLa Cells, HEK293 Cells, Exosome Multienzyme Ribonuclease Complex metabolism, Exosome Multienzyme Ribonuclease Complex genetics, Polyadenylation, Nucleocytoplasmic Transport Proteins genetics, Nucleocytoplasmic Transport Proteins metabolism, Introns genetics, RNA Nucleotidyltransferases, Exons genetics, Heterogeneous-Nuclear Ribonucleoprotein K metabolism, Heterogeneous-Nuclear Ribonucleoprotein K genetics, RNA, Messenger genetics, RNA, Messenger metabolism, RNA-Binding Proteins metabolism, RNA-Binding Proteins genetics
- Abstract
RNA surveillance systems degrade aberrant RNAs that result from defective transcriptional termination, splicing, and polyadenylation. Defective RNAs in the nucleus are recognized by RNA-binding proteins and MTR4, and are degraded by the RNA exosome complex. Here, we detect aberrant RNAs in MTR4-depleted cells using long-read direct RNA sequencing and 3' sequencing. MTR4 destabilizes intronic polyadenylated transcripts generated by transcriptional read-through over one or more exons, termed 3' eXtended Transcripts (3XTs). MTR4 also associates with hnRNPK, which recognizes 3XTs with multiple exons. Moreover, the aberrant protein translated from KCTD13 3XT is a target of the hnRNPK-MTR4-RNA exosome pathway and forms aberrant condensates, which we name KCTD13 3eXtended Transcript-derived protein (KeXT) bodies. Our results suggest that RNA surveillance in human cells inhibits the formation of condensates of a defective polyadenylated transcript-derived protein., (© 2024. The Author(s).)
- Published
- 2024
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23. Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
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Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, and Hashiguchi T
- Subjects
- Humans, Mutation, Antibodies, Neutralizing immunology, Binding Sites, Protein Conformation, Models, Molecular, Spike Glycoprotein, Coronavirus metabolism, Spike Glycoprotein, Coronavirus chemistry, Spike Glycoprotein, Coronavirus genetics, SARS-CoV-2 metabolism, SARS-CoV-2 chemistry, Angiotensin-Converting Enzyme 2 metabolism, Angiotensin-Converting Enzyme 2 chemistry, Protein Binding, COVID-19 virology, COVID-19 metabolism, Protein Domains
- Abstract
Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the RBD in the down-conformation to facilitate the conformational shift to RBD-up remains unclear. Herein, we present the structures of the BA.2.86 and the JN.1 spike proteins bound to ACE2. Notably, we successfully observed the ACE2-bound down-RBD, indicating an intermediate structure before the RBD-up conformation. The wider and mobile angle of RBDs in the up-state provides space for ACE2 to interact with the down-RBD, facilitating the transition to the RBD-up state. The K356T, but not N354-linked glycan, contributes to both of infectivity and neutralizing-antibody evasion in BA.2.86. These structural insights the spike-protein dynamics would help understand the mechanisms underlying SARS-CoV-2 infection and its neutralization., (© 2024. The Author(s).)
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- 2024
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24. Neurotransmitter recognition by human vesicular monoamine transporter 2.
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Im D, Jormakka M, Juge N, Kishikawa JI, Kato T, Sugita Y, Noda T, Uemura T, Shiimura Y, Miyaji T, Asada H, and Iwata S
- Subjects
- Humans, HEK293 Cells, Models, Molecular, Vesicular Monoamine Transport Proteins metabolism, Vesicular Monoamine Transport Proteins chemistry, Cryoelectron Microscopy, Tetrabenazine analogs & derivatives, Tetrabenazine metabolism, Tetrabenazine chemistry, Dopamine metabolism, Neurotransmitter Agents metabolism
- Abstract
Human vesicular monoamine transporter 2 (VMAT2), a member of the SLC18 family, plays a crucial role in regulating neurotransmitters in the brain by facilitating their uptake and storage within vesicles, preparing them for exocytotic release. Because of its central role in neurotransmitter signalling and neuroprotection, VMAT2 is a target for neurodegenerative diseases and movement disorders, with its inhibitor being used as therapeutics. Despite the importance of VMAT2 in pharmacophysiology, the molecular basis of VMAT2-mediated neurotransmitter transport and its inhibition remains unclear. Here we show the cryo-electron microscopy structure of VMAT2 in the substrate-free state, in complex with the neurotransmitter dopamine, and in complex with the inhibitor tetrabenazine. In addition to these structural determinations, monoamine uptake assays, mutational studies, and pKa value predictions were performed to characterize the dynamic changes in VMAT2 structure. These results provide a structural basis for understanding VMAT2-mediated vesicular transport of neurotransmitters and a platform for modulation of current inhibitor design., (© 2024. The Author(s).)
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- 2024
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25. Normothermic ex vivo kidney perfusion preserves mitochondrial and graft function after warm ischemia and is further enhanced by AP39.
