1
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Matsuoka S, Sakakura K, Akinaga Y, Akisawa K, Okuwaki K, Doi H, Mochizuki Y. Enhancement of energy decomposition analysis in fragment molecular orbital calculations. J Comput Chem 2024; 45:898-902. [PMID: 38158621 DOI: 10.1002/jcc.27297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Energy decomposition analysis is one of the most attractive features of fragment molecular orbital (FMO) calculations from the point of view of practical applications. Here we report some enhancements for PIEDA in the ABINIT-MP program. One is a separation of the dispersion-type stabilization from the electron correlation energy, traditionally referred to as the "dispersion interaction" (DI). Another is an alternative evaluation of the electrostatic (ES) interaction using the restrained electrostatic potential (RESP) charges. The GA:CT stacked base pair and the Trp-Cage miniprotein were used as illustrative examples.
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Affiliation(s)
- Sota Matsuoka
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | | | | | - Kazuki Akisawa
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | - Koji Okuwaki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
- JSOL Corp., Kudan-Kaikan Terrace, Tokyo, Japan
| | - Hideo Doi
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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2
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Kawaji T, Fujibayashi M, Abe K. Goal-directed and flexible modulation of syllable sequence within birdsong. Nat Commun 2024; 15:3419. [PMID: 38658545 DOI: 10.1038/s41467-024-47824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Songs constitute a complex system of vocal signals for inter-individual communication in songbirds. Here, we elucidate the flexibility which songbirds exhibit in the organizing and sequencing of syllables within their songs. Utilizing a newly devised song decoder for quasi-real-time annotation, we execute an operant conditioning paradigm, with rewards contingent upon specific syllable syntax. Our analysis reveals that birds possess the capacity to modify the contents of their songs, adjust the repetition length of particular syllables and employing specific motifs. Notably, birds altered their syllable sequence in a goal-directed manner to obtain rewards. We demonstrate that such modulation occurs within a distinct song segment, with adjustments made within 10 minutes after cue presentation. Additionally, we identify the involvement of the parietal-basal ganglia pathway in orchestrating these flexible modulations of syllable sequences. Our findings unveil an unappreciated aspect of songbird communication, drawing parallels with human speech.
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Affiliation(s)
- Takuto Kawaji
- Lab of Brain Development, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Sendai, Miyagi, 980-8577, Japan
| | - Mizuki Fujibayashi
- Lab of Brain Development, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Sendai, Miyagi, 980-8577, Japan
| | - Kentaro Abe
- Lab of Brain Development, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Sendai, Miyagi, 980-8577, Japan.
- Division for the Establishment of Frontier Sciences of the Organization for Advanced Studies, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
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3
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Jung J, Tan C, Sugita Y. GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Nat Commun 2024; 15:3370. [PMID: 38643169 PMCID: PMC11032353 DOI: 10.1038/s41467-024-47654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.
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Affiliation(s)
- Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Cheng Tan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan.
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4
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Heiss JE, Zhong P, Lee SM, Yamanaka A, Kilduff TS. Distinct lateral hypothalamic CaMKIIα neuronal populations regulate wakefulness and locomotor activity. Proc Natl Acad Sci U S A 2024; 121:e2316150121. [PMID: 38593074 PMCID: PMC11032496 DOI: 10.1073/pnas.2316150121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
For nearly a century, evidence has accumulated indicating that the lateral hypothalamus (LH) contains neurons essential to sustain wakefulness. While lesion or inactivation of LH neurons produces a profound increase in sleep, stimulation of inhibitory LH neurons promotes wakefulness. To date, the primary wake-promoting cells that have been identified in the LH are the hypocretin/orexin (Hcrt) neurons, yet these neurons have little impact on total sleep or wake duration across the 24-h period. Recently, we and others have identified other LH populations that increase wakefulness. In the present study, we conducted microendoscopic calcium imaging in the LH concomitant with EEG and locomotor activity (LMA) recordings and found that a subset of LH neurons that express Ca2+/calmodulin-dependent protein kinase IIα (CaMKIIα) are preferentially active during wakefulness. Chemogenetic activation of these neurons induced sustained wakefulness and greatly increased LMA even in the absence of Hcrt signaling. Few LH CaMKIIα-expressing neurons are hypocretinergic or histaminergic while a small but significant proportion are GABAergic. Ablation of LH inhibitory neurons followed by activation of the remaining LH CaMKIIα neurons induced similar levels of wakefulness but blunted the LMA increase. Ablated animals showed no significant changes in sleep architecture but both spontaneous LMA and high theta (8 to 10 Hz) power during wakefulness were reduced. Together, these findings indicate the existence of two subpopulations of LH CaMKIIα neurons: an inhibitory population that promotes locomotion without affecting sleep architecture and an excitatory population that promotes prolonged wakefulness even in the absence of Hcrt signaling.
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Affiliation(s)
- Jaime E. Heiss
- Center for Neuroscience, Biosciences Division, SRI International, Menlo Park, CA94025
| | - Peng Zhong
- Center for Neuroscience, Biosciences Division, SRI International, Menlo Park, CA94025
| | - Stephanie M. Lee
- Center for Neuroscience, Biosciences Division, SRI International, Menlo Park, CA94025
| | - Akihiro Yamanaka
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya464-8601, Japan
| | - Thomas S. Kilduff
- Center for Neuroscience, Biosciences Division, SRI International, Menlo Park, CA94025
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5
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Nishito Y, Kamimura Y, Nagamatsu S, Yamamoto N, Yasui H, Kambe T. Zinc and manganese homeostasis closely interact in mammalian cells. FASEB J 2024; 38:e23605. [PMID: 38597508 DOI: 10.1096/fj.202400181r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
Understanding the homeostatic interactions among essential trace metals is important for explaining their roles in cellular systems. Recent studies in vertebrates suggest that cellular Mn metabolism is related to Zn metabolism in multifarious cellular processes. However, the underlying mechanism remains unclear. In this study, we examined the changes in the expression of proteins involved in cellular Zn and/or Mn homeostatic control and measured the Mn as well as Zn contents and Zn enzyme activities to elucidate the effects of Mn and Zn homeostasis on each other. Mn treatment decreased the expression of the Zn homeostatic proteins metallothionein (MT) and ZNT1 and reduced Zn enzyme activities, which were attributed to the decreased Zn content. Moreover, loss of Mn efflux transport protein decreased MT and ZNT1 expression and Zn enzyme activity without changing extracellular Mn content. This reduction was not observed when supplementing with the same Cu concentrations and in cells lacking Cu efflux proteins. Furthermore, cellular Zn homeostasis was oppositely regulated in cells expressing Zn and Mn importer ZIP8, depending on whether Zn or Mn concentration was elevated in the extracellular milieu. Our results provide novel insights into the intricate interactions between Mn and Zn homeostasis in mammalian cells and facilitate our understanding of the physiopathology of Mn, which may lead to the development of treatment strategies for Mn-related diseases in the future.
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Affiliation(s)
- Yukina Nishito
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yoshiki Kamimura
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shino Nagamatsu
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nao Yamamoto
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hiroyuki Yasui
- Department of Analytical and Bioinorganic Chemistry, Division of Analytical and Physical Sciences, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Taiho Kambe
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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6
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Otake S, Saito K, Chiba Y, Yamada A, Fukumoto S. S100a6 knockdown promotes the differentiation of dental epithelial cells toward the epidermal lineage instead of the odontogenic lineage. FASEB J 2024; 38:e23608. [PMID: 38593315 DOI: 10.1096/fj.202302412rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Tooth development is a complex process involving various signaling pathways and genes. Recent findings suggest that ion channels and transporters, including the S100 family of calcium-binding proteins, may be involved in tooth formation. However, our knowledge in this regard is limited. Therefore, this study aimed to investigate the expression of S100 family members and their functions during tooth formation. Tooth germs were extracted from the embryonic and post-natal mice and the expression of S100a6 was examined. Additionally, the effects of S100a6 knockdown and calcium treatment on S100a6 expression and the proliferation of SF2 cells were examined. Microarrays and single-cell RNA-sequencing indicated that S100a6 was highly expressed in ameloblasts. Immunostaining of mouse tooth germs showed that S100a6 was expressed in ameloblasts but not in the undifferentiated dental epithelium. Additionally, S100a6 was localized to the calcification-forming side in enamel-forming ameloblasts. Moreover, siRNA-mediated S100a6 knockdown in ameloblasts reduced intracellular calcium concentration and the expression of ameloblast marker genes, indicating that S100a6 is associated with ameloblast differentiation. Furthermore, S100a6 knockdown inhibited the ERK/PI3K signaling pathway, suppressed ameloblast proliferation, and promoted the differentiation of the dental epithelium toward epidermal lineage. Conclusively, S100a6 knockdown in the dental epithelium suppresses cell proliferation via calcium and intracellular signaling and promotes differentiation of the dental epithelium toward the epidermal lineage.
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Grants
- 23H03109 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21J21873 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H03296 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H00488 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20K20612 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Shinji Otake
- Division of Pediatric Dentistry, Department of Community Social Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Kan Saito
- Division of Pediatric Dentistry, Department of Community Social Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Yuta Chiba
- Division of Pediatric Dentistry, Department of Community Social Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Aya Yamada
- Division of Pediatric Dentistry, Department of Community Social Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoshi Fukumoto
- Division of Pediatric Dentistry, Department of Community Social Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
- Section of Pediatric Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
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7
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Sakurai R, Fukuda Y, Tada C. Circular metagenome-assembled genome of Candidatus Patescibacteria recovered from anaerobic digestion sludge. Microbiol Resour Announc 2024; 13:e0008324. [PMID: 38526092 PMCID: PMC11008200 DOI: 10.1128/mra.00083-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
A single-contig, circular metagenome-assembled genome (cMAG) of Candidatus (Ca.) Patescibacteria was reconstructed from a mesophilic full-scale food waste treatment plant in Japan. The genome is of small size and lacks fundamental biosynthetic pathways. Taxonomic analysis using the Genome Taxonomy Database revealed that this cMAG belonged to the genus JAEZRQ01 (Ca. Parcubacteria).
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Affiliation(s)
- Riku Sakurai
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
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8
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Homma H, Yoshioka Y, Fujita K, Shirai S, Hama Y, Komano H, Saito Y, Yabe I, Okano H, Sasaki H, Tanaka H, Okazawa H. Dynamic molecular network analysis of iPSC-Purkinje cells differentiation delineates roles of ISG15 in SCA1 at the earliest stage. Commun Biol 2024; 7:413. [PMID: 38594382 PMCID: PMC11003991 DOI: 10.1038/s42003-024-06066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 03/18/2024] [Indexed: 04/11/2024] Open
Abstract
Better understanding of the earliest molecular pathologies of all neurodegenerative diseases is expected to improve human therapeutics. We investigated the earliest molecular pathology of spinocerebellar ataxia type 1 (SCA1), a rare familial neurodegenerative disease that primarily induces death and dysfunction of cerebellum Purkinje cells. Extensive prior studies have identified involvement of transcription or RNA-splicing factors in the molecular pathology of SCA1. However, the regulatory network of SCA1 pathology, especially central regulators of the earliest developmental stages and inflammatory events, remains incompletely understood. Here, we elucidated the earliest developmental pathology of SCA1 using originally developed dynamic molecular network analyses of sequentially acquired RNA-seq data during differentiation of SCA1 patient-derived induced pluripotent stem cells (iPSCs) to Purkinje cells. Dynamic molecular network analysis implicated histone genes and cytokine-relevant immune response genes at the earliest stages of development, and revealed relevance of ISG15 to the following degradation and accumulation of mutant ataxin-1 in Purkinje cells of SCA1 model mice and human patients.
