Biophysics and Physicobiology最新文献

Description of peptide bond planarity from high-resolution neutron crystallography. 通过高分辨率中子晶体学描述肽键的平面性。

Biophysics and Physicobiology Pub Date : 2023-09-06 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0035

Yuya Hanazono, Yu Hirano, Taro Tamada, Kunio Miki

引用次数: 0

Population dynamics models for various forms of adaptation. 各种适应形式的人口动态模型。

Biophysics and Physicobiology Pub Date : 2023-09-02 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0034

So Nakashima, Tetsuya J Kobayashi

{"title":"Population dynamics models for various forms of adaptation.","authors":"So Nakashima, Tetsuya J Kobayashi","doi":"10.2142/biophysico.bppb-v20.0034","DOIUrl":"10.2142/biophysico.bppb-v20.0034","url":null,"abstract":"Adaptability to changing environments is one of the universal characteristics of living organisms. Because individual modes of adaptation are diverse, a unified understanding of these diverse modes is essential to comprehend adaptation. Adaptations can be categorized from at least two perspectives with respect to information. One is the passivity and activity of adaptation and the other is the type of information transmission. In Darwinian natural selection, organisms are selected among randomly generated traits under which individual organisms are passive in the sense that they do not process any environmental information. On the other hand, organisms can also adapt by sensing their environment and changing their traits. This is an active adaptation in that it makes use of environmental information. In terms of information transfer, adaptation through phenotypic heterogeneity, such as bacterial bet-hedging, is intragenerational in which traits are not passed on to the next generation. In contrast, adaptation through genetic diversity is intergenerational. The theory of population dynamics enables us to unify these various modes of adaptations and their properties can be analyzed qualitatively and quantitatively using techniques from quantitative genetics and information thermodynamics. In addition, such methods can be applied to situations where organisms can learn from past experiences and pass them on from generation to generation. In this work, we introduce the unified theory of biological adaptation based on population dynamics and show its potential applications to evaluate the fitness value of information and to analyze experimental lineage tree data. Finally, we discuss future perspectives for its development. This review article is an extended version of the Japanese article in SEIBUTSU BUTSURI Vol. 57, p. 287-290 (2017).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79827191","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

Frontiers of microbial movement research. 微生物运动研究的前沿。

Biophysics and Physicobiology Pub Date : 2023-08-31 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0033

Tohru Minamino, Daisuke Nakane, Shuichi Nakamura, Hana Kiyama, Yusuke V Morimoto, Makoto Miyata

引用次数: 0

Unveiling the physics underlying symmetry breaking of the actin cytoskeleton: An artificial cell-based approach. 揭示肌动蛋白细胞骨架对称性破坏的物理学基础：基于人工细胞的方法

Biophysics and Physicobiology Pub Date : 2023-08-19 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0032

Ryota Sakamoto, Yusuke T Maeda

{"title":"Unveiling the physics underlying symmetry breaking of the actin cytoskeleton: An artificial cell-based approach.","authors":"Ryota Sakamoto, Yusuke T Maeda","doi":"10.2142/biophysico.bppb-v20.0032","DOIUrl":"10.2142/biophysico.bppb-v20.0032","url":null,"abstract":"Single-cell behaviors cover many biological functions, such as cell division during morphogenesis and tissue metastasis, and cell migration during cancer cell invasion and immune cell responses. Symmetry breaking of the positioning of organelles and the cell shape are often associated with these biological functions. One of the main players in symmetry breaking at the cellular scale is the actin cytoskeleton, comprising actin filaments and myosin motors that generate contractile forces. However, because the self-organization of the actomyosin network is regulated by the biochemical signaling in cells, how the mechanical contraction of the actin cytoskeleton induces diverse self-organized behaviors and drives the cell-scale symmetry breaking remains unclear. In recent times, to understand the physical underpinnings of the symmetry breaking exhibited in the actin cytoskeleton, artificial cell models encapsulating the cytoplasmic actomyosin networks covered with lipid monolayers have been developed. By decoupling the actomyosin mechanics from the complex biochemical signaling within living cells, this system allows one to study the self-organization of actomyosin networks confined in cell-sized spaces. We review the recent developments in the physics of confined actomyosin networks and provide future perspectives on the artificial cell-based approach. This review article is an extended version of the Japanese article, The Physical Principle of Cell Migration Under Confinement: Artificial Cell-based Bottom-up Approach, published in SEIBUTSU BUTSURI Vol. 63, p. 163-164 (2023).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80408913","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