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Kawamura M, Parmentier C, Ray S, Clotet-Freixas S, Leung S, John R, Mazilescu L, Nogueira E, Noguchi Y, Goto T, Arulratnam B, Ganesh S, Tamang T, Lees K, Reichman TW, Andreazza AC, Kim PK, Konvalinka A, Selzner M, and Robinson LA
- Subjects
- Animals, Male, Swine, Hydrogen Sulfide metabolism, Hydrogen Sulfide pharmacology, Adenosine Triphosphate metabolism, Oxidative Stress, Organophosphorus Compounds, Thiones, Kidney Transplantation, Mitochondria metabolism, Kidney metabolism, Organ Preservation methods, Warm Ischemia, Perfusion methods
- Abstract
We previously reported that normothermic ex vivo kidney perfusion (NEVKP) is superior in terms of organ protection compared to static cold storage (SCS), which is still the standard method of organ preservation, but the mechanisms are incompletely understood. We used a large animal kidney autotransplant model to evaluate mitochondrial function during organ preservation and after kidney transplantation, utilizing live cells extracted from fresh kidney tissue. Male porcine kidneys stored under normothermic perfusion showed preserved mitochondrial function and higher ATP levels compared to kidneys stored at 4 °C (SCS). Mitochondrial respiration and ATP levels were further enhanced when AP39, a mitochondria-targeted hydrogen sulfide donor, was administered during warm perfusion. Correspondingly, the combination of NEVKP and AP39 was associated with decreased oxidative stress and inflammation, and with improved graft function after transplantation. In conclusion, our findings suggest that the organ-protective effects of normothermic perfusion are mediated by maintenance of mitochondrial function and enhanced by AP39 administration. Activation of mitochondrial function through the combination of AP39 and normothermic perfusion could represent a new therapeutic strategy for long-term renal preservation., (© 2024. The Author(s).)
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- 2024
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26. Phospholipid scrambling induced by an ion channel/metabolite transporter complex.
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Niu H, Maruoka M, Noguchi Y, Kosako H, and Suzuki J
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- Humans, HEK293 Cells, Ion Channels metabolism, Ion Channels genetics, Animals, CRISPR-Cas Systems, Calcium metabolism, Phospholipid Transfer Proteins metabolism, Phospholipid Transfer Proteins genetics, Phospholipids metabolism
- Abstract
Cells establish the asymmetrical distribution of phospholipids and alter their distribution by phospholipid scrambling (PLS) to adapt to environmental changes. Here, we demonstrate that a protein complex, consisting of the ion channel Tmem63b and the thiamine transporter Slc19a2, induces PLS upon calcium (Ca
2+ ) stimulation. Through revival screening using a CRISPR sgRNA library on high PLS cells, we identify Tmem63b as a PLS-inducing factor. Ca2+ stimulation-mediated PLS is suppressed by deletion of Tmem63b, while human disease-related Tmem63b mutants induce constitutive PLS. To search for a molecular link between Ca2+ stimulation and PLS, we perform revival screening on Tmem63b-overexpressing cells, and identify Slc19a2 and the Ca2+ -activated K+ channel Kcnn4 as PLS-regulating factors. Deletion of either of these genes decreases PLS activity. Biochemical screening indicates that Tmem63b and Slc19a2 form a heterodimer. These results demonstrate that a Tmem63b/Slc19a2 heterodimer induces PLS upon Ca2+ stimulation, along with Kcnn4 activation., (© 2024. The Author(s).)- Published
- 2024
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27. Electric-field-enhanced second-harmonic domain contrast and nonreciprocity in a van der Waals antiferromagnet.
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Wang Z, Wang M, Lehmann J, Shiomi Y, Arima TH, Nagaosa N, Tokura Y, and Ogawa N
- Abstract
Imaging antiferromagnetic 180° domains with actively controlled visibility is vital for both fundamental science and sophisticated applications. While optical second-harmonic generation (SHG) is a well-known technique for distinguishing such domains in non-centrosymmetric antiferromagnets, a general material-based strategy to control domain contrast remains elusive. Using van der Waals antiferromagnet MnPS
3 as a proof of concept, we demonstrate the tuning of nonreciprocity-induced domain contrast in SHG through applying an in-plane electric field that transforms the magnetic point group to its unitary subgroup. The interference among intrinsic electric-dipole, magnetic-dipole, and field-induced electric-dipole transitions, each carrying distinct characters under space-inversion ( P ) and time-reversal ( T ) operations, enables large tuning of domain contrast and nonreciprocity in a broad spectral range. This strategy, generically applicable to systems characterized by P T -symmetric magnetic groups with a polar unitary subgroup, offers a path to fast electrical modulation of nonlinear nonreciprocal photonic behaviors using antiferromagnets., (© 2024. The Author(s).)- Published
- 2024
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28. Distinct roles of monkey OFC-subcortical pathways in adaptive behavior.
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Oyama K, Majima K, Nagai Y, Hori Y, Hirabayashi T, Eldridge MAG, Mimura K, Miyakawa N, Fujimoto A, Hori Y, Iwaoki H, Inoue KI, Saunders RC, Takada M, Yahata N, Higuchi M, Richmond BJ, and Minamimoto T
- Subjects
- Animals, Male, Behavior, Animal physiology, Adaptation, Psychological physiology, Caudate Nucleus physiology, Caudate Nucleus diagnostic imaging, Reward, Positron-Emission Tomography, Macaca mulatta, Neural Pathways physiology, Choice Behavior physiology, Decision Making physiology, Thalamus physiology, Thalamus diagnostic imaging, Brain Mapping methods, Prefrontal Cortex physiology, Prefrontal Cortex diagnostic imaging
- Abstract
Primates must adapt to changing environments by optimizing their behavior to make beneficial choices. At the core of adaptive behavior is the orbitofrontal cortex (OFC) of the brain, which updates choice value through direct experience or knowledge-based inference. Here, we identify distinct neural circuitry underlying these two separate abilities. We designed two behavioral tasks in which two male macaque monkeys updated the values of certain items, either by directly experiencing changes in stimulus-reward associations, or by inferring the value of unexperienced items based on the task's rules. Chemogenetic silencing of bilateral OFC combined with mathematical model-fitting analysis revealed that monkey OFC is involved in updating item value based on both experience and inference. In vivo imaging of chemogenetic receptors by positron emission tomography allowed us to map projections from the OFC to the rostromedial caudate nucleus (rmCD) and the medial part of the mediodorsal thalamus (MDm). Chemogenetic silencing of the OFC-rmCD pathway impaired experience-based value updating, while silencing the OFC-MDm pathway impaired inference-based value updating. Our results thus demonstrate dissociable contributions of distinct OFC projections to different behavioral strategies, and provide new insights into the neural basis of value-based adaptive decision-making in primates., (© 2024. The Author(s).)