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Affiliation(s)
- Hidenori Homma
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Yuki Yoshioka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kyota Fujita
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Research Center for Child Mental Development, Kanazawa University, 13-1 Takaramachi, Kanazawa-shi, Ishikawa, 920-8640, Japan
| | - Shinichi Shirai
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Yuka Hama
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Hajime Komano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yuko Saito
- Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Ichiro Yabe
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hidenao Sasaki
- Department of Neurology, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Hikari Tanaka
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Hitoshi Okazawa
- Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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9
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Temma K, Oketani R, Kubo T, Bando K, Maeda S, Sugiura K, Matsuda T, Heintzmann R, Kaminishi T, Fukuda K, Hamasaki M, Nagai T, Fujita K. Selective-plane-activation structured illumination microscopy. Nat Methods 2024:10.1038/s41592-024-02236-3. [PMID: 38580844 DOI: 10.1038/s41592-024-02236-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
The background light from out-of-focus planes hinders resolution enhancement in structured illumination microscopy when observing volumetric samples. Here we used selective plane illumination and reversibly photoswitchable fluorescent proteins to realize structured illumination within the focal plane and eliminate the out-of-focus background. Theoretical investigation of the imaging properties and experimental demonstrations show that selective plane activation is beneficial for imaging dense microstructures in cells and cell spheroids.
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Affiliation(s)
- Kenta Temma
- Department of Applied Physics, Osaka University, Osaka, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Ryosuke Oketani
- Department of Applied Physics, Osaka University, Osaka, Japan
- Department of Chemistry, Kyushu University, Fukuoka, Japan
| | - Toshiki Kubo
- Department of Applied Physics, Osaka University, Osaka, Japan
| | - Kazuki Bando
- Department of Applied Physics, Osaka University, Osaka, Japan
| | - Shunsuke Maeda
- Department of Applied Physics, Osaka University, Osaka, Japan
| | - Kazunori Sugiura
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Tomoki Matsuda
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller University Jena, Jena, Germany
| | - Tatsuya Kaminishi
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koki Fukuda
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Takeharu Nagai
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
- Research Institute for Electronic Science, Hokkaido University, Hokkaido, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, Osaka, Japan.
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Osaka, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.
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10
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Koga S, Takazono T, Namie H, Okuno D, Ito Y, Nakada N, Hirayama T, Takeda K, Ide S, Iwanaga N, Tashiro M, Sakamoto N, Watanabe A, Izumikawa K, Yanagihara K, Tanaka Y, Mukae H. Human Vγ9Vδ2 T cells exhibit antifungal activity against Aspergillus fumigatus and other filamentous fungi. Microbiol Spectr 2024; 12:e0361423. [PMID: 38426765 DOI: 10.1128/spectrum.03614-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/11/2024] [Indexed: 03/02/2024] Open
Abstract
Invasive aspergillosis (IA) and mucormycosis are life-threatening diseases, especially among immunocompromised patients. Drug-resistant Aspergillus fumigatus strains have been isolated worldwide, which can pose a serious clinical problem. As IA mainly occurs in patients with compromised immune systems, the ideal therapeutic approach should aim to bolster the immune system. In this study, we focused on Vγ9Vδ2 T cells that exhibit immune effector functions and examined the possibility of harnessing this unconventional T cell subset as a novel therapeutic modality for IA. A potent antifungal effect was observed when A. fumigatus (Af293) hyphae were challenged by Vγ9Vδ2 T cells derived from peripheral blood. In addition, Vγ9Vδ2 T cells exhibited antifungal activity against hyphae of all Aspergillus spp., Cunninghamella bertholletiae, and Rhizopus microsporus but not against their conidia. Furthermore, Vγ9Vδ2 T cells also exhibited antifungal activity against azole-resistant A. fumigatus, indicating that Vγ9Vδ2 T cells could be used for treating drug-resistant A. fumigatus. The antifungal activity of Vγ9Vδ2 T cells depended on cell-to-cell contact with A. fumigatus hyphae, and degranulation characterized by CD107a mobilization seems essential for this activity against A. fumigatus. Vγ9Vδ2 T cells could be developed as a novel modality for treating IA or mucormycosis. IMPORTANCE Invasive aspergillosis (IA) and mucormycosis are often resistant to treatment with conventional antifungal agents and have a high mortality rate. Additionally, effective antifungal treatment is hindered by drug toxicity, given that both fungal and human cells are eukaryotic, and antifungal agents are also likely to act on human cells, resulting in adverse effects. Therefore, the development of novel therapeutic agents specifically targeting fungi is challenging. This study demonstrated the antifungal activity of Vγ9Vδ2 T cells against various Aspergillus spp. and several Mucorales in vitro and discussed the mechanism underlying their antifungal activity. We indicate that adoptive immunotherapy using Vγ9Vδ2 T cells may offer a new therapeutic approach to IA.
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Affiliation(s)
- Satoru Koga
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Takahiro Takazono
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hodaka Namie
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Daisuke Okuno
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Yuya Ito
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Nana Nakada
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
- Health Center, Nagasaki University, Nagasaki, Japan
| | - Tatsuro Hirayama
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
- Department of Pharmacotherapeutics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kazuaki Takeda
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Shotaro Ide
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
- Infectious Diseases Experts Training Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Naoki Iwanaga
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Masato Tashiro
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Noriho Sakamoto
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, Nagasaki, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
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11
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Shinozaki D, Takayama E, Kawakami N, Yoshimoto K. Autophagy maintains endosperm quality during seed storage to preserve germination ability in Arabidopsis. Proc Natl Acad Sci U S A 2024; 121:e2321612121. [PMID: 38530890 PMCID: PMC10998590 DOI: 10.1073/pnas.2321612121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
To preserve germination ability, plant seeds must be protected from environmental stresses during the storage period. Here, we demonstrate that autophagy, an intracellular degradation system, maintains seed germination ability in Arabidopsis thaliana. The germination ability of long-term (>5 years) stored dry seeds of autophagy-defective (atg) mutant and wild-type (WT) plants was compared. Long-term stored (old) seeds of atg mutants showed lower germination ability than WT seeds, although short-term stored (new) seeds of atg mutants did not show such a phenotype. After removal of the seed coat and endosperm from old atg mutant seeds, the embryos developed into seedlings. Autophagic flux was maintained in endosperm cells during the storage period, and autophagy defect resulted in the accumulation of oxidized proteins and accelerated endosperm cell death. Consistent with these findings, the transcripts of genes, ENDO-β-MANNANASE 7 and EXPANSIN 2, which are responsible for degradation/remodeling of the endosperm cell wall during germination, were reduced in old atg mutant seeds. We conclude that autophagy maintains endosperm quality during seed storage by suppressing aging-dependent oxidative damage and cell death, which allows the endosperm to perform optimal functions during germination, i.e., cell wall degradation/remodeling, even after long-term storage.
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Grants
- 16H07255 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 19H05713 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20H03281 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- S1411023 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 23H02506 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21J11995 MEXT | Japan Society for the Promotion of Science (JSPS)
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Affiliation(s)
- Daiki Shinozaki
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki214-8571, Kanagawa, Japan
| | - Erina Takayama
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
| | - Kohki Yoshimoto
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
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12
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Anzai I, Fujita J, Ono C, Kosaka Y, Miyamoto Y, Shichinohe S, Takada K, Torii S, Taguwa S, Suzuki K, Makino F, Kajita T, Inoue T, Namba K, Watanabe T, Matsuura Y. Characterization of a neutralizing antibody that recognizes a loop region adjacent to the receptor-binding interface of the SARS-CoV-2 spike receptor-binding domain. Microbiol Spectr 2024; 12:e0365523. [PMID: 38415660 DOI: 10.1128/spectrum.03655-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Although the global crisis caused by the coronavirus disease 2019 (COVID-19) pandemic is over, the global epidemic of the disease continues. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of COVID-19, initiates infection via the binding of the receptor-binding domain (RBD) of its spike protein to the human angiotensin-converting enzyme II (ACE2) receptor, and this interaction has been the primary target for the development of COVID-19 therapeutics. Here, we identified neutralizing antibodies against SARS-CoV-2 by screening mouse monoclonal antibodies and characterized an antibody, CSW1-1805, that targets a narrow region at the RBD ridge of the spike protein. CSW1-1805 neutralized several variants in vitro and completely protected mice from SARS-CoV-2 infection. Cryo-EM and biochemical analyses revealed that this antibody recognizes the loop region adjacent to the ACE2-binding interface with the RBD in both a receptor-inaccessible "down" state and a receptor-accessible "up" state and could stabilize the RBD conformation in the up-state. CSW1-1805 also showed different binding orientations and complementarity determining region properties compared to other RBD ridge-targeting antibodies with similar binding epitopes. It is important to continuously characterize neutralizing antibodies to address new variants that continue to emerge. Our characterization of this antibody that recognizes the RBD ridge of the spike protein will aid in the development of future neutralizing antibodies.IMPORTANCESARS-CoV-2 cell entry is initiated by the interaction of the viral spike protein with the host cell receptor. Therefore, mechanistic findings regarding receptor recognition by the spike protein help uncover the molecular mechanism of SARS-CoV-2 infection and guide neutralizing antibody development. Here, we characterized a SARS-CoV-2 neutralizing antibody that recognizes an epitope, a loop region adjacent to the receptor-binding interface, that may be involved in the conformational transition of the receptor-binding domain (RBD) of the spike protein from a receptor-inaccessible "down" state into a receptor-accessible "up" state, and also stabilizes the RBD in the up-state. Our mechanistic findings provide new insights into SARS-CoV-2 receptor recognition and guidance for neutralizing antibody development.
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Grants
- JP16H06429, JP16K21723, JP16H06432 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06429, JP16K21723, JP16H06434 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15042 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP25K000013 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K22630 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP223fa627002, JP22am0401030, JP23fk0108659, JP20jk0210021, JP22gm1610010, JP19fk0108113 Japan Agency for Medical Research and Development (AMED)
- JP223fa627002 Japan Agency for Medical Research and Development (AMED)
- JP19fk0108113, JP20fk0108281, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP21am0101117, JP17pc0101020 Japan Agency for Medical Research and Development (AMED)
- JPMJOP1861 MEXT | Japan Science and Technology Agency (JST)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Itsuki Anzai
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Chikako Ono
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | | | | | - Shintaro Shichinohe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shuhei Taguwa
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- JEOL Ltd., Akishima, Tokyo, Japan
| | | | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research and Spring-8 Center, Suita, Osaka, Japan
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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13
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Matsuda K, Nakahara Y, Choirunnisa AR, Arima K, Wakimoto T. Phylogeny-guided Characterization of Bacterial Hydrazine Biosynthesis Mediated by Cupin/methionyl tRNA Synthetase-like Enzymes. Chembiochem 2024; 25:e202300838. [PMID: 38403952 DOI: 10.1002/cbic.202300838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/27/2024] [Accepted: 02/25/2024] [Indexed: 02/27/2024]
Abstract
Cupin/methionyl-tRNA synthetase (MetRS)-like didomain enzymes catalyze nitrogen-nitrogen (N-N) bond formation between Nω-hydroxylamines and amino acids to generate hydrazines, key biosynthetic intermediates of various natural products containing N-N bonds. While the combination of these two building blocks leads to the creation of diverse hydrazine products, the full extent of their structural diversity remains largely unknown. To explore this, we herein conducted phylogeny-guided genome-mining of related hydrazine biosynthetic pathways consisting of two enzymes: flavin-dependent Nω-hydroxylating monooxygenases (NMOs) that produce Nω-hydroxylamine precursors and cupin/MetRS-like enzymes that couple the Nω-hydroxylamines with amino acids via N-N bonds. A phylogenetic analysis identified the largely unexplored sequence spaces of these enzyme families. The biochemical characterization of NMOs demonstrated their capabilities to produce various Nω-hydroxylamines, including those previously not known as precursors of N-N bonds. Furthermore, the characterization of cupin/MetRS-like enzymes identified five new hydrazine products with novel combinations of building blocks, including one containing non-amino acid building blocks: 1,3-diaminopropane and putrescine. This study substantially expanded the variety of N-N bond forming pathways mediated by cupin/MetRS-like enzymes.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuto Nakahara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Atina Rizkiya Choirunnisa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kuga Arima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
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14
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Ando R, Shimozono S, Ago H, Takagi M, Sugiyama M, Kurokawa H, Hirano M, Niino Y, Ueno G, Ishidate F, Fujiwara T, Okada Y, Yamamoto M, Miyawaki A. StayGold variants for molecular fusion and membrane-targeting applications. Nat Methods 2024; 21:648-656. [PMID: 38036853 PMCID: PMC11009113 DOI: 10.1038/s41592-023-02085-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023]
Abstract
Although StayGold is a bright and highly photostable fluorescent protein, its propensity for obligate dimer formation may hinder applications in molecular fusion and membrane targeting. To attain monovalent as well as bright and photostable labeling, we engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, we disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. We applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. We achieved cell-wide, high-spatiotemporal resolution and sustained imaging of dynamic subcellular events, including the targeting of endogenous condensin I to mitotic chromosomes, the movement of the Golgi apparatus and its membranous derivatives along microtubule networks, the distribution of cortical filamentous actin and the remolding of cristae membranes within mobile mitochondria.
