Article
Chemistry, Organic
Chao Yang, Dong-Ting Dai, Huan-Xuan Lu, Feng-Lian Zhang, Yao Fu, Yun-He Xu
Summary: Unprecedented palladium-catalysed regio- and stereo-selective coupling reactions of homoallenylboronates with various reactants in aqueous solution resulted in high yields of products with specific stereoselectivity, demonstrating the potential of homoallenylboronates as powerful and flexible platform molecules for the formation of complex 1,3-dienyl compounds.
ORGANIC CHEMISTRY FRONTIERS
(2021)
Article
Chemistry, Organic
Cong Shen, Yuhang Zhu, Shuqi Jin, Kejie Xu, Shuxin Luo, Lixia Xu, Guofu Zhong, Liangjun Zhong, Jian Zhang
Summary: This study reports on the alpha- and beta-olefinic C-H alkenylation of aryl alkenes in ethanol using N,N-bidentate chelation assistance, yielding aryl dienes/trienes with excellent selectivities. The reaction features mild conditions, wide functionality tolerance, and scalable preparation.
ORGANIC CHEMISTRY FRONTIERS
(2022)
Article
Food Science & Technology
Yanli Chang, Kai Huang, Fan Yang, Yanyan Gao, Yan Zhang, Sen Li, Bin Liu, Shuzhen Guo
Summary: This study aimed to identify the active metabolites responsible for improving myocardial hypertrophy. Caffeic acid, methyl caffeate, and dihydrocaffeic acid were found to be the active metabolites.
JOURNAL OF FUNCTIONAL FOODS
(2022)
Article
Cell Biology
Laura Rodriguez-Pascau, Anna Vilalta, Marc Cerrada, Estefania Traver, Sonja Forss-Petter, Isabelle Weinhofer, Jan Bauer, Stephan Kemp, Guillem Pina, Silvia Pascual, Uwe Meya, Patricia L. Musolino, Johannes Berger, Marc Martinell, Pilar Pizcueta
Summary: Leriglitazone shows promising neuroprotective effects in X-ALD, reducing oxidative stress and toxicity in primary neurons and astrocytes. It also improves motor function, restores markers of oxidative stress and inflammation in spinal cord tissues, and decreases neurological disability in animal models of neuroinflammation.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Chemistry, Physical
Richard Batsa Odonkor, Richard Tia, Evans Adei
Summary: In this study, density functional theory (DFT) was used to investigate the [3+2] cycloaddition reaction of N-propadienylindole derivatives and C, N-diarylnitrone derivatives, resulting in the formation of 5-and 4-methyleneisoxazolidine derivatives. The transition structure geometries revealed an asynchronous one-step mechanism for the cycloaddition. The preferential formation of the 4-methyleneisoxazolidine isomer was observed. Electron-releasing and electron-withdrawing groups on the reactants were found to influence the formation of different regioisomers. The reaction was found to be kinetically controlled in all cases.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Pratik Aryal, Ismail Syed, Jennifer Lee, Rucha Patel, Andrew T. Nelson, Dionicio Siegel, Alan Saghatelian, Barbara B. Kahn
Summary: FAHFAs have specific biological actions including enhancing glucose stimulated insulin secretion, insulin sensitivity, and anti-inflammatory effects. Some FAHFAs activate G protein-coupled receptor 40 and attenuate chemokine and cytokine expression and secretion in immune cells. The study suggests that FAHFAs with unsaturated acyl chains and higher branched structures are more likely to enhance insulin secretion, while those with lower branching are more likely to have anti-inflammatory effects.
JOURNAL OF LIPID RESEARCH
(2021)
Article
Chemistry, Organic
Wisdom Kwaku Samba, Richard Tia, Evans Adei
Summary: This study investigated the reaction pathways of five-membered cyclodiene derivatives with itaconic anhydride using density functional theory calculations. The results showed that the initial Diels-Alder reaction pathways have lower activation barriers than esterification reaction pathways. The reactions are stereo-selective towards S-enantiomers with lower activation barriers compared to R-enantiomers.
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Physical
Wisdom Kwaku Samba, Anthony Amoah, Richard Tia, Evans Adei
Summary: The research focused on the 1,3-dipolar cycloadditions of nitrones and nitrile oxides to N-vinylindole, revealing lower activation energies and preferential formation of cis-stereoisomers. The study provided insights into the formation of isoxazolidines and 5-indolyl-substituted isoxazolines, with consistent results in terms of electrophilicity indices and molecular orbital coefficients.