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- 2024
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29. The significance of electrical signals in maturing spermatozoa for phosphoinositide regulation through voltage-sensing phosphatase.
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Kawai T, Morioka S, Miyata H, Andriani RT, Akter S, Toma G, Nakagawa T, Oyama Y, Iida-Norita R, Sasaki J, Watanabe M, Sakimura K, Ikawa M, Sasaki T, and Okamura Y
- Subjects
- Animals, Male, Mice, Sperm Capacitation physiology, Gene Knock-In Techniques, Humans, Mutation, Spermatozoa metabolism, Spermatozoa physiology, Phosphatidylinositols metabolism, Sperm Motility physiology, Phosphoric Monoester Hydrolases metabolism, Phosphoric Monoester Hydrolases genetics
- Abstract
Voltage-sensing phosphatase (VSP) exhibits voltage-dependent phosphatase activity toward phosphoinositides. VSP generates a specialized phosphoinositide environment in mammalian sperm flagellum. However, the voltage-sensing mechanism of VSP in spermatozoa is not yet characterized. Here, we found that VSP is activated during sperm maturation, indicating that electric signals in immature spermatozoa are essential. Using a heterologous expression system, we show the voltage-sensing property of mouse VSP (mVSP). The voltage-sensing threshold of mVSP is approximately -30 mV, which is sensitive enough to activate mVSP in immature spermatozoa. We also report several knock-in mice in which we manipulate the voltage-sensitivity or electrochemical coupling of mVSP. Notably, the V312R mutant, with a minor voltage-sensitivity change, exhibits abnormal sperm motility after, but not before, capacitation. Additionally, the V312R mutant shows a significant change in the acyl-chain profile of phosphoinositide. Our findings suggest that electrical signals during sperm maturation are crucial for establishing the optimal phosphoinositide environment in spermatozoa., (© 2024. The Author(s).)
- Published
- 2024
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30. Atypical and non-classical CD45RB lo memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19.
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Priest DG, Ebihara T, Tulyeu J, Søndergaard JN, Sakakibara S, Sugihara F, Nakao S, Togami Y, Yoshimura J, Ito H, Onishi S, Muratsu A, Mitsuyama Y, Ogura H, Oda J, Okusaki D, Matsumoto H, and Wing JB
- Subjects
- Humans, Male, Antibodies, Viral immunology, Antibodies, Viral blood, Middle Aged, Female, COVID-19 Vaccines immunology, Vaccination, Adult, Immunologic Memory immunology, mRNA Vaccines immunology, B-Lymphocytes immunology, Aged, COVID-19 immunology, Leukocyte Common Antigens metabolism, SARS-CoV-2 immunology, Memory B Cells immunology, BNT162 Vaccine immunology
- Abstract
Resting memory B cells can be divided into classical or atypical groups, but the heterogenous marker expression on activated memory B cells makes similar classification difficult. Here, by longitudinal analysis of mass cytometry and CITE-seq data from cohorts with COVID-19, bacterial sepsis, or BNT162b2 mRNA vaccine, we observe that resting B cell memory consist of classical CD45RB
+ memory and CD45RBlo memory, of which the latter contains of two distinct groups of CD11c+ atypical and CD23+ non-classical memory cells. CD45RB levels remain stable in these cells after activation, thereby enabling the tracking of activated B cells and plasmablasts derived from either CD45RB+ or CD45RBlo memory B cells. Moreover, in both COVID-19 patients and mRNA vaccination, CD45RBlo B cells formed the majority of SARS-CoV2 specific memory B cells and correlated with serum antibodies, while CD45RB+ memory are activated by bacterial sepsis. Our results thus identify that stably expressed CD45RB levels can be exploited to trace resting memory B cells and their activated progeny, and suggest that atypical and non-classical CD45RBlo memory B cells contribute to SARS-CoV-2 infection and vaccination., (© 2024. The Author(s).)- Published
- 2024
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31. Disease-relevant upregulation of P2Y 1 receptor in astrocytes enhances neuronal excitability via IGFBP2.
- Author
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Shigetomi E, Suzuki H, Hirayama YJ, Sano F, Nagai Y, Yoshihara K, Koga K, Tateoka T, Yoshioka H, Shinozaki Y, Kinouchi H, Tanaka KF, Bito H, Tsuda M, and Koizumi S
- Subjects
- Animals, Humans, Male, Mice, Calcium Signaling, Disease Models, Animal, Epilepsy metabolism, Epilepsy genetics, Epilepsy physiopathology, Mice, Inbred C57BL, Mice, Transgenic, Astrocytes metabolism, Insulin-Like Growth Factor Binding Protein 2 metabolism, Insulin-Like Growth Factor Binding Protein 2 genetics, Neurons metabolism, Receptors, Purinergic P2Y1 metabolism, Receptors, Purinergic P2Y1 genetics, Up-Regulation
- Abstract
Reactive astrocytes play a pivotal role in the pathogenesis of neurological diseases; however, their functional phenotype and the downstream molecules by which they modify disease pathogenesis remain unclear. Here, we genetically increase P2Y
1 receptor (P2Y1R) expression, which is upregulated in reactive astrocytes in several neurological diseases, in astrocytes of male mice to explore its function and the downstream molecule. This astrocyte-specific P2Y1R overexpression causes neuronal hyperexcitability by increasing both astrocytic and neuronal Ca2+ signals. We identify insulin-like growth factor-binding protein 2 (IGFBP2) as a downstream molecule of P2Y1R in astrocytes; IGFBP2 acts as an excitatory signal to cause neuronal excitation. In neurological disease models of epilepsy and stroke, reactive astrocytes upregulate P2Y1R and increase IGFBP2. The present findings identify a mechanism underlying astrocyte-driven neuronal hyperexcitability, which is likely to be shared by several neurological disorders, providing insights that might be relevant for intervention in diverse neurological disorders., (© 2024. The Author(s).)- Published
- 2024
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32. Single-shot laser-driven neutron resonance spectroscopy for temperature profiling.
