Physical biology最新文献

{"title":"Quantitative modeling of EGF receptor ligand discrimination via internalization proofreading.","authors":"Jaleesa A Leblanc,&nbsp;Michael G Sugiyama,&nbsp;Costin N Antonescu,&nbsp;Aidan I Brown","doi":"10.1088/1478-3975/aceecd","DOIUrl":"10.1088/1478-3975/aceecd","url":null,"abstract":"<p><p>The epidermal growth factor receptor (EGFR) is a central regulator of cell physiology that is stimulated by multiple distinct ligands. Although ligands bind to EGFR while the receptor is exposed on the plasma membrane, EGFR incorporation into endosomes following receptor internalization is an important aspect of EGFR signaling, with EGFR internalization behavior dependent upon the type of ligand bound. We develop quantitative modeling for EGFR recruitment to and internalization from clathrin domains, focusing on how internalization competes with ligand unbinding from EGFR. We develop two model versions: a kinetic model with EGFR behavior described as transitions between discrete states and a spatial model with EGFR diffusion to circular clathrin domains. We find that a combination of spatial and kinetic proofreading leads to enhanced EGFR internalization ratios in comparison to unbinding differences between ligand types. Various stages of the EGFR internalization process, including recruitment to and internalization from clathrin domains, modulate the internalization differences between receptors bound to different ligands. Our results indicate that following ligand binding, EGFR may encounter multiple clathrin domains before successful recruitment and internalization. The quantitative modeling we have developed describes competition between EGFR internalization and ligand unbinding and the resulting proofreading.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10420722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phase transitions in insect swarms.","authors":"Andy M Reynolds","doi":"10.1088/1478-3975/aceece","DOIUrl":"10.1088/1478-3975/aceece","url":null,"abstract":"<p><p>In contrast with laboratory insect swarms, wild insect swarms display significant coordinated behaviour. It has been hypothesised that the presence of a fluctuating environment drives the formation of transient, local order (synchronized subgroups), and that this local order pushes the swarm into a new state that is robust to environmental perturbations. The hypothesis is supported by observations of swarming mosquitoes. Here I provide numerical evidence that the formation of transient, local order is an accidental by-product of the strengthening of short-range repulsion which is expected in the presence of environmental fluctuations. The results of the numerical simulations reveal that this strengthening of the short-range can drive swarms into a crystalline phase containing subgroups that participate in cooperative ring exchanges-a new putative form of collective animal movement lacking velocity correlation. I thereby demonstrate that the swarm state and structure may be tuneable with environmental noise as a control parameter. Predicted properties of the collective modes are consistent with observations of transient synchronized subgroups in wild mosquito swarms that contend with environmental disturbances. When mutual repulsion becomes sufficiently strong, swarms are, in accordance with observations, predicted to form near stationary crystalline states. The analysis suggests that the many different forms of swarming motions observed across insect species are not distinctly different phenomena but are instead different phases of a single phenomenon.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10401954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Out-of-equilibrium gene expression fluctuations in the presence of extrinsic noise.","authors":"Marta Biondo, Abhyudai Singh, Michele Caselle, Matteo Osella","doi":"10.1088/1478-3975/acea4e","DOIUrl":"10.1088/1478-3975/acea4e","url":null,"abstract":"<p><p>Cell-to-cell variability in protein concentrations is strongly affected by extrinsic noise, especially for highly expressed genes. Extrinsic noise can be due to fluctuations of several possible cellular factors connected to cell physiology and to the level of key enzymes in the expression process. However, how to identify the predominant sources