Biophysics and physicobiology最新文献

{"title":"Neuron with well-designed ionic system.","authors":"Takayoshi Tsubo","doi":"10.2142/biophysico.bppb-v21.0028","DOIUrl":"10.2142/biophysico.bppb-v21.0028","url":null,"abstract":"<p><p>Neurons have an ionic system with several types of ion pumps and ion channels on their membranes. Each ion pump creates a specific difference in ion concentration inside and outside the neuron, and the energy resulting from this difference in concentration is maintained inside the neuron as a resting potential. Each ion channel senses the necessary situation, opens the channel, and allows the corresponding ion to pass through to perform its corresponding role. This ionic system realizes important functions such as (i) fast conduction of action potentials, (ii) achieving synaptic integration in response to several inputs with a time lag, and (iii) the information processing functions by neural circuits. However, the mechanisms by which these functions are realized have remained unclear. Therefore, based on the reports on various highly polymeric ion pumps, ion channels, cell membranes, and other components that have been elucidated so far, author analyzed how this ionic system can realize the above important functions from an electrical circuit designer point of view. As a result of a series of analyses, it was found that neurons realize each function by making full use of high-density packaging technology based on basic electrical principles and making maximum use of the extremely high dielectric properties of the ionic fluid of neurons. In other words, neuron looks to equip well designed ionic system which is the collaboration by designers of proteins and membranes that perform advanced functions and designers of electrical circuits that utilize them to achieve important functions electrically.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210028"},"PeriodicalIF":1.6,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11830477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443085","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":"Comparative study of alpha-glucosidase inhibition of four Vietnamese medicinal plants <i>Combretum quadrangulare</i>, <i>Dicranopteris linearis</i>, <i>Psychotria adenophylla</i>, and <i>Garcinia schomburgkiana</i>: <i>In vitro</i> and <i>in vivo</i> studies.","authors":"Thi-Hong-Tuoi Do, Thuc-Huy Duong, Huu-Hung Nguyen, Thanh-Sang Vo, Ngoc-Hong Nguyen, Huong Thuy Le","doi":"10.2142/biophysico.bppb-v21.0027","DOIUrl":"10.2142/biophysico.bppb-v21.0027","url":null,"abstract":"<p><p>Four medicinal plants <i>C. quadrangulare</i>, <i>D. linearis</i>, <i>P. adenophylla</i>, and <i>G. schomburgkiana</i> growing in the South of Vietnam were investigated for their alpha-glucosidase inhibition. The crude methanol extract of <i>C. quadrangulare</i> was determined to be the most active extract, then was selected for further <i>in vivo</i> assays including antidiabetic study and toxicity. <i>In vitro</i> alpha-glucosidase inhibition of four medicinal plants <i>C. quadrangulare</i>, <i>D. linearis</i>, <i>P. adenophylla</i>, and <i>G. schomburgkiana</i> was screened using standard procedures. <i>In vivo</i> antidiabetic activity, acute toxicity and subchronical toxicity of <i>C. quadrangulare</i> leaves was assessed on Swiss albino mice. Swiss albino mice were induced with diabetes by intraperitoneal injection of alloxan at a dose of 150 mg/kg body weight. High-performance liquid chromatography with evaporative light scattering detector (HPLC-ELSD) were used to detect the bioactive components of <i>C. quadrangulare</i> leaves. All crude extracts from the studied plants showed promising alpha-glucosidase inhibition, with IC₅₀ values ranging from 2.4 to 35.3 μg/mL. The methanol extract of <i>C. quadrangulare</i> leaves was determined to be the most active extract. This extract was then selected for antidiabetic assay using alloxan induced model of type 2 diabetes mellitus mice. The results indicated that the extract at a dose of 400 mg/kg can effectively decrease blood glucose levels that is comparable to that of glibenclamide 2 mg/kg. This compound showed moderate activity toward alpha-glucosidase. Therefore, our study indicated that <i>C. quadrangulare</i>, <i>D. linearis</i>, <i>P. adenophylla</i>, and <i>G. schomburgkiana</i> extract are potential materials for producing α-glucosidase inhibitor drugs.