- Author
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Lan Z, Arikawa Y, Mirfayzi SR, Morace A, Hayakawa T, Sato H, Kamiyama T, Wei T, Tatsumi Y, Koizumi M, Abe Y, Fujioka S, Mima K, Kodama R, and Yogo A
- Abstract
The temperature measurement of material inside of an object is one of the key technologies for control of dynamical processes. For this purpose, various techniques such as laser-based thermography and phase-contrast imaging thermography have been studied. However, it is, in principle, impossible to measure the temperature of an element inside of an object using these techniques. One of the possible solutions is measurements of Doppler brooding effect in neutron resonance absorption (NRA). Here we present a method to measure the temperature of an element or an isotope inside of an object using NRA with a single neutron pulse of approximately 100 ns width provided from a high-power laser. We demonstrate temperature measurements of a tantalum (Ta) metallic foil heated from the room temperature up to 617 K. Although the neutron energy resolution is fluctuated from shot to shot, we obtain the temperature dependence of resonance Doppler broadening using a reference of a silver (Ag) foil kept to the room temperature. A free gas model well reproduces the results. This method enables element(isotope)-sensitive thermometry to detect the instantaneous temperature rise in dynamical processes., (© 2024. The Author(s).)
- Published
- 2024
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33. Multiscale chemogenetic dissection of fronto-temporal top-down regulation for object memory in primates.
- Author
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Hirabayashi T, Nagai Y, Hori Y, Hori Y, Oyama K, Mimura K, Miyakawa N, Iwaoki H, Inoue KI, Suhara T, Takada M, Higuchi M, and Minamimoto T
- Subjects
- Animals, Male, Macaca mulatta, Memory physiology, Magnetic Resonance Imaging, Frontal Lobe physiology, Memory, Short-Term physiology, Brain Mapping, Prefrontal Cortex physiology, Temporal Lobe physiology, Neurons physiology
- Abstract
Visual object memory is a fundamental element of various cognitive abilities, and the underlying neural mechanisms have been extensively examined especially in the anterior temporal cortex of primates. However, both macroscopic large-scale functional network in which this region is embedded and microscopic neuron-level dynamics of top-down regulation it receives for object memory remains elusive. Here, we identified the orbitofrontal node as a critical partner of the anterior temporal node for object memory by combining whole-brain functional imaging during rest and a short-term object memory task in male macaques. Focal chemogenetic silencing of the identified orbitofrontal node downregulated both the local orbitofrontal and remote anterior temporal nodes during the task, in association with deteriorated mnemonic, but not perceptual, performance. Furthermore, imaging-guided neuronal recordings in the same monkeys during the same task causally revealed that orbitofrontal top-down modulation enhanced stimulus-selective mnemonic signal in individual anterior temporal neurons while leaving bottom-up perceptual signal unchanged. Furthermore, similar activity difference was also observed between correct and mnemonic error trials before silencing, suggesting its behavioral relevance. These multifaceted but convergent results provide a multiscale causal understanding of dynamic top-down regulation of the anterior temporal cortex along the ventral fronto-temporal network underpinning short-term object memory in primates., (© 2024. The Author(s).)
- Published
- 2024
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34. Intrinsic signaling pathways modulate targeted protein degradation.
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Mori Y, Akizuki Y, Honda R, Takao M, Tsuchimoto A, Hashimoto S, Iio H, Kato M, Kaiho-Soma A, Saeki Y, Hamazaki J, Murata S, Ushijima T, Hattori N, and Ohtake F
- Subjects
- Humans, HSP90 Heat-Shock Proteins metabolism, Cell Line, Tumor, Apoptosis drug effects, Cyclin-Dependent Kinase 9 metabolism, Cyclin-Dependent Kinase 9 antagonists & inhibitors, Nuclear Proteins metabolism, Nuclear Proteins genetics, Bromodomain Containing Proteins, Signal Transduction drug effects, Proteolysis drug effects, Transcription Factors metabolism, Transcription Factors genetics, Cell Cycle Proteins metabolism, Ubiquitination
- Abstract
Targeted protein degradation is a groundbreaking modality in drug discovery; however, the regulatory mechanisms are still not fully understood. Here, we identify cellular signaling pathways that modulate the targeted degradation of the anticancer target BRD4 and related neosubstrates BRD2/3 and CDK9 induced by CRL2
VHL - or CRL4CRBN -based PROTACs. The chemicals identified as degradation enhancers include inhibitors of cellular signaling pathways such as poly-ADP ribosylation (PARG inhibitor PDD00017273), unfolded protein response (PERK inhibitor GSK2606414), and protein stabilization (HSP90 inhibitor luminespib). Mechanistically, PARG inhibition promotes TRIP12-mediated K29/K48-linked branched ubiquitylation of BRD4 by facilitating chromatin dissociation of BRD4 and formation of the BRD4-PROTAC-CRL2VHL ternary complex; by contrast, HSP90 inhibition promotes BRD4 degradation after the ubiquitylation step. Consequently, these signal inhibitors sensitize cells to the PROTAC-induced apoptosis. These results suggest that various cell-intrinsic signaling pathways spontaneously counteract chemically induced target degradation at multiple steps, which could be liberated by specific inhibitors., (© 2024. The Author(s).)- Published
- 2024
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35. Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography.