THEORETICAL CHEMISTRY ACCOUNTS
(2021)
Article
Multidisciplinary Sciences
Dina S. Ghallab, Eman Shawky, Reham S. Ibrahim, Mohamed M. Mohyeldin
Summary: The present study used UPLC-MS metabolite fingerprinting to characterize the metabolites of four marine algae species. It was found that some of these metabolites exhibited cytotoxic activity, providing insight into the chemistry and activity relationship of these algae species.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Rui Yang, Yanmei Dong, Fei Gao, Jingyi Li, Zora Dajic Stevanovic, Hui Li, Lei Shi
Summary: This paper assessed the bioactive compounds and antioxidant capacity of four traditionally used thyme species. The study found a positive correlation between the content of total polyphenols and total flavonoids, and their antioxidant activity. Flavonoids were identified as the key contributors to the high antioxidant capacity of thyme species.
Article
Chemistry, Multidisciplinary
Jian Xu, Han Yang, Chengdong Nie, Tao Wang, Xiangyu Qin, Jie Yang, Yuanhang Chang, Siming Nie, Yujie Fu
Summary: This study compared the phytochemical profiles, antioxidant and antiproliferative activities of lingonberry's fruits, leaves, and stems from different regions of China. The results showed that lingonberry contains abundant bioactive compounds in different parts and exhibits strong antioxidant and antiproliferative effects.
Article
Cell Biology
Yumiko Saito-Nakano, Ratna Wahyuni, Kumiko Nakada-Tsukui, Kentaro Tomii, Tomoyoshi Nozaki
Summary: Rab small GTPases play important roles in regulating membrane traffic and cytoskeletal dynamics, which are crucial for the pathogenesis of Entamoeba histolytica. E. histolytica contains over 100 Rab proteins, including unique subgroups like Rab7D, which is involved in phagocytosis and trogocytosis.
CELLULAR MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hironori Takeda, Akihisa Tsutsumi, Tomohiro Nishizawa, Caroline Lindau, Jon Busto, Lena-Sophie Wenz, Lars Ellenrieder, Kenichiro Imai, Sebastian P. Straub, Waltraut Mossmann, Jian Qiu, Yu Yamamori, Kentaro Tomii, Junko Suzuki, Takeshi Murata, Satoshi Ogasawara, Osamu Nureki, Thomas Becker, Nikolaus Pfanner, Nils Wiedemann, Masahide Kikkawa, Toshiya Endo
Summary: The study reveals that beta-barrel proteins in the mitochondrial outer membrane are inserted by the multisubunit mitochondrial SAM complex. The structure of the SAM complex, determined using cryo-electron microscopy, shows the involvement of proteins such as Sam50, Sam35, Sam37, and Mdm10 in the process.
Article
Chemistry, Physical
Yu Yamamori, Kentaro Tomii
Summary: In this study, a new post-processing method was proposed to optimize the weighting factors of MD simulation snapshots for better agreement with experimental data without altering the distribution generated by the simulation. The method focuses on minimizing Kullback-Leibler divergence between optimized and original probability distribution, as long as the error between experimental and calculated values is within a certain threshold. This reweighting method was applied to ethane in a vacuum and lysozyme in a solvent as examples.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Andriy Kryshtafovych, John Moult, Wendy M. Billings, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnoyic, Chaok Seok, Ceslovas Venclovas, Jonghun Won
Summary: CASP aims to advance protein structure prediction technology and successfully conducted a project to compute the structures of proteins in the SARS-CoV-2 genome. Models from the AlphaFold2 group showed good agreement with experimental structures.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Mathys Grapotte, Manu Saraswat, Chloe Bessiere, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyamas, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C. Frith, Clement Chatelain, Piero Carninci, Michiel J. L. de Hoom, Wyeth W. Wasserman, Laurent Brehelin, Charles-Henri Lecellieree
Summary: The FANTOM5 consortium used CAGE technology to map transcription start sites, finding that a large portion of non-coding transcription initiates at microsatellites. They developed Cap Trap RNA-seq to confirm this transcription, and trained deep learning models to predict CAGE signal at STRs with high accuracy. These models revealed the importance of STR surrounding sequences for distinguishing STR classes and predicting transcription initiation levels.
NATURE COMMUNICATIONS
(2021)
Article
Medicine, Research & Experimental
Kazutoshi Murotomi, Hirosuke Tawara, Mitsuko Sutoh, Mayu Yasunaga
Summary: Non-alcoholic steatohepatitis (NASH) is influenced by the complex interaction between the liver and other organs. This study found that iron-accumulating splenocytes can induce inflammation and exacerbate NASH. Therefore, the regulation of iron metabolism in the spleen is crucial for the development of novel therapeutic targets for NASH.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Keisuke Kimura, Fumihiro Kawai, Hisako Kubota-Kawai, Yasunori Watanabe, Kentaro Tomii, Rieko Kojima, Kunio Hirata, Yu Yamamori, Toshiya Endo, Yasushi Tamura
Summary: The study demonstrates the functional role of Tam41-type CDP-DAG synthase in certain prokaryotic cells and proposes a molecular mechanism for CDP-DAG synthesis in bacterial cells and mitochondria through crystal structure analysis and modeling.