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Affiliation(s)
- Ryoko Ando
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
- Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, Wako-city, Japan
- Department of Optical Biomedical Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Satoshi Shimozono
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research (CPR), Saitama, Japan
| | - Mayu Sugiyama
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Hiroshi Kurokawa
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Masahiko Hirano
- Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, Wako-city, Japan
| | - Yusuke Niino
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Japan
| | - Fumiyoshi Ishidate
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
- Department of Cell Biology, Department of Physics, UBI and WPI-IRCN, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan.
- Biotechnological Optics Research Team, RIKEN Center for Advanced Photonics, Wako-city, Japan.
- Laboratory of Bioresponse Analysis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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15
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Uneme Y, Maeda R, Nakayama G, Narita H, Takeda N, Hiramatsu R, Nishihara H, Nakato R, Kanai Y, Araki K, Siomi MC, Yamanaka S. Morc1 reestablishes H3K9me3 heterochromatin on piRNA-targeted transposons in gonocytes. Proc Natl Acad Sci U S A 2024; 121:e2317095121. [PMID: 38502704 PMCID: PMC10990106 DOI: 10.1073/pnas.2317095121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/23/2024] [Indexed: 03/21/2024] Open
Abstract
To maintain fertility, male mice re-repress transposable elements (TEs) that were de-silenced in the early gonocytes before their differentiation into spermatogonia. However, the mechanism of TE silencing re-establishment remains unknown. Here, we found that the DNA-binding protein Morc1, in cooperation with the methyltransferase SetDB1, deposits the repressive histone mark H3K9me3 on a large fraction of activated TEs, leading to heterochromatin. Morc1 also triggers DNA methylation, but TEs targeted by Morc1-driven DNA methylation only slightly overlapped with those repressed by Morc1/SetDB1-dependent heterochromatin formation, suggesting that Morc1 silences TEs in two different manners. In contrast, TEs regulated by Morc1 and Miwi2, the nuclear PIWI-family protein, almost overlapped. Miwi2 binds to PIWI-interacting RNAs (piRNAs) that base-pair with TE mRNAs via sequence complementarity, while Morc1 DNA binding is not sequence specific, suggesting that Miwi2 selects its targets, and then, Morc1 acts to repress them with cofactors. A high-ordered mechanism of TE repression in gonocytes has been identified.
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Affiliation(s)
- Yuta Uneme
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Ryu Maeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Gen Nakayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Haruka Narita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Naoki Takeda
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
| | - Ryuji Hiramatsu
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Hidenori Nishihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara631-8505, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo113-0032, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
- Faculty of Life Sciences, Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Honjo, Kumamoto860-8556, Japan
| | - Mikiko C. Siomi
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
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16
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Akutsu T, Tezuka T, Maruko M, Hirata A, Ohnishi Y. The ssgB gene is required for the early stages of sporangium formation in Actinoplanes missouriensis. J Bacteriol 2024; 206:e0042823. [PMID: 38353530 PMCID: PMC10956132 DOI: 10.1128/jb.00428-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/26/2024] [Indexed: 03/22/2024] Open
Abstract
In Streptomyces, multiple paralogs of SsgA-like proteins (SALPs) are involved in spore formation from aerial hyphae. However, the functions of SALPs have not yet been elucidated in other actinobacterial genera. Here, we report the primary function of an SsgB ortholog (AmSsgB) in Actinoplanes missouriensis, which develops terminal sporangia on the substrate mycelia via short sporangiophores. Importantly, AmSsgB is the sole SALP in A. missouriensis. The transcription of AmssgB was upregulated during sporangium formation, consistent with our previous findings that AmssgB is a member of the AmBldD regulon. The AmssgB null mutant (ΔAmssgB) strain formed non-globose irregular structures on the substrate mycelium. Transmission electron microscopy revealed that the irregular structures contained abnormally septate hypha-like cells, without an intrasporangial matrix. These phenotypic changes were restored by complementation with AmssgB. Additionally, analysis of the heterologous expression of seven SALP-encoding genes from Streptomyces coelicolor A3(2) (ssgA-G) in the ΔAmssgB strain revealed that only ssgB could compensate for AmSsgB deficiency. This indicated that SsgB of S. coelicolor A3(2) and AmSsgB have comparable functions in A. missouriensis. In contrast to the ΔAmssgB strain, the ftsZ-disrupted strain showed a severe growth defect and produced small sporangium-like structures that swelled to some extent. These findings indicate that AmSsgB is crucial for the early stages of sporangium formation, not for spore septum formation in the late stages. We propose that AmSsgB is involved in sporangium formation by promoting the expansion of the "presporangium" structures formed on the tips of the substrate hyphae. IMPORTANCE SsgB has been proposed as an archetypical SsgA-like protein with an evolutionarily conserved function in the morphological development of spore-forming actinomycetes. SsgB in Streptomyces coelicolor A3(2) is involved in spore septum formation. However, it is unclear whether this is the primary function of SsgBs in actinobacteria. This study demonstrated that the SsgB ortholog (AmSsgB) in Actinoplanes missouriensis is essential for sporangium expansion, which does not seem to be related to spore septum formation. However, the heterologous expression of ssgB from S. coelicolor A3(2) restored morphological abnormalities in the ΔAmssgB mutant. We propose that the primary function of SsgB is to initiate sporulation in differentiating cells (e.g., aerial hyphae in Streptomyces and "presporangium" cells in A. missouriensis) although its molecular mechanism remains unknown.
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Affiliation(s)
- Takuya Akutsu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Manato Maruko
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Aiko Hirata
- Bioimaging Center, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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17
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Sadaoka N, Le MNT, Kawada-Matsuo M, Eng S, Zendo T, Nakanishi J, Takeda K, Shiba H, Komatsuzawa H. Opposing genetic polymorphisms of two ABC transporters contribute to the variation of nukacin resistance in Streptococcus mutans. Appl Environ Microbiol 2024; 90:e0208423. [PMID: 38411065 PMCID: PMC10952377 DOI: 10.1128/aem.02084-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
Streptococcus mutans is a cariogenic bacterium that produces a variety of bacteriocins and retains resistance to these bacteriocins. In this study, we investigated the susceptibility of 127 S. mutans strains to nukacins produced by Staphylococcus spp., which are commensal bacteria in humans. We detected diverse susceptibilities among strains. Nineteen strains had a disrupted LctF (type I), which is responsible for nukacin susceptibility, whereas the remaining 108 strains had an intact LctF (type II) and displayed resistance to nukacins. However, the type I strains still showed resistance to nukacins to some extent. Interestingly, 18/19 (94.7%) type I strains carried a mukA-T locus, which is related to the synthesis of mutacin K8, and mukFEG, an ABC transporter. In contrast, among type II strains, only 6/108 strains (5.6%) had both the mukA-T locus and mukFEG, 19/108 strains (17.6%) carried only mukFEG, and 83/108 strains (76.9%) harbored neither mukA-T nor mukFEG. We also found that MukF had two variants: 305 amino acids (type α) and 302 amino acids (type β). All type I strains showed a type α (MukFα), whereas most type II strains with mukFEG (22/25 strains) had a type β (MukFβ). Then, we constructed a mukFEG-deletion mutant complemented with MukFαEG or MukFβEG and found that only MukFαEG was involved in nukacin resistance. The nukacin resistance capability of type II-LctFEG was stronger than that of MukFαEG. In conclusion, we identified a novel nukacin resistance factor, MukFEG, and either LctFEG or MukFEG was active in most strains via genetic polymorphisms depending on mukA-T genes. IMPORTANCE Streptococcus mutans is an important pathogenic bacterium not only for dental caries but also for systemic diseases. S. mutans is known to produce a variety of bacteriocins and to retain resistance these bacteriocins. In this study, two ABC transporters, LctFEG and MukFEG, were implicated in nukacin resistance and each ABC transporter has two subtypes, active and inactive. Of the two ABC transporters, only one ABC transporter was always resistant, while the other ABC transporter was inactivated by genetic mutation. Interestingly, this phenomenon was defined by the presence or absence of the mutacin K8 synthesis gene region, one of the bacteriocins of S. mutans. This suggests that the resistance acquisition is tightly controlled in each strain. This study provides important evidence that the insertion of bacteriocin synthesis genes is involved in the induction of genetic polymorphisms and suggests that bacteriocin synthesis genes may play an important role in bacterial evolution.
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Affiliation(s)
- Naoki Sadaoka
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Mi Nguyen-Tra Le
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Centre for Oral Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Miki Kawada-Matsuo
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Centre for Oral Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Sopongselamuny Eng
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Takeshi Zendo
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Jun Nakanishi
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Katsuhiro Takeda
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hideki Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Centre for Oral Infectious Diseases, Hiroshima University, Hiroshima, Japan
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18
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Tabata K, Son S, Miyata J, Toriumi K, Miyashita M, Suzuki K, Itokawa M, Takahashi H, Murai T, Arai M. Association of homocysteine with white matter dysconnectivity in schizophrenia. Schizophrenia (Heidelb) 2024; 10:39. [PMID: 38509166 PMCID: PMC10954654 DOI: 10.1038/s41537-024-00458-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Several studies have shown white matter (WM) dysconnectivity in people with schizophrenia (SZ). However, the underlying mechanism remains unclear. We investigated the relationship between plasma homocysteine (Hcy) levels and WM microstructure in people with SZ using diffusion tensor imaging (DTI). Fifty-three people with SZ and 83 healthy controls (HC) were included in this retrospective observational study. Tract-Based Spatial Statistics (TBSS) were used to evaluate group differences in WM microstructure. A significant negative correlation between plasma Hcy levels and WM microstructural disruption was noted in the SZ group (Spearman's ρ = -.330, P = 0.016) but not in the HC group (Spearman's ρ = .041, P = 0.712). These results suggest that increased Hcy may be associated with WM dysconnectivity in SZ, and the interaction between Hcy and WM dysconnectivity could be a potential mechanism of the pathophysiology of SZ. Further, longitudinal studies are required to investigate whether high Hcy levels subsequently cause WM microstructural disruption in people with SZ.
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Grants
- 19K17061 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 18H02749 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 18H05130 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20H05064 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 23H04979 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21H02849 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21H05173 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 23H02844 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP18dm0307008 Japan Agency for Medical Research and Development (AMED)
- JP21uk1024002 Japan Agency for Medical Research and Development (AMED)
- JPMJCR22P3 MEXT | JST | Core Research for Evolutional Science and Technology (CREST)
- The Novartis Pharma Research Grant; SENSHIN Medical Research Foundation; SUZUKEN Memorial Foundation; the Takeda Science Foundation.