- Author
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Maity B, Shoji M, Luo F, Nakane T, Abe S, Owada S, Kang J, Tono K, Tanaka R, Pham TT, Kojima M, Hishikawa Y, Tanaka J, Tian J, Nagama M, Suzuki T, Noya H, Nakasuji Y, Asanuma A, Yao X, Iwata S, Shigeta Y, Nango E, and Ueno T
- Subjects
- Crystallography, X-Ray, Porosity, Coordination Complexes chemistry, Models, Molecular, Animals, Carbon Monoxide chemistry, Time Factors, Chickens, Muramidase chemistry, Manganese chemistry
- Abstract
Determining short-lived intermediate structures in chemical reactions is challenging. Although ultrafast spectroscopic methods can detect the formation of transient intermediates, real-space structures cannot be determined directly from such studies. Time-resolved serial femtosecond crystallography (TR-SFX) has recently proven to be a powerful method for capturing molecular changes in proteins on femtosecond timescales. However, the methodology has been mostly applied to natural proteins/enzymes and limited to reactions promoted by synthetic molecules due to structure determination challenges. This work demonstrates the applicability of TR-SFX for investigations of chemical reaction mechanisms of synthetic metal complexes. We fix a light-induced CO-releasing Mn(CO)
3 reaction center in porous hen egg white lysozyme (HEWL) microcrystals. By controlling light exposure and time, we capture the real-time formation of Mn-carbonyl intermediates during the CO release reaction. The asymmetric protein environment is found to influence the order of CO release. The experimentally-observed reaction path agrees with quantum mechanical calculations. Therefore, our demonstration offers a new approach to visualize atomic-level reactions of small molecules using TR-SFX with real-space structure determination. This advance holds the potential to facilitate design of artificial metalloenzymes with precise mechanisms, empowering design, control and development of innovative reactions., (© 2024. The Author(s).)- Published
- 2024
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36. Shape of the first mitotic spindles impacts multinucleation in human embryos.
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Ono Y, Shirasawa H, Takahashi K, Goto M, Ono T, Sakaguchi T, Okabe M, Hirakawa T, Iwasawa T, Fujishima A, Sugawara T, Makino K, Miura H, Fukunaga N, Asada Y, Kumazawa Y, and Terada Y
- Subjects
- Humans, Zygote cytology, Zygote metabolism, Embryo, Mammalian cytology, Microscopy, Confocal, Centrosome metabolism, Embryonic Development physiology, Female, Spindle Apparatus metabolism, Mitosis, Cell Nucleus metabolism
- Abstract
During human embryonic development, early cleavage-stage embryos are more susceptible to errors. Studies have shown that many problems occur during the first mitosis, such as direct cleavage, chromosome segregation errors, and multinucleation. However, the mechanisms whereby these errors occur during the first mitosis in human embryos remain unknown. To clarify this aspect, in the present study, we image discarded living human two-pronuclear stage zygotes using fluorescent labeling and confocal microscopy without microinjection of DNA or mRNA and investigate the association between spindle shape and nuclear abnormality during the first mitosis. We observe that the first mitotic spindles vary, and low-aspect-ratio-shaped spindles tend to lead to the formation of multiple nuclei at the 2-cell stage. Moreover, we observe defocusing poles in many of the first mitotic spindles, which are strongly associated with multinucleation. Additionally, we show that differences in the positions of the centrosomes cause spindle abnormality in the first mitosis. Furthermore, many multinuclei are modified to form mononuclei after the second mitosis because the occurrence of pole defocusing is firmly reduced. Our study will contribute markedly to research on the occurrence of mitotic errors during the early cleavage of human embryos., (© 2024. The Author(s).)
- Published
- 2024
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37. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques.
- Author
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Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, and Susaki EA
- Subjects
- Animals, Mice, Humans, Cell Line, Tumor, Brain diagnostic imaging, Microscopy, Fluorescence methods, Microscopy, Fluorescence instrumentation, Imaging, Three-Dimensional methods
- Abstract
Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies., (© 2024. The Author(s).)
- Published
- 2024
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38. Three stepwise pH progressions in stratum corneum for homeostatic maintenance of the skin.
- Author
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Fukuda K, Ito Y, Furuichi Y, Matsui T, Horikawa H, Miyano T, Okada T, van Logtestijn M, Tanaka RJ, Miyawaki A, and Amagai M
- Subjects
- Hydrogen-Ion Concentration, Animals, Skin metabolism, Mice, Humans, Cell Differentiation, Tight Junctions metabolism, Male, Female, Mice, Inbred C57BL, Homeostasis, Keratinocytes metabolism, Epidermis metabolism
- Abstract
The stratum corneum is the outermost skin layer with a vital role in skin barrier function. It is comprised of dead keratinocytes (corneocytes) and is known to maintain its thickness by shedding cells, although, the precise mechanisms that safeguard stratum corneum maturation and homeostasis remain unclear. Previous ex vivo studies have suggested a neutral-to-acidic pH gradient in the stratum corneum. Here, we use intravital pH imaging at single-corneocyte resolution to demonstrate that corneocytes actually undergo differentiation to develop three distinct zones in the stratum corneum, each with a distinct pH value. We identified a moderately acidic lower, an acidic middle, and a pH-neutral upper layer in the stratum corneum, with tight junctions playing a key role in their development. The upper pH neutral zone can adjust its pH according to the external environment and has a neutral pH under steady-state conditions owing to the influence of skin microbiota. The middle acidic pH zone provides a defensive barrier against pathogens. With mathematical modeling, we demonstrate the controlled protease activation of kallikrein-related peptidases on the stratum corneum surface that results in proper corneocyte shedding in desquamation. This work adds crucial information to our understanding of how stratum corneum homeostasis is maintained., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
