Article
Biochemistry & Molecular Biology
Remi Vuillemot, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Summary: This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD), to obtain atomic models of cryo-EM maps more efficiently and accurately.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Lenka Kuncicka, Radim Kocich
Summary: This study focuses on assessing the effects of initial temperature (in)homogeneity on a hot-stamped medical gas valve fitting and optimizing temperature distribution within the product. Preheating the product with a certain temperature gradient is favorable, as it can result in better structural properties and avoid the occurrence of forming defects.
ADVANCED ENGINEERING MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Remi Vuillemot, Alex Mirzaei, Mohamad Harastani, Ilyes Hamitouche, Leo Frechin, Bruno P. Klaholz, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Summary: This article presents a new method for extracting atomic-resolution landscapes of continuous conformational variability of biomolecular complexes from cryo-EM single particle images. The method, called MDSPACE, uses a 3D-to-2D flexible fitting method based on molecular dynamics simulation and is embedded in an iterative conformational-landscape refinement scheme. The article describes the MDSPACE approach and demonstrates its performance using synthetic and experimental datasets.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Chaojian Hou, Kun Wang, Wenqi Zhang, Donglei Chen, Xiaokai Wang, Lu Fan, Chunyang Li, Jing Zhao, Lixin Dong
Summary: The current state-of-the-art in situ transmission electron microscopy (TEM) characterization technology can manipulate specimens at the nanoscale and provide atom-level material attributes. However, there is a barrier between material attributes investigations and device-level application explorations due to immature in situ TEM manufacturing technology and sufficient external stimuli. This study proposes an in situ opto-electromechanical TEM characterization platform by integrating an ultra-flexible micro-cantilever chip with optical, mechanical, and electrical coupling fields. The platform enables static and dynamic in situ device-level TEM characterizations using molybdenum disulfide (MoS2) as the channel material. The experiments demonstrate electron-beam modulation behavior and bending of MoS2 nanodevices, revealing piezoresistive and opto-electromechanical coupling properties. Real-time atom-level characterization is achieved using this approach, providing a step towards advanced in situ device-level TEM characterization technology.
ADVANCED MATERIALS
(2023)
Article
Nanoscience & Nanotechnology
F. Ruebeling, Y. Xu, G. Richter, D. Dini, P. Gumbsch, C. Greiner
Summary: Near the interface of two contacting metallic bodies in relative motion, the microstructure changes, influencing the tribological behavior. This study reveals the influence of normal load and counter body size on tribologically induced microstructures in copper, identifying the presence of dislocation trace lines in the subsurface area. The results demonstrate the generality of the trace line phenomena and provide a basis for modeling microstructure evolution under sliding contact.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Multidisciplinary
Franz-Philipp Schmidt, Arthur Losquin, Michal Horak, Ulrich Hohenester, Michael Stoger-Pollach, Joachim R. Krenn
Summary: The study utilizes cathodoluminescence (CL) spectroscopy in a transmission electron microscope to investigate the radial breathing mode of plasmonic silver nanodisks. It reveals a spectral shift in the CL spectra acquired from both sides induced by the electron beam, confirmed through numerical simulations. The interference of CL emission patterns of an electron-beam-induced dipole and the breathing mode is identified as a physical effect that can limit fidelity in CL measurements.
Article
Chemistry, Multidisciplinary
Hikaru Saito, Daichi Yoshimoto, Yuto Moritake, Taeko Matsukata, Naoki Yamamoto, Takumi Sannomiya
Summary: Using gap surface plasmons for high index contrasting, a wide-bandgap valley plasmonic crystal has been achieved for waveguiding in the near-infrared-visible range, providing a practical platform for transferring angular momentum between photons and carriers.
Article
Plant Sciences
Sergey Mursalimov, Nobuhiko Ohno, Mami Matsumoto, Sergey Bayborodin, Elena Deineko
Summary: The study using SBF-SEM revealed that intercellular nuclear migration (INM) occurs in 90-100% of tobacco meiocytes, suggesting it is a normal part of tobacco meiosis, yet the reason for such behavior of nuclei remains unclear. The results obtained highlight the potential of SBF-SEM in unveiling unexplored features of plant meiosis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
Karina Godoy, Cristian Sandoval, Claudio Vasquez, Carlos Manterola-Barroso, Barbara Toledo, Joel Calfuleo, Carolina Beltran, Marion Bustamante, Sebastian Valderrama, Mariana Rojas, Luis A. Salazar
Summary: In this study, we evaluated the gene expression during bone formation and regeneration and their relationship with mineralization in rainbow trout with mandibular deformation. The results showed marked elevation of bone morphogenetic protein 2 (Bmp2) and distinct expression patterns for transcriptional factors. This deformation was characterized by demineralization, increased porosity, and a moderate decrease in bone mineral content.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Engineering, Manufacturing
Xin Wang, Xianhu Liu, Xiao Ge, Dirk W. Schubert
Summary: Developing strain sensors with higher sensitivity and larger monitoring range is crucial for the potential applications in intelligent electronics, motion signal analysis, and human monitoring. This study presents a high-performance flexible strain sensor fabricated by embedding silver nanowires on a carbon black-modified electrospun thermoplastic polyurethane fabric film. The sensor exhibits excellent electrical response abilities, with superior sensitivity (gauge factor >16,000) over a strain range of 360% and exceptional durability and reliability (>10,000 cycles). Mathematical fitting models are proposed to quantitatively describe the variation of conductive pathways and inter-particles distance, providing valuable insights for the manufacturing and improvement of flexible strain sensors.
COMPOSITES PART A-APPLIED SCIENCE AND MANUFACTURING
(2023)
Article
Materials Science, Multidisciplinary
Mayank Kumar, Ajay M. Sidpara, Vikranth Racherla
Summary: This study utilizes the solvent casting method to create a flexible polyurethane tool embedded with SiC abrasive particles. Characterizations reveal the pore structure, distribution of abrasive particles, and mechanical behavior of the tools. Preliminary results suggest that these tools have the potential to achieve the desired level of finishing at a rapid rate and minimal cost.
MATERIALS TODAY COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Jorge J. Saenz Noval, Ruben Gomez-Merchan, Juan A. Lenero-Bardallo, Lionel C. Gontard
Summary: This study proposes an algorithm for measuring particle size distributions in electron microscopy images. Unlike AI-based methods, this non-AI algorithm is accurate, quick to set up, and can be applied to new experimental images. An open dataset of images and ground truth measurements is provided to overcome the lack of standards in NP metrology.
PARTICLE & PARTICLE SYSTEMS CHARACTERIZATION
(2023)
News Item
Optics
Yuya Morimoto
Summary: A transmission electron microscopy technique allows the recording of movies capturing the dynamic behavior of optical near-fields with a temporal resolution surpassing the oscillation of optical electric fields.
Article
Chemistry, Applied
Xueqing Lei, Zhiwei Qin, Bo Ye, Yao Wu, Ling Liu
Summary: The study found that under low pH conditions, oxyhemoglobin gradually transformed into methemoglobin, and the shape of heme in fluorescence electron microscopy changed. Compared to other pH values, at pH 5.7, the distance between amino acids in hemoglobin structure is longer, leading to more severe protein damage and lipid oxidation.
Article
Biochemistry & Molecular Biology
Sotaro Fuchigami, Shoji Takada
Summary: High-speed atomic force microscopy (HS-AFM) is a powerful technique for imaging the structural dynamics of biomolecules. In this study, the authors developed a flexible fitting molecular dynamics (MD) simulation method to infer the conformational and chemical states of a molecular motor, myosin V, from AFM images.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Dusan Kolarski, Simon Miller, Tsuyoshi Oshima, Yoshiko Nagai, Yugo Aoki, Piermichele Kobauri, Ashutosh Srivastava, Akiko Sugiyama, Kazuma Amaike, Ayato Sato, Florence Tama, Wiktor Szymanski, Ben L. Feringa, Kenichiro Itami, Tsuyoshi Hirota
Summary: CRY1 and CRY2 proteins are essential components of the circadian clock. Developing CRY1-selective compounds that can be manipulated through light-dependent mechanisms allows for a better understanding of the specific functions of CRY1 and CRY2. By utilizing benzophenone derivatives to interact with the photo lyase region of CRY1, researchers were able to activate CRY1 without affecting CRY2, demonstrating a potential for spatiotemporal regulation of CRY1 activity for health and disease research.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Medicinal
Sandhya P. Tiwari, Florence Tama, Osamu Miyashita
Summary: XFEL scattering technology faces challenges in studying single biomolecular complexes, leading to the proposal of an alternative method to find potential 3D biological shape models for further analysis.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Kunio Nakata, Naoyuki Miyazaki, Hiroki Yamaguchi, Mika Hirose, Tatsuki Kashiwagi, Nidamarthi H. Kutumbarao, Osamu Miyashita, Florence Tama, Hiroshi Miyano, Toshimi Mizukoshi, Kenji Iwasaki
Summary: The three-dimensional structure of phosphoketolase (PKT) from Bifidobacterium longum was determined using cryo-EM single-particle analysis. The study observed interesting structural features and multiple conformations of amino acid residues, as well as the presence of water molecules. The conformational changes of the QN-loop were found to be related to the enzymatic function of PKT.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maki Kuzuya, Hidemi Hirano, Kenichi Hayashida, Masakatsu Watanabe, Kazumi Kobayashi, Tohru Terada, Md Iqbal Mahmood, Florence Tama, Kazutoshi Tani, Yoshinori Fujiyoshi, Atsunori Oshima
Summary: In this study, the cryo-EM structures of human PANX1 in lipid nanodiscs were analyzed to elucidate the gating mechanism and its regulation by the amino terminus in phospholipids. The results showed that the amino-terminal domain plays an essential role in channel opening and is associated with lipid movement.
Article
Biochemistry & Molecular Biology
Albert M. Schulte, Dusan Kolarski, Vidya Sundaram, Ashutosh Srivastava, Florence Tama, Ben L. Feringa, Wiktor Szymanski
Summary: Protein kinases play a crucial role in cellular processes and signaling pathways, and their dysfunction is associated with various diseases. Photopharmacology, as an unconventional approach, uses light-controlled bioactive molecules to selectively activate drugs for kinase inhibition. This study presents the discovery and optimization of a photoswitchable inhibitor targeting casein kinase 1 delta (CK1 delta), which is involved in important signaling processes such as cell differentiation, circadian rhythm, DNA repair, and apoptosis. The optimized photoswitchable inhibitor showed improved properties, including high photostationary state distributions and solubility, as well as a 10-fold difference in activity between irradiated and thermally adapted samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Remi Vuillemot, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Summary: This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD), to obtain atomic models of cryo-EM maps more efficiently and accurately.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Optics
Miki Nakano, Osamu Miyashita, Yasumasa Joti, Akihiro Suzuki, Hideyuki Mitomo, Yoshiya Niida, Ying Yang, Hirokatsu Yumoto, Takahisa Koyama, Kensuke Tono, Haruhiko Ohashi, Makina Yabashi, Tetsuya Ishikawa, Yoshitaka Bessho, Kuniharu Ijiro, Yoshinori Nishino, Florence Tama
Summary: The study demonstrates the reconstruction of the three-dimensional structure of a gold nanoparticle from XFEL diffraction data using microliquid enclosure arrays (MLEAs) sample holders. The quality of the restored structure was significantly improved by background subtraction, achieving a resolution of 5 nm.
Article
Multidisciplinary Sciences
Reika Isoda, Zoltan Palmai, Akira Yoshinari, Li-Qing Chen, Florence Tama, Wolf B. Frommer, Masayoshi Nakamura
Summary: SWEET sucrose transporters play important roles in the allocation of sucrose in plants and have been shown to mediate transport of the plant growth regulator gibberellin (GA). The study reveals a functional connection between sucrose and GA and demonstrates that sucrose is the physiologically relevant substrate. These findings are important for understanding the role of SWEETs in pathogen susceptibility and male fertility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Simon Miller, Manish Kesherwani, Priscilla Chan, Yoshiko Nagai, Moeri Yagi, Jamie Cope, Florence Tama, Steve A. Kay, Tsuyoshi Hirota
Summary: This study elucidated the selectivity of SHP656 for CRY2 and identified the R form of SHP656 as the active isomer. The findings suggest a direct role of CRY2 in glioblastoma antitumorigenesis and provide a rationale for the selective modulation of CRY isoforms in the therapeutic treatment of glioblastoma and other circadian clock-related diseases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Remi Vuillemot, Alex Mirzaei, Mohamad Harastani, Ilyes Hamitouche, Leo Frechin, Bruno P. Klaholz, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Summary: This article presents a new method for extracting atomic-resolution landscapes of continuous conformational variability of biomolecular complexes from cryo-EM single particle images. The method, called MDSPACE, uses a 3D-to-2D flexible fitting method based on molecular dynamics simulation and is embedded in an iterative conformational-landscape refinement scheme. The article describes the MDSPACE approach and demonstrates its performance using synthetic and experimental datasets.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Miki Nakano, Osamu Miyashita, Florence Tama
Summary: Single-particle analysis using x-ray free-electron lasers is a novel method for obtaining structural information of samples. This study evaluates the resolution of three-dimensional structures obtained from XFEL single-particle reconstruction using synthetic data. It is found that larger molecules can be restored with higher detail relative to their size, but achieving high absolute resolution is challenging.
STRUCTURAL DYNAMICS-US
(2023)
Article
Biochemistry & Molecular Biology
Osamu Miyashita, Florence Tama
Summary: Flexible fitting based on molecular dynamics simulation is a technique for structure modeling from cryo-EM data that has been used for nearly two decades. It provides a way to extract atomistic details of conformational changes encoded in cryo-EM data and improve the quality of structural models. Additionally, it enables the characterization of conformational heterogeneity in cryo-EM data. We will summarize the advancements made in these techniques and highlight recent developments in this field.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Paula Olaya, Silvina Caino-Lores, Vanessa Lama, Ria Patel, Ariel Keller Rorabaugh, Osamu Miyashita, Florence Tama, Michela Taufer
Summary: Capturing the structural information of biological molecules is crucial for understanding their function and mechanism. This research presents a framework, XPSI, which utilizes X-ray Free Electron Lasers to accurately predict the orientation, conformation, and protein type of molecules from their diffraction patterns. Compared to other machine learning methods, XPSI shows low computational cost and high prediction accuracy.
2022 IEEE 18TH INTERNATIONAL CONFERENCE ON E-SCIENCE (ESCIENCE 2022)
(2022)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Ria Patel, Ariel Keller Rorabaugh, Paula Olaya, Silvina Caino-Lores, Georgia Channing, Catherine Schuman, Osamu Miyashita, Florence Tama, Michela Taufer
Summary: Neural networks are crucial for successful management of high-throughput scientific workflows. This study utilizes a multi-objective neural architecture search approach to generate accurate neural networks while optimizing for computational efficiency. By selecting and refining a subset of networks, efficient networks suitable for data analysis are obtained.
2022 IEEE 18TH INTERNATIONAL CONFERENCE ON E-SCIENCE (ESCIENCE 2022)
(2022)
Article
Biochemistry & Molecular Biology
Han Asi, Bhaskar Dasgupta, Tetsuro Nagai, Osamu Miyashita, Florence Tama
Summary: XFEL has huge potential in structural biology, but experimental difficulties and complex data analysis make it challenging to reconstruct 3D structures of biological molecules. In this study, we propose a hybrid approach that combines low-resolution XFEL diffraction pattern with a known conformation to characterize biomolecular conformational transitions. Our algorithm successfully describes the transitions and demonstrates the effect of incident beam orientation on the accuracy of 3D structure modeling.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