- the Brain/MINDS Beyond program (23dm0307008) from the Japan Agency for Medical Research
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Affiliation(s)
- Koichi Tabata
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shuraku Son
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Jun Miyata
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuya Toriumi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Mitsuhiro Miyashita
- Unit for Mental Health Promotion, Research Center for Social Science & Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kazuhiro Suzuki
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Psychiatry, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Hidehiko Takahashi
- Department of Psychiatry and Behavioral Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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19
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Polyakova Z, Hatanaka N, Chiken S, Nambu A. Subthalamic Activity for Motor Execution and Cancelation in Monkeys. J Neurosci 2024; 44:e1911222024. [PMID: 38290848 PMCID: PMC10957207 DOI: 10.1523/jneurosci.1911-22.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/01/2024] Open
Abstract
The subthalamic nucleus (STN) receives cortical inputs via the hyperdirect and indirect pathways, projects to the output nuclei of the basal ganglia, and plays a critical role in the control of voluntary movements and movement disorders. STN neurons change their activity during execution of movements, while recent studies emphasize STN activity specific to cancelation of movements. To address the relationship between execution and cancelation functions, we examined STN activity in two Japanese monkeys (Macaca fuscata, both sexes) who performed a goal-directed reaching task with a delay that included Go, Cancel, and NoGo trials. We first examined responses to the stimulation of the forelimb regions in the primary motor cortex and/or supplementary motor area. STN neurons with motor cortical inputs were found in the dorsal somatomotor region of the STN. All these STN neurons showed activity changes in Go trials, suggesting their involvement in execution of movements. Part of them exhibited activity changes in Cancel trials and sustained activity during delay periods, suggesting their involvement in cancelation of planed movements and preparation of movements, respectively. The STN neurons rarely showed activity changes in NoGo trials. Go- and Cancel-related activity was selective to the direction of movements, and the selectivity was higher in Cancel trials than in Go trials. Changes in Go- and Cancel-related activity occurred early enough to initiate and cancel movements, respectively. These results suggest that the dorsal somatomotor region of the STN, which receives motor cortical inputs, is involved in preparation and execution of movements and cancelation of planned movements.
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Affiliation(s)
- Zlata Polyakova
- Division of System Neurophysiology, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
- Center for Human Nature, Artificial Intelligence, and Neuroscience, Hokkaido University, Sapporo 060-0812, Japan
| | - Nobuhiko Hatanaka
- Division of System Neurophysiology, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Satomi Chiken
- Division of System Neurophysiology, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
| | - Atsushi Nambu
- Division of System Neurophysiology, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
- Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585, Japan
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20
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Ohta K, Saka N, Nishi Y, Nishio M. Nairovirus polymerase mutations associated with the establishment of persistent infection in human cells. J Virol 2024; 98:e0169823. [PMID: 38358288 PMCID: PMC10949423 DOI: 10.1128/jvi.01698-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV), a tick-borne virus of the Orthonairovirus genus, persistently infects tick cells. It has been reported to establish persistent infection in non-human primates, but virological analysis has not yet been performed in human cells. Here, we investigated whether and how nairoviruses persistently infect human cells using Hazara orthonairovirus (HAZV), a surrogate model for CCHFV. We established a human cell line that was persistently infected with HAZV. Surprisingly, virions of persistently infected HAZV (HAZVpi) were not observed in the culture supernatants. There were five mutations (mut1, mut2, mut3, mut4, and mut5) in L protein of HAZVpi. Mutations in L protein of HAZVpi contribute to non-detection of virion in the supernatants. Lmut4 was found to cause low viral growth rate, despite its high polymerase activity. The low growth rate was restored by Lmut2, Lmut3, and Lmut5. The polymerase activity of Lmut1 was extremely low, and recombinant HAZV carrying Lmut1 (rHAZV/Lmut1) was not released into the supernatants. However, genomes of rHAZV/Lmut1 were retained in the infected cells. All mutations (Lmut1-5) found in L protein of HAZVpi were required for experimental reproduction of HAZVpi, and only Lmut1 and Lmut4 were insufficient. We demonstrated that point mutations in viral polymerase contribute to the establishment of persistent HAZV infection. Furthermore, innate immunity was found to be suppressed in HAZVpi-infected cells, which also potentially contributes to viral persistence. This is the first presentation of a possible mechanism behind how nairoviruses establish persistent infection in human cells. IMPORTANCE We investigated whether and how nairoviruses persistently infect human cells, using Hazara orthonairovirus (HAZV), a surrogate model for Crimean-Congo hemorrhagic fever virus. We established a human cell line that was persistently infected with HAZV. Five mutations were found in L protein of persistently infected HAZV (HAZVpi): mut1, mut2, mut3, mut4, and mut5. Among them, Lmut1 and Lmut4 restricted viral growth by low polymerase activity and low growth rate, respectively, leading to inhibition of viral overgrowth. The restriction of viral growth caused by Lmut1 and Lmut4 was compensated by other mutations, including Lmut2, Lmut3, and Lmut5. Each of the mutations found in L protein of HAZVpi was concluded to cooperatively modulate viral growth, which facilitates the establishment of persistent infection. Suppression of innate immunity also potentially contributes to virus persistence. This is the first presentation of a possible mechanism behind how nairoviruses establish persistent infection in human cells.
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Affiliation(s)
- Keisuke Ohta
- Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Naoki Saka
- Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yuzuha Nishi
- Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Machiko Nishio
- Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan
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21
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Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H. Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire. J Virol 2024; 98:e0199523. [PMID: 38323813 PMCID: PMC10949447 DOI: 10.1128/jvi.01995-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024] Open
Abstract
Historically, antibody reactivity to pathogens and vaccine antigens has been evaluated using serological measurements of antigen-specific antibodies. However, it is difficult to evaluate all antibodies that contribute to various functions in a single assay, such as the measurement of the neutralizing antibody titer. Bulk antibody repertoire analysis using next-generation sequencing is a comprehensive method for analyzing the overall antibody response; however, it is unreliable for estimating antigen-specific antibodies due to individual variation. To address this issue, we propose a method to subtract the background signal from the repertoire of data of interest. In this study, we analyzed changes in antibody diversity and inferred the heavy-chain complementarity-determining region 3 (CDRH3) sequences of antibody clones that were selected upon influenza virus infection in a mouse model using bulk repertoire analysis. A decrease in the diversity of the antibody repertoire was observed upon viral infection, along with an increase in neutralizing antibody titers. Using kernel density estimation of sequences in a high-dimensional sequence space with background signal subtraction, we identified several clusters of CDRH3 sequences induced upon influenza virus infection. Most of these repertoires were detected more frequently in infected mice than in uninfected control mice, suggesting that infection-specific antibody sequences can be extracted using this method. Such an accurate extraction of antigen- or infection-specific repertoire information will be a useful tool for vaccine evaluation in the future. IMPORTANCE As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
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Affiliation(s)
- Masashi Shingai
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Iida
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoko Kawai
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Naoki Nomura
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Chimuka Handabile
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Tomomi Kawakita
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuo Ohnishi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kimihito Ito
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
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22
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Hara T, Meng S, Tsuji Y, Arao Y, Saito Y, Sato H, Motooka D, Uchida S, Ishii H. RN7SL1 may be translated under oncogenic conditions. Proc Natl Acad Sci U S A 2024; 121:e2312322121. [PMID: 38478683 PMCID: PMC10962956 DOI: 10.1073/pnas.2312322121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/29/2024] [Indexed: 03/27/2024] Open
Abstract
RN7SL1 (RNA component of signal recognition particle 7SL1), a component of the signal recognition particle, is a non-coding RNA possessing a small ORF (smORF). However, whether it is translated into peptides is unknown. Here, we generated the RN7SL1-Green Fluorescent Protein (GFP) gene, in which the smORF of RN7SL1 was replaced by GFP, introduced it into 293T cells, and observed cells emitting GFP fluorescence. Furthermore, RNA-seq of GFP-positive cells revealed that they were in an oncogenic state, suggesting that RN7SL1 smORF may be translated under special conditions.
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Affiliation(s)
- Tomoaki Hara
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
| | - Sikun Meng
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
| | - Yoshiko Tsuji
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
| | - Yasuko Arao
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
| | - Yoshiko Saito
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
| | - Hiromichi Sato
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka565-0871, Japan
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen SVDK-2450, Denmark
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka565-0871, Japan
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23
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Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K. Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport. Nat Commun 2024; 15:2404. [PMID: 38493152 PMCID: PMC10944485 DOI: 10.1038/s41467-024-46747-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn2+-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.
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Affiliation(s)
- Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kento Yonezawa
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Mariko Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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24
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Kikuchi Y, Yoshida M, Kuwae A, Asami Y, Inahashi Y, Abe A. Correlation between the spread of IMP-producing bacteria and the promoter strength of bla IMP genes. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00715-5. [PMID: 38491135 DOI: 10.1038/s41429-024-00715-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/10/2024] [Accepted: 02/21/2024] [Indexed: 03/18/2024]
Abstract
The first report of transmissible carbapenem resistance encoded by blaIMP-1 was discovered in Pseudomonas aeruginosa GN17203 in 1988, and blaIMP-1 has since been detected in other bacteria, including Enterobacterales. Currently, many variants of blaIMPs exist, and point mutations in the blaIMP promoter have been shown to alter promoter strength. For example, the promoter (Pc) of blaIMP-1, first reported in P. aeruginosa GN17203, was a weak promoter (PcW) with low-level expression intensity. This study investigates whether point mutations in the promoter region have helped to create strong promoters under antimicrobial selection pressure. Using bioinformatic approaches, we retrieved 115 blaIMPs from 14,529 genome data of Pseudomonadota and performed multiple alignment analyses. The results of promoter analysis of the 115 retrieved blaIMPs showed that most of them used the Pc located in class 1 integrons (n = 112, 97.4%). The promoter analysis by year revealed that the blaIMP population with the strong promoter, PcS, was transient. In contrast, the PcW-TG population, which had acquired a TGn-extended -10 motif in PcW and had an intermediate promoter strength, gradually spread throughout the world. An inverse correlation between Pc promoter strength and Intl1 integrase excision efficiency has been reported previously [1]. Because of this trade-off, it is unlikely that blaIMPs with strong promoters will increase rapidly, but the possibility that promoter strength will increase with the use of other integrons cannot be ruled out. Monitoring of the blaIMP genes, including promoter analysis, is necessary for global surveillance of carbapenem-resistant bacteria.
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Affiliation(s)
- Yuta Kikuchi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
| | - Mariko Yoshida
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
| | - Asaomi Kuwae
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
| | - Yukihiro Asami
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan
| | - Akio Abe
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan.
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-Ku, Tokyo, 108-8641, Japan.
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25
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Jang S, Ishigami K, Mergaert P, Kikuchi Y. Ingested soil bacteria breach gut epithelia and prime systemic immunity in an insect. Proc Natl Acad Sci U S A 2024; 121:e2315540121. [PMID: 38437561 PMCID: PMC10945853 DOI: 10.1073/pnas.2315540121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/11/2024] [Indexed: 03/06/2024] Open
Abstract
Insects lack acquired immunity and were thought to have no immune memory, but recent studies reported a phenomenon called immune priming, wherein sublethal dose of pathogens or nonpathogenic microbes stimulates immunity and prevents subsequential pathogen infection. Although the evidence for insect immune priming is accumulating, the underlying mechanisms are still unclear. The bean bug Riptortus pedestris acquires its gut microbiota from ambient soil and spatially structures them into a multispecies and variable community in the anterior midgut and a specific, monospecies Caballeronia symbiont population in the posterior region. We demonstrate that a particular Burkholderia strain colonizing the anterior midgut stimulates systemic immunity by penetrating gut epithelia and migrating into the hemolymph. The activated immunity, consisting of a humoral and a cellular response, had no negative effect on the host fitness, but on the contrary protected the insect from subsequent infection by pathogenic bacteria. Interruption of contact between the Burkholderia strain and epithelia of the gut weakened the host immunity back to preinfection levels and made the insects more vulnerable to microbial infection, demonstrating that persistent acquisition of environmental bacteria is important to maintain an efficient immunity.
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Affiliation(s)
- Seonghan Jang
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 062-8517Sapporo, Japan
| | - Kota Ishigami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 062-8517Sapporo, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, 91198Gif-sur-Yvette, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 062-8517Sapporo, Japan
- Unit of Applied Biological Chemistry, Graduate School of Agriculture, Hokkaido University, 060-8589Sapporo, Japan
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26
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Nakai R, Munekawa S, Murai Y, Ohmura Y, Tani K. Diversity profiling of microbiomes associated with selected alpine plants and lichens from Mt. Suisho, Japan. Microbiol Resour Announc 2024; 13:e0127023. [PMID: 38363134 DOI: 10.1128/mra.01270-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/03/2024] [Indexed: 02/17/2024] Open
Abstract
We report 16S rRNA gene amplicon data for the microbiomes in selected alpine plants (genera Artemisia, Parnassia, and Phyllodoce) and lichens (genera Cladonia and a mixture of Miriquidica and Rhizocarpon) from Mt. Suisho, Japan. Most of these samples were dominated by Pseudomonadota, while some contained the rarely cultivated phylum Vulcanimicrobiota (Candidatus Eremiobacterota/WPS-2).
