Biophysics and Physicobiology最新文献

{"title":"Accelerating biophysical studies and applications by label-free nanopore sensing.","authors":"Hirohito Yamazaki, Kan Shoji","doi":"10.2142/biophysico.bppb-v20.0010","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0010","url":null,"abstract":"Label-free single-molecule sensing technologies are attractive tools for investigating the properties of biological molecules via the understanding of molecular functionality. Among these technologies, nanopore sensing has become one of the growing technologies [1,2]. Nanopore sensing operates in the principle of resistive pulse sensing, where sensing molecules, such as DNA, RNA, and protein, pass through a pore under the electrical field, resulting in a blockade current due to the molecular occupation in a pore. The physical properties of sensing entities were obtained by analyzing blockade current, which can provide a fingerprint of sensing molecules (Figure 1) [3]. In this commentary article, we review the eight presentations at the symposium “Innovative label-free nanopore sensing toward biophysical studies and applications” of the 60th Annual Meeting of the Biophysical Society of Japan held in September 2022 and introduce how this sensing technology can be used as a tool to open new biophysical science or applications other than DNA sequencing. Kyle Briggs at Ottawa University/ Northern Nanopore Instruments talked about an automated method of electricalbased nanopore fabrication, which is one of the gold standard fabrication methods in the lab, and introduced how to accelerate solid-state nanopore research using this method [4,5]. He also presented the automated muti-pore fabrication tools having multi-channels fluidic flow cells with multi-membrane chips. Finally, he showed the nanopore trace analysis software, Nanolyzer, which has multiple functions such as multi-level blockade current fitting, overlay translocation events, kernel density estimation, etc. Kan Shoji at Nagaoka University of Technology presented a probe-type planer bilayer lipid membrane (pBLM) system [6,7] and its application for scanning ion conductance microscopy (SICM) [8]. In this system, pBLMs can be repeatedly formed at the tip of probes by inserting probes into a layered bath solution of an oil/lipid mixture and electrolyte. He mounted the probe into a SICM setup and demonstrated spatially-resolved chemical sensing by manipulating the probe. Additionally, he introduced an efficient current measurement system for synthetic DNA nanopores. Although DNA nanopore structures are expected to be applied for nanopore sensing, it is challenging to efficiently insert DNA nanopores into pBLMs. He prepared DNA nanopore-tethered gold electrodes and formed pBLMs on the surface of electrodes by inserting electrodes into the bath solution. Resultantly, efficient insertions of DNA nanopores were observed, and this method potentially accelerates applications of DNA nanopores for nanopore sensing. Figure 1 The fundamental working principle of nanopore sensing © 2023 THE BIOPHYSICAL SOCIETY OF JAPAN doi: 10.2142/biophysico.bppb-v20.0010","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200010"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/43/bc/20_e200010.PMC10205581.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9531815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving two-photon excitation microscopy for sharper and faster biological imaging.","authors":"Kohei Otomo,&nbsp;Hirokazu Ishii,&nbsp;Tomomi Nemoto","doi":"10.2142/biophysico.bppb-v20.0009","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0009","url":null,"abstract":"<p><p>Two-photon excitation laser scanning microscopy (TPLSM) has provided many insights into the life sciences, especially for thick biological specimens, because of its superior penetration depth and less invasiveness owing to the near-infrared wavelength of its excitation laser light. This paper introduces our four kinds of studies to improve TPLSM by utilizing several optical technologies as follows: (1) A high numerical aperture objective lens significantly deteriorates the focal spot size in deeper regions of specimens. Thus, approaches to adaptive optics were proposed to compensate for optical aberrations for deeper and sharper intravital brain imaging. (2) TPLSM spatial resolution has been improved by applying super-resolution microscopic techniques. We also developed a compact stimulated emission depletion (STED) TPLSM that utilizes electrically controllable components, transmissive liquid crystal devices, and laser diode-based light sources. The spatial resolution of the developed system was five times higher than conventional TPLSM. (3) Most TPLSM systems adopt moving mirrors for single-point laser beam scanning, resulting in the temporal resolution caused by the limited physical speed of these mirrors. For high-speed TPLSM imaging, a confocal spinning-disk scanner and newly-developed high-peak-power laser light sources enabled approximately 200 foci scanning. (4) Several researchers have proposed various volumetric imaging technologies. However, most technologies require large-scale and complicated optical setups based on deep expertise for microscopic technologies, resulting in a high threshold for biologists. Recently, an easy-to-use light-needle-creating device was proposed for conventional TPLSM systems to achieve one-touch volumetric imaging.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200009"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7d/15/20_e200009.PMC10205574.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9526625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanisms of the high performance of spider silks revealed through multi-omics analysis.","authors":"Yasuha Watanabe,&nbsp;Kazuharu Arakawa","doi":"10.2142/biophysico.bppb-v20.0014","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0014","url":null,"abstract":"<p><p>Spider silk is considered a promising next-generation biomaterial due to its exceptional toughness, coupled with its renewability and biodegradability. Contrary to the conventional view that spider silk is mainly composed of two types of silk proteins (spidroins), MaSp1 and MaSp2, multi-omics strategies are increasingly revealing that the inclusion of complex components confers the higher mechanical properties to the material. In this review, we focus on several recent findings that report essential components and mechanisms that are necessary to reproduce the properties of natural spider silk. First, we discuss the discovery of MaSp3, a newly identified spidroin that is a major component in the composition of spider silk, in addition to the previously understood MaSp1 and MaSp2. Moreover, the role of the Spider-silk Constituting Element (SpiCE), which is present in trace amounts but has been found to significantly increase the tensile strength of artificial spider silk, is explored. We also delve into the process of spidroin fibril formation through liquid-liquid phase separation (LLPS) that forms the hierarchical structure of spider silk. In addition, we review the correlation between amino acid sequences and mechanical properties such as toughness and supercontraction, as revealed by an analysis of 1,000 spiders. In conclusion, these recent findings contribute to the comprehensive understanding of the mechanisms that give spider silk its high mechanical properties and help to improve artificial spider silk production.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200014"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b3/c4/20_e200014.PMC10338049.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9825845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Announcement of BPPB paper awards 2022.","authors":"Haruki Nakamura","doi":"10.2142/biophysico.bppb-v19.0042","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0042","url":null,"abstract":"There are two kinds of paper awards given to the authors of the original articles, which have been published from Biophysics and Physicobiology (BPPB): Award for Outstanding BPPB Paper and BPPB Editors' Choice Award. The former is given by the Biophysical Society of Japan (BSJ) to the authors, who contributed to the advancement of biophysics by their groundbreaking article, published between 2015 and 2020. This year, the committee organized in the BSJ for the 11th Award for Outstanding BPPB paper has selected Drs. Akira Kitamura and Masataka Kinjo in Hokkaido University, for their article “Determination of diffusion coefficients in live cells using fluorescence recovery after photobleaching with wide-field fluorescence microscopy” Biophys. Physicobiol. 15, 1-7 (2018) [1]. At the 60th Annual Meeting of the BSJ held in September 2022, the awardee, Dr. Akira Kitamura, was commended, and he made the Award Seminar. The latter one, the 9th BPPB Editors' Choice Award, is given by the BSJ to the authors of the articles in the BPPB, who made scientifically unique contributions to biophysics, published in 2021. This year, the awardees are the following four authors. Dr. Ryo Yoshizawa in RIKEN [2], Dr. Takashi Yoshidome in Tohoku Univ. [3], Dr. Masayuki Oda in Kyoto Prefectural Univ. [4], and Dr. Katsumasa Irie in Wakayama Medical Univ. [5]. At the 60th Annual Meeting of the BSJ, the awardees were announced, and they made brief comments for their works.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190042"},"PeriodicalIF":0.0,"publicationDate":"2022-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/76/d4/19_e190042.PMC9592885.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tackle \"Molecular Engine\" by early-career researchers.","authors":"Akihiro Otomo,&nbsp;Takahiro Kosugi","doi":"10.2142/biophysico.bppb-v19.0039","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0039","url":null,"abstract":"1 Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan 2 Department of Functional Molecular Science, School of Physical Science, SOKENDAI, Hayama, Kanagawa 2400193, Japan 3 Research Center of Integrative Molecular Systems, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan 4 Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan 5 Department of Structural Molecular Science, School of Physical Sciences, SOKENDAI, Hayama, Kanagawa 2400193, Japan 6 PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190039"},"PeriodicalIF":0.0,"publicationDate":"2022-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ad/b4/19_e190039.PMC9592889.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation on substrate specificity and catalytic activity of serine protease neuropsin.","authors":"Masami Lintuluoto,&nbsp;Mitsumasa Abe,&nbsp;Yota Horioka,&nbsp;Yoshifumi Fukunishi,&nbsp;Hideki Tamura,&nbsp;Juha M Lintuluoto","doi":"10.2142/biophysico.bppb-v19.0040","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0040","url":null,"abstract":"<p><p>Neuropsin is one of serine proteases mainly found at the hippocampus and the amygdala, where it contributes to the long-term potentiation and memory acquisition by rebuilding of synaptic connections. Despite of the importance of neuropsin, the substrate specificity and regulation mechanisms of neuropsin have been unclear. Thus, we investigated the substrate specificity and the catalytic activity of neuropsin by the protein-ligand docking and molecular dynamics (MD) simulations and succeeded to reproduce the trend of the experimental results. Our study revealed that the substrate specificity and the activity of neuropsin depended on multiple factors: the substrate charge, the substrate orientation, the hydrogen bond network within the catalytic triad and the substrate, and the formation of the oxyanion hole. The apo neuropsin was not reactive without proper alignment of catalytic triad. The substrate binding induced the reactive alignment of catalytic triad. Then the substrate-neuropsin interaction forms the oxyanion hole that stabilizes the transition state and reduces the free-energy barrier of the following scission reaction.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190040"},"PeriodicalIF":0.0,"publicationDate":"2022-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/05/41/19_e190040.PMC9592888.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of gap junctions upon Ca²⁺ propagation from stimulated keratinocytes to DRG neurons.","authors":"Chiaki Seto,&nbsp;Kenta Toyoda,&nbsp;Kousuke Inada,&nbsp;Kotaro Oka,&nbsp;Etsuro Ito","doi":"10.2142/biophysico.bppb-v19.0041","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0041","url":null,"abstract":"<p><p>Epidermal cells, such as keratinocytes, are regarded as the first sensory cells to transmit nociception and mechanoreception to free nerve endings extended from the dorsal root ganglion (DRG). Previous studies suggested that this transmission occurs as Ca²⁺ propagation via ATP receptors. Conversely, the influence of gap junctions on this Ca²⁺ propagation is largely unknown. Thus, we examined the localization and the role of connexin 43 among keratinocytes and DRG neurons. We co-cultured keratinocytes and DRG neurons and investigated the effect of pharmacological blockade of gap junctions on Ca²⁺ propagation upon stimulation of a single keratinocyte. Immunocytochemical experiments showed that connexin 43 is localized between keratinocytes and between keratinocytes and DRG neurons. Octanol, a gap junction inhibitor, significantly suppressed the concentrical Ca²⁺ propagation. Therefore, we conclude that the Ca²⁺ propagation mechanism via gap junctions from stimulated keratinocytes to free nerve endings should be taken into account.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190041"},"PeriodicalIF":0.0,"publicationDate":"2022-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/29/c6/19_e190041.PMC9592570.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Announcement of new Editorial Board members","authors":"Haruki Nakamura","doi":"10.2142/biophysico.bppb-v19.0038","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0038","url":null,"abstract":"In this September 2022, the following four biophysicists join the Editorial Board of the Biophysics and Physicobiology (BPPB): Prof. Gautam Basu in Bose Institute, India, Prof. Raymond S. Norton in Monash University, Australia, Prof. Steve Pressé in Arizona State University, USA, and Prof. Jie Yan in National University of Singapore. Prof. Basu works in the field of structural bioinformatics and biochemistry using both experimental and computational tools [1]. Prof. Norton is a specialist in studies of peptides and proteins from venomous organisms by a range of biophysical approaches, including NMR, SPR, ITC and X-ray crystallography [2]. Prof. Pressé is a data scientist in chemical and biological physics, performing experiments to understand bacterial hunting dynamics and developing theoretical models [3]. Prof. Yan studies molecular and cell biology by combining theoretical modeling and his own single-molecule biophysical methods, single-molecule manipulation and imaging [4]. At the same time, we invite Prof. Lee-Wei Yang in National Tsing-Hua University, Taiwan as one of the Associate Editors, together with the following three new Advisory Board members: Prof. Robert E. Campbell in both The University of Alberta, Canada and The University of Tokyo, Dr. Damien R. Hall in Kanazawa University, Japan, and Prof. Soichi Wakatsuki in Stanford University, USA. We expect those fresh Editorial Board members, an Associate Editor, and Advisory Board members in various biophysics field will surely contribute to the BPPB very much, to publish many valuable articles and to provide novel biophysical information and knowledge to all over the world.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79447424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Standardization of luminescence, fluorescence measurements, and light microscopy: Current situation and perspectives.","authors":"Akira Sasaki,&nbsp;Yoshihiro Ohmiya","doi":"10.2142/biophysico.bppb-v19.0037","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0037","url":null,"abstract":"Improving reproducibility and confidence are important challenges in biomedical measurements, such as luminescence and fluorescence measurements [1]. In general, biomedical measurement results using luminescence and fluorescence are described in terms of optical signals. Although the quantitative aspects of luminescence, fluorescence measurement, and light microscopy are increasingly critical for experimental outputs, the measurement values are still described in arbitrary units. This makes it difficult to compare the results obtained using different equipment because the factors used to determine the optical signal value depend on the type of measurement system and detector used, the spectral properties of the optical components in the light path, and the day the measurement is taken. Standardizing system calibration and verification procedures and establishing reference materials as a common “scale” support a universal comparison between measurement results obtained under different instruments and conditions, thereby ensuring improved result reproducibility and reliability. At the 60th Annual Meeting of the Biophysical Society of Japan, held in September 2022, we organize a symposium session to introduce this research goal.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190037"},"PeriodicalIF":0.0,"publicationDate":"2022-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/37/9b/19_e190037.PMC9592890.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interplay among cell migration, shaping, and traction force on a matrix with cell-scale stiffness heterogeneity.","authors":"Hiroyuki Ebata,&nbsp;Satoru Kidoaki","doi":"10.2142/biophysico.bppb-v19.0036","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0036","url":null,"abstract":"<p><p>In living tissues where cells migrate, the spatial distribution of mechanical properties, especially matrix stiffness, is generally heterogeneous, with cell scales ranging from 10 to 1000 μm. Since cell migration in the body plays a critical role in morphogenesis, wound healing, and cancer metastasis, it is essential to understand the migratory dynamics on the matrix with cell-scale stiffness heterogeneity. In general, cell migration is driven by the extension and contraction of the cell body owing to the force from actin polymerization and myosin motors in the actomyosin cytoskeleton. When a cell is placed on a matrix with a simple stiffness gradient, directional migration called durotaxis emerges because of the asymmetric extension and contraction of the pseudopodia, which is accompanied by the asymmetric distribution of focal adhesions. Similarly, to determine cell migration on a matrix with cell-scale stiffness heterogeneity, the interaction between cell-scale stiffness heterogeneity and cellular responses, such as the dynamics of the cell-matrix adhesion site, intracellular prestress, and cell shape, should play a key role. In this review, we summarize systematic studies on the dynamics of cell migration, shaping, and traction force on a matrix with cell-scale stiffness heterogeneity using micro-elastically patterned hydrogels. We also outline the cell migration model based on cell-shaping dynamics that explains the general durotaxis induced by cell-scale stiffness heterogeneity. This review article is an extended version of the Japanese article, Dynamics of Cell Shaping and Migration on the Matrix with Cell-scale Stiffness-heterogeneity, published in SEIBUTSU BUTSURI Vol. 61, p. 152-156 (2021).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190036"},"PeriodicalIF":0.0,"publicationDate":"2022-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/01/5d/19_e190036.PMC9592569.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}