39. Nonmagnetic framboid and associated iron nanoparticles with a space-weathered feature from asteroid Ryugu.
- Author
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Kimura Y, Kato T, Anada S, Yoshida R, Yamamoto K, Tanigaki T, Akashi T, Kasai H, Kurosawa K, Nakamura T, Noguchi T, Sato M, Matsumoto T, Morita T, Kikuiri M, Amano K, Kagawa E, Yada T, Nishimura M, Nakato A, Miyazaki A, Yogata K, Abe M, Okada T, Usui T, Yoshikawa M, Saiki T, Tanaka S, Terui F, Nakazawa S, Yurimoto H, Okazaki R, Yabuta H, Naraoka H, Sakamoto K, Watanabe SI, Tsuda Y, and Tachibana S
- Abstract
Extraterrestrial minerals on the surface of airless Solar System bodies undergo gradual alteration processes known as space weathering over long periods of time. The signatures of space weathering help us understand the phenomena occurring in the Solar System. However, meteorites rarely retain the signatures, making it impossible to study the space weathering processes precisely. Here, we examine samples retrieved from the asteroid Ryugu by the Hayabusa2 spacecraft and discover the presence of nonmagnetic framboids through electron holography measurements that can visualize magnetic flux. Magnetite particles, which normally provide a record of the nebular magnetic field, have lost their magnetic properties by reduction via a high-velocity (>5 km s
-1 ) impact of a micrometeoroid with a diameter ranging from 2 to 20 μm after destruction of the parent body of Ryugu. Around these particles, thousands of metallic-iron nanoparticles with a vortex magnetic domain structure, which could have recorded a magnetic field in the impact event, are found. Through measuring the remanent magnetization of the iron nanoparticles, future studies are expected to elucidate the nature of the nebular/interplanetary magnetic fields after the termination of aqueous alteration in an asteroid., (© 2024. The Author(s).)- Published
- 2024
- Full Text
- View/download PDF
40. NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity.
- Author
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Toyama Y and Shimada I
- Subjects
- Humans, Thermodynamics, Magnetic Resonance Spectroscopy, Models, Molecular, Nucleic Acid Conformation, DEAD-box RNA Helicases metabolism, DEAD-box RNA Helicases chemistry, RNA metabolism, RNA chemistry, Protein Binding
- Abstract
The DEAD-box RNA helicase (DDX) plays a central role in many aspects of RNA metabolism by remodeling the defined structure of RNA molecules. While a number of structural studies have revealed the atomistic details of the interaction between DDX and RNA ligands, the molecular mechanism of how this molecule unwinds a structured RNA into an unstructured single-stranded RNA (ssRNA) has largely remained elusive. This is due to challenges in structurally characterizing the unwinding intermediate state and the lack of thermodynamic details underlying this process. In this study, we use solution nuclear magnetic resonance (NMR) spectroscopy to characterize the interaction of human DDX3X, a member of the DDX family, with various RNA ligands. Our results show that the inherent binding affinity of DDX3X for ssRNA is significantly higher than that for structured RNA elements. This preferential binding, accompanied by the formation of a domain-closed conformation in complex with ssRNA, effectively stabilizes the denatured ssRNA state and thus underlies the unwinding activity of DDX3X. Our results provide a thermodynamic and structural basis for the DDX function, whereby DDX can recognize and remodel a distinct set of structured RNAs to participate in a wide range of physiological processes., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
41. Large-volume focus control at 10 MHz refresh rate via fast line-scanning amplitude-encoded scattering-assisted holography.
- Author
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Shibukawa A, Higuchi R, Song G, Mikami H, Sudo Y, and Jang M
- Abstract
The capability of focus control has been central to optical technologies that require both high temporal and spatial resolutions. However, existing varifocal lens schemes are commonly limited to the response time on the microsecond timescale and share the fundamental trade-off between the response time and the tuning power. Here, we propose an ultrafast holographic focusing method enabled by translating the speed of a fast 1D beam scanner into the speed of the complex wavefront modulation of a relatively slow 2D spatial light modulator. Using a pair of a digital micromirror device and a resonant scanner, we demonstrate an unprecedented refresh rate of focus control of 31 MHz, which is more than 1,000 times faster than the switching rate of a digital micromirror device. We also show that multiple micrometer-sized focal spots can be independently addressed in a range of over 1 MHz within a large volume of 5 mm × 5 mm × 5.5 mm, validating the superior spatiotemporal characteristics of the proposed technique - high temporal and spatial precision, high tuning power, and random accessibility in a three-dimensional space. The demonstrated scheme offers a new route towards three-dimensional light manipulation in the 100 MHz regime., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
42. Highly efficient multi-resonance thermally activated delayed fluorescence material toward a BT.2020 deep-blue emitter.