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Affiliation(s)
- Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Shouno Munekawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Yoshinori Murai
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Yoshihito Ohmura
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Kenichiro Tani
- Department of Geology and Paleontology, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
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27
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Nakamura T, Ohyama C, Sakamoto M, Toma T, Tateishi H, Matsuo M, Chirifu M, Ikemizu S, Morioka H, Fujita M, Inoue JI, Yamagata Y. TIFAB regulates the TIFA-TRAF6 signaling pathway involved in innate immunity by forming a heterodimer complex with TIFA. Proc Natl Acad Sci U S A 2024; 121:e2318794121. [PMID: 38442163 PMCID: PMC10945758 DOI: 10.1073/pnas.2318794121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Nuclear factor κB (NF-κB) is activated by various inflammatory and infectious molecules and is involved in immune responses. It has been elucidated that ADP-β-D-manno-heptose (ADP-Hep), a metabolite in gram-negative bacteria, activates NF-κB through alpha-kinase 1 (ALPK1)-TIFA-TRAF6 signaling. ADP-Hep stimulates the kinase activity of ALPK1 for TIFA phosphorylation. Complex formation between phosphorylation-dependent TIFA oligomer and TRAF6 promotes the polyubiquitination of TRAF6 for NF-κB activation. TIFAB, a TIFA homolog lacking a phosphorylation site and a TRAF6 binding motif, is a negative regulator of TIFA-TRAF6 signaling and is implicated in myeloid diseases. TIFAB is indicated to regulate TIFA-TRAF6 signaling through interactions with TIFA and TRAF6; however, little is known about its biological function. We demonstrated that TIFAB forms a complex not with the TIFA dimer, an intrinsic form of TIFA involved in NF-κB activation, but with monomeric TIFA. The structural analysis of the TIFA/TIFAB complex and the biochemical and cell-based analyses showed that TIFAB forms a stable heterodimer with TIFA, inhibits TIFA dimer formation, and suppresses TIFA-TRAF6 signaling. The resultant TIFA/TIFAB complex is a "pseudo-TIFA dimer" lacking the phosphorylation site and TRAF6 binding motif in TIFAB and cannot form the orderly structure as proposed for the phosphorylated TIFA oligomer involved in NF-κB activation. This study elucidated the molecular and structural basis for the regulation of TIFA-TRAF6 signaling by TIFAB.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Chiaki Ohyama
- School of Pharmacy, Kumamoto University, Kumamoto862-0973, Japan
| | - Madoka Sakamoto
- School of Pharmacy, Kumamoto University, Kumamoto862-0973, Japan
| | - Tsugumasa Toma
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Hiroshi Tateishi
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mihoko Matsuo
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mikako Fujita
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Jun-ichiro Inoue
- The University of Tokyo Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), 4-6-1 Shirokanedai, Minato-ku, Tokyo108-0071, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto862-8678, Japan
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28
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Islam MS, Yamamoto K, Morita N, Yumoto I, Kato S, Nakai R, Igarashi K. Complete genome sequence of Opitutales bacterium strain ASA1, isolated from soil. Microbiol Resour Announc 2024; 13:e0103223. [PMID: 38329357 DOI: 10.1128/mra.01032-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
We present the complete genome of Opitutales bacterium ASA1, isolated from soil. The genome is 5,821,695 bp with 4,638 protein-coding sequences. The genome data suggest that this strain belongs to the class Opitutae of the phylum Verrucomicrobiota, and its genome has six unique biosynthetic gene clusters associated with secondary metabolites.
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Affiliation(s)
- Md Samiul Islam
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Naoki Morita
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Isao Yumoto
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Souichiro Kato
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
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Horiguchi H, Kadomatsu T, Yamashita T, Yumoto S, Horino T, Sato M, Terada K, Miyata K, Ichigozaki Y, Kimura T, Fukushima S, Moroishi T, Oike Y. Tumor stroma-derived ANGPTL2 potentiates immune checkpoint inhibitor efficacy. Cancer Gene Ther 2024:10.1038/s41417-024-00757-9. [PMID: 38467764 DOI: 10.1038/s41417-024-00757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Use of immune checkpoint inhibitors (ICIs) as cancer immunotherapy has advanced rapidly in the clinic. We recently reported that tumor stroma-derived angiopoietin-like protein 2 (ANGPTL2) has tumor suppressive activity by enhancing dendritic cell-mediated CD8+ T cell anti-tumor immune responses. However, a direct impact of ANGPTL2 on ICI anti-tumor effect remains unclear. Here, we use a murine syngeneic model to show that host ANGPTL2 facilitates CD8+ T cell cross-priming and contributes to anti-tumor responses to ICIs in this context. Importantly, our analysis of public datasets indicated that ANGPTL2 expression is associated with positive responses to ICI therapy by human melanoma patients. We conclude that ANGPTL2-mediated stromal cell crosstalk facilitates anti-tumor immunity and ICI responsiveness. These findings overall provide novel insight into ANGPTL2 anti-tumor function and regulation of ICI-induced anti-tumor immunity.
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Affiliation(s)
- Haruki Horiguchi
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.
- Department of Aging and Geriatric Medicine, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.
| | - Tsuyoshi Kadomatsu
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
- Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Tomoya Yamashita
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Shinsei Yumoto
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Taichi Horino
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Michio Sato
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Kazutoyo Terada
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
- Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Keishi Miyata
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Yuki Ichigozaki
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Toshihiro Kimura
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Satoshi Fukushima
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Toshiro Moroishi
- Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
- Department of Molecular and Medical Pharmacology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.
- Department of Aging and Geriatric Medicine, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.
- Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto, 860-8556, Japan.
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30
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Carreras J, Ikoma H, Kikuti YY, Miyaoka M, Hiraiwa S, Tomita S, Kondo Y, Ito A, Nagase S, Miura H, Kawada H, Roncador G, Campo E, Hamoudi R, Nakamura N. Mutational, immune microenvironment, and clinicopathological profiles of diffuse large B-cell lymphoma and follicular lymphoma with BCL6 rearrangement. Virchows Arch 2024:10.1007/s00428-024-03774-z. [PMID: 38462571 DOI: 10.1007/s00428-024-03774-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
Abstract
BCL6-rearrangement (BCL6-R) is associated with a favorable prognosis of follicular lymphoma (FL), but the mechanism is unknown. We analyzed the clinicopathological, immune microenvironment (immune checkpoint, immuno-oncology markers), and mutational profiles of 10 BCL6-R-positive FL, and 19 BCL6-R-positive diffuse large B-cell lymphoma (DLBCL) cases (both BCL2-R and MYC-R negative). A custom-made panel included 168 genes related to aggressive B-cell lymphomas and FL. FL cases were nodal, histological grade 3A in 70%, low Ki67; and had a favorable overall and progression-free survival. DLBCL cases were extranodal in 60%, IPI high in 63%, non-GCB in 60%, EBER-negative; and had a progression-free survival comparable to that of DLBCL NOS. The microenvironment had variable infiltration of M2-like tumor-associated macrophages (TAMs) that were CD163, CSF1R, LAIR1, PD-L1, and CD85A (LILRB3) positive; but had low IL10 and PTX3 expression. In comparison to FL, DLBCL had higher TAMs, IL10, and PTX3 expression. Both lymphoma subtypes shared a common mutational profile with mutations in relevant pathogenic genes such as KMT2D, OSBPL10, CREBBP, and HLA-B (related to chromatin remodeling, metabolism, epigenetic modification, and antigen presentation). FL cases were characterized by a higher frequency of mutations of ARID1B, ATM, CD36, RHOA, PLOD2, and PRPRD (p < 0.05). DLBCL cases were characterized by mutations of BTG2, and PIM1; and mutations of HIST1H1E and MFHAS1 to disease progression (p < 0.05). Interestingly, mutations of genes usually associated with poor prognosis, such as NOTCH1/2 and CDKN2A, were infrequent in both lymphoma subtypes. Some high-confidence variant calls were likely oncogenic, loss-of-function. MYD88 L265P gain-of-function was found in 32% of DLBCL. In conclusion, both BCL6-R-positive FL and BCL6-R-positive DLBCL had a common mutational profile; but also, differences. DLBCL cases had a higher density of microenvironment markers.
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Grants
- 23K06454 the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 15K19061 the Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 18K15100 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 24590430 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 2021-B04 Tokai University School of Medicine research incentive assistant plan
- VRI-20-10 ASPIRE, the technology program management pillar of Abu Dhabi's Advanced Technology Research Council (ATRC), via the ASPIRE Precision Medicine Research Institute Abu Dhabi (AS-PIREPMRIAD) award
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Affiliation(s)
- Joaquim Carreras
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan.
| | - Haruka Ikoma
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Yara Yukie Kikuti
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Masashi Miyaoka
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Shinichiro Hiraiwa
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Sakura Tomita
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Yusuke Kondo
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Atsushi Ito
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Shunsuke Nagase
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Hisanobu Miura
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
| | - Hiroshi Kawada
- Department of Hematology, School of Medicine, Tokai University, Tokyo, Japan
| | - Giovanna Roncador
- Monoclonal Antibodies Core Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Elias Campo
- Department of Pathology, Esther Koplowitz Center (CEK), Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Hospital Clinic Barcelona, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Rifat Hamoudi
- Research Institute for Medical and Health Science, Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, UK
- BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah, United Arab Emirates
| | - Naoya Nakamura
- Department of Pathology, School of Medicine, Tokai University, Tokyo, Japan
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31
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Apostolopoulos A, Kawamoto N, Chow SYA, Tsuiji H, Ikeuchi Y, Shichino Y, Iwasaki S. dCas13-mediated translational repression for accurate gene silencing in mammalian cells. Nat Commun 2024; 15:2205. [PMID: 38467613 PMCID: PMC10928199 DOI: 10.1038/s41467-024-46412-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Current gene silencing tools based on RNA interference (RNAi) or, more recently, clustered regularly interspaced short palindromic repeats (CRISPR)‒Cas13 systems have critical drawbacks, such as off-target effects (RNAi) or collateral mRNA cleavage (CRISPR‒Cas13). Thus, a more specific method of gene knockdown is needed. Here, we develop CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13). Owing to its tight association with mRNA, dCas13 serves as a physical roadblock for scanning ribosomes during translation initiation and does not affect mRNA stability. Guide RNAs covering the start codon lead to the highest efficacy regardless of the translation initiation mechanism: cap-dependent, internal ribosome entry site (IRES)-dependent, or repeat-associated non-AUG (RAN) translation. Strikingly, genome-wide ribosome profiling reveals the ultrahigh gene silencing specificity of CRISPRδ. Moreover, the fusion of a translational repressor to dCas13 further improves the performance. Our method provides a framework for translational repression-based gene silencing in eukaryotes.
