PRX Life最新文献

Emergent chirality in active solid rotation of pancreas spheres 胰腺球主动固体旋转中出现的手性

PRX Life Pub Date : 2024-08-08 DOI: 10.1103/prxlife.2.033006

Tzer Han Tan, Aboutaleb Amiri, Irene Seijo-Barandiarán, Michael F Staddon, Anne Materne, Sandra Tomas, C. Duclut, Marko Popović, A. Grapin-Botton, Frank Jülicher

{"title":"Emergent chirality in active solid rotation of pancreas spheres","authors":"Tzer Han Tan, Aboutaleb Amiri, Irene Seijo-Barandiarán, Michael F Staddon, Anne Materne, Sandra Tomas, C. Duclut, Marko Popović, A. Grapin-Botton, Frank Jülicher","doi":"10.1103/prxlife.2.033006","DOIUrl":"https://doi.org/10.1103/prxlife.2.033006","url":null,"abstract":"Collective cell dynamics play a crucial role in many developmental and physiological contexts. While two-dimensional (2D) cell migration has been widely studied, how three-dimensional (3D) geometry and topology interplay with collective cell behavior to determine dynamics and functions remains an open question. In this work, we elucidate the biophysical mechanism underlying rotation in spherical tissues, a phenomenon widely reported both and . Using murine pancreas-derived organoids as a model system, we find that epithelial spheres exhibit persistent rotation, rotational axis drift, and rotation arrest. Using a 3D vertex model, we demonstrate how the combined action of traction force and polarity alignment can account for these distinct rotational dynamics near a solid to flow transition. Furthermore, our analysis shows that the spherical tissue rotates as an active solid occasionally switching to a flowing state and exhibits spontaneous chiral symmetry breaking. Using a continuum model, we demonstrate how the topological defects in the polarity field underlie this symmetry breaking process, which is revealed by asymmetries in the cell elongation pattern. For cell elongation to reveal the chiral asymmetry, shear flow is required in addition to the solid body rotation. Altogether, our work reveals a robust chiral symmetry breaking mechanism with potential implications for left-right symmetry breaking processes in morphogenetic events.\u0000 \u0000 \u0000 \u0000 \u0000 Published by the American Physical Society\u0000 2024\u0000 \u0000 \u0000","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"111 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141926590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In and Out of Criticality? State-Dependent Scaling in the Rat Visual Cortex 进出临界状态？大鼠视觉皮层的状态依赖性缩放

PRX Life Pub Date : 2024-05-21 DOI: 10.1103/prxlife.2.023008

Daniel M. Castro, Thaís Feliciano, Nivaldo A. P. de Vasconcelos, C. Soares-Cunha, B. Coimbra, A. Rodrigues, Pedro V. Carelli, Mauro Copelli

{"title":"In and Out of Criticality? State-Dependent Scaling in the Rat Visual Cortex","authors":"Daniel M. Castro, Thaís Feliciano, Nivaldo A. P. de Vasconcelos, C. Soares-Cunha, B. Coimbra, A. Rodrigues, Pedro V. Carelli, Mauro Copelli","doi":"10.1103/prxlife.2.023008","DOIUrl":"https://doi.org/10.1103/prxlife.2.023008","url":null,"abstract":"The presumed proximity to a critical point is believed to endow the brain with scale-invariant statistics, which are thought to confer various functional advantages in terms of its information processing, storage, and transmission capabilities. To assess the relationship between scaling and cortical states, we apply a phenomenological renormalization group analysis to 3-h spiking data recordings from the urethane-anesthetized rat's visual cortex. Under this type of anesthesia, cortical states dynamically shift across a spectrum of synchronization levels, defined by population spiking rate variability. By developing a scaling criterion based on the kurtosis of the momentum-space activity distribution, our study combines the coarse-graining method with state-dependent analysis. We find that scaling signatures only appear as spiking variability surpasses a specified threshold. Notably, within this regime, scaling exponents show relative stability. Conversely, subthreshold activity is primarily asynchronous and fails to meet the scaling criterion. Our results suggest that a wide range of cortical states corresponds to small deviations around a critical point, with the system fluctuating in and out of criticality, spending roughly three-quarters of the experiment duration within a scaling regime.\u0000 \u0000 \u0000 \u0000 \u0000 Published by the American Physical Society\u0000 2024\u0000 \u0000 \u0000","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"27 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141117251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of Linker Length on Biomolecular Condensate Formation 连接体长度对生物分子缩合物形成的影响