- Author
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Ochi J, Yamasaki Y, Tanaka K, Kondo Y, Isayama K, Oda S, Kondo M, and Hatakeyama T
- Abstract
An ultrapure deep-blue multi-resonance-induced thermally activated delayed fluorescence material (DOB2-DABNA-A) is designed and synthesized. Benefiting from a fully resonating extended helical π-conjugated system, this compound has a small ΔE
ST value of 3.6 meV and sufficient spin-orbit coupling to exhibit a high-rate constant for reverse intersystem crossing (kRISC = 1.1 × 106 s-1 ). Furthermore, an organic light-emitting diode employing DOB2-DABNA-A as an emitter is fabricated; it exhibits ultrapure deep-blue emission at 452 nm with a small full width at half maximum of 24 nm, corresponding to Commission Internationale de l'Éclairage (CIE) coordinates of (0.145, 0.049). The high kRISC value reduces the efficiency roll-off, resulting in a high external quantum efficiency (EQE) of 21.6% at 1000 cd m-2 ., (© 2024. The Author(s).)- Published
- 2024
- Full Text
- View/download PDF
43. Broadened quantum critical ground state in a disordered superconducting thin film.
- Author
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Ienaga K, Tamoto Y, Yoda M, Yoshimura Y, Ishigami T, and Okuma S
- Abstract
A superconductor-insulator transition (SIT) in two dimensions is a prototypical quantum phase transition (QPT) with a clear quantum critical point (QCP) at zero temperature (T = 0). The SIT is induced by a field B and observed in disordered thin films. In some of weakly disordered or crystalline thin films, however, an anomalous metallic (AM) ground state emerges over a wide B range between the superconducting and insulating phases. It remains a fundamental open question how the QPT picture of the SIT is modified when the AM state appears. Here we present measurements of the Nernst effect N, which has great sensitivity to the fluctuations of the superconducting order parameter. From a thorough contour map of N in the B-T plane, we found a thermal-to-quantum crossover line of the superconducting fluctuations, a so-called ghost-temperature line associated with the QPT, as well as a ghost-field line associated with a thermal transition. The QCP is identified as a T = 0 intercept of the ghost-temperature line inside the AM state, which verifies that the AM state is a broadened critical state of the SIT., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
44. Delivery of a BET protein degrader via a CEACAM6-targeted antibody-drug conjugate inhibits tumour growth in pancreatic cancer models.
- Author
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Nakazawa Y, Miyano M, Tsukamoto S, Kogai H, Yamamoto A, Iso K, Inoue S, Yamane Y, Yabe Y, Umihara H, Taguchi J, Akagi T, Yamaguchi A, Koga M, Toshimitsu K, Hirayama T, Mukai Y, and Machinaga A
- Subjects
- Humans, Mice, Animals, Cell Line, Tumor, Tumor Microenvironment, Antigens, CD, Cell Adhesion Molecules, GPI-Linked Proteins, Immunoconjugates pharmacology, Immunoconjugates therapeutic use, Pancreatic Neoplasms genetics, Carcinoma, Pancreatic Ductal genetics
- Abstract
Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis of all cancers. To improve PDAC therapy, we establish screening systems based on organoid and co-culture technologies and find a payload of antibody-drug conjugate (ADC), a bromodomain and extra-terminal (BET) protein degrader named EBET. We select CEACAM6/CD66c as an ADC target and developed an antibody, #84.7, with minimal reactivity to CEACAM6-expressing normal cells. EBET-conjugated #84.7 (84-EBET) has lethal effects on various PDAC organoids and bystander efficacy on CEACAM6-negative PDAC cells and cancer-associated fibroblasts. In mouse studies, a single injection of 84-EBET induces marked tumor regression in various PDAC-patient-derived xenografts, with a decrease in the inflammatory phenotype of stromal cells and without significant body weight loss. Combination with standard chemotherapy or PD-1 antibody induces more profound and sustained regression without toxicity enhancement. Our preclinical evidence demonstrates potential efficacy by delivering BET protein degrader to PDAC and its microenvironment via CEACAM6-targeted ADC., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
45. Superconductivity in a van der Waals layered quasicrystal.
- Author
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Tokumoto Y, Hamano K, Nakagawa S, Kamimura Y, Suzuki S, Tamura R, and Edagawa K
- Abstract
Van der Waals layered transition-metal chalcogenides are drawing significant attention owing to their intriguing physical properties. This group of materials consists of abundant members with various elements, having a variety of different structures. However, they are all crystalline materials, and the physical properties of van der Waals layered quasicrystals have never been studied to date. Here, we report on the discovery of superconductivity in a van der Waals layered quasicrystal of Ta
1.6 Te. The electrical resistivity, magnetic susceptibility, and specific heat of the quasicrystal unambiguously validate the occurrence of bulk superconductivity at a transition temperature of ~1 K. This discovery can promote new research on assessing the physical properties of novel van der Waals layered quasicrystals as well as two-dimensional quasicrystals; moreover, it paves the way toward new frontiers of superconductivity in thermodynamically stable quasicrystals., (© 2024. The Author(s).)- Published
