Biophysics and physicobiology最新文献_第4页

Monitoring of enzymatic cleavage reaction of GST-fusion protein on biolayer interferometry sensor. 利用生物层干涉仪传感器监测 GST 融合蛋白的酶裂解反应。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-18 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0019

Sena Tarumoto, Sei Inoue, Rina Yanagimoto, Takashi Saitoh

{"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":"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 Plasmodium falciparum was expressed and purified as a GST-tagged fusion protein, GST-Tic22, in Escherichia coli. 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.","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}

引用次数: 0

Experience of Hands-on training program on DNA Nanomachine at IUPAB2024. DNA纳米机器在IUPAB2024的实践培训计划的经验。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-13 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2004

Koki Yoshida

引用次数: 0

Function of nodal cilia in left-right determination: Mechanical regulation in initiation of symmetry breaking. 节点纤毛在左右决定中的功能：启动对称性破坏过程中的机械调节

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-06 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0018

Takanobu A Katoh

{"title":"Function of nodal cilia in left-right determination: Mechanical regulation in initiation of symmetry breaking.","authors":"Takanobu A Katoh","doi":"10.2142/biophysico.bppb-v21.0018","DOIUrl":"10.2142/biophysico.bppb-v21.0018","url":null,"abstract":"Visceral organs in vertebrates are arranged with left-right asymmetry; for example, the heart is located on the left side of the body. Cilia at the node of mouse early embryos play an essential role in determining this left-right asymmetry. Using information from the anteroposterior axis, motile cilia at the central region of the node generate leftward nodal flow. Immotile cilia at the periphery of the node mechanically sense the direction of leftward nodal flow in a manner dependent on the polarized localization of Pkd2, which is localized on the dorsal side of cilia. Therefore, only left-side cilia are activated by leftward nodal flow. This activation results in frequent calcium transients in the cilia via the Pkd2 channel, which leads to the degradation of Dand5 mRNA only at the left-side crown-cells. This process is the mechanism of initial determination of the left-side-specific signal. In this review, we provide an overview of initial left-right symmetry breaking that occurs at the node, focusing mainly on a recent biophysical study that revealed the function of nodal immotile cilia using advanced microscopic techniques, such as optical tweezers and super-resolution microscopy.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 3","pages":"e210018"},"PeriodicalIF":1.6,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11718168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974232","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

Feeling a nanoworld with optical tweezers: Hands on training at IUPAB 2024. 用光学镊子感受纳米世界：IUPAB 2024的实践培训。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-05 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2003

Zuzana Johanovská

引用次数: 0

Editorial: IUPAB2024 Congress in Kyoto. 社论：IUPAB2024年京都大会。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-08-29 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2001

Hiroyuki Noji

引用次数: 0

Hands-on training experience of C-trap. C-trap的实际培训经验。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-08-29 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2002

Yuze Sun

引用次数: 0

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":"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":"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