Biophysics and physicobiology最新文献_第2页

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

Real-time imaging of human endothelial-to-hematopoietic transition in vitro using pluripotent stem cell derived hemogenic endothelium. 利用多能干细胞衍生的造血内皮对体外人体内皮细胞向造血细胞转变进行实时成像。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-03-22 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s015

Yuriko Yoneda, Hisaya Kato, Yoshiro Maezawa, Koutaro Yokote, Mio Nakanishi

{"title":"Real-time imaging of human endothelial-to-hematopoietic transition in vitro using pluripotent stem cell derived hemogenic endothelium.","authors":"Yuriko Yoneda, Hisaya Kato, Yoshiro Maezawa, Koutaro Yokote, Mio Nakanishi","doi":"10.2142/biophysico.bppb-v21.s015","DOIUrl":"10.2142/biophysico.bppb-v21.s015","url":null,"abstract":"During embryogenesis, human hematopoietic stem cells (HSCs) first emerge in the aorta-gonad-mesonephros (AGM) region via transformation of specialized hemogenic endothelial (HE) cells into premature HSC precursors. This process is termed endothelial-to-hematopoietic transition (EHT), in which the HE cells undergo drastic functional and morphological changes from flat, anchorage-dependent endothelial cells to free-floating round hematopoietic cells. Despite its essential role in human HSC development, molecular mechanisms underlying the EHT are largely unknown. This is due to lack of methods to visualize the emergence of human HSC precursors in real time in contrast to mouse and other model organisms. In this study, by inducing HE from human pluripotent stem cells in feeder-free monolayer cultures, we achieved real-time observation of the human EHT in vitro. By continuous observation and single-cell tracking in the culture, it was possible to visualize a process that a single endothelial cell gives rise to a hematopoietic cell and subsequently form a hematopoietic-cell cluster. The EHT was also confirmed by a drastic HE-to-HSC switching in molecular marker expressions. Notably, HSC precursor emergence was not linked to asymmetric cell division, whereas the hematopoietic cell cluster was formed through proliferation and assembling of the floating cells after the EHT. These results reveal unappreciated dynamics in the human EHT, and we anticipate that our human EHT model in vitro will provide an opportunity to improve our understanding of the human HSC development.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 Supplemental","pages":"e211015"},"PeriodicalIF":1.6,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11339020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142038672","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

Editorial: Singularity Biology and Beyond. 社论：奇点生物学及其他

IF 1.6

Biophysics and physicobiology Pub Date : 2024-03-15 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s013

Takeharu Nagai

引用次数: 0

Model systems for discovering evolutionary singularity of bilaterian physiological regulation: lessons from studies on simple/primitive flatworms. 发现两栖动物生理调节进化奇异性的模式系统：从简单/原始扁形虫研究中汲取的教训。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-03-02 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s012

Shunsuke Mori, Aoshi Kobayashi, Hirotaka Sakamoto, Mayuko Hamada, Tatsuya Sakamoto, Ryo Nakamura

引用次数: 0

Visualizing Singularity Phenomenon. 奇点现象可视化。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-02-22 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s011

Tomonobu M Watanabe, Tsuyoshi Shiina

引用次数: 0

Unraveling T-cell dynamics using fluorescent timer: Insights from the Tocky system. 利用荧光计时器揭示 T 细胞动态：从 Tocky 系统获得的启示。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-02-16 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s010

Masahiro Ono

{"title":"Unraveling T-cell dynamics using fluorescent timer: Insights from the Tocky system.","authors":"Masahiro Ono","doi":"10.2142/biophysico.bppb-v21.s010","DOIUrl":"10.2142/biophysico.bppb-v21.s010","url":null,"abstract":"Understanding the temporal dynamics of T-cell transcription is crucial for insights into immune cell function and development. In this study, we show the features of the Timer-of-Cell-Kinetics-and-Activity (Tocky) system, which enables analysis of temporal dynamics of cell activities and differentiation, leveraging Fluorescent Timer protein, which spontaneously changes its emission spectrum from blue to red fluorescence in known kinetics, as reporters. The current study examines the properties of the Tocky system, highlighting the Timer-Angle approach, which is a core algorithm of Tocky analysis and converts Timer Blue and Red fluorescence into Timer Angle and Intensity by trigonometric transformation. Importantly, Tocky analyzes time-related events within individual cells by the two phases of measurements, distinguishing between (1) the temporal sequence of cellular activities and differentiation within the time domain, and (2) the transcription frequency within the frequency domain. The transition from time measurement to frequency analysis, particularly at the Persistent locus that bridges these domains, highlights that system's unique property in what is measured and analyzed by Tocky. Intriguingly, the sustained transcriptional activities observed in cells at the Persistent locus may have unique biological features as demonstrated in activated regulatory T-cells (Treg) and pathogenic T-cells, respectively, using Foxp3-Tocky and Nr4a3-Tocky models. In conclusion, the Tocky system can provide crucial data for advancing our understanding of T-cell dynamics and function.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 Supplemental","pages":"e211010"},"PeriodicalIF":1.6,"publicationDate":"2024-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142038677","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

Chromophore-assisted light inactivation of target proteins for singularity biology. 用于奇异生物学的色团辅助光灭活目标蛋白质。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-02-15 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s009

Hisashi Shidara, Susumu Jitsuki, Kiwamu Takemoto

引用次数: 0