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Grants
- JP20H05784 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05278 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05734 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H04268 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05786 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP23H02415 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K07016 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23K05648 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15023 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP23KJ2175 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005h0001 Japan Agency for Medical Research and Development (AMED)
- JP23gm6910005 Japan Agency for Medical Research and Development (AMED)
- JP20gm1410001 Japan Agency for Medical Research and Development (AMED)
- Pioneering Projects MEXT | RIKEN
- Pioneering Projects MEXT | RIKEN
- Exploratory Research Center on Life and Living Systems (ExCELLS), 23EX601
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Affiliation(s)
- Antonios Apostolopoulos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Naohiro Kawamoto
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hitomi Tsuiji
- Education and Research Division of Pharmacy, School of Pharmacy, Aichi Gakuin University, Nagoya, Aichi, 464-8650, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
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32
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Matsuda K, Wakimoto T. Bacterial Hydrazine Biosynthetic Pathways Featuring Cupin/Methionyl tRNA Synthetase-like Enzymes. Chembiochem 2024:e202300874. [PMID: 38458972 DOI: 10.1002/cbic.202300874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/26/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
Nitrogen-Nitrogen (N-N) bond-containing functional groups in natural products and synthetic drugs play significant roles in exerting biological activities. The mechanisms of N-N bond formation in natural organic molecules have garnered increasing attention over the decades. Recent advances have illuminated various enzymatic and nonenzymatic strategies, and our understanding of natural N-N bond construction is rapidly expanding. A group of didomain proteins with zinc-binding cupin/methionyl-tRNA synthetase (MetRS)-like domains, also known as hydrazine synthetases, generates amino acid-based hydrazines, which serve as key biosynthetic precursors of diverse N-N bond-containing functionalities such as hydrazone, diazo, triazene, pyrazole, and pyridazinone groups. In this review, we summarize the current knowledge on hydrazine synthetase mechanisms and the various pathways employing this unique bond-forming machinery.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
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Shiraishi T, Katayama Y, Nishiyama M, Shoji H, Miyakawa T, Mizoo T, Matsumoto A, Hijikata A, Shirai T, Mayanagi K, Nakayama KI. The complex etiology of autism spectrum disorder due to missense mutations of CHD8. Mol Psychiatry 2024:10.1038/s41380-024-02491-y. [PMID: 38438524 DOI: 10.1038/s41380-024-02491-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024]
Abstract
CHD8 is an ATP-dependent chromatin-remodeling factor encoded by the most frequently mutated gene in individuals with autism spectrum disorder (ASD). Although many studies have examined the consequences of CHD8 haploinsufficiency in cells and mice, few have focused on missense mutations, the most common type of CHD8 alteration in ASD patients. We here characterized CHD8 missense mutations in ASD patients according to six prediction scores and experimentally examined the effects of such mutations on the biochemical activities of CHD8, neural differentiation of embryonic stem cells, and mouse behavior. Only mutations with high prediction scores gave rise to ASD-like phenotypes in mice, suggesting that not all CHD8 missense mutations detected in ASD patients are directly responsible for the development of ASD. Furthermore, we found that mutations with high scores cause ASD by mechanisms either dependent on or independent of loss of chromatin-remodeling function. Our results thus provide insight into the molecular underpinnings of ASD pathogenesis caused by missense mutations of CHD8.
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Affiliation(s)
- Taichi Shiraishi
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Yuta Katayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Masaaki Nishiyama
- Department of Histology and Cell Biology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Hirotaka Shoji
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Taisuke Mizoo
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Kouta Mayanagi
- Department of Drug Discovery Structural Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Fukuoka, Fukuoka, 812-8582, Japan.
- Anticancer Strategies Laboratory, TMDU Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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Moriyama Y, Koga H, Tsukaya H. Decoding the leaf apical meristem of Guarea glabra Vahl (Meliaceae): insight into the evolution of indeterminate pinnate leaves. Sci Rep 2024; 14:5166. [PMID: 38431750 PMCID: PMC10908829 DOI: 10.1038/s41598-024-55882-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/27/2024] [Indexed: 03/05/2024] Open
Abstract
In seed plants, growth of shoots and roots is indeterminate, while leaves are typically determinate organs that cease to grow after a certain developmental stage. This is due to the characteristics of the leaf meristem, where cell proliferation activity is retained only for a limited period. However, several plants exhibit indeterminacy in their leaves, exemplified by the pinnate compound leaves of Guarea and Chisocheton genera in the Meliaceae family. In these plants, the leaf meristem at the tip of the leaf retains meristematic activity and produces leaflets over years, resulting in a single leaf that resembles a twig. The molecular mechanism underlying the indeterminate leaf meristem of these plants has not been examined. In this research, we used Guarea glabra as a model to investigate the development of indeterminate pinnate leaves. Transcriptome analyses revealed that the gene expression profile in leaf apex tissue differed from that in the shoot apex. However, a class 1 KNOTTED-LIKE HOMEOBOX (KNOX1) gene which is lost in Brassicaceae was highly expressed in both tissues. We established an in situ hybridisation system for this species using Technovit 9100 to analyse the spatial expression patterns of genes. We revealed that the leaf meristematic region of G. glabra expresses KNOX1, LEAFY and ANGUSTIFORIA3 simultaneously, suggesting the involvement of these genes in the indeterminacy of the leaf meristem.
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Affiliation(s)
- Yasutake Moriyama
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, Japan
| | - Hiroyuki Koga
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, Japan.
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35
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Sakata R, Araie M, Yoshitomi T. Factors associated with visual field or structure progression occurring first in a prospective study on patients with untreated open-angle glaucoma with normal intraocular pressure. Eye (Lond) 2024; 38:737-744. [PMID: 37798361 PMCID: PMC10920799 DOI: 10.1038/s41433-023-02766-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND/OBJECTIVES To identify factors associated with disc/retina deterioration in stereo fundus photographs preceding that of the visual field (VF), as determined with a Humphrey Field Analyzer (HFA) (Structure First deterioration) and factors associated with the latter preceding the former (Field First deterioration) in open-angle glaucoma (OAG) with lower normal intraocular pressure (IOP). SUBJECTS/METHODS Prospective cohort study. Ninety eyes of 90 patients with OAG and a baseline IOP < 15 mmHg participated in a 5-year prospective study without treatment. IOP measurements and HFA 24-2 Swedish Interactive Test Algorithm Standard tests were performed every 3 months, and fundus photographs were obtained every 6 months. VF deterioration was determined by Guided Progression Analysis and deterioration of disc/retina was determined on stereophotographs by an independent committee. A multivariable Cox proportional hazard model was used to identify factors associated with Structure First deterioration, and with Field First deterioration. RESULTS The average baseline age and mean deviation were 53.9 ± 9.8 years and -2.8 ± 2.8 dB, respectively. During the 5-year follow-up, the probability of Field First deterioration was 49% ± 6.6% (standard error) and that of Structure First deterioration was 33% ± 6.4% (P = 0.062, log-rank test). Disc hemorrhage (DH) prior to the event (P = 0.006) was associated with Structure First deterioration, and older age was associated with Field First deterioration (P = 0.040). CONCLUSIONS In OAG eyes with lower normal IOP, DH was significantly associated with Structure First deterioration, and age was significantly associated with Field First deterioration.
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Affiliation(s)
- Rei Sakata
- Department of Ophthalmology, Graduate of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Makoto Araie
- Department of Ophthalmology, Graduate of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Ophthalmology, Kanto Central Hospital of the Mutual Aid Association of Public School Teachers, Tokyo, Japan
| | - Takeshi Yoshitomi
- Department of Orthoptics, Fukuoka International University of Health and Welfare, Fukuoka, Japan
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Sakamoto R, Kamoda T, Sato K, Ogoh S, Katayose M, Neki T, Iwamoto E. Acute aerobic exercise enhances cerebrovascular shear-mediated dilation in young adults: the role of cerebral shear. J Appl Physiol (1985) 2024; 136:535-548. [PMID: 38153849 DOI: 10.1152/japplphysiol.00543.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023] Open
Abstract
Exercise-induced increases in shear rate (SR) acutely improve peripheral endothelial function, but the presence of this mechanism in cerebral arteries remains unclear. Thus, we evaluated shear-mediated dilation of the internal carotid artery (ICA), which is an index of cerebrovascular endothelial function, before and after exercise. Shear-mediated dilation was measured with 30 s of hypercapnia in 16 young adults before and 10 min after 30 min of sitting rest (CON) or three cycling exercises on four separate days. The target exercise intensity was 80% of oxygen uptake at the ventilatory threshold. To manipulate the ICA SR during exercise, participants breathed spontaneously (ExSB, SR increase) or hyperventilated without (ExHV, no increase in SR) or with ([Formula: see text], restoration of SR increase) addition of CO2 to inspiratory air. Shear-mediated dilation was calculated as a percent increase in diameter from baseline. Doppler ultrasound measures ICA velocity and diameter. The CON trial revealed that 30 min of sitting did not alter shear-mediated dilation (4.34 ± 1.37% to 3.44 ± 1.23%, P = 0.052). ICA dilation after exercise compared with preexercise levels increased in the ExSB trial (3.32 ± 1.37% to 4.74 ± 1.84%, P < 0.01), remained unchanged in the ExHV trial (4.07 ± 1.55% to 3.21 ± 1.48%, P = 0.07), but was elevated in the [Formula: see text] trial (3.35 ± 1.15% to 4.33 ± 2.12%, P = 0.04). Our results indicate that exercise-induced increases in cerebral shear may play a crucial role in improving cerebrovascular endothelial function after acute exercise in young adults.NEW & NOTEWORTHY We found that 30-min cycling (target intensity was 80% of the ventilatory threshold) with increasing shear of the internal carotid artery (ICA) enhanced transient hypercapnia-induced shear-mediated dilation of the ICA, reflecting improved cerebrovascular endothelial function. This enhancement of ICA dilation was diminished by suppressing the exercise-induced increase in ICA shear via hyperventilation. Our results indicate that increases in cerebral shear may be a key stimulus for improving cerebrovascular endothelial function after exercise in young adults.
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Affiliation(s)
- Rintaro Sakamoto
- Graduate School of Health Sciences, Sapporo Medical University, Sapporo, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Tatsuki Kamoda
- Graduate School of Health Sciences, Sapporo Medical University, Sapporo, Japan
| | - Kohei Sato
- Graduate School of Health Sciences, Sapporo Medical University, Sapporo, Japan
| | - Shigehiko Ogoh
- Department of Biomedical Engineering, Toyo University, Kawagoe, Japan
| | - Masaki Katayose
- Graduate School of Health Sciences, Sapporo Medical University, Sapporo, Japan
- School of Health Sciences, Sapporo Medical University, Sapporo, Japan
| | - Toru Neki
- School of Health Sciences, Sapporo Medical University, Sapporo, Japan
| | - Erika Iwamoto
- School of Health Sciences, Sapporo Medical University, Sapporo, Japan
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37
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Toyofuku T, Ishikawa T, Nojima S, Kumanogoh A. Efficacy against Lung Cancer Is Augmented by Combining Aberrantly N-Glycosylated T Cells with a Chimeric Antigen Receptor Targeting Fragile X Mental Retardation 1 Neighbor. J Immunol 2024; 212:917-927. [PMID: 38214607 PMCID: PMC10876419 DOI: 10.4049/jimmunol.2300618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/17/2023] [Indexed: 01/13/2024]
Abstract
The adaptive transfer of T cells redirected to cancer cells via chimeric Ag receptors (CARs) has produced clinical benefits for the treatment of hematologic diseases. To extend this approach to solid cancer, we screened CARs targeting surface Ags on human lung cancer cells using (to our knowledge) novel expression cloning based on the Ag receptor-induced transcriptional activation of IL-2. Isolated CARs were directed against fragile X mental retardation 1 neighbor (FMR1NB), a cancer-testis Ag that is expressed by malignant cells and adult testicular germ cells. Anti-FMR1NB CAR human T cells demonstrated target-specific cytotoxicity and successfully controlled tumor growth in mouse xenograft models of lung cancer. Furthermore, to protect CAR T cells from immune-inhibitory molecules, which are present in the tumor microenvironment, we introduced anti-FMR1NB CARs into 2-deoxy-glucose (2DG)-treated human T cells. These cells exhibited reduced binding affinity to immune-inhibitory molecules, and the suppressive effects of these molecules were resisted through blockade of the N-glycosylation of their receptors. Anti-FMR1NB CARs in 2DG-treated human T cells augmented target-specific cytotoxicity in vitro and in vivo. Thus, our findings demonstrated the feasibility of eradicating lung cancer cells using 2DG-treated human T cells, which are able to direct tumor-specific FMR1NB via CARs and survive in the suppressive tumor microenvironment.
