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Inhibition of topoisomerase IIα and induction of DNA damage in cholangiocarcinoma cells by altholactone and its halogenated benzoate derivatives

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Biomedicine and Pharmacotherapy 2020年 127卷 110149-110149页

作者： Kitdumrongthum, Sarunya Reabroi, Somrudee Suksen, Kanoknetr Tuchinda, Patoomratana Munyoo, Bamroong Mahalapbutr, Panupong Rungrotmongkol, Thanyada Ounjai, Puey Chairoungdua, Arthit Toxicology Graduate Program Faculty of Science Mahidol University Bangkok Thailand Excellent Center for Drug Discovery (ECDD) Mahidol University Bangkok Thailand Department of Pharmacology Faculty of Science Mahidol University Bangkok Thailand Department of Physiology Faculty of Science Mahidol University Bangkok Thailand Department of Chemistry Faculty of Science Mahidol University Bangkok Thailand Structural and Computational Biology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok Thailand Department of Biology Faculty of Science Mahidol University Bangkok Thailand

Topoisomerase IIα enzyme (Topo IIα) plays a critical function in DNA replication process and is considered to be a promising target of anti-cancer drugs. In the present study, we reported that the altholactone derivatives modified by adding a halogenated benzoate group showed greater inhibitory activity on Topo IIα enzyme in cell-free system concomitant with cytotoxicity against the CCA cell lines (KKU-M055 and KKU-M213) than those of the parent altholactone. However, the cytotoxic activities of four halogenated benzoate altholactone derivatives including iodo-, fluoro-, chloro-, and bromobenzoate derivatives (compound 1, 2, 3, and 4, respectively) were of equal potency. The fluorobenzoate derivative (compound 2) was chosen for investigating the underlying mechanism in CCA cells. Compound 2 arrested CCA cell cycle at sub G1 phase and induced apoptotic cell death. It markedly inhibited Topo IIα protein expression in both KKU-M055 and KKU-M213 cells, which was accompanied by DNA double-strand breaks demonstrated by an increase in phosphorylated H2A.X protein. Interestingly, KKU-M055 cells, which express higher Topo IIα mRNA compared to KKU-M213 cells, showed greater sensitivity to the compound, indicating the selectivity of the compound to Topo IIα enzyme. By computational docking analysis, the binding affinity of altholactone (-52.5 kcal/mol) and compound 2 (-56.7 kcal/mol) were similar to that of the Topo II poison salvicine (-53.7 kcal/mol). The aromatic moiety of both altholactones embedded in a hydrophobic pocket of Topo II ATPase domain. In addition, compound 2 induced the formation of linear DNA in Topo II-mediated cleavage assay. Collectively, our results demonstrate that the addition of fluorobenzoyl group to altholactone enhances potency and selectivity to inhibit type IIα topoisomerases. Atholactone and fluorobenzoate derivative act as Topo II cleavage complexes stabilizing compounds or Topo II poisons preferentially through binding at ATPase domain of Topo

关键词： Altholactone Cholangiocarcinoma Halogenated benzoate Topoisomerase IIα

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Polaronic quasiparticle picture for generation dynamics of coherent phonons in semiconductors: Transient and nonlinear Fano resonance

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Physical Review B 2017年第1期95卷 014301-014301页

作者： Yohei Watanabe Ken-ichi Hino Muneaki Hase Nobuya Maeshima Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba Tsukuba Ibaraki 305-8573 Japan Division of Materials Science Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba 305-8573 Japan Center for Computational Sciences University of Tsukuba Tsukuba 305-8577 Japan Division of Applied Physics Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba 305-8573 Japan