PRX Life Pub Date : 2023-12-26 DOI: 10.1103/prxlife.1.023013

Trevor GrandPre, Yaojun Zhang, Andrew G. T. Pyo, Benjamin G. Weiner, Je-Luen Li, M. Jonikas, N. Wingreen

引用次数: 0

Mapping Stochastic Collective Behavior Distinguishes Subtle Mutations in Social Bacteria 绘制随机集体行为图，区分社会性细菌中的微妙突变

PRX Life Pub Date : 2023-12-21 DOI: 10.1103/prxlife.1.023011

Merrill E. Asp, Eduardo A. Caro, Roy D. Welch, Alison E. Patteson

引用次数: 0

Models of Cell Processes are Far from the Edge of Chaos 细胞过程模型远离混沌边缘

PRX Life Pub Date : 2023-12-15 DOI: 10.1103/prxlife.1.023009

Kyu Hyong Park, F. Costa, Luis M. Rocha, Réka Albert, Jordan C. Rozum

引用次数: 0

Tension Remodeling Regulates Topological Transitions in Epithelial Tissues 张力重塑调节上皮组织的拓扑转变

PRX Life Pub Date : 2023-11-27 DOI: 10.1103/prxlife.1.023006

Fernanda Pérez-Verdugo, Shiladitya Banerjee

引用次数: 0

Information Bottleneck in Molecular Sensing 分子传感的信息瓶颈

PRX Life Pub Date : 2023-11-15 DOI: 10.1103/prxlife.1.023005

Marianne Bauer, William Bialek

引用次数: 0

Confinement Mechanisms for Epigenetic Modifications of Nucleosomes 核小体表观遗传修饰的约束机制

PRX Life Pub Date : 2023-09-05 DOI: 10.1103/prxlife.1.013013

J. F. Nickels, K. Sneppen

引用次数: 0

Bacterial Replication Initiation as Precision Control by Protein Counting 通过蛋白质计数精确控制细菌复制起始

PRX Life Pub Date : 2023-08-28 DOI: 10.1103/prxlife.1.013011

Haochen Fu, Fangzhou Xiao, S. Jun

{"title":"Bacterial Replication Initiation as Precision Control by Protein Counting","authors":"Haochen Fu, Fangzhou Xiao, S. Jun","doi":"10.1103/prxlife.1.013011","DOIUrl":"https://doi.org/10.1103/prxlife.1.013011","url":null,"abstract":"Balanced biosynthesis is the hallmark of bacterial cell physiology, where the concentrations of stable proteins remain steady. However, this poses a conceptual challenge to modeling the cell-cycle and cell-size controls in bacteria, as prevailing concentration-based eukaryote models are not directly applicable. In this study, we revisit and signiﬁcantly extend the initiator-titration model, proposed 30 years ago, and we explain how bacteria precisely and robustly control replication initiation based on the mechanism of protein copy-number sensing. Using a mean-ﬁeld approach, we ﬁrst derive an analytical expression of the cell size at initiation based on three biological mechanistic control parameters for an extended initiator-titration model. We also study the stability of our model analytically and show that initiation can become unstable in multifork replication conditions. Using simulations, we further show that the presence of the conversion between active and inactive initiator protein forms signiﬁcantly represses initiation instability. Importantly, the two-step Poisson process set by the initiator titration step results in signiﬁcantly improved initiation synchrony with CV ∼ 1 / N scaling rather than the standard 1 / √ N scaling in the Poisson process, where N is the total number of initiators required for initiation. Our results answer two long-standing questions in replication initiation: (i) Why do bacteria produce almost two orders of magnitude more DnaA, the master initiator proteins, than required for initiation? (ii) Why does DnaA exist in active (DnaA-ATP) and inactive (DnaA-ADP) forms if only the active form is competent for initiation? The mechanism presented in this work provides a satisfying general solution to how the cell can achieve precision control without sensing protein concentrations, with broad implications from evolution to the design of synthetic cells. DOI","PeriodicalId":420529,"journal":{"name":"PRX Life","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116115387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Quantitative Theory of Viral-Immune Coevolution May Be within Reach 病毒免疫协同进化的定量理论可能触手可及

PRX Life Pub Date : 2023-08-22 DOI: 10.1103/prxlife.1.011001

T. Mora, A. Walczak

引用次数: 1