Biophysics and physicobiology最新文献

Chemical tongues as multipurpose bioanalytical tools for the characterization of complex biological samples. 化学舌作为多用途生物分析工具，用于表征复杂的生物样本。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-08-20 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0017

Shunsuke Tomita, Hiroka Sugai

{"title":"Chemical tongues as multipurpose bioanalytical tools for the characterization of complex biological samples.","authors":"Shunsuke Tomita, Hiroka Sugai","doi":"10.2142/biophysico.bppb-v21.0017","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v21.0017","url":null,"abstract":"Chemical tongues are emerging powerful bioanalytical tools that mimic the mechanism of the human taste system to recognize the comprehensive characteristics of complex biological samples. By using an array of chromogenic or fluorogenic probes that interact non-specifically with various components in the samples, this tool generates unique colorimetric or fluorescence patterns that reflect the biological composition of a sample. These patterns are then analyzed using multivariate analysis or machine learning to distinguish and classify the samples. This review focuses on our efforts to provide an overview of the fundamental principles of chemical tongues, probe design, and their applications as versatile tools for analyzing proteins, cells, and bacteria in biological samples. Compared to conventional methods that rely on specific targeting (e.g., antibodies or enzymes) or comprehensive omics analyses, chemical tongues offer advantages in terms of cost and the ability to analyze samples without the need for specific biomarkers. The complementary use of chemical tongues and conventional methods is expected to enable a more detailed understanding of biological samples and lead to the elucidation of new biological phenomena.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 3","pages":"e210017"},"PeriodicalIF":1.6,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11467466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485131","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}

引用次数: 0

Unraveling the fastest myosin: Discovery history and structure-function relationships of algae Chara myosin XI. 揭开最快肌球蛋白的神秘面纱：藻类查拉肌球蛋白 XI 的发现历史和结构功能关系。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-07-17 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0016

Kohji Ito, Takeshi Haraguchi

引用次数: 0

Internal structure of Mycoplasma mobile gliding machinery analyzed by negative staining electron tomography. 通过负染色电子断层扫描分析支原体移动滑行机械的内部结构。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-05-28 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0015

Minoru Fukushima, Takuma Toyonaga, Yuhei O Tahara, Daisuke Nakane, Makoto Miyata

{"title":"Internal structure of Mycoplasma mobile gliding machinery analyzed by negative staining electron tomography.","authors":"Minoru Fukushima, Takuma Toyonaga, Yuhei O Tahara, Daisuke Nakane, Makoto Miyata","doi":"10.2142/biophysico.bppb-v21.0015","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v21.0015","url":null,"abstract":"Mycoplasma mobile is a parasitic bacterium that forms gliding machinery on the cell pole and glides on a solid surface in the direction of the cell pole. The gliding machinery consists of both internal and surface structures. The internal structure is divided into a bell at the front and chain structure extending from the bell. In this study, the internal structures prepared under several conditions were analyzed using negative-staining electron microscopy and electron tomography. The chains were constructed by linked motors containing two complexes similar to ATP synthase. A cylindrical spacer with a maximum diameter of 6 nm and a height of 13 nm, and anonymous linkers with a diameter of 0.9-8.3 nm and length of 14.7±6.9 nm were found between motors. The bell is bowl-shaped and features a honeycomb surface with a periodicity of 8.4 nm. The chains of the motor are connected to the rim of the bell through a wedge-shaped structure. These structures may play roles in the assembly and cooperation of gliding machinery units.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 2","pages":"e210015"},"PeriodicalIF":1.6,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11347822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142116818","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}

引用次数: 0

Application of single-molecule analysis to singularity phenomenon of cells. 将单分子分析应用于细胞的奇异现象。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-05-08 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s018

Michio Hiroshima, Hiroko Bannai, Gen Matsumoto, Masahiro Ueda

{"title":"Application of single-molecule analysis to singularity phenomenon of cells.","authors":"Michio Hiroshima, Hiroko Bannai, Gen Matsumoto, Masahiro Ueda","doi":"10.2142/biophysico.bppb-v21.s018","DOIUrl":"10.2142/biophysico.bppb-v21.s018","url":null,"abstract":"Single-molecule imaging in living cells is an effective tool for elucidating the mechanisms of cellular phenomena at the molecular level. However, the analysis was not designed for throughput and requires high expertise, preventing it from reaching large scale, which is necessary when searching for rare cells that induce singularity phenomena. To overcome this limitation, we have automated the imaging procedures by combining our own focusing device, artificial intelligence, and robotics. The apparatus, called automated in-cell single-molecule imaging system (AiSIS), achieves a throughput that is a hundred-fold higher than conventional manual imaging operations, enabling the analysis of molecular events by individual cells across a large population. Here, using AiSIS, we demonstrate the single-molecule imaging of molecular behaviors and reactions related to tau protein aggregation, which is considered a singularity phenomenon in neurological disorders. Changes in the dynamics and kinetics of molecular events were observed inside and on the basal membrane of cells after the induction of aggregation. Additionally, to detect rare cells based on the molecular behavior, we developed a method to identify the state of individual cells defined by the quantitative distribution of molecular mobility and clustering. Using this method, cellular variations in receptor behavior were shown to decrease following ligand stimulation. This cell state analysis based on large-scale single-molecule imaging by AiSIS will advance the study of molecular mechanisms causing singularity phenomena.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 Supplemental","pages":"e211018"},"PeriodicalIF":1.6,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142038667","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}

