Proceedings of the Japan Academy. Series B, Physical and Biological Sciences最新文献

f₄-statistics-based ancestry profiling and convolutional neural network phenotyping shed new light on the structure of genetic and spike shape diversity in Aegilops tauschii Coss. 基于统计分析和卷积神经网络表型分析的方法，揭示了陶氏Aegilops tauschii遗传结构和穗形多样性。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-05-21 DOI: 10.2183/pjab.101.023

Yoshihiro Koyama, Mizuki Nasu, Yoshihiro Matsuoka

{"title":"f4-statistics-based ancestry profiling and convolutional neural network phenotyping shed new light on the structure of genetic and spike shape diversity in Aegilops tauschii Coss.","authors":"Yoshihiro Koyama, Mizuki Nasu, Yoshihiro Matsuoka","doi":"10.2183/pjab.101.023","DOIUrl":"https://doi.org/10.2183/pjab.101.023","url":null,"abstract":"Aegilops tauschii Coss., a progenitor of bread wheat, is an important wild genetic resource for breeding. The species comprises three genetically defined lineages (TauL1, TauL2, and TauL3), each displaying distinctive phenotypes in various agronomic traits, including spike shape. In the present work, we studied the relationship between population structure and spike shape variation patterns using a collection of 249 accessions. f4-statistics-based ancestry profiling confirmed the previously identified lineages and revealed a genetic component derived from TauL3 in the genomes of some southern Caspian and Transcaucasus TauL1 and TauL2 accessions. Spike shape variation patterns were analyzed using a convolutional neural network-based approach, trained on green and dry spike image datasets. This analysis showed that spike shape diversity is structured according to lineages and demonstrated that the lineages can be distinguished based on spike shape. The implications of these findings for the origins of common wheat and the intraspecific taxonomy of Ae. tauschii are discussed.","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Conformational dynamics and molecular interactions of natural products: unveiling functional structures in biological membranes. 天然产物的构象动力学和分子相互作用：揭示生物膜的功能结构。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-05-09 Epub Date: 2025-03-31 DOI: 10.2183/pjab.101.016

Michio Murata, Masayuki Satake, Nobuaki Matsumori

引用次数: 0

Mechanism of puberulic acid contamination in red yeast rice tablets that caused a serious food poisoning outbreak in Japan. 红曲米片剂中微嫩酸污染导致日本严重食物中毒的机理。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-05-09 Epub Date: 2025-03-31 DOI: 10.2183/pjab.101.017

Tomoya Yoshinari, Maiko Watanabe, Wataru Aoki, Seiji Tanaka, Naoko Masumoto, Michiho Ito, Takahiro Ohnishi

{"title":"Mechanism of puberulic acid contamination in red yeast rice tablets that caused a serious food poisoning outbreak in Japan.","authors":"Tomoya Yoshinari, Maiko Watanabe, Wataru Aoki, Seiji Tanaka, Naoko Masumoto, Michiho Ito, Takahiro Ohnishi","doi":"10.2183/pjab.101.017","DOIUrl":"10.2183/pjab.101.017","url":null,"abstract":"In Japan, serious food poisoning among individuals who took supplement tablets for lowering plasma cholesterol levels have been publicized since late March 2024. The tablets were prepared from red yeast rice (RYR), a product of Monascus pilosus. Puberulic acid (PA) was detected as an unexpected compound in tablets that caused food poisoning. We conducted an on-site investigation at the RYR production factory to determine the cause of PA contamination of the tablets. Fungi capable of producing PA were detected in wipe samples from the factory and were identified as Penicillium adametzioides. To understand the route through which P. adametzioides contaminated RYR and produced PA, coculture experiments with M. pilosus and P. adametzioides were performed. P. adametzioides grew on rice covered with M. pilosus and produced PA. These results suggest that PA-producing P. adametzioides inhabited the RYR production factory and accidently contaminated the culture of M. pilosus. Consequently, RYR tablets contaminated with PA were manufactured and caused the food poisoning outbreak.","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":" ","pages":"302-316"},"PeriodicalIF":4.4,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization. 染色质结构的转变范式：从30纳米染色质纤维到液体状组织。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-04-25 DOI: 10.2183/pjab.101.020

Kazuhiro Maeshima

引用次数: 0

A thermostable and highly active fungal GH3 β-glucosidase generated by random and saturation mutagenesis. 一种耐热高活性真菌GH3 β-葡萄糖苷酶，由随机诱变和饱和诱变产生。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-03-11 Epub Date: 2025-02-20 DOI: 10.2183/pjab.101.011

Chiaki Matsuzaki, Masafumi Hidaka, Yukari Nakashima, Yuji Honda, Takashi Koyanagi, Kazuhiko Ishikawa, Toshihiko Katoh, Takane Katayama, Hidehiko Kumagai

