Biophysics and physicobiology最新文献_第5页

Regulation of long-term memory by a few clock neurons in Drosophila. 果蝇中少数时钟神经元对长期记忆的调控

IF 1.6

Biophysics and physicobiology Pub Date : 2024-01-24 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s002

Rei Shirakawa, Yuto Kurata, Takaomi Sakai

{"title":"Regulation of long-term memory by a few clock neurons in Drosophila.","authors":"Rei Shirakawa, Yuto Kurata, Takaomi Sakai","doi":"10.2142/biophysico.bppb-v21.s002","DOIUrl":"10.2142/biophysico.bppb-v21.s002","url":null,"abstract":"Identification of the neural circuits in the brain regulating animal behavior and physiology is critical for understanding brain functions and is one of the most challenging goals in neuroscience research. The fruitfly Drosophila melanogaster has often been used to identify the neural circuits involved in the regulation of specific behaviors because of the many neurogenetic tools available to express target genes in particular neurons. Neurons controlling sexual behavior, feeding behavior, and circadian rhythms have been identified, and the number of neurons responsible for controlling these phenomena is small. The search for a few neurons controlling a specific behavior is an important first step to clarify the overall picture of the neural circuits regulating that behavior. We previously found that the clock gene period (per), which is essential for circadian rhythms in Drosophila, is also essential for long-term memory (LTM). We have also found that a very limited number of per-expressing clock neurons in the adult brain are required for the consolidation and maintenance of LTM. In this review, we focus on LTM in Drosophila, introduce the concept of LTM regulation by a few clock neurons that we have recently discovered, and discuss how a few clock neurons regulate Drosophila LTM.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 Supplemental","pages":"e211002"},"PeriodicalIF":1.6,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142038673","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

The Asian Biophysics Association: Reborn from the COVID-19 pandemic. 亚洲生物物理协会：从 COVID-19 大流行中重生。

Biophysics and physicobiology Pub Date : 2024-01-24 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0009

Shang-Te Danny Hsu

引用次数: 0

Resonance frequency measurement to identify stiffness variations based on photoacoustic imaging. 基于光声成像的共振频率测量，用于识别硬度变化。

Biophysics and physicobiology Pub Date : 2024-01-20 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0008

Ananta Kusuma Yoga Pratama, Andreas Setiawan, Rini Widyaningrum, Mitrayana

引用次数: 0

Analysis of the singularity cells controlling the pattern formation in multi-cellular systems. 控制多细胞系统模式形成的奇异细胞分析。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s001

Kazuki Horikawa, Tatsuya Takemoto

引用次数: 0

Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor. 小鼠丁香酚 O- 工厂受体中气味氢键诱导的结构动态交叉相关性的分子动力学模拟分析。

Biophysics and physicobiology Pub Date : 2024-01-18 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0007

Chisato Okamoto, Koji Ando

{"title":"Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor.","authors":"Chisato Okamoto, Koji Ando","doi":"10.2142/biophysico.bppb-v21.0007","DOIUrl":"10.2142/biophysico.bppb-v21.0007","url":null,"abstract":"Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlphaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2-4 ns. The lifetime of the H-bond was in the range of 1-20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the α-carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 → Phe182 → (Leu259 or Tyr260) → Tyr291 induced by the ligand binding with a time scale of 4-6 ns.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210007"},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159367","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

Observation of sarcomere chaos induced by changes in calcium concentration in cardiomyocytes. 观察心肌细胞中钙浓度变化引起的肌节混乱。

Biophysics and physicobiology Pub Date : 2024-01-12 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0006

Seine A Shintani

{"title":"Observation of sarcomere chaos induced by changes in calcium concentration in cardiomyocytes.","authors":"Seine A Shintani","doi":"10.2142/biophysico.bppb-v21.0006","DOIUrl":"10.2142/biophysico.bppb-v21.0006","url":null,"abstract":"Heating cardiomyocytes to 38-42°C induces hyperthermal sarcomeric oscillations (HSOs), which combine chaotic instability and homeostatic stability. These properties are likely important for achieving periodic and rapid ventricular expansion during the diastole phase of the heartbeat. Compared with spontaneous oscillatory contractions in cardiomyocytes, which are sarcomeric oscillations induced in the presence of a constant calcium concentration, we found that calcium concentration fluctuations cause chaotic instability during HSOs. We believe that the experimental fact that sarcomeres, autonomously oscillating, exhibit such instability due to the action of calcium concentration changes is important for understanding the physiological function of sarcomeres. Therefore, we have named this chaotic sarcomere instability that appears under conditions involving changes in calcium concentration as Sarcomere Chaos with Changes in Calcium Concentration (S4C). Interestingly, sarcomere instability that could be considered S4C has also been observed in the relaxation dynamics of EC coupling. Unlike ADP-SPOCs and Cell-SPOCs under constant calcium concentration conditions, fluctuations in oscillation amplitude indistinguishable from HSOs were observed. Additionally, like HSO, a positive Lyapunov exponent was measured. S4C is likely a crucial sarcomeric property supporting the rapid and flexible ventricular diastole with each heartbeat of the heart.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210006"},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159256","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

Physicochemical mechanisms of aggregation and fibril formation of α-synuclein and apolipoprotein A-I. α-突触核蛋白和脂蛋白 A-I 的聚集和纤维形成的物理化学机制。

Biophysics and physicobiology Pub Date : 2023-12-29 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0005

