Article
Chemistry, Applied
Jui-Hsin Su, Chih- Liu, Mei-Chin Lu, Chi- Chang, Min-Ying Hsieh, Yu-Chi Lin, Chang-Feng Dai, Ya-Han Zhang, Zheng-Yu Lin, Yun-Sheng Lin
Summary: A long-term research on Taiwanese soft coral led to the discovery of various diterpenoids, including a new xenicane-type compound. These compounds were found in the tissues of the coral during spawning and non-spawning periods, showing different activities.
NATURAL PRODUCT RESEARCH
(2021)
Article
Environmental Sciences
Elena Prado, Alberto Abad-Uribarren, Ruben Ramo, Sergio Sierra, Cesar Gonzalez-Pola, Javier Cristobo, Pilar Rios, Rocio Grana, Eneko Aierbe, Juan Manuel Rodriguez, Cristina Rodriguez-Cabello, Larissa Modica, Augusto Rodriguez-Basalo, Francisco Sanchez
Summary: This study used a benthic lander to monitor the activity of gorgonian polyps as a proxy for their feeding activity. Using deep learning, more than 1000 images of gorgonian specimens were analyzed to describe their feeding patterns. The study also used oceanographic sensors to continuously monitor the hydrographic conditions and correlated feeding activity with current dynamics.
Article
Chemistry, Applied
Shubhajit Dhara, Kajal Chakraborty
Summary: Chemical analysis of the organic extract from intertidal brown seaweed Sargassum ilicifolium revealed a previously undescribed xenicane-type diterpenoid with significant antioxidant and anti-inflammatory properties. The compound showed higher selectivity index and potential free radical quenching compared to ibuprofen. The electronic parameters and docking score supported the compound's significant anti-inflammatory properties against 5-lipoxygenase.
NATURAL PRODUCT RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Hanan I. Althagbi, Fitri Budiyanto, Ahmed Abdel-Lateff, Khalid O. Al-Footy, Nahed O. Bawakid, Mohamed A. Ghandourah, Mohammad Y. Alfaifi, Serag Eldin I. Elbehairi, Walied M. Alarif
Summary: Seven isoprenoid derivatives isolated from the soft coral Xenia umbellata exhibited cytotoxic effects against breast adenocarcinoma, hepatocellular carcinoma, and cervix adenocarcinoma cells, with compound 3 showing the most potent cytotoxic effect among them. Late apoptosis was prominent after treatment with compound 7 on all cancer cells.
Article
Chemistry, Medicinal
Chi-Jen Tai, Chiung-Yao Huang, Atallah F. Ahmed, Raha S. Orfali, Walied M. Alarif, Yusheng M. Huang, Yi-Hsuan Wang, Tsong-Long Hwang, Jyh-Horng Sheu
Summary: Chemical investigation of a Red Sea Spongia sp. led to the isolation of four new compounds, with compounds 1 and 5 showing strong anti-inflammatory activity by significantly reducing superoxide anion generation and elastase release in human neutrophil cells.
Article
Biology
Timothy D. O'Hara, Ben Thuy, Andrew F. Hugall
Summary: The deep-seafloor in the tropical Indo-Pacific harbours a rich and diverse benthic fauna with numerous palaeoendemics. The discovery of a new species, genus and family of brittle-star in this region, along with similar microfossil remains from Early Jurassic sediments in Normandy, France, highlights the importance of ongoing taxonomic research in the deep-sea environment.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Fisheries
Lorenzo Bramanti, Elisabetta Manea, Bruna Giordano, Tristan Estaque, Olivier Bianchimani, Justine Richaume, Bastien Merigot, Quentin Schull, Stephane Sartoretto, Joaquim Garrabou, Katell Guizien
Summary: Climate change poses a significant threat to coastal areas, with increasing intensity and frequency of marine heat waves. This study focuses on the impact of marine heat waves on the red gorgonian Paramuricea clavata populations in the Western Mediterranean Sea. Results show that shallow populations were predominantly affected by mass mortality events during the summer of 2022, while populations at mesophotic depths experienced less mortality. This suggests the presence of a depth refuge hypothesis, supporting further investigations and monitoring of potential deep refuge areas for gorgonians.
MEDITERRANEAN MARINE SCIENCE
(2023)
Article
Plant Sciences
Maria-Eleni Grafakou, Christina Barda, Joerg Heilmann, Helen Skaltsa
Summary: Euphorbia deflexa, an endemic spurge from Greece, was investigated for its diterpene constituents, resulting in the isolation of 22 diterpenoids, including 16 previously undescribed compounds, which exhibited activity against human cancer cell lines.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Chemistry, Multidisciplinary
Jiao Liu, Song-Wei Li, Qing-Min Zhao, Zai-Yong Zhang, Li-Gong Yao, Yu-Cheng Gu, Le-Fu Lan, Yue-Wei Guo
Summary: Nanolobatone A, a compound with an unprecedented tricyclo[10.3.0.0(1,2)]pentadecane carbon skeleton, as well as four new polyoxygenated compounds and four rare endoperoxide-bridged casbane-type diterpenoids, were isolated from the Hainan soft coral Sinularia nanolobata. The structures of the new compounds were determined through extensive spectroscopic analysis, X-ray diffraction analysis, and time-dependent density functional theory/electronic circular dichroism calculations. A possible biosynthetic pathway for the new isolates was proposed. Bioassays showed that nanolobatone A exhibited weak antibacterial activity against the Gram-positive bacteria Streptococcus pyogenes.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Yanan Li, Zongfu Chen, Peng Zhang, Feng Gao, Junfeng Wang, Li Lin, Haibin Zhang
Summary: In this study, a novel copper-zinc superoxide dismutase (CuZnSOD) was cloned and characterized from a new sea cucumber species Psychropotes verruciaudatus (PVCuZnSOD). The PVCuZnSOD showed optimum temperature at 20 degrees C and maintained high activity from 0-60 degrees C. It also exhibited strong tolerance to various ions and chemical reagents, indicating its potential applications in medicine, food, and other products.
Article
Fisheries
Charley Gros, Jan Jansen, Candice Untiedt, Tabitha R. R. Pearman, Rachel Downey, David K. A. Barnes, David A. Bowden, Dirk C. Welsford, Nicole A. Hill
Summary: A multi-criteria approach to vulnerable marine ecosystem (VME) identification is proposed, considering the vulnerabilities of different indicator taxa to fishing disturbance. Using annotated imagery data, an index of cumulative abundance and overall richness was computed to quantify assemblage-level vulnerability and characterize different assemblages. This method aims to enhance VME identification and provide context to bycatch events.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Environmental Sciences
Xiaogu Wang, Lifen Bai, Chunsheng Wang, Bo Lu, Yujie Li, Qinyi Lin, Xinyu Huang, Paulo Fontoura
Summary: This study investigated the structure and diversity of marine tardigrade communities in the deep sea of the South China Sea. A total of 17 species were found, with two species belonging to the Angursa genus being the most abundant.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Christian Bailly
Summary: The roots of Euphorbia ebracteolata Hayata have long been used in traditional Chinese medicine for the treatment of various diseases. Several bioactive compounds, including diterpenoids, have been isolated from this plant, some of which have anti-inflammatory and anticancer properties. The origin, structural diversity, and properties of these little-known natural products are discussed.
Review
Environmental Sciences
Eva Paulus
Summary: The deep sea is one of the most biodiverse habitats on Earth, but is facing threats from human activities. Despite many mysteries remaining, there are challenges such as overfishing and environmental degradation that must be addressed to protect biodiversity in the deep sea.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Ecology
Christiane Schmidt, Emmanuelle Geslin, Joan M. Bernhard, Charlotte LeKieffre, Mette Marianne Svenning, Helene Roberge, Magali Schweizer, Giuliana Panieri
Summary: Researchers conducted an experiment to investigate whether certain foraminifera feed on methane-oxidizing bacteria. The results showed that foraminifera can ingest methane-oxidizing bacteria through untargeted grazing. This study is important for understanding the role of foraminifera in the benthic food web.
Article
Chemistry, Physical
Hiromi Nakai, Masato Kobayashi, Takeshi Yoshikawa, Junji Seino, Yasuhiro Ikabata, Yoshifumi Nishimura
Summary: Fragmentation and embedding schemes are crucial in applying quantum-chemical calculations to complex and attractive targets. This feature article discusses the DC-based schemes developed by the authors over the last two decades, inspired by the pioneering study of the DC self-consistent field method. Theoretical aspects of DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, along with the introduction of two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and three programs including DC-based schemes. Illustrative applications demonstrate the accuracy and feasibility of the DC-based schemes.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Dentistry, Oral Surgery & Medicine
Hidetake Tachinami, Kei Tomihara, Shin-ichi Yamada, Atsushi Ikeda, Shuichi Imaue, Hideaki Hirai, Hiromi Nakai, Tomoko Sonoda, Kazuto Kurohara, Yukio Yoshioka, Takumi Hasegawa, Tomofumi Naruse, Takashi Niiyama, Tetsu Shimane, Michihiro Ueda, Souichi Yanamoto, Masaya Akashi, Masahiro Umeda, Hiroshi Kurita, Akihiro Miyazaki, Naoya Arai, Ryuji Hayashi, Makoto Noguchi
Summary: The immune checkpoint inhibitor nivolumab has greatly improved the treatment of recurrent and metastatic oral cancer. However, the response rate to nivolumab remains low, and there is a need to identify predictors of response. This study evaluated the association between neutrophil-to-lymphocyte ratio (NLR) and nivolumab treatment outcome in oral squamous cell carcinoma (OSCC) patients.
BRITISH JOURNAL OF ORAL & MAXILLOFACIAL SURGERY
(2023)
Article
Chemistry, Physical
Takeshi Yoshikawa, Yasuhiro Ikabata, Hiromi Nakai, Kentaro Ogawa, Ken Sakata
Summary: Conical intersections (CIs) play a crucial role in various photophysical, photochemical, and photobiological processes, but the systematic interpretation of minimum energy CI (MECI) geometries is unclear. A previous study investigated the MECI between the ground and first excited electronic states (S0/S1 MECI) using frozen orbital analysis (FZOA), identifying two controlling factors. However, one of the factors was found to be invalid for spin-flip TDDFT (SF-TDDFT). This study revisited the controlling factors using FZOA for the SF-TDDFT method and confirmed the control factors of S0/S1 MECI through numerical applications of a revised formula.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yoshifumi Nishimura, Hiromi Nakai
Summary: In this study, a large-scale quantum chemical calculation program, Dcdftbmd, was integrated with a Python-based advanced atomistic simulation program, i-PI. The implementation of a client-server model enabled hierarchical parallelization with respect to replicas and force evaluations. The established framework demonstrated that quantum path integral molecular dynamics simulations can be executed with high efficiency for systems consisting of a few tens of replicas and containing thousands of atoms. The application of the framework to bulk water systems, with and without an excess proton, demonstrated that nuclear quantum effects are significant for intra- and inter-molecular structural properties, including oxygen-hydrogen bond distance and radial distribution function around the hydrated excess proton.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Parasitology
Yasuyuki Goto, Haruka Mizobuchi
Summary: Macrophages are crucial in determining the fate of Leishmania infection and can either limit or allow parasite growth, leading to disease development or control. They also contribute to pathological outcomes during infection through various molecular and cellular responses, including inflammatory responses, reactive oxygen species-induced cell damage, and disordered phagocytosis. Importantly, the severity of leishmaniasis does not always correlate with parasite burdens, highlighting that the pathological roles of macrophages are not solely dependent on their ability to kill parasites. In this review, we focus on the roles of macrophages in leishmaniasis and their contribution to disease development.
PARASITOLOGY INTERNATIONAL
(2023)
Article
Microbiology
Hana Hirai, Jing Hong, Wataru Fujii, Chizu Sanjoba, Yasuyuki Goto
Summary: The shedding of cell surface receptors can have synergistic outcomes by disrupting cell signaling and binding with ligands. Soluble receptors, such as SIRPa, have biological and diagnostic importance in immunological disorders. In this study, increased levels of soluble SIRPa were observed in mice infected with Leishmania donovani, suggesting its potential role as a biomarker for disorders like hemophagocytosis and anemia.
Article
Chemistry, Physical
Chinami Takashima, Hiromi Nakai
Summary: The Cholesky decomposition and lower-upper decomposition methods were utilized to handle the two-electron integral matrices in an infinite-order two-component relativistic Hamiltonian. CD was used to calculate the symmetric TEI matrices, such as Coulomb-like and specific spin-free interaction terms, while LUD was used for the asymmetric TEI matrix, namely the Darwin-like term. Unitary transformation was performed on the decomposed matrices. Numerical assessments suggest that the proposed method can reduce the computational cost without sacrificing accuracy.
CHEMICAL PHYSICS LETTERS
(2023)
Review
Biochemistry & Molecular Biology
Yasuyuki Goto, Tatsumi Ito, Souradeepa Ghosh, Budhaditya Mukherjee
Summary: Iron plays vital roles in various biochemical processes and is crucial for the survival and defense of Leishmania parasites. These parasites acquire and utilize iron and heme from host macrophages and employ iron superoxide dismutase to counter oxidative stress. Therefore, understanding the iron acquisition and utilization strategies of these parasites is of great significance for the development of antileishmanial drugs.
JOURNAL OF BIOCHEMISTRY
(2023)
Article
Chemistry, Physical
Tatsuki Hanada, Hiroki Uratani, Hiromi Nakai
Summary: In this study, the feasibility of N?I phase transition by vibrational excitation using infrared irradiation is investigated. Nonadiabatic molecular dynamics approach combined with real-time electron dynamics at the level of a semiempirical quantum chemical model is used to simulate the photoinduced phase transition processes. The results highlight the importance of vibronic interactions in the phase transition, suggesting the possibility of N?I phase transition driven by vibrational excitations with infrared irradiation.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Permono Adi Putro, Aditya Wibawa Sakti, Faozan Ahmad, Hiromi Nakai, Husin Alatas
Summary: Extensive metadynamics simulations were conducted to accurately predict the maximum UV-Vis wavelength (Amax) values of capsanthin-based red natural dyes using the LC-TD-DFT-D4/?B97X/def2-SVP method, which exhibited the effect of conformational changes on calculated wavelengths. Additionally, the inexpensive and efficient LC-TD-DFTB method reproduced experimental ?(max) values insensitive to conformational changes.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Infectious Diseases
Prakash Ghosh, Rajashree Chowdhury, Md. Abu Rahat, Faria Hossain, Nur E. Arpha, Mojca Kristan, Matthew Higgins, Ahmed Abd El Wahed, Yasuyuki Goto, M. M. Towhidul Islam, Susana Campino, Mary Cameron, Malcom S. Duthie, Rashidul Haque, Dinesh Mondal
Summary: The study demonstrates the excellent diagnostic efficiency of dried blood spots (DBS) for serological assays and suggests it as a viable alternative to whole blood sampling procedures. However, the sensitivity and specificity of molecular assays using DBS for DNA detection are lower compared to whole blood. The low cost and field feasibility of DBS, coupled with serology-based detection, make it suitable for mass surveillance in detecting residual visceral leishmaniasis transmission.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Immunology
Mahmud Usman, Audu Joseph Natala, Isa Danladi Jatau, Ndudim Isaac Ogo, Ghulam Jeelani, Yasuyuki Goto, Tomoyoshi Nozaki, James H. Mckerrow, Emmanuel Oluwadare Balogun
Summary: This study investigated the species of sand flies and the Leishmania species they transmit in Sokoto State, Nigeria. The findings revealed that P. papatasi and sand flies belonging to the genus Sergentomyia are the most prevalent sand flies in the area, and they solely harbor and transmit L. infantum. This sheds light on the predominance of visceral leishmaniasis in the region.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Chemistry, Physical
Hiromi Nakai, Masato Kobayashi, Takeshi Yoshikawa, Junji Seino, Yasuhiro Ikabata, Yoshifumi Nishimura
Summary: Fragmentation and embedding schemes are crucial in quantum-chemical calculations for complex targets. This feature article presents various divide-and-conquer (DC)-based schemes developed by the authors, inspired by the pioneering study of DC self-consistent field method. It covers theoretical aspects of DC-based SCF, electron correlation, excited-state, and nuclear orbital methods, as well as the introduction of two-component relativistic theory, quantum mechanical molecular dynamics simulation, and three programs. Illustrative applications validate the accuracy and feasibility of the DC-based schemes.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Hiroki Uratani, Hiromi Nakai
Summary: This study presents real-time simulations of charge-transfer processes in donor-acceptor interfaces of organic photovoltaics using a new computational method. The results provide atomic resolution insights into the charge-transfer pathway and explain the dependence of charge transfer on excitation energy. Moreover, the study demonstrates the significant role of nuclear motion in modulating the molecular orbital energies and influencing the charge-transfer process.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Materials Science, Composites
Dhea Afrisa Darmawan, Evi Yulianti, Qolby Sabrina, Kensuke Ishida, Aditya Wibawa Sakti, Hiromi Nakai, Edi Pramono, Sun Theo Constan Lotebulo Ndruru
Summary: This study investigates the effect of lithium acetate salt on carboxymethyl cellulose-based solid polymer electrolytes. The results show that the complex of 30% (wt) LiCH3COO salt with CMC exhibits good ionic conductivity and thermal stability.
POLYMER COMPOSITES
(2023)