SATORI: Amplification-free digital RNA detection method for the diagnosis of viral infections. SATORI：用于病毒感染诊断的无扩增数字 RNA 检测方法。

Biophysics and Physicobiology Pub Date : 2023-07-12 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0031

Tatsuya Iida, Hajime Shinoda, Rikiya Watanabe

{"title":"SATORI: Amplification-free digital RNA detection method for the diagnosis of viral infections.","authors":"Tatsuya Iida, Hajime Shinoda, Rikiya Watanabe","doi":"10.2142/biophysico.bppb-v20.0031","DOIUrl":"10.2142/biophysico.bppb-v20.0031","url":null,"abstract":"With the recent global outbreak of COVID-19, there is an urgent need to establish a versatile diagnostic method for viral infections. Gene amplification test or antigen test are widely used to diagnose viral infections; however, these methods generally have technical drawbacks either in terms of sensitivity, accuracy, or throughput. To address this issue, we recently developed an amplification-free digital RNA detection method (SATORI), which can identify and detect viral genes at the single-molecule level in approximately 9 min, satisfying almost all detection performance requirements for the diagnosis of viral infections. In addition, we also developed practical platforms for SATORI, such as an automated platform (opn-SATORI) and a low-cost compact fluorescence imaging system (COWFISH), with the aim of application in clinical settings. Our latest technologies can be inherently applied to diagnose a variety of RNA viral infections, such as COVID-19 and Influenza A/B, and therefore, we expect that SATORI will be established as a versatile platform for point-of-care testing of a wide range of infectious diseases, thus contributing to the prevention of future epidemics. This article is an extended version of the Japanese article published in the SEIBUTSU BUTSURI Vol. 63, p. 115-118 (2023).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89113319","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

Joule heating involving ion currents through channel proteins. 焦耳加热涉及通过通道蛋白的离子电流。

Biophysics and Physicobiology Pub Date : 2023-06-28 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0030

Tetsuichi Wazawa, Takeharu Nagai

{"title":"Joule heating involving ion currents through channel proteins.","authors":"Tetsuichi Wazawa, Takeharu Nagai","doi":"10.2142/biophysico.bppb-v20.0030","DOIUrl":"10.2142/biophysico.bppb-v20.0030","url":null,"abstract":"Ion currents associated with channel proteins in the presence of membrane potential are ubiquitous in cellular and organelle membranes. When an ion current occurs through a channel protein, Joule heating should occur. However, this Joule heating seems to have been largely overlooked in biology. Here we show theoretical investigation of Joule heating involving channel proteins in biological processes. We used electrochemical potential to derive the Joule's law for an ion current through an ion transport protein in the presence of membrane potential, and we suggest that heat production and absorption can occur. Simulation of temperature distribution around a single channel protein with the Joule heating revealed that the temperature increase was as small as <10-3 K, although an ensemble of channel proteins was suggested to exhibit a noticeable temperature increase. Thereby, we theoretically investigated the Joule heating of systems containing ensembles of channel proteins. Nerve is known to undergo rapid heat production followed by heat absorption during the action potential, and our simulation of Joule heating for a squid giant axon combined with the Hodgkin-Huxley model successfully reproduced the feature of the heat. Furthermore, we extended the theory of Joule heating to uncoupling protein 1 (UCP1), a solute carrier family transporter, which is important to the non-shivering thermogenesis in brown adipose tissue mitochondria (BATM). Our calculations showed that the Joule heat involving UCP1 was comparable to the literature calorimetry data of BATM. Joule heating of ion transport proteins is likely to be one of important mechanisms of cellular thermogenesis.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75616610","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

Methods to spontaneously generate three dimensionally arrayed microdroplets triggered by capillarity for bioassays and bioengineering. 利用毛细管自发生成三维阵列微滴的方法，用于生物测定和生物工程。