- 2024
- Full Text
- View/download PDF
46. Japanese wolves are most closely related to dogs and share DNA with East Eurasian dogs.
- Author
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Gojobori J, Arakawa N, Xiaokaiti X, Matsumoto Y, Matsumura S, Hongo H, Ishiguro N, and Terai Y
- Subjects
- Dogs, Animals, Phylogeny, Japan, DNA, Mitochondrial genetics, Genome, Wolves genetics
- Abstract
Although the domestic dog's origin is still unclear, this lineage is believed to have been domesticated from an extinct population of gray wolves, which is expected to be more closely related to dogs than to other populations of gray wolves. Here, we sequence the whole genomes of nine Japanese wolves (7.5-100x: Edo to Meiji periods) and 11 modern Japanese dogs and analyze them together with those from other populations of dogs and wolves. A phylogenomic tree shows that, among the gray wolves, Japanese wolves are closest to the dog, suggesting that the ancestor of dogs is closely related to the ancestor of the Japanese wolf. Based on phylogenetic and geographic relationships, the dog lineage has most likely originated in East Asia, where it diverged from a common ancestor with the Japanese wolf. Since East Eurasian dogs possess Japanese wolf ancestry, we estimate an introgression event from the ancestor of the Japanese wolf to the ancestor of the East Eurasian dog that occurred before the dog's arrival in the Japanese archipelago., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
47. Phosphorylation of plasma membrane H + -ATPase Thr881 participates in light-induced stomatal opening.
- Author
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Hayashi Y, Fukatsu K, Takahashi K, Kinoshita SN, Kato K, Sakakibara T, Kuwata K, and Kinoshita T
- Subjects
- Phosphorylation, Light, Plant Stomata metabolism, Proton-Translocating ATPases genetics, Proton-Translocating ATPases metabolism, Cell Membrane metabolism, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism
- Abstract
Plasma membrane (PM) H
+ -ATPase is crucial for light-induced stomatal opening and phosphorylation of a penultimate residue, Thr948 (pen-Thr, numbering according to Arabidopsis AHA1) is required for enzyme activation. In this study, a comprehensive phosphoproteomic analysis using guard cell protoplasts from Vicia faba shows that both red and blue light increase the phosphorylation of Thr881, of PM H+ -ATPase. Light-induced stomatal opening and the blue light-induced increase in stomatal conductance are reduced in transgenic Arabidopsis plants expressing mutant AHA1-T881A in aha1-9, whereas the blue light-induced phosphorylation of pen-Thr is unaffected. Auxin and photosynthetically active radiation induce the phosphorylation of both Thr881 and pen-Thr in etiolated seedlings and leaves, respectively. The dephosphorylation of phosphorylated Thr881 and pen-Thr are mediated by type 2 C protein phosphatase clade D isoforms. Taken together, Thr881 phosphorylation, in addition of the pen-Thr phosphorylation, are important for PM H+ -ATPase function during physiological responses, such as light-induced stomatal opening in Arabidopsis thaliana., (© 2024. The Author(s).)- Published
- 2024
- Full Text
- View/download PDF
48. Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant.
- Author
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Tamura T, Irie T, Deguchi S, Yajima H, Tsuda M, Nasser H, Mizuma K, Plianchaisuk A, Suzuki S, Uriu K, Begum MM, Shimizu R, Jonathan M, Suzuki R, Kondo T, Ito H, Kamiyama A, Yoshimatsu K, Shofa M, Hashimoto R, Anraku Y, Kimura KT, Kita S, Sasaki J, Sasaki-Tabata K, Maenaka K, Nao N, Wang L, Oda Y, Ikeda T, Saito A, Matsuno K, Ito J, Tanaka S, Sato K, Hashiguchi T, Takayama K, and Fukuhara T
- Subjects
- Animals, Cricetinae, Humans, Codon, Nonsense, Phylogeny, SARS-CoV-2 genetics, Biological Assay, COVID-19
- Abstract
Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
49. Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases.
- Author
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Furuta Y, Yamamoto H, Hirakawa T, Uemura A, Pelayo MA, Iimura H, Katagiri N, Takeda-Kamiya N, Kumaishi K, Shirakawa M, Ishiguro S, Ichihashi Y, Suzuki T, Goh T, Toyooka K, Ito T, and Yamaguchi N
- Subjects
- Flowers genetics, Reactive Oxygen Species metabolism, Autophagy, Chromatin metabolism, Gene Expression Regulation, Plant, Arabidopsis genetics, Cyclopentanes, Oxylipins
- Abstract
In angiosperms, the transition from floral-organ maintenance to abscission determines reproductive success and seed dispersion. For petal abscission, cell-fate decisions specifically at the petal-cell base are more important than organ-level senescence or cell death in petals. However, how this transition is regulated remains unclear. Here, we identify a jasmonic acid (JA)-regulated chromatin-state switch at the base of Arabidopsis petals that directs local cell-fate determination via autophagy. During petal maintenance, co-repressors of JA signaling accumulate at the base of petals to block MYC activity, leading to lower levels of ROS. JA acts as an airborne signaling molecule transmitted from stamens to petals, accumulating primarily in petal bases to trigger chromatin remodeling. This allows MYC transcription factors to promote chromatin accessibility for downstream targets, including NAC DOMAIN-CONTAINING PROTEIN102 (ANAC102). ANAC102 accumulates specifically at the petal base prior to abscission and triggers ROS accumulation and cell death via AUTOPHAGY-RELATED GENEs induction. Developmentally induced autophagy at the petal base causes maturation, vacuolar delivery, and breakdown of autophagosomes for terminal cell differentiation. Dynamic changes in vesicles and cytoplasmic components in the vacuole occur in many plants, suggesting JA-NAC-mediated local cell-fate determination by autophagy may be conserved in angiosperms., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
50. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders.
- Author
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Yang Q, Wang B, Lemey P, Dong L, Mu T, Wiebe RA, Guo F, Trovão NS, Park SW, Lewis N, Tsui JL, Bajaj S, Cheng Y, Yang L, Haba Y, Li B, Zhang G, Pybus OG, Tian H, and Grenfell B
- Subjects
- Animals, Animals, Wild, Birds, Phylogeny, Poultry, Influenza A virus genetics, Influenza in Birds transmission, Animal Migration
- Abstract
Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
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