Biophysics and physicobiology最新文献_第3页

Integration of single-cell manipulation, whole transcriptome analysis, and image-based deep learning for studying "Singularity Biology". 整合单细胞操作、全转录组分析和基于图像的深度学习，研究 "奇点生物学"。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-02-09 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s005

Katsuyuki Shiroguchi

引用次数: 0

Current advances in the development of bioluminescent probes toward spatiotemporal trans-scale imaging. 开发生物发光探针以实现跨尺度时空成像的最新进展。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-02-02 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s004

Akihiro Sakama, Mariko Orioka, Yuki Hiruta

引用次数: 0

Search for singularity cells at the onset of brain disorders using whole-brain imaging. 利用全脑成像技术寻找脑部疾病发病时的奇异细胞。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-02-02 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s003

Hitoshi Hashimoto, Takanobu Nakazawa

引用次数: 0

Pioneering artificial cell-like structures with DNA nanotechnology-based liquid-liquid phase separation. 利用基于 DNA 纳米技术的液-液相分离技术开创人工类细胞结构。

Biophysics and physicobiology Pub Date : 2024-01-30 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0010

Yusuke Sato, Masahiro Takinoue

{"title":"Pioneering artificial cell-like structures with DNA nanotechnology-based liquid-liquid phase separation.","authors":"Yusuke Sato, Masahiro Takinoue","doi":"10.2142/biophysico.bppb-v21.0010","DOIUrl":"10.2142/biophysico.bppb-v21.0010","url":null,"abstract":"Recent studies have revealed that liquid-liquid phase separation (LLPS) plays crucial roles in various cellular functions. Droplets formed via LLPS within cells, often referred to as membraneless organelles, serve to concentrate specific molecules, thus enhancing biochemical reactions. Artificial LLPS systems have been utilized to construct synthetic cell models, employing a range of synthetic molecules. LLPS systems based on DNA nanotechnology are particularly notable for their designable characteristics in droplet formation, dynamics, properties, and functionalities. This review surveys recent advancements in DNA-based LLPS systems, underscoring the programmability afforded by DNA's base-pair specific interactions. We discuss the fundamentals of DNA droplet formation, including temperature-dependence and physical properties, along with the precise control achievable through sequence design. Attention is given to the phase separation of DNA nanostructures on two-dimensional closed interfaces, which results in spatial pattern formation at the interface. Furthermore, we spotlight the potential of DNA droplet computing for cancer diagnostics through specific microRNA pattern recognition. We envision that DNA-based LLPS presents a versatile platform for the exploration of cellular mimicry and opens innovative ways for the development of functional synthetic cells.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210010"},"PeriodicalIF":0.0,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159213","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

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