Biophysics and Physicobiology Pub Date : 2023-06-09 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0029

Hiroki Yasuga

{"title":"Methods to spontaneously generate three dimensionally arrayed microdroplets triggered by capillarity for bioassays and bioengineering.","authors":"Hiroki Yasuga","doi":"10.2142/biophysico.bppb-v20.0029","DOIUrl":"10.2142/biophysico.bppb-v20.0029","url":null,"abstract":"Herein, I review our recent work toward developing methods for generating three-dimensional (3D) droplet arrays driven by capillarity. Microdroplet array-based systems are useful for bioassays and bioengineering because they require only small amounts of samples and reagents and provide the high throughput. Various methods have been developed for preparing droplet arrays, among which methods based on capillarity have attracted considerable attention owing to their simplicity. I and collaborators have developed such methods based on capillary flow, including a method for preparing droplet arrays via oil-water replacement. We recently proposed our own concept of \"fluid-fluid interfacial energy driven 3D structure emergence in a micropillar scaffold (FLUID3EAMS)\" and its application. FLUID3EAMS allows a 3D droplet (or hydrogel bead) array to be generated in a micropillar scaffold by passing a fluid-fluid interface through the scaffold. This approach is useful for applications requiring ordered or arrayed microdroplets in biosensors, biophysics, biology, and tissue engineering. This review is an extended version of the article \"FLUID3EAMS: Fluid-Fluid Interfacial Energy Driven 3D Structure Emergence in a Micropillar Scaffold and Development in Bioengineering\" published in Seibutsu Butsuri (vol. 62, p. 110-113, 2022).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81168039","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

LOV2-based photoactivatable CaMKII and its application to single synapses: Local Optogenetics. 基于 LOV2 的可光激活 CaMKII 及其在单突触中的应用：局部光遗传学。

Biophysics and Physicobiology Pub Date : 2023-06-06 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0027

Yutaro Nagasawa, Hiromi H Ueda, Haruka Kawabata, Hideji Murakoshi

{"title":"LOV2-based photoactivatable CaMKII and its application to single synapses: Local Optogenetics.","authors":"Yutaro Nagasawa, Hiromi H Ueda, Haruka Kawabata, Hideji Murakoshi","doi":"10.2142/biophysico.bppb-v20.0027","DOIUrl":"10.2142/biophysico.bppb-v20.0027","url":null,"abstract":"Optogenetic techniques offer a high spatiotemporal resolution to manipulate cellular activity. For instance, Channelrhodopsin-2 with global light illumination is the most widely used to control neuronal activity at the cellular level. However, the cellular scale is much larger than the diffraction limit of light (<1 μm) and does not fully exploit the features of the \"high spatial resolution\" of optogenetics. For instance, until recently, there were no optogenetic methods to induce synaptic plasticity at the level of single synapses. To address this, we developed an optogenetic tool named photoactivatable CaMKII (paCaMKII) by fusing a light-sensitive domain (LOV2) to CaMKIIα, which is a protein abundantly expressed in neurons of the cerebrum and hippocampus and essential for synaptic plasticity. Combining photoactivatable CaMKII with two-photon excitation, we successfully activated it in single spines, inducing synaptic plasticity (long-term potentiation) in hippocampal neurons. We refer to this method as \"Local Optogenetics\", which involves the local activation of molecules and measurement of cellular responses. In this review, we will discuss the characteristics of LOV2, the recent development of its derivatives, and the development and application of paCaMKII.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89954682","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

Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life. 为什么我们是由蛋白质和核酸组成的：关于外星生命的结构生物学观点。

Biophysics and Physicobiology Pub Date : 2023-06-02 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0026

Shunsuke Tagami

引用次数: 0

Mathematical model for promotion of wound closure with ATP release. 利用 ATP 释放促进伤口闭合的数学模型。

Biophysics and Physicobiology Pub Date : 2023-05-24 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0023

Kenta Odagiri, Hiroshi Fujisaki, Hiroya Takada, Rei Ogawa

引用次数: 0