{"title":"A thermostable and highly active fungal GH3 β-glucosidase generated by random and saturation mutagenesis.","authors":"Chiaki Matsuzaki, Masafumi Hidaka, Yukari Nakashima, Yuji Honda, Takashi Koyanagi, Kazuhiko Ishikawa, Toshihiko Katoh, Takane Katayama, Hidehiko Kumagai","doi":"10.2183/pjab.101.011","DOIUrl":"10.2183/pjab.101.011","url":null,"abstract":"Enhancing the thermostability of cellulose-degrading enzymes is pivotal for establishing an efficient bioconversion system from cellulosic materials to value-added compounds. Here, by introducing random and saturation mutagenesis into the Thermoascus aurantiacus β-glucosidase gene, we generated a hyperthermostable mutant with five amino acid substitutions. Analysis of temperature-induced unfolding revealed the involvement of each replacement in the increased Tm value. Structural analysis showed that all replacements are located at the periphery of the catalytic pocket. D433N replacement, which had a pronounced thermostabilizing effect (ΔTm ＝ 4.5°C), introduced an additional hydrogen bond with a backbone carbonyl oxygen in a long loop structure. The mutant enzyme expressed in Kluyveromyces marxianus exhibited a Tm of 82°C and hydrolyzed cellobiose with kcat and Km values of 200 s－1 and 1.8 mM, respectively. When combined with a thermostable endoglucanase, the mutant enzyme released 20％ more glucose than wild-type enzyme from cellulosic material. The mutant enzyme is therefore a noteworthy addition to the existing repertoire of thermostable β-glucosidases.","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":" ","pages":"177-195"},"PeriodicalIF":4.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Thrombomodulin: A key regulator of intravascular blood coagulation, fibrinolysis, and inflammation, and a treatment for disseminated intravascular coagulation. 凝血调节素-血管内凝血和炎症的关键调节因子，以及弥散性血管内凝血的治疗方法。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-02-10 Epub Date: 2024-12-18 DOI: 10.2183/pjab.101.006

Koji Suzuki

{"title":"Thrombomodulin: A key regulator of intravascular blood coagulation, fibrinolysis, and inflammation, and a treatment for disseminated intravascular coagulation.","authors":"Koji Suzuki","doi":"10.2183/pjab.101.006","DOIUrl":"10.2183/pjab.101.006","url":null,"abstract":"Thrombomodulin (TM) is an important regulator of intravascular blood coagulation, fibrinolysis, and inflammation. TM inhibits the procoagulant and proinflammatory activities of thrombin and promotes the thrombin-induced activation of protein C (PC) bound to the endothelial PC receptor (EPCR). Activated PC (APC) inactivates coagulation factors Va and VIIIa, thereby inhibiting blood clotting. APC bound to EPCR exerts anti-inflammatory and cytoprotective effects on vascular endothelial cells. TM promotes the activation of thrombin-activatable fibrinolysis inhibitor, and also protects cells in blood vessels from inflammation caused by pathogen-associated and damaged cell-associated molecules. Excessive anticoagulant, fibrinolytic, anti-inflammatory, and tissue regenerative effects in the TM-PC pathway are controlled by PC inhibitor. A recombinant TM drug (TM), a soluble form of natural TM developed from the cloned human TM gene, has been evaluated for efficacy in many clinical trials and approved as a treatment for disseminated intravascular coagulation (DIC) caused by diseases such as sepsis, solid tumors, hematopoietic tumors, and trauma. It is currently widely used to treat DIC in Japan.","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":" ","pages":"75-97"},"PeriodicalIF":4.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11893221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855135","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}

引用次数: 0

Cellular senescence as a source of chronic microinflammation that promotes the aging process. 细胞衰老是促进衰老过程的慢性微炎症的来源。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-01-01 DOI: 10.2183/pjab.101.014

Makoto Nakanishi

{"title":"Cellular senescence as a source of chronic microinflammation that promotes the aging process.","authors":"Makoto Nakanishi","doi":"10.2183/pjab.101.014","DOIUrl":"https://doi.org/10.2183/pjab.101.014","url":null,"abstract":"Why and how do we age? This physiological phenomenon that we all experience remains a great mystery, largely unexplained even in this age of scientific and technological progress. Aging is a significant risk factor for numerous diseases, including cancer. However, underlying mechanisms responsible for this association remain to be elucidated. Recent findings have elucidated the significance of the accumulation of senescent cells and other inflammatory cells in organs and tissues with age, and their deleterious effects, such as the induction of inflammation in the microenvironment, as underlying factors contributing to organ dysfunction and disease development. Cellular senescence is a cellular phenomenon characterized by a permanent cessation of cell proliferation and secretion of several proinflammatory cytokines (senescence associated secretory phenotypes). Notably, the elimination of senescent cells from aging individuals has been demonstrated to alleviate age-related organ and tissue dysfunction, as well as various geriatric diseases. This review summarizes the molecular mechanisms by which senescent cells are induced and contribute to age-related diseases, as well as the technologies that ameliorate them.","PeriodicalId":20707,"journal":{"name":"Proceedings of the Japan Academy. Series B, Physical and Biological Sciences","volume":"101 4","pages":"224-237"},"PeriodicalIF":4.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Common and distinct features of diverse macrophage populations in the central nervous system. 中枢神经系统中不同巨噬细胞群的共同和独特特征。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-01-01 DOI: 10.2183/pjab.101.013

Takahiro Masuda

引用次数: 0

Pursuing the identity of a natural medicine licorice by Dr. Shoji Shibata that he firstly investigated half a century before. 寻找柴田正二博士在半个世纪前首次研究的天然药物甘草的身份。

IF 4.4 3区综合性期刊

Proceedings of the Japan Academy. Series B, Physical and Biological Sciences Pub Date : 2025-01-01 DOI: 10.2183/pjab.101.018

Michiho Ito

引用次数: 0

Multi-region processing during sleep for memory and cognition. 睡眠中记忆和认知的多区域加工。