JOURNAL OF BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Yu Yamamori, Kentaro Tomii
Summary: This study proposes a method for constructing atomic structure models based on cryo-EM maps with low-to-medium resolution, which combines sensitive and accurate homology modeling with molecular dynamics simulation. Benchmark applications were used to evaluate the model constructions of two target proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Yoshiki Hayashi, Soshiro Kashio, Kazutoshi Murotomi, Shinjiro Hino, Woojin Kang, Kenji Miyado, Mitsuyoshi Nakao, Masayuki Miura, Satoru Kobayashi, Masakazu Namihira
Summary: Tissue aging is a major factor contributing to disabilities and shortened lifespan. The mechanism of tissue aging is not completely understood, but this study suggests that the biosynthesis of S-adenosyl-methionine (SAM) can accelerate aging-related defects during Drosophila oogenesis. The study also reveals an aging-related increase in SAM levels in mouse reproductive tissue and the brain.
SCIENTIFIC REPORTS
(2022)
Article
Allergy
Hirohisa Ogawa, Masahiko Azuma, Aya Umeno, Mayuko Shimizu, Kazutoshi Murotomi, Yasukazu Yoshida, Yasuhiko Nishioka, Koichi Tsuneyama
Summary: In this study, the roles of neutrophils and nerve growth factor (NGF) in refractory asthma were examined. The results showed that neutrophil myeloperoxidase (MPO)-derived singlet oxygen induces increased NGF production, leading to airway hyperreactivity (AHR) and the production of specific markers. These findings contribute to the development of new therapies and biomarkers for non-type 2 and refractory asthma.
ALLERGOLOGY INTERNATIONAL
(2022)
Correction
Biochemistry & Molecular Biology
Hironori Takeda, Jon V. Busto, Caroline Lindau, Akihisa Tsutsumi, Kentaro Tomii, Kenichiro Imai, Yu Yamamori, Takatsugu Hirokawa, Chie Motono, Iniyan Ganesan, Lena-Sophie Wenz, Thomas Becker, Masahide Kikkawa, Nikolaus Pfanner, Nils Wiedemann, Toshiya Endo
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hironori Takeda, Jon V. Busto, Caroline Lindau, Akihisa Tsutsumi, Kentaro Tomii, Kenichiro Imai, Yu Yamamori, Takatsugu Hirokawa, Chie Motono, Iniyan Ganesan, Lena-Sophie Wenz, Thomas Becker, Masahide Kikkawa, Nikolaus Pfanner, Nils Wiedemann, Toshiya Endo
Summary: Mitochondrial beta-barrel proteins play a vital role in transporting metabolites, ions, and proteins. The SAM complex is responsible for guiding their folding and inserting them into membranes. Our study presents the cryo-electron microscopy structure of the yeast SAM complex containing an early eukaryotic beta-barrel folding intermediate. The research reveals a multipoint guidance mechanism for mitochondrial beta-barrel folding, including the involvement of Sam50 and Sam37 in the process.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Biophysics
Yuko Tsuchiya, Yu Yamamori, Kentaro Tomii
Summary: This review introduces a wide array of computational methods for estimating PPIs including antibody-antigen interactions, offering both historical and forward-looking perspectives.
BIOPHYSICAL REVIEWS
(2022)
Article
Engineering, Biomedical
Mayu Yasunaga, Fumiko Kobayashi, Yu Sogo, Kazutoshi Murotomi, Motohiro Hirose, Yuki Hara, Masashi Yamazaki, Atsuo Ito
Summary: This study demonstrated the enhancing effects of low-molecular-weight heparin (LMWH) incorporated into fibroblast growth factor-2 (FGF-2)-calcium phosphate composite layers on the biological activity of FGF-2 in vitro. The presence of LMWH increased the stability and amount of FGF-2 in the composite layers, leading to enhanced mitogenic and endothelial tube-forming activities, as well as osteogenic differentiation gene expression. These findings suggest that the LMWH-FGF-2-calcium phosphate composite layer holds promise as a coating for orthopedic and dental implants.
ACTA BIOMATERIALIA
(2022)
Article
Cell Biology
Tomohiro Takano, Miwa Morikawa, Yu Adachi, Kiyomi Kabasawa, Nicolas Sax, Saya Moriyama, Lin Sun, Masanori Isogawa, Ayae Nishiyama, Taishi Onodera, Kazutaka Terahara, Keisuke Tonouchi, Masashi Nishimura, Kentaro Tomii, Kazuo Yamashita, Takayuki Matsumura, Masaharu Shinkai, Yoshimasa Takahashi
Summary: By applying high-dimensional immune profiling, the study identified vaccine-induced immune dynamics that correlate with neutralizing antibody levels, adverse event severity, or both. Natural killer cells, dendritic cell subsets, and NKT-like cells were found to play important roles in these immune dynamics.
CELL REPORTS MEDICINE
(2022)