引用次数: 0

X-ray diffraction recording from a small amount of fibrous protein materials oriented by a micro shear-flow cell. 通过微型剪切流池定向的少量纤维蛋白质材料的 X 射线衍射记录。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-04-20 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0014

Hiroyuki Iwamoto, Kazuhiro Oiwa, Kogiku Shiba, Kazuo Inaba

引用次数: 0

Optimizing tumor treating fields for blood cancer therapy: Analysis of electric field distribution and dose density. 优化血癌治疗的肿瘤治疗场：电场分布和剂量密度分析

IF 1.6

Biophysics and physicobiology Pub Date : 2024-04-18 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0013

Nasori Nasori, Miftakhul Firdhaus, Ulya Farahdina, Rini Khamimatul Ula

{"title":"Optimizing tumor treating fields for blood cancer therapy: Analysis of electric field distribution and dose density.","authors":"Nasori Nasori, Miftakhul Firdhaus, Ulya Farahdina, Rini Khamimatul Ula","doi":"10.2142/biophysico.bppb-v21.0013","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v21.0013","url":null,"abstract":"Blood cancer is a condition in which white blood cells grow uncontrollably. Tumor treating fields (TTF) are a modality of cancer treatment that utilizes electric fields to target malignant cells. To optimize the efficacy of TTF, it is necessary to investigate the distribution of electric field through varying electrode configurations and input parameters. This allows for enhancement of electric field intensity in targeted areas while minimizing intensity in sensitive areas. Analysis of electric field distribution was conducted through simulation of brachial models with varying electrode configurations and input parameters, utilizing the COMSOL Multiphysics 5.4 software. Additionally, investigations were carried out to assess tissue dose density. The dose density value at primary target for all electrode configurations and input parameters do not exceed the threshold value (770 W/m3), whereas the electric field value at the primary target satisfied the threshold value (100 V/m) on the system that used 4 plate-shaped electrodes and arm contour-shaped electrodes with an input voltage of 20 V, and at the input voltage 15 V, only 4 arm contour-shaped electrodes that satisfied the threshold value. An increase in input voltage, electrodes addition, and electrodes adjustment to skin contour shape result in an enhancement of electric field distribution and average electric field value at primary targets.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 2","pages":"e210013"},"PeriodicalIF":1.6,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11347819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142116819","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}

引用次数: 0

Charge block-driven liquid-liquid phase separation: A mechanism of how phosphorylation regulates phase behavior of disordered proteins. 电荷块驱动的液-液相分离：磷酸化如何调节无序蛋白质相行为的机制

IF 1.6

Biophysics and physicobiology Pub Date : 2024-03-28 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0012

Hisashi Shimamura, Hiroya Yamazaki, Shige H Yoshimura

{"title":"Charge block-driven liquid-liquid phase separation: A mechanism of how phosphorylation regulates phase behavior of disordered proteins.","authors":"Hisashi Shimamura, Hiroya Yamazaki, Shige H Yoshimura","doi":"10.2142/biophysico.bppb-v21.0012","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v21.0012","url":null,"abstract":"Phosphorylation regulates protein function by modulating stereospecific interactions between protein-protein or enzyme-ligand. On the other hand, many bioinformatics studies have demonstrated that phosphorylation preferably occurs in intrinsically disordered regions (IDRs), which do not have any secondary and tertiary structures. Although studies have demonstrated that phosphorylation changes the phase behavior of IDRs, the mechanism, which is distinct from the \"stereospecific\" effect, had not been elucidated. Here, we describe how phosphorylation in IDRs regulates the protein function by modulating phase behavior. Mitotic phosphorylation in the IDRs of Ki-67 and NPM1 promotes or suppresses liquid-liquid phase separation, respectively, by altering the \"charge blockiness\" along the polypeptide chain. The phosphorylation-mediated regulation of liquid-liquid phase separation by enhancing or suppressing \"charge blockiness,\" rather than by modulating stereospecific interactions, may provide one of the general mechanisms of protein regulation by posttranslational modifications and the role of multiple phosphorylations.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 2","pages":"e210012"},"PeriodicalIF":1.6,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11347820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142116817","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}