Takashi Ohgita, Hiroki Kono, Norihiro Namba, Hiroyuki Saito

{"title":"Physicochemical mechanisms of aggregation and fibril formation of α-synuclein and apolipoprotein A-I.","authors":"Takashi Ohgita, Hiroki Kono, Norihiro Namba, Hiroyuki Saito","doi":"10.2142/biophysico.bppb-v21.0005","DOIUrl":"10.2142/biophysico.bppb-v21.0005","url":null,"abstract":"Deposition and accumulation of amyloid fibrils is a hallmark of a group of diseases called amyloidosis and neurodegenerative disorders. Although polypeptides potentially have a fibril-forming propensity, native proteins have evolved into proper functional conformations to avoid aggregation and fibril formation. Understanding the mechanism for regulation of fibril formation of native proteins provides clues for the rational design of molecules for inhibiting fibril formation. Although fibril formation is a complex multistep reaction, experimentally obtained fibril formation curves can be fitted with the Finke-Watzky (F-W) two-step model for homogeneous nucleation followed by autocatalytic fibril growth. The resultant F-W rate constants for nucleation and fibril formation provide information on the chemical kinetics of fibril formation. Using the F-W two-step model analysis, we investigated the physicochemical mechanisms of fibril formation of a Parkinson's disease protein α-synuclein (αS) and a systemic amyloidosis protein apolipoprotein A-I (apoA-I). The results indicate that the C-terminal region of αS enthalpically and entropically suppresses nucleation through the intramolecular interaction with the N-terminal region and the intermolecular interaction with existing fibrils. In contrast, the nucleation of the N-terminal fragment of apoA-I is entropically driven likely due to dehydration of large hydrophobic segments in the molecule. Based on our recent findings, we discuss the similarity and difference of the fibril formation mechanisms of αS and the N-terminal fragment of apoA-I from the physicochemical viewpoints.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210005"},"PeriodicalIF":0.0,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159208","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

Shape of scaffold controlling the direction of cell migration. 控制细胞迁移方向的支架形状。

Biophysics and physicobiology Pub Date : 2023-12-29 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0004

Hiroshi Sunami, Yusuke Shimizu, Hidehiro Kishimoto

{"title":"Shape of scaffold controlling the direction of cell migration.","authors":"Hiroshi Sunami, Yusuke Shimizu, Hidehiro Kishimoto","doi":"10.2142/biophysico.bppb-v21.0004","DOIUrl":"10.2142/biophysico.bppb-v21.0004","url":null,"abstract":"Cell migration plays an important role in the development and maintenance of multicellular organisms. Factors that induce cell migration and mechanisms controlling their expression are important for determining the mechanisms of factor-induced cell migration. Despite progress in the study of factor-induced cytotaxis, including chemotaxis and haptotaxis, precise control of the direction of cell migration over a wide area has not yet been achieved. Success in this area would update the cell migration assays, superior cell separation technologies, and artificial organs with high biocompatibility. The present study therefore sought to control the direction of cell migration over a wide area by adjusting the three-dimensional shape of the cell scaffold. The direction of cell migration was influenced by the shape of the cell scaffold, thereby optimizing cell adhesion and protrusion. Anisotropic arrangement of these three-dimensional shapes into a periodic structure induced unidirectional cell migration. Three factors were required for unidirectional cell migration: 1) the sizes of the anisotropic periodic structures had to be equal to or lower than the size of the spreading cells, 2) cell migration was restricted to a runway approximately the width of the cell, and 3) cells had to be prone to extension of long protrusions in one direction. Because the first two factors had been identified previously in studies of cell migration in one direction using two-dimensional shaped patterns, these three factors are likely important for the mechanism by which cell scaffold shapes regulate cell migration.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210004"},"PeriodicalIF":0.0,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159222","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

The potential of nanopore technologies toward empowering biophysical research: Brief history, basic principle and applications. 纳米孔技术在加强生物物理研究方面的潜力：简史、基本原理和应用。

Biophysics and physicobiology Pub Date : 2023-12-26 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0003

Hirohito Yamazaki, Zugui Peng, Ryuji Kawano, Kan Shoji

引用次数: 0

Concepts of a synthetic minimal cell: Information molecules, metabolic pathways, and vesicle reproduction. 合成最小细胞的概念：信息分子、代谢途径和囊泡繁殖。

Biophysics and physicobiology Pub Date : 2023-12-19 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0002

Minoru Kurisu, Masayuki Imai

{"title":"Concepts of a synthetic minimal cell: Information molecules, metabolic pathways, and vesicle reproduction.","authors":"Minoru Kurisu, Masayuki Imai","doi":"10.2142/biophysico.bppb-v21.0002","DOIUrl":"10.2142/biophysico.bppb-v21.0002","url":null,"abstract":"How do the living systems emerge from non-living molecular assemblies? What physical and chemical principles supported the process? To address these questions, a promising strategy is to artificially reconstruct living cells in a bottom-up way. Recently, the authors developed the \"synthetic minimal cell\" system showing recursive growth and division cycles, where the concepts of information molecules, metabolic pathways, and cell reproduction were artificially and concisely redesigned with the vesicle-based system. We intentionally avoided using the sophisticated molecular machinery of the biological cells and tried to redesign the cells in the simplest forms. This review focuses on the similarities and differences between the biological cells and our synthetic minimal cell concerning each concept of cells. Such comparisons between natural and artificial cells will provide insights on how the molecules should be assembled to create living systems to the wide readers in the field of synthetic biology, artificial cells, and protocells research. This review article is an extended version of the Japanese article \"Growth and division of vesicles coupled with information molecules,\" published in SEIBUTSU-BUTSURI vol. 61, p. 378-381 (2021).","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210002"},"PeriodicalIF":0.0,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159252","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