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Affiliation(s)
- Toshihiko Toyofuku
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, The Center of Medical Innovation and Translational Research, Osaka University, Suita, Osaka, Japan
| | - Takako Ishikawa
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, The Center of Medical Innovation and Translational Research, Osaka University, Suita, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
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38
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Zhang NJ, Lin JX, Chichinadze DV, Wang Y, Watanabe K, Taniguchi T, Fu L, Li JIA. Angle-resolved transport non-reciprocity and spontaneous symmetry breaking in twisted trilayer graphene. Nat Mater 2024; 23:356-362. [PMID: 38388731 DOI: 10.1038/s41563-024-01809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
The identification and characterization of spontaneous symmetry breaking is central to our understanding of strongly correlated two-dimensional materials. In this work, we utilize the angle-resolved measurements of transport non-reciprocity to investigate spontaneous symmetry breaking in twisted trilayer graphene. By analysing the angular dependence of non-reciprocity in both longitudinal and transverse channels, we are able to identify the symmetry axis associated with the underlying electronic order. We report that a hysteretic rotation in the mirror axis can be induced by thermal cycles and a large current bias, supporting the spontaneous breaking of rotational symmetry. Moreover, the onset of non-reciprocity with decreasing temperature coincides with the emergence of orbital ferromagnetism. Combined with the angular dependence of the superconducting diode effect, our findings uncover a direct link between rotational and time-reversal symmetry breaking. These symmetry requirements point towards exchange-driven instabilities in momentum space as a possible origin for transport non-reciprocity in twisted trilayer graphene.
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Affiliation(s)
| | - Jiang-Xiazi Lin
- Department of Physics, Brown University, Providence, RI, USA
| | | | - Yibang Wang
- Department of Physics, Brown University, Providence, RI, USA
| | - Kenji Watanabe
- Research Center for Functional Materials, National Institute for Materials Science, Tsukuba, Japan
| | - Takashi Taniguchi
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Liang Fu
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J I A Li
- Department of Physics, Brown University, Providence, RI, USA.
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39
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Yokoyama R, Ago Y, Igarashi H, Higuchi M, Tanuma M, Shimazaki Y, Kawai T, Seiriki K, Hayashida M, Yamaguchi S, Tanaka H, Nakazawa T, Okamura Y, Hashimoto K, Kasai A, Hashimoto H. (R)-ketamine restores anterior insular cortex activity and cognitive deficits in social isolation-reared mice. Mol Psychiatry 2024:10.1038/s41380-024-02419-6. [PMID: 38388704 DOI: 10.1038/s41380-024-02419-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 02/24/2024]
Abstract
Chronic social isolation increases the risk of mental health problems, including cognitive impairments and depression. While subanesthetic ketamine is considered effective for cognitive impairments in patients with depression, the neural mechanisms underlying its effects are not well understood. Here we identified unique activation of the anterior insular cortex (aIC) as a characteristic feature in brain-wide regions of mice reared in social isolation and treated with (R)-ketamine, a ketamine enantiomer. Using fiber photometry recording on freely moving mice, we found that social isolation attenuates aIC neuronal activation upon social contact and that (R)-ketamine, but not (S)-ketamine, is able to counteracts this reduction. (R)-ketamine facilitated social cognition in social isolation-reared mice during the social memory test. aIC inactivation offset the effect of (R)-ketamine on social memory. Our results suggest that (R)-ketamine has promising potential as an effective intervention for social cognitive deficits by restoring aIC function.
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Affiliation(s)
- Rei Yokoyama
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yukio Ago
- Department of Cellular and Molecular Pharmacology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Hisato Igarashi
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Momoko Higuchi
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masato Tanuma
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuto Shimazaki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takafumi Kawai
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kaoru Seiriki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Misuzu Hayashida
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shun Yamaguchi
- Department of Morphological Neuroscience, Graduate School of Medicine, Gifu University, Gifu, Gifu, 501-1194, Japan
- Center for One Medicine Innovative Translational Research, Institute for Advanced Study, Gifu University, Gifu, Gifu, 501-1194, Japan
| | - Hirokazu Tanaka
- Faculty of Information Technology, Tokyo City University, Setagaya, Tokyo, 158-8557, Japan
| | - Takanobu Nakazawa
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, 156-8502, Japan
| | - Yasushi Okamura
- Laboratory of Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chuo, Chiba, 260-8670, Japan
| | - Atsushi Kasai
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.
- Systems Brain Science Project, Drug Innovation Center, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan.
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Suita, Osaka, 565-0871, Japan.
- Division of Bioscience, Institute for Datability Science, Osaka University, Suita, Osaka, 565-0871, Japan.
- Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Molecular Pharmaceutical Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
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40
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Miyake K, Ito J, Takahashi K, Nakabayashi J, Brombacher F, Shichino S, Yoshikawa S, Miyake S, Karasuyama H. Single-cell transcriptomics identifies the differentiation trajectory from inflammatory monocytes to pro-resolving macrophages in a mouse skin allergy model. Nat Commun 2024; 15:1666. [PMID: 38396021 PMCID: PMC10891131 DOI: 10.1038/s41467-024-46148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Both monocytes and macrophages are heterogeneous populations. It was traditionally understood that Ly6Chi classical (inflammatory) monocytes differentiate into pro-inflammatory Ly6Chi macrophages. Accumulating evidence has suggested that Ly6Chi classical monocytes can also differentiate into Ly6Clo pro-resolving macrophages under certain conditions, while their differentiation trajectory remains to be fully elucidated. The present study with scRNA-seq and flow cytometric analyses reveals that Ly6ChiPD-L2lo classical monocytes recruited to the allergic skin lesion sequentially differentiate into Ly6CloPD-L2hi pro-resolving macrophages, via intermediate Ly6ChiPD-L2hi macrophages but not Ly6Clo non-classical monocytes, in an IL-4 receptor-dependent manner. Along the differentiation, classical monocyte-derived macrophages display anti-inflammatory signatures followed by metabolic rewiring concordant with their ability to phagocytose apoptotic neutrophils and allergens, therefore contributing to the resolution of inflammation. The failure in the generation of these pro-resolving macrophages drives the IL-1α-mediated cycle of inflammation with abscess-like accumulation of necrotic neutrophils. Thus, we clarify the stepwise differentiation trajectory from Ly6Chi classical monocytes toward Ly6Clo pro-resolving macrophages that restrain neutrophilic aggravation of skin allergic inflammation.
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Affiliation(s)
- Kensuke Miyake
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Junya Ito
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazufusa Takahashi
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Jun Nakabayashi
- College of Liberal Arts and Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Frank Brombacher
- Institute of Infectious Disease and Molecular Medicine, International Center for Genetic and Biotechnology Cape Town Component & University of Cape Town, Cape Town, South Africa
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Soichiro Yoshikawa
- Department of Immunology, Juntendo University School of Medicine, Tokyo, Japan
| | - Sachiko Miyake
- Department of Immunology, Juntendo University School of Medicine, Tokyo, Japan
| | - Hajime Karasuyama
- Inflammation, Infection and Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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41
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Hayashi Y, Fukatsu K, Takahashi K, Kinoshita SN, Kato K, Sakakibara T, Kuwata K, Kinoshita T. Phosphorylation of plasma membrane H +-ATPase Thr881 participates in light-induced stomatal opening. Nat Commun 2024; 15:1194. [PMID: 38378616 PMCID: PMC10879185 DOI: 10.1038/s41467-024-45248-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
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.
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Affiliation(s)
- Yuki Hayashi
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Kohei Fukatsu
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Koji Takahashi
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | | | - Kyohei Kato
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Taku Sakakibara
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan.
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42
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Takenaka N, Ko S, Kitada A, Yamada A. Liquid Madelung energy accounts for the huge potential shift in electrochemical systems. Nat Commun 2024; 15:1319. [PMID: 38374056 PMCID: PMC10876980 DOI: 10.1038/s41467-023-44582-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/20/2023] [Indexed: 02/21/2024] Open
Abstract
Achievement of carbon neutrality requires the development of electrochemical technologies suitable for practical energy storage and conversion. In any electrochemical system, electrode potential is the central variable that regulates the driving force of redox reactions. However, quantitative understanding of the electrolyte dependence has been limited to the classic Debye-Hückel theory that approximates the Coulombic interactions in the electrolyte under the dilute limit conditions. Therefore, accurate expression of electrode potential for practical electrochemical systems has been a holy grail of electrochemistry research for over a century. Here we show that the 'liquid Madelung potential' based on the conventional explicit treatment of solid-state Coulombic interactions enables quantitatively accurate expression of the electrode potential, with the Madelung shift obtained from molecular dynamics reproducing a hitherto-unexplained huge experimental shift for the lithium metal electrode. Thus, a long-awaited method for the description of the electrode potential in any electrochemical system is now available.
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Affiliation(s)
- Norio Takenaka
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Seongjae Ko
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Atsushi Kitada
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Atsuo Yamada
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Sungkyunkwan University Institute of Energy Science & Technology (SIEST), Sungkyunkwan University, Suwon, Korea.
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43
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Fujikawa T, Ishihara JI, Vincent WF, Uchida M, Tsuji M. Draft genome sequence of the basidiomycetous yeast Mrakia hoshinonis JCM 32575 T isolated from Ellesmere Island, Canadian High Arctic. Microbiol Resour Announc 2024; 13:e0082023. [PMID: 38179911 PMCID: PMC10868207 DOI: 10.1128/mra.00820-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Mrakia hoshinonis JCM 32575 was isolated from glacial sediments on Ellesmere Island in the Canadian High Arctic and described as a new basidiomycetous yeast. This species does not require amino acids and vitamins for growth and can grow at sub-zero temperatures. Here, we report a draft genome sequence of this strain.
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Affiliation(s)
- Tatsuya Fujikawa
- Department of Materials Chemistry, National Institute of Technology (KOSEN), Asahikawa College, Asahikawa, Hokkaido, Japan
| | | | - Warwick F. Vincent
- Département de Biologie & Centre for Northern Studies (CEN), Université Laval, Quebec, Canada
| | - Masaki Uchida
- National Institute of Polar Research (NIPR), Tachikawa, Tokyo, Japan
- Department of Polar Science, The Graduate University for Advanced Studies, Tachikawa, Tokyo, Japan
| | - Masaharu Tsuji
- Department of Materials Chemistry, National Institute of Technology (KOSEN), Asahikawa College, Asahikawa, Hokkaido, Japan
- National Institute of Polar Research (NIPR), Tachikawa, Tokyo, Japan
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44
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Okutani A, Okugawa S, Fujimoto F, Ikeda M, Tsutsumi T, Moriya K, Maeda K. Draft genome sequence including the capsule operon of a Bacillus cereus strain isolated from a patient with bacteremia in Japan. Microbiol Resour Announc 2024; 13:e0076623. [PMID: 38179945 PMCID: PMC10868262 DOI: 10.1128/mra.00766-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/23/2023] [Indexed: 01/06/2024] Open
Abstract
Bacillus cereus, which causes opportunistic infections in hospitals as well as food poisoning, is genetically similar to Bacillus anthracis. We herein report the draft genome including the capsule operon of B. cereus BCER1 isolated from the blood of a hospital patient in Japan.
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Affiliation(s)
- Akiko Okutani
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu Okugawa
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Fumie Fujimoto
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Mahoko Ikeda
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Takeya Tsutsumi
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
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45
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Seto Y, Ogihara R, Takizawa K, Eiraku M. In vitro induction of patterned branchial arch-like aggregate from human pluripotent stem cells. Nat Commun 2024; 15:1351. [PMID: 38355589 PMCID: PMC10867012 DOI: 10.1038/s41467-024-45285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Early patterning of neural crest cells (NCCs) in the craniofacial primordium is important for subsequent development of proper craniofacial structures. However, because of the complexity of the environment of developing tissues, surveying the early specification and patterning of NCCs is difficult. In this study, we develop a simplified in vitro 3D model using human pluripotent stem cells to analyze the early stages of facial development. In this model, cranial NCC-like cells spontaneously differentiate from neural plate border-like cells into maxillary arch-like mesenchyme after a long-term culture. Upon the addition of EDN1 and BMP4, these aggregates are converted into a mandibular arch-like state. Furthermore, temporary treatment with EDN1 and BMP4 induces the formation of spatially separated domains expressing mandibular and maxillary arch markers within a single aggregate. These results suggest that this in vitro model is useful for determining the mechanisms underlying cell fate specification and patterning during early facial development.
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Affiliation(s)
- Yusuke Seto
- Laboratory of Developmental Systems, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
| | - Ryoma Ogihara
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Kaori Takizawa
- Laboratory of Developmental Systems, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Mototsugu Eiraku
- Laboratory of Developmental Systems, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
- Institute for Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
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Kadowaki S, Wakano JY, Tamura T, Watanabe A, Hirose M, Suga E, Tsukada K, Tarawneh O, Massadeh S. Delayed increase in stone tool cutting-edge productivity at the Middle-Upper Paleolithic transition in southern Jordan. Nat Commun 2024; 15:610. [PMID: 38326315 PMCID: PMC10850154 DOI: 10.1038/s41467-024-44798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Although the lithic cutting-edge productivity has long been recognized as a quantifiable aspect of prehistoric human technological evolution, there remains uncertainty how the productivity changed during the Middle-to-Upper Paleolithic transition. Here we present the cutting-edge productivity of eight lithic assemblages in the eastern Mediterranean region that represent a chrono-cultural sequence including the Late Middle Paleolithic, Initial Upper Paleolithic, the Early Upper Paleolithic, and the Epipaleolithic. The results show that a major increase in the cutting-edge productivity does not coincide with the conventional Middle-Upper Paleolithic boundary characterized by the increase in blades in the Initial Upper Paleolithic, but it occurs later in association with the development of bladelet technology in the Early Upper Paleolithic. Given increasing discussions on the complexity of Middle-Upper Paleolithic cultural changes, it may be fruitful to have a long-term perspective and employ consistent criteria for diachronic comparisons to make objective assessment of how cultural changes proceeded across conventional chrono-cultural boundaries.
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Affiliation(s)
- Seiji Kadowaki
- Nagoya University Museum, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Joe Yuichiro Wakano
- School of Interdisciplinary Mathematical Sciences, Meiji University, Nakano 4-21-1, Nakano-ku, Tokyo, 164-8525, Japan
| | - Toru Tamura
- Geological Survey of Japan, AIST, Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Ayami Watanabe
- Nagoya University Museum, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Masato Hirose
- Laboratory of Archaeology, Kiso Regional Union, Nagano, 399-6101, Japan
| | - Eiki Suga
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kazuhiro Tsukada
- Nagoya University Museum, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Oday Tarawneh
- Department of Antiquities, Third Circle, Jabal Amman, Amman, Jordan
| | - Sate Massadeh
- Ministry of Tourism and Antiquities, Third Circle, Jabal Amman, Amman, Jordan
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47
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Shimamura T, Takeo Y, Moriya F, Kimura T, Shimura M, Senba Y, Kishimoto H, Ohashi H, Shimba K, Jimbo Y, Mimura H. Ultracompact mirror device for forming 20-nm achromatic soft-X-ray focus toward multimodal and multicolor nanoanalyses. Nat Commun 2024; 15:665. [PMID: 38326328 PMCID: PMC10850520 DOI: 10.1038/s41467-023-44269-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 12/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nanoscale soft-X-ray microscopy is a powerful analysis tool in biological, chemical, and physical sciences. To enhance its probe sensitivity and leverage multimodal soft-X-ray microscopy, precise achromatic focusing devices, which are challenging to fabricate, are essential. Here, we develop an ultracompact Kirkpatrick-Baez (ucKB) mirror, which is ideal for the high-performance nanofocusing of broadband-energy X-rays. We apply our advanced fabrication techniques and short-focal-length strategy to realize diffraction-limited focusing over the entire soft-X-ray range. We achieve a focus size of 20.4 nm at 2 keV, which represents a significant improvement in achromatic soft-X-ray focusing. The ucKB mirror extends soft-X-ray fluorescence microscopy by producing a bicolor nanoprobe with a 1- or 2-keV photon energy. We propose a subcellular chemical mapping method that allows a comprehensive analysis of specimen morphology and the distribution of light elements and metal elements. ucKB mirrors will improve soft-X-ray nanoanalyses by facilitating photon-hungry, multimodal, and polychromatic methods, even with table-top X-ray sources.
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Affiliation(s)
- Takenori Shimamura
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan.
- Japan Synchrotron Radiation Research Institute, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5198, Japan.
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan.
| | - Yoko Takeo
- Japan Synchrotron Radiation Research Institute, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5198, Japan
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Fumika Moriya
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Takashi Kimura
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Mari Shimura
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5148, Japan
- Department of Refractory Viral Infection, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo, 162-8655, Japan
| | - Yasunori Senba
- Japan Synchrotron Radiation Research Institute, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5148, Japan
| | - Hikaru Kishimoto
- Japan Synchrotron Radiation Research Institute, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5198, Japan
| | - Haruhiko Ohashi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5148, Japan
| | - Kenta Shimba
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Yasuhiko Jimbo
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Hidekazu Mimura
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo, Sayo District, Hyogo, 679-5148, Japan.
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, 153-8904, Japan.
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Nonaka H, Sakamoto S, Shiraiwa K, Ishikawa M, Tamura T, Okuno K, Kondo T, Kiyonaka S, Susaki EA, Shimizu C, Ueda HR, Kakegawa W, Arai I, Yuzaki M, Hamachi I. Bioorthogonal chemical labeling of endogenous neurotransmitter receptors in living mouse brains. Proc Natl Acad Sci U S A 2024; 121:e2313887121. [PMID: 38294939 PMCID: PMC10861872 DOI: 10.1073/pnas.2313887121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 12/16/2023] [Indexed: 02/02/2024] Open
Abstract
Neurotransmitter receptors are essential components of synapses for communication between neurons in the brain. Because the spatiotemporal expression profiles and dynamics of neurotransmitter receptors involved in many functions are delicately governed in the brain, in vivo research tools with high spatiotemporal resolution for receptors in intact brains are highly desirable. Covalent labeling by chemical reaction (chemical labeling) of proteins without genetic manipulation is now a powerful method for analyzing receptors in vitro. However, selective target receptor labeling in the brain has not yet been achieved. This study shows that ligand-directed alkoxyacylimidazole (LDAI) chemistry can be used to selectively tether synthetic probes to target endogenous receptors in living mouse brains. The reactive LDAI reagents with negative charges were found to diffuse well over the whole brain and could selectively label target endogenous receptors, including AMPAR, NMDAR, mGlu1, and GABAAR. This simple and robust labeling protocol was then used for various applications: three-dimensional spatial mapping of endogenous receptors in the brains of healthy and disease-model mice; multi-color receptor imaging; and pulse-chase analysis of the receptor dynamics in postnatal mouse brains. Here, results demonstrated that bioorthogonal receptor modification in living animal brains may provide innovative molecular tools that contribute to the in-depth understanding of complicated brain functions.
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Affiliation(s)
- Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Kazuki Shiraiwa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Mamoru Ishikawa
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
| | - Kyohei Okuno
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
| | - Takumi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya464-8603, Japan
| | - Shigeki Kiyonaka
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya464-8603, Japan
| | - Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo113-8421, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Wataru Kakegawa
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Itaru Arai
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Michisuke Yuzaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto615-8510, Japan
- Hamachi Innovative Molecular Technology for Neuroscience, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Kyoto615-8530, Japan
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Sawamura T, Yuki N, Aoki K, Horii K, Horii Y, Naitou K, Tsukamoto S, Shiina T, Shimizu Y. Alterations in descending brain-spinal pathways regulating colorectal motility in a rat model of Parkinson's disease. Am J Physiol Gastrointest Liver Physiol 2024; 326:G195-G204. [PMID: 38111988 DOI: 10.1152/ajpgi.00181.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 12/20/2023]
Abstract
Patients with Parkinson's disease (PD) often have constipation. It is assumed that a disorder of the regulatory mechanism of colorectal motility by the central nervous system is involved in the constipation, but this remains unclear. The aim of this study was to investigate whether central neural pathways can modulate colorectal motility in a rat model of PD. PD model rats were generated by injection of 6-hydroxydopamine into a unilateral medial forebrain bundle and destruction of dopaminergic neurons in the substantia nigra. Colorectal motility was measured in vivo in anesthetized rats. Intraluminal administration of capsaicin, as a noxious stimulus, induced colorectal motility in sham-operated rats but not in PD rats. Intrathecally administered dopamine (DA) and serotonin (5-HT), which mediate the prokinetic effect of capsaicin, at the L6-S1 levels enhanced colorectal motility in PD rats similarly to that in sham-operated rats. In PD rats, capsaicin enhanced colorectal motility only when a GABAA receptor antagonist was preadministered into the lumbosacral spinal cord. Capsaicin-induced colorectal motility was abolished by intrathecal administration of a D2-like receptor antagonist but not by administration of 5-HT2 and 5-HT3 receptor antagonists. These findings demonstrate that the inhibitory GABAergic component becomes operative and the stimulatory serotonergic component is suppressed in PD rats. The alteration of the central regulatory mechanism of colorectal motility is thought to be related to the occurrence of constipation in PD patients. Our findings provide a new insight into the pathogenesis of defecation disorders observed in PD.NEW & NOTEWORTHY In a rat model of Parkinson's disease, the component of descending brain-spinal pathways that regulate colorectal motility through a mediation of the lumbosacral defecation center was altered from stimulatory serotonergic neurons to inhibitory GABAergic neurons. Our findings suggest that chronic constipation in Parkinson's disease patients may be associated with alterations in central regulatory mechanisms of colorectal motility. The plasticity in the descending pathway regulating colorectal motility may contribute to other disease-related defecation abnormalities.
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Affiliation(s)
- Tomoya Sawamura
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Natsufu Yuki
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Kanae Aoki
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Kazuhiro Horii
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Division of Biological Principles, Department of Physiology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Yuuki Horii
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Kiyotada Naitou
- Department of Basic Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Shumpei Tsukamoto
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Takahiko Shiina
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Yasutake Shimizu
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Department of Basic Veterinary Science, Laboratory of Physiology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
- Division of Animal Medical Science, Center for One Medicine Innovative Translational Research (COMIT), Gifu University Institute for Advanced Study, Gifu, Japan
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50
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Venkatachalam B, Biswa BB, Nagayama H, Koide T. Association of tameness and sociability but no sign of domestication syndrome in mice selectively bred for active tameness. Genes Brain Behav 2024; 23:e12887. [PMID: 38373143 PMCID: PMC10876149 DOI: 10.1111/gbb.12887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
Domesticated animals have been developed by selecting desirable traits following the initial unconscious selection stage, and now exhibit phenotypes desired by humans. Tameness is a common behavioural trait found in all domesticated animals. At the same time, these domesticated animals exhibit a variety of morphological, behavioural, and physiological traits that differ from their wild counterparts of their ancestral species. These traits are collectively referred to as domestication syndrome. However, whether this phenomenon exists is debatable. Previously, selective breeding has been used to enhance active tameness, a motivation to interact with humans, in wild heterogeneous stock mice derived from eight wild inbred strains. In the current study, we used tame mice to study how selective breeding for active tameness affects behavioural and morphological traits. A series of behavioural and morphological analyses on mice showed an increased preference for social stimuli and a longer duration of engagement in non-aggressive behaviour. However, no differences were observed in exploratory or anxiety-related behaviours. Similarly, selection for tameness did not affect ultrasonic vocalisations in mice, and no changes were observed in known morphological traits associated with domestication syndrome. These results suggest that there may be a link between active tameness and sociability and provide insights into the relationship between tameness and other behaviours in the context of domestication.
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Affiliation(s)
- Bharathi Venkatachalam
- Mouse Genomics Resource LaboratoryNational Institute of GeneticsMishimaShizuokaJapan
- Graduate Institute for Advanced StudiesSOKENDAIMishimaShizuokaJapan
| | - Bhim B. Biswa
- Mouse Genomics Resource LaboratoryNational Institute of GeneticsMishimaShizuokaJapan
- Graduate Institute for Advanced StudiesSOKENDAIMishimaShizuokaJapan
| | - Hiromichi Nagayama
- Mouse Genomics Resource LaboratoryNational Institute of GeneticsMishimaShizuokaJapan
- Graduate Institute for Advanced StudiesSOKENDAIMishimaShizuokaJapan
| | - Tsuyoshi Koide
- Mouse Genomics Resource LaboratoryNational Institute of GeneticsMishimaShizuokaJapan
- Graduate Institute for Advanced StudiesSOKENDAIMishimaShizuokaJapan
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