引用次数: 0

Strength in numbers: Unleashing the potential of trans-scale scope AMATERAS for massive cell quantification. 数字的力量：释放跨尺度范围 AMATERAS 的潜力，实现大规模细胞定量。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-03-23 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s017

Taro Ichimura, Taishi Kakizuka, Yuki Sato, Yoichiro Fujioka, Yusuke Ohba, Kazuki Horikawa, Takeharu Nagai

{"title":"Strength in numbers: Unleashing the potential of trans-scale scope AMATERAS for massive cell quantification.","authors":"Taro Ichimura, Taishi Kakizuka, Yuki Sato, Yoichiro Fujioka, Yusuke Ohba, Kazuki Horikawa, Takeharu Nagai","doi":"10.2142/biophysico.bppb-v21.s017","DOIUrl":"10.2142/biophysico.bppb-v21.s017","url":null,"abstract":"Singularity biology is a scientific field that targets drastic state changes in multicellular systems, aiming to discover the key cells that induce the state change and investigate the mechanisms behind them. To achieve this goal, we developed a trans-scale optical imaging system (trans-scale scope), that is capable of capturing both macroscale changes across the entire system and the micro-scale behavior of individual cells, surpassing the cell observation capabilities of traditional microscopes. We developed two units of the trans-scale scope, named AMATERAS-1 and -2, which demonstrated the ability to observe multicellular systems consisting of over one million cells in a single field of view with sub-cellular resolution. This flagship instrument has been used to observe the dynamics of various cell species, with the advantage of being able to observe a large number of cells, allowing the detection and analysis of rare events and cells such as leader cells in multicellular pattern formation and cells that spontaneously initiate calcium waves. In this paper, we present the design concept of AMATERAS, the optical configuration, and several examples of observations, and demonstrate how the strength-in-numbers works in life sciences.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 Supplemental","pages":"e211017"},"PeriodicalIF":1.6,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142038676","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}

引用次数: 0

Yuragi biomarker concept for evaluating human induced pluripotent stem cells using heterogeneity-based Raman finger-printing. 利用基于异质性的拉曼指纹图谱评估人类诱导多能干细胞的 Yuragi 生物标记概念。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-03-22 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s016

Hideaki Fujita, Takayuki Haruki, Kazuhiro Sudo, Yumiko Koga, Yukio Nakamura, Kuniya Abe, Yasuhiko Yoshida, Keiichi Koizumi, Tomonobu M Watanabe

{"title":"Yuragi biomarker concept for evaluating human induced pluripotent stem cells using heterogeneity-based Raman finger-printing.","authors":"Hideaki Fujita, Takayuki Haruki, Kazuhiro Sudo, Yumiko Koga, Yukio Nakamura, Kuniya Abe, Yasuhiko Yoshida, Keiichi Koizumi, Tomonobu M Watanabe","doi":"10.2142/biophysico.bppb-v21.s016","DOIUrl":"10.2142/biophysico.bppb-v21.s016","url":null,"abstract":"Considering the fundamental mechanism causing singularity phenomena, we performed the following abduction: Assuming that a multicellular system is driven by spontaneous fluctuation of each cell and dynamic interaction of the cells, state transition of the system would be experimentally predictable from cellular heterogeneity. This study evaluates the abductive hypothesis by analyzing cellular heterogeneity to distinguish pre-state of state transition of differentiating cells with Raman spectroscopy and human induced pluripotent stem cells (hiPSCs) technique. Herein, we investigated the time development of cellular heterogeneity in Raman spectra during cardiomyogenesis of six hiPSC lines and tested two types of analyses for heterogeneity. As expected, some spectral peaks, possibly attributed to glycogen, correctively exhibited higher heterogeneity, prior to intensity changes of the spectrum in the both analyses in the all cell-lines tested. The combination of spectral data and heterogeneity-based analysis will be an approach to the arrival of biology that uses not only signal intensity but also heterogeneity as a biological index.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 Supplemental","pages":"e211016"},"PeriodicalIF":1.6,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142038679","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}

引用次数: 0

Inferring the roles of individuals in collective systems using information-theoretic measures of influence. 利用信息论的影响力衡量标准推断个人在集体系统中的角色。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-03-22 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s014

Sulimon Sattari, Udoy S Basak, M Mohiuddin, Mikito Toda, Tamiki Komatsuzaki

引用次数: 0