We examine generation dynamics of coherent phonons in both polar and nonpolar semiconductors, such as GaAs and Si, based on a polaronic-quasiparticle (PQ) model. In this model, the PQ operator is composed of two kinds of operators: one is a quasiboson operator, defined as a linear combination of a set of pairs of electron operators, and the other is a longitudinal optical (LO) phonon operator. In particular, the problem of transient and nonlinear Fano resonance (FR) is tackled, where the vestige of this quantum interference effect was observed exclusively in lightly n-doped Si immediately after carriers were excited by an ultrashort pulse laser [M. Hase et al., Nature (London) 426, 51 (2003)], although not observed yet in GaAs. The PQ model enables us to show straightforwardly that the phonon energy state is embedded in continuum states formed by a set of adiabatic eigenstates of the quasiboson; this energy configuration is a necessary condition of the manifestation of the transient FR in the present optically nonlinear system. Numerical calculations are done for photoemission spectra relevant to the retarded longitudinal dielectric function of transient photoexcited states and for power spectra relevant to the LO-phonon displacement function of time. The photoemission spectra show that in undoped Si, an asymmetric spectral profile characteristic of FR comes into existence immediately after the instantaneous carrier excitation to fade out gradually, whereas in undoped GaAs, no asymmetry in spectra appears in the whole temporal region. The similar results are also obtained in the power spectra. These results are in harmony with the reported experimental results. It is found that the obtained difference in spectral profile between undoped Si and GaAs is attributed to a phase factor of an effective interaction between the LO phonon and the quasiboson. More detailed discussion of the FR dynamics is made in the text.

关键词： Optical phonons Polarons Ultrafast phenomena Elemental semiconductors Semiconductor compounds Semiconductors Linear response theory

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Multiomics Reveals Induction of Neuroblastoma SK-N-BE(2)C Cell Death by Mitochondrial Division Inhibitor 1 through Multiple Effects

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Journal of Proteome Research 2024年第1期23卷 301-315页

作者： Wang, Wei-Hsuan Kao, Yi-Chun Hsieh, Chiao-Hui Tsai, Shin-Yu Cheung, Chantal Hoi Yin Huang, Hsuan-Cheng Juan, Hsueh-Fen Genome and Systems Biology Degree Program Academia Sinica and National Taiwan University Taipei 106 Taiwan Department of Life Science National Taiwan University Taipei 106 Taiwan Center for Computational and Systems Biology National Taiwan University Taipei 106 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 112 Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei 106 Taiwan Center for Advanced Computing and Imaging in Biomedicine National Taiwan University Taipei 106 Taiwan

Mitochondrial division inhibitor 1 (Mdivi-1) is a well-known synthetic compound aimed at inhibiting dynamin-related protein 1 (Drp1) to suppress mitochondrial fission, making it a valuable tool for studying mitochondrial dynamics. However, its specific effects beyond Drp1 inhibition remain to be confirmed. In this study, we employed integrative proteomics and phosphoproteomics to delve into the molecular responses induced by Mdivi-1 in SK-N-BE(2)C cells. A total of 3070 proteins and 1945 phosphorylation sites were identified, with 880 of them represented as phosphoproteins. Among these, 266 proteins and 97 phosphorylation sites were found to be sensitive to the Mdivi-1 treatment. Functional enrichment analysis unveiled their involvement in serine biosynthesis and extrinsic apoptotic signaling pathways. Through targeted metabolomics, we observed that Mdivi-1 enhanced intracellular serine biosynthesis while reducing the production of C24:1-ceramide. Within these regulated phosphoproteins, dynamic dephosphorylation of proteasome subunit alpha type 3 serine 250 (PSMA3-S250) occurred after Mdivi-1 treatment. Further site-directed mutagenesis experiments revealed that the dephosphorylation-deficient mutant PSMA3-S250A exhibited a decreased cell survival. This research confirms that Mdivi-1’s inhibition of mitochondrial division leads to various side effects, ultimately influencing cell survival, rather than solely targeting Drp1 inhibition. © 2023 American Chemical Society.

关键词： Mdivi-1 multiomics neuroblastoma phosphoproteome proteome targeted metabolome

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Floquet-Weyl semimetals generated by an optically resonant interband-transition

arXiv

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arXiv 2022年

作者： Zhang, Runnan Hino, Ken-Ichi Maeshima, Nobuya Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba Ibaraki Tsukuba305-8573 Japan Division of Materials Science Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba305-8573 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan

Floquet-Weyl semimetals (FWSMs) generated by irradiation of a continuous-wave laser with left-hand circular polarization (rotating in counterclockwise sense with time) on the group II-V narrow gap semiconductor Zn3As2 are theoretically investigated, where the frequency of the laser is set nearly resonant with a band gap of the crystal. It is found that the excitation of the crystal by such a laser induce two types of FWSM phases that differ absolutely in characters. To be specific, the associated two pairs of Weyl points are stably formed by band touching between Floquet sidebands ascribable to a valence band labeled as Jz = ±3/2 and a conduction band labeled as Jz = ±1/2, where Jz represents the z-component of total angular momentum quantum number of Γ-point and a double sign corresponds. Here, one FWSM state composed of the up-spin Floquet sidebands relevant to Jz = 3/2 and 1/2 shows almost quadratic band-touching in the vicinity of the associated pair of Weyl points, while the other FWSM state composed of the down-spin Floquet sidebands relevant to Jz = −3/2 and −1/2 shows linear band-touching. Further, it is revealed that both up-spin and down-spin sidebands host nontrivial two-dimensional surface states that are pinned to the respective pairs of the Weyl points. Both surface states also show different energy dispersions and physical properties. More detailed discussion is made in the text on the origin of the above findings, chirality of the FWSM phases, alteration of topological order, laser-induced magnetic properties, and so on. © 2022, CC BY.

关键词： Continuous wave lasers

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Modelling the Human Immune System Response to the ChAdOx1 nCoV-19 Vaccine

Modelling the Human Immune System Response to the ChAdOx1 nC...

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2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

作者： Xavier, Maicom Peters Pompei, Lara T. De O. Vieira, Ana Carolina G. De Paula, Matheus A. M. Bonin, Carla R. B. Reis, Ruy F. Pigozzo, Alexandre B. Quintela, Barbara De M. Dos Santos, Rodrigo W. Lobosco, Marcelo Federal University of Juiz de Fora Graduate Program on Computational Modeling Juiz de Fora Brazil Federal University of Juiz de Fora FISIOCOMP Juiz de Fora Brazil Federal University of Juiz de Fora GET-EngComp Juiz de Fora Brazil IF Sudeste MG Cataguases Advanced Campus Cataguases Brazil Federal University of Juiz de Fora Computer Science Department Juiz de Fora Brazil Federal University of São João Del-Rei Computer Science Department São João Del-Rei Brazil

ISBN: (纸本)9781665401265

About seven months after the start of the COVID-19 pandemic, the first vaccine against the disease was approved for emergency use. Since then, twenty-three more vaccines have been approved, while more than three hundred are in development. Despite being one of the fastest vaccines ever created, several questions about it remain open. computational models can be useful to answer some of these questions. This paper aims to evaluate whether a computer model previously used to reproduce the effects of the yellow fever vaccine in the body is also capable of reproducing the effects of a distinct vaccine: ChAdOx1 nCoV-19. Preliminary results show that the model is a promising tool to achieve this goal since it was able to reproduce the antibody curves observed in individuals vaccinated with ChAdOx1 nCoV-19. © 2021 IEEE.

关键词： Coronavirus

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Edge states of Floquet-Dirac semimetal in a laser-driven semiconductor quantum-well

arXiv

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arXiv 2020年

作者： Zhang, Boyuan Maeshima, Nobuya Hino, Ken-Ichi Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba Tsukuba Ibaraki305-8573 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan Division of Materials Science Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba305-8573 Japan

Band crossings observed in a wide range of condensed matter systems are recognized as a key to understand low-energy fermionic excitations that behave as massless Dirac particles. Despite rapid progress in this field, the exploration of non-equilibrium topological states remains scarce and it has potential ability of providing a new platform to create unexpected massless Dirac states. Here we show that in a cw-laser driven semiconductor quantum-well, the optical Stark effect conducts bulk-band crossing, and the resulting Floquet-Dirac semimetallic phase supports an unconventional edge state in the projected one-dimensional Brillouin zone. Further, we reveal that this edge state mediates a transition between topological and non-topological edge states that is caused by tuning the laser intensity. The existence of the respective edge states and the related topological numbers are understood in a unified manner in terms of the laser-induced polarization reflecting parity hybridization in the bulk Brillouin zone. Copyright © 2020, The Authors. All rights reserved.

关键词： Semiconductor quantum wells

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A Neuro-Inspired Approach to Solve a Simultaneous Location and Mapping Task Using Shared Information in Multiple Robots Systems

A Neuro-Inspired Approach to Solve a Simultaneous Location a...

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International Conference on Control, Automation, Robotics and Vision

作者： Matheus Chaves Menezes Edison Pignaton de Freitas Sen Cheng Alexandre Cesar Muniz de Oliveira Paulo Rogerio de Almeida Ribeiro Graduate Program on Computer Science Federal University of Maranhão São Luís Brazil Graduate Program on Computer Science Federal University of Rio Grande do Sul Porto Alegre Brazil Computational Neuroscience Ruhr University Bochum Bochum Germany Department of Informatics Federal University of Maranhão São Luís Maranhão Department of Computer Engineering Federal University of Maranhão São Luís Maranhão

This paper presents a neuro-inspired mapping approach that uses partial information shared by multiple robots to reduce the time to create a map of an entire environment. Robots using a neurobiologically inspired algorithm, namely RatSLAM, map an environment sharing video information among themselves. RatSLAM, which is based on the navigation system present in the hippocampus of rodents' brain, has been widely used on simultaneous localization and mapping (SLAM) problem. This proposal has been able to generate suitable maps mainly when there is redundant information, e.g. a scene is seen more than once, since this fact activates local view cells that inject activity inside the pose cells via an excitatory link. The work here reported extends this approach by merging partial information acquired by multiple robots. The results from the performed experiments show that the final map built by two robots with shared information is similar to one built by two robots performing the same mapping task individually, i.e. without sharing information. However, the time spent to generate the whole map with the proposed shared approach was smaller than the one without the shared information. Thus, the current approach allows creating a complete map of an environment within a reduced time using multiple robots.

关键词： Navigation Simultaneous localization and mapping Feature extraction Robot vision systems Task analysis Hippocampus

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Data-augmented modeling of intracranial pressure

arXiv

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arXiv 2018年

作者： Wang, Jian-Xun Hu, Xiao Shadden, Shawn C. Mechanical Engineering University of California BerkeleyCA United States Aerospace and Mechanical Engineering Center of Informatics and Computational Science University of Notre Dame Notre DameIN United States Department of Physiological Nursing Department of Neurological surgery Institute of Computational Health Sciences UCSF Joint Bio-Engineering Graduate Program University of California San FranciscoCA United States

Precise management of patients with cerebral diseases often requires intracranial pressure (ICP) monitoring, which is highly invasive and requires a specialized ICU setting. The ability to noninvasively estimate ICP is highly compelling as an alternative to, or screening for, invasive ICP measurement. Most existing approaches for noninvasive ICP estimation aim to build a regression function that maps noninvasive measurements to an ICP estimate using statistical learning techniques. These data-based approaches have met limited success, likely because the amount of training data needed is onerous for this complex applications. In this work, we discuss an alternative strategy that aims to better utilize noninvasive measurement data by leveraging mechanistic understanding of physiology. Specifically, we developed a Bayesian framework that combines a multiscale model of intracranial physiology with noninvasive measurements of cerebral blood flow using transcranial Doppler. Virtual experiments with synthetic data are conducted to verify and analyze the proposed framework. A preliminary clinical application study on two patients is also performed in which we demonstrate the ability of this method to improve ICP prediction. Copyright © 2018, The Authors. All rights reserved.

关键词： Diagnosis

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Correction: Spatial organization of B lymphocytes and prognosis prediction in patients with gastric cancer

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Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association 2025年 2025 May 16页

作者： Ryan Yong Kiat Tay Manavi Sachdeva Haoran Ma Young-Woo Kim Myeong-Cherl Kook Hyunki Kim Jae-Ho Cheong Lindsay C Hewitt Katharina Nekolla Günter Schmidt Takaki Yoshikawa Takashi Oshima Tomio Arai Supriya Srivastava Ming Teh Xuewen Ong Su Ting Tay Taotao Sheng Joseph J Zhao Patrick Tan Heike I Grabsch Raghav Sundar Yong Loo Lin School of Medicine National University of Singapore 1E Kent Ridge Road Singapore 119228 Singapore. Department of Haematology-Oncology National University Cancer Institute National University Hospital Singapore Singapore. Cancer and Stem Cell Biology Program Duke-NUS Medical School Singapore Singapore. Department of Cancer Policy and Population Health National Cancer Center Graduate School of Cancer Science and Policy and Center for Gastric Cancer and Department of Surgery National Cancer Center Goyang Republic of Korea. Center for Gastric Cancer Department of Pathology National Cancer Center Goyang Republic of Korea. Department of Pathology Yonsei University College of Medicine Seoul Republic of Korea. Department of Surgery Yonsei University College of Medicine Seoul Republic of Korea. Department of Pathology GROW Research Institute for Oncology and Reproduction Maastricht University Medical Center+ Maastricht The Netherlands. Department of Precision Medicine GROW School for Oncology and Reproduction Maastricht University Center+ Maastricht The Netherlands. Computational Pathology Oncology R&D AstraZeneca Munich Germany. Department of Surgery Kanagawa Cancer Center Yokohama Japan. Department of Surgery Yokohama City University Yokohama Japan. Department of Surgery Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital Tokyo Japan. Department of Pathology Tokyo Metropolitan Institute for Geriatrics and Gerontology Tokyo Japan. Department of Medicine National University of Singapore Singapore Singapore. Department of Pathology National University Hospital Singapore Singapore. Genome Institute of Singapore Agency for Science Technology and Research Singapore Singapore. Cancer Science Institute of Singapore National University of Singapore Singapore Singapore. Cellular and Molecular Research National Cancer Centre Singapore Singapore. Singhealth/Duke-NUS Institute of Precision Medicine National Heart Centre Singapore

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Homogenisation for the monodomain model in the presence of microscopic fibrotic structures

arXiv

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arXiv 2020年

作者： Lawson, Brodie A.J. dos Santos, Rodrigo Weber Turner, Ian W. Bueno-Orovio, Alfonso Burrage, Pamela Burrage, Kevin Centre for Data Science Queensland University of Technology QLD Australia ARC Centre of Excellence for Mathematical and Statistical Frontiers Queensland University of Technology QLD Australia Graduate Program on Computational Modeling Universidade de Juiz de Fora Minas Gerais Brazil Department of Computer Science University of Oxford Oxfordshire United Kingdom

MSC Codes 35B27computational models in cardiac electrophysiology are notorious for long runtimes, restricting the numbers of nodes and mesh elements in the numerical discretisations used for their solution. This makes it particularly challenging to incorporate structural heterogeneities on small spatial scales, preventing a full understanding of the critical arrhythmogenic effects of conditions such as cardiac fibrosis. In this work, we explore the technique of homogenisation by volume averaging for the inclusion of non-conductive micro-structures into larger-scale cardiac meshes with minor computational overhead. Importantly, our approach is not restricted to periodic patterns, enabling homogenised models to represent, for example, the intricate patterns of collagen deposition present in different types of fibrosis. We first highlight the importance of appropriate boundary condition choice for the closure problems that define the parameters of homogenised models. Then, we demonstrate the technique’s ability to correctly upscale the effects of fibrotic patterns with a spatial resolution of 10 µm into much larger numerical mesh sizes of 100-250 µm. The homogenised models using these coarser meshes correctly predict critical pro-arrhythmic effects of fibrosis, including slowed conduction, source/sink mismatch, and stabilisation of re-entrant activation patterns. As such, this approach to homogenisation represents a significant step towards whole organ simulations that unravel the effects of microscopic cardiac tissue heterogeneities. © 2020, CC BY.

关键词： Heart

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