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210027"},"PeriodicalIF":1.6,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11832248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442916","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":"Electrophysiological analysis of hyperkalemic cardiomyocytes using a multielectrode array system.","authors":"Kentaro Kito, Masahito Hayashi, Tomoyuki Kaneko","doi":"10.2142/biophysico.bppb-v21.0026","DOIUrl":"10.2142/biophysico.bppb-v21.0026","url":null,"abstract":"<p><p>The action potential of cardiomyocytes is controlled by electrolytes in serum such as Na⁺, K⁺ and Ca²⁺. Hyperkalemia, which refers to an abnormally high concentration of K⁺ in the blood, can induce lethal arrythmia. In this study, the extracellular potentials on a sheet of chick embryonic cardiomyocytes were investigated at increasing K⁺ concentrations using a multielectrode array system. We observed that the interspike interval (ISI) was prolonged by approximately 3.5 times; dV/dt (the slope of a waveform) was decreased by more than five times; the field potential duration (FPD) was shortened by 20%, and the conduction velocity was about half at 12 mM K⁺ against the control (4 mM K⁺). In calcium therapy for hyperkalemia, although the prolongation of ISI under hyperkalemic conditions was restored, the slowing of conduction velocity, the decrease in dV/dt, and the shortening of FPD were not recovered by increasing the extracellular Ca²⁺ concentration. These findings provide a comprehensive understanding of cardiomyocytes in hyperkalemic conditions. Electrophysiological analysis by varying the extracellular concentrations of multiple types of electrolytes will be useful for the further discussion of the results of this study and for the interpretation of the waveforms obtained by measuring the extracellular potential.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210026"},"PeriodicalIF":1.6,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11832246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442882","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 2024.","authors":"Haruki Nakamura","doi":"10.2142/biophysico.bppb-v21.0025","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v21.0025","url":null,"abstract":"","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210025"},"PeriodicalIF":1.6,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11830474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442872","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":"Rapid in vitro method to assemble and transfer DNA fragments into the JCVI-syn3B minimal synthetic bacterial genome through Cre/<i>loxP</i> system.","authors":"Atsuko Uenoyama, Hana Kiyama, Mone Mimura, Makoto Miyata","doi":"10.2142/biophysico.bppb-v21.0024","DOIUrl":"10.2142/biophysico.bppb-v21.0024","url":null,"abstract":"<p><p>JCVI-syn3B (syn3B), a minimal synthetic bacterium that only possesses essential genes, facilitates the examination of heterogeneous gene functions in minimal life. Conventionally, <i>Escherichia coli</i> is used to construct DNA fragments for gene transfer into the syn3B genome through Cre/<i>loxP</i> system. However, the construction process is challenging and time-consuming due to various issues, including the inhibition of <i>E. coli</i> growth and unexpected recombination, especially with AT-rich DNA sequences such as those found in <i>Mycoplasma</i> genes. Therefore, in this study, we aimed to develop a new transformation method to overcome these issues. We assembled the vector and target DNA fragments using an in vitro homologous recombination system and subsequently transferred the products into the syn3B genome. We obtained approximately 10³~10⁴ recombinant colonies per milliliter of the original culture in eight days, which is four days shorter than the conventional period, without any recombination issues, even for AT-rich DNA. This method may be applicable to other gene manipulation systems based on Cre/<i>loxP</i> system.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210024"},"PeriodicalIF":1.6,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11830475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443089","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":"Inducing aggresome and stable tau aggregation in Neuro2a cells with an optogenetic tool.","authors":"Shigeo Sakuragi, Tomoya Uchida, Naoki Kato, Boxiao Zhao, Toshiki Takahashi, Akito Hattori, Yoshihiro Sakata, Yoshiyuki Soeda, Akihiko Takashima, Hideaki Yoshimura, Gen Matsumoto, Hiroko Bannai","doi":"10.2142/biophysico.bppb-v21.0023","DOIUrl":"10.2142/biophysico.bppb-v21.0023","url":null,"abstract":"<p><p>Tauopathy is a spectrum of diseases characterized by fibrillary tau aggregate formation in neurons and glial cells in the brain. Tau aggregation originates in the brainstem and entorhinal cortex and then spreads throughout the brain in Alzheimer's disease (AD), which is the most prevalent type of tauopathy. Understanding the mechanism by which locally developed tau pathology propagates throughout the brain is crucial for comprehending AD pathogenesis. Therefore, a novel model of tau pathology that artificially induces tau aggregation in targeted cells at specific times is essential. This study describes a novel optogenetic module, OptoTau, which is a human tau with the P301L mutation fused with a photosensitive protein CRY2olig, inducing various forms of tau according to the temporal pattern of blue light illumination pattern. Continuous blue light illumination for 12 h to Neuro2a cells that stably express OptoTau (OptoTauKI cells) formed clusters along microtubules, many of which eventually accumulated in aggresomes. Conversely, methanol-resistant tau aggregation was formed when alternating light exposure and darkness in 30-min cycles for 8 sets per day were repeated over 8 days. Methanol-resistant tau was induced more rapidly by repeating 5-min illumination followed by 25-min darkness over 24 h. These results indicate that OptoTau induced various tau aggregation stages based on the temporal pattern of blue light exposure. Thus, this technique exhibits potential as a novel approach to developing specific tau aggregation in targeted cells at desired time points.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210023"},"PeriodicalIF":1.6,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11832247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442976","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":"Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves.","authors":"Sakura Takada, Kei Fujiwara","doi":"10.2142/biophysico.bppb-v21.0022","DOIUrl":"10.2142/biophysico.bppb-v21.0022","url":null,"abstract":"<p><p>Intracellular positional information is crucial for the precise control of biological phenomena, including cell division, polarity, and motility. Intracellular reaction-diffusion (iRD) waves are responsible for regulating positional information within cells as morphogens in multicellular tissues. However, iRD waves are explained by the coupling of biochemical reactions and molecular diffusion which indicates nonlinear systems under far from equilibrium conditions. Because of this complexity, experiments using defined elements rather than living cells containing endogenous factors are necessary to elucidate their pattern formation mechanisms. In this review, we summarize the effectiveness of artificial cell systems for investigating iRD waves derived from their high controllability and ability to emulate cell-size space effects. We describe how artificial cell systems reveal the characteristics of iRD waves, including the mechanisms of wave generation, mode selection, and period regulation. Furthermore, we introduce remaining open questions and discuss future challenges even in Min waves and in applying artificial cell systems to various iRD waves.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210022"},"PeriodicalIF":1.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11830476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442950","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":"Data-driven score tuning for ChooseLD: A structure-based drug design algorithm with empirical scoring and evaluation of ligand-protein docking predictability.","authors":"Akihiro Masuda, Daichi Sadato, Mitsuo Iwadate","doi":"10.2142/biophysico.bppb-v21.0021","DOIUrl":"10.2142/biophysico.bppb-v21.0021","url":null,"abstract":"<p><p>Computerized molecular docking methodologies are pivotal in <i>in-silico</i> screening, a crucial facet of modern drug design. ChooseLD, a docking simulation software, combines structure- and ligand-based drug design methods with empirical scoring. Despite advancements in computerized molecular docking methodologies, there remains a gap in optimizing the predictive capabilities of docking simulation software. Accordingly, using the docking scores output by ChooseLD, we evaluated its performance in predicting the bioactivity of G-protein coupled receptor (GPCR) and kinase bioactivity, specifically focusing on Ki and IC₅₀ values. We evaluated the accuracy of our algorithm through a comparative analysis using force-field-based predictions from AutoDock Vina. Our findings suggested that the modified ChooseLD could accurately predict the bioactivity, especially in scenarios with a substantial number of known ligands. These findings highlight the importance of selecting algorithms based on the characteristics of the prediction targets. Furthermore, addressing partial model fitting with database knowledge was demonstrated to be effective in overcoming this challenge. Overall, these findings contribute to the refinement and optimization of methodologies in computer-aided drug design, ultimately advancing the efficiency and reliability of <i>in-silico</i> screening processes.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 3","pages":"e210021"},"PeriodicalIF":1.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11718169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974184","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":"Four-color single-molecule imaging system for tracking GPCR dynamics with fluorescent HiBiT peptide.","authors":"Toshiki Yoda, Yasushi Sako, Asuka Inoue, Masataka Yanagawa","doi":"10.2142/biophysico.bppb-v21.0020","DOIUrl":"10.2142/biophysico.bppb-v21.0020","url":null,"abstract":"<p><p>Single-molecule imaging provides information on diffusion dynamics, oligomerization, and protein-protein interactions in living cells. To simultaneously monitor different types of proteins at the single-molecule level, orthogonal fluorescent labeling methods with different photostable dyes are required. G-protein-coupled receptors (GPCRs), a major class of drug targets, are prototypical membrane receptors that have been studied using single-molecule imaging techniques. Here we developed a method for labeling cell-surface GPCRs inspired by the HiBiT system, which utilizes the high affinity complementation between LgBiT and HiBiT fragments of the NanoLuc luciferase. We synthesized four fluorescence-labeled HiBiT peptides (F-FiBiTs) with a different color dye (Setau-488, TMR, SaraFluor 650 and SaraFluor 720). We constructed a multicolor total internal reflection fluorescence microscopy system that allows us to track four color dyes simultaneously. As a proof-of-concept experiment, we labeled an N-terminally LgBiT-fused GPCR (Lg-GPCR) with a mixture of the four F-FiBiTs and successfully tracked each dye within a cell at the single-molecule level. The F-FiBiT-labeled Lg-GPCRs showed agonist-dependent changes in the diffusion dynamics and accumulation into the clathrin-coated pits as observed with a conventional method using a C-terminally HaloTag-fused GPCR. Taking advantage of luciferase complementation by the F-FiBiT and Lg-GPCRs, the F-FiBiT was also applicable to bioluminescence plate-reader-based assays. By combining existing labeling methods such as HaloTag, SNAP-tag, and fluorescent proteins, the F-FiBiT method will be useful for multicolor single-molecule imaging and will enhance our understanding of GPCR signaling at the single-molecule level.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 3","pages":"e210020"},"PeriodicalIF":1.6,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11718171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974224","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":"Monitoring of enzymatic cleavage reaction of GST-fusion protein on biolayer interferometry sensor.","authors":"Sena Tarumoto, Sei Inoue, Rina Yanagimoto, Takashi Saitoh","doi":"10.2142/biophysico.bppb-v21.0019","DOIUrl":"10.2142/biophysico.bppb-v21.0019","url":null,"abstract":"<p><p>Biolayer interferometry (BLI) is an optical sensor-based analytical method primarily used for analyzing interactions between biomolecules. In this study, we explored the application of BLI to observe the cleavage reaction of glutathione S-transferase (GST)-tagged fusion protein by human rhinovirus (HRV) 3C protease on a BLI sensor as a new application of the BLI method. The soluble domain of the Tic22 protein from <i>Plasmodium falciparum</i> was expressed and purified as a GST-tagged fusion protein, GST-Tic22, in <i>Escherichia coli</i>. A cleavage sequence for HRV 3C protease was inserted between the GST tag and the soluble domain of Tic22. First, we confirmed that GST-Tic22 was specifically cleaved at the inserted sequence by HRV 3C protease using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Following this, GST-Tic22 was immobilized on a BLI sensor, and enzymatic cleavage by the HRV 3C protease was monitored. We observed that the soluble domain of Tic22 was cleaved and released into the buffer over time, and this reaction was dependent on the enzyme concentration. This result demonstrates that the BLI method can be used to evaluate the cleavage of the GST tag by the HRV 3C protease in real time under different conditions. This method enables a more efficient search for the optimal conditions for the tag cleavage reaction in fusion proteins, a process that has historically required a substantial amount of time and effort.</p>","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 3","pages":"e210019"},"PeriodicalIF":1.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11718170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974260","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}