{"title":"Mannose-binding analysis and biological application of pradimicins.","authors":"Yu Nakagawa, Yukishige Ito","doi":"10.2183/pjab.98.002","DOIUrl":"https://doi.org/10.2183/pjab.98.002","url":null,"abstract":"<p><p>Pradimicins (PRMs) are an exceptional family of natural products that specifically bind d-mannose (Man). In the past decade, their scientific significance has increased greatly, with the emergence of biological roles of Man-containing glycans. However, research into the use of PRMs has been severely limited by their inherent tendency to form water-insoluble aggregates. Recently, we have established a derivatization strategy to suppress PRM aggregation, providing an opportunity for practical application of PRMs in glycobiological research. This article first outlines the challenges in studying Man-binding mechanisms and structural modifications of PRMs, and then describes our approach to address them. We also present our recent attempts toward the development of PRM-based research tools.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"98 1","pages":"15-29"},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/85/6d/pjab-98-015.PMC8795531.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39685142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Central regulation of body fluid homeostasis.","authors":"Masaharu Noda, Takashi Matsuda","doi":"10.2183/pjab.98.016","DOIUrl":"https://doi.org/10.2183/pjab.98.016","url":null,"abstract":"<p><p>Extracellular fluids, including blood, lymphatic fluid, and cerebrospinal fluid, are collectively called body fluids. The Na<sup>+</sup> concentration ([Na<sup>+</sup>]) in body fluids is maintained at 135-145 mM and is broadly conserved among terrestrial animals. Homeostatic osmoregulation by Na<sup>+</sup> is vital for life because severe hyper- or hypotonicity elicits irreversible organ damage and lethal neurological trauma. To achieve \"body fluid homeostasis\" or \"Na homeostasis\", the brain continuously monitors [Na<sup>+</sup>] in body fluids and controls water/salt intake and water/salt excretion by the kidneys. These physiological functions are primarily regulated based on information on [Na<sup>+</sup>] and relevant circulating hormones, such as angiotensin II, aldosterone, and vasopressin. In this review, we discuss sensing mechanisms for [Na<sup>+</sup>] and hormones in the brain that control water/salt intake behaviors, together with the responsible sensors (receptors) and relevant neural pathways. We also describe mechanisms in the brain by which [Na<sup>+</sup>] increases in body fluids activate the sympathetic neural activity leading to hypertension.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"98 7","pages":"283-324"},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d2/0f/pjab-98-283.PMC9363595.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40657596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Developments of GNSS buoy for a synthetic geohazard monitoring system.","authors":"Teruyuki Kato, Yukihiro Terada, Keiichi Tadokoro, Akira Futamura","doi":"10.2183/pjab.98.004","DOIUrl":"https://doi.org/10.2183/pjab.98.004","url":null,"abstract":"<p><p>A global navigation satellite system (GNSS) buoy system for early tsunami warnings has been developed for more than 20 years. The first GNSS buoy system using a real-time kinematic algorithm (RTK) was implemented in the Nationwide Ocean Wave information network for Ports and HArbourS (NOWPHAS) wave monitoring system in Japan in 2008. The records of NOWPHAS were used to update the tsunami alert by the Japan Meteorological Agency (JMA), owing to the tsunami generated by the 2011 Tohoku-oki earthquake (Mw9.0). However, considering that the distance limit is less than 20 km for the RTK algorithm, a new system was designed by introducing a new positioning algorithm and satellite data transmission to place the buoy much farther from the coast. A new technique for the continuous monitoring of ocean-bottom crustal movements was also implemented in the new system. The new buoy system can be used for weather forecasting and ionospheric monitoring as well.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"98 2","pages":"49-71"},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/fb/29/pjab-98-049.PMC8890997.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39776036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Therapeutic siRNA targeting the cancer cell stemness regulator PRDI-BF1 and RIZ domain zinc finger protein 14.","authors":"Kohzoh Imai, Hiroaki Taniguchi","doi":"10.2183/pjab.98.017","DOIUrl":"https://doi.org/10.2183/pjab.98.017","url":null,"abstract":"<p><p>PRDI-BF1 and RIZ (PR) domain zinc finger protein 14 (PRDM14), first reported in 2007 to be overexpressed in breast cancer, plays an important role in breast cancer proliferation. Subsequent studies reported that PRDM14 is expressed in embryonic stem cells, primordial germ cells, and various cancers. PRDM14 was reported to confer stemness properties to cancer cells. These properties induce cancer initiation, cancer progression, therapeutic resistance, distant metastasis, and recurrence in refractory tumors. Therefore, PRDM14 may be an ideal therapeutic target for various types of tumors. Silencing PRDM14 expression using PRDM14-specific siRNA delivered through an innovative intravenous drug delivery system reduced the size of inoculated tumors, incidence of distant metastases, and increased overall survival in nude mice without causing adverse effects. Therapeutic siRNA targeting PRDM14 is now being evaluated in a human phase I clinical trial for patients with refractory breast cancer, including triple-negative breast cancer.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"98 7","pages":"325-335"},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/13/04/pjab-98-325.PMC9363597.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40657594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"An interpretation of COVID-19 in Tokyo using a combination of SIR models.","authors":"Koichiro Maki","doi":"10.2183/pjab.98.006","DOIUrl":"https://doi.org/10.2183/pjab.98.006","url":null,"abstract":"<p><p>A year and a half has passed since the outbreak of the COVID-19 pandemic. Mathematical models to predict infection are expected and many studies have been conducted. In this study, a new interpretation was created that could reproduce the daily positive cases in Tokyo using only a simple SIR model. In addition, the data on the ratio of transfer to delta variants could also be simulated. It is anticipated that this interpretation will be a basis for the development of forecasting methods.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"98 2","pages":"87-92"},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d6/13/pjab-98-087.PMC8890995.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39790222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Phenine design for nanocarbon molecules.","authors":"Koki Ikemoto, Toshiya M Fukunaga, Hiroyuki Isobe","doi":"10.2183/pjab.98.020","DOIUrl":"https://doi.org/10.2183/pjab.98.020","url":null,"abstract":"<p><p>With the name \"phenine\" given to 1,3,5-trisubstituted benzene for a fundamental trigonal planar unit to weave nanometer-sized networks, a series of curved nanocarbon molecules have been designed and synthesized. Since the 6π-phenine units were amenable to modern biaryl coupling reactions mediated by transition metals, concise syntheses of >400π-nanocarbon molecules were readily achieved. In addition, the phenine design allowed for installing of heteroatoms and/or transition metals doped at specific positions of the large π-systems of the nanocarbon molecules. Fundamental tools were also developed to specify and describe the locations of defects/dopants, quantify pyramidalizations of trigonal panels and estimate molecular Gauss curvatures of the discrete surface. Unique features of phenine nanocarbons, such as stereoisomerism, entropy-driven molecular assembly and effects of dopants on electronic/magnetic characteristics, were revealed during the first half-decade of investigations.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"98 8","pages":"379-400"},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/3d/9e/pjab-98-379.PMC9614209.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33498510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"JF1/B6F1 Ngly1<sup>-/-</sup> mouse as an isogenic animal model of NGLY1 deficiency.","authors":"Makoto Asahina, Reiko Fujinawa, Haruhiko Fujihira, Yuki Masahara-Negishi, Tomohiro Andou, Ryuichi Tozawa, Tadashi Suzuki","doi":"10.2183/pjab.97.005","DOIUrl":"10.2183/pjab.97.005","url":null,"abstract":"<p><p>N-Glycanase 1 (NGLY1) deficiency is a congenital disorder caused by mutations in the NGLY1 gene. Because systemic Ngly1<sup>-/-</sup> mice with a C57BL/6 (B6) background are embryonically lethal, studies on the mechanism of NGLY1 deficiency using mice have been problematic. In this study, B6-Ngly1<sup>-/+</sup> mice were crossed with Japanese wild mice-originated Japanese fancy mouse 1 (JF1) mice to produce viable F<sub>2</sub> Ngly1<sup>-/-</sup> mice from (JF1×B6)F<sub>1</sub> Ngly1<sup>-/+</sup> mice. Systemic Ngly1<sup>-/-</sup> mice with a JF1 mouse background were also embryonically lethal. Hybrid F1 Ngly1<sup>-/-</sup> (JF1/B6F1) mice, however, showed developmental delay and motor dysfunction, similar to that in human patients. JF1/B6F1 Ngly1<sup>-/-</sup> mice showed increased levels of plasma and urinary aspartylglycosamine, a potential biomarker for NGLY1 deficiency. JF1/B6F1 Ngly1<sup>-/-</sup> mice are a useful isogenic animal model for the preclinical testing of therapeutic options and understanding the precise pathogenic mechanisms responsible for NGLY1 deficiency.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"97 2","pages":"89-102"},"PeriodicalIF":4.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7897899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25353638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development and present status of seismic evaluation and seismic retrofit of existing reinforced concrete buildings in Japan.","authors":"Tsuneo Okada","doi":"10.2183/pjab.97.021","DOIUrl":"https://doi.org/10.2183/pjab.97.021","url":null,"abstract":"<p><p>This paper describes the development and present status of seismic evaluation and seismic retrofit of existing buildings mainly for low-rise and medium-rise reinforced concrete buildings in Japan. First, since the seismic evaluation of existing buildings has close relationships with the seismic design of new buildings, a brief history of the development of seismic design, seismic evaluation, and seismic retrofit is provided in terms of major earthquake disasters mostly in Japan and associated with some major events in the U.S. Then, the development of seismic evaluation and retrofit is reviewed, focusing on the items in which the author has been deeply involved. This provides insight into previous earthquake damage, methodologies for seismic evaluation, the basic concept of the Standard for Seismic Evaluation of Existing Reinforced Concrete Buildings, studies on the demand criteria for seismic safety, and the present status of seismic evaluation and retrofit. Finally, the typical methods of seismic retrofit and some examples of retrofitted buildings in Japan are explained.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"97 7","pages":"402-422"},"PeriodicalIF":3.1,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8403529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39304106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Insight into chemical mechanisms of sepal color development and variation in hydrangea.","authors":"Kumi Yoshida, Kin-Ichi Oyama, Tadao Kondo","doi":"10.2183/pjab.97.003","DOIUrl":"10.2183/pjab.97.003","url":null,"abstract":"<p><p>Hydrangea (Hydrangea macrophylla) is a unique flower because it is composed of sepals rather than true petals that have the ability to change color. In the early 20th century, it was known that soil acidity and Al<sup>3+</sup> content could intensify the blue hue of the sepals. In the mid-20th century, the anthocyanin component 3-O-glucosyldelphinidin (1) and the copigment components 5-O-caffeoylquinic, 5-O-p-coumaroylquinic, and 3-O-caffeoylquinic acids (2-4) were reported. Interestingly, all hydrangea colors from red to purple to blue are produced by the same organic components. We were interested in this phenomenon and the chemical mechanisms underlying hydrangea color variation. In this review, we summarize our recent studies on the chemical mechanisms underlying hydrangea sepal color development, including the structure of the blue complex, transporters involved in accumulation of aluminum ion (Al<sup>3+</sup>), and distribution of the blue complex and aluminum ions in living sepal tissue.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"97 2","pages":"51-68"},"PeriodicalIF":4.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7897900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25353636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"LUBAC-mediated linear ubiquitination: a crucial regulator of immune signaling.","authors":"Kazuhiro Iwai","doi":"10.2183/pjab.97.007","DOIUrl":"10.2183/pjab.97.007","url":null,"abstract":"<p><p>Ubiquitination is a reversible post-translational modification in which ubiquitin chains are conjugated to target proteins to modulate protein function. The type of ubiquitin chain determines the mode of protein regulation. It has been shown that ubiquitin chains are formed via one of seven Lys residues in ubiquitin, and several types of ubiquitin chains are found in cells. We identified a new type of linear ubiquitin chain linked through the N-terminal Met of ubiquitin and assembled by the linear ubiquitin chain assembly complex (LUBAC), which is specific for linear chains. The discovery of linear ubiquitin chains and LUBAC is considered as a paradigm shift in ubiquitin research because linear ubiquitination is exclusive to animals, despite the existence of ubiquitination throughout eukaryotic kingdoms. Linear ubiquitination plays a critical role in immune signaling and cell death regulation. Dysregulation of LUBAC-mediated linear ubiquitination underlies various human diseases, including autoinflammation, autoimmunity, infection, and malignant tumors. This review summarizes the current status of linear ubiquitination research.</p>","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"97 3","pages":"120-133"},"PeriodicalIF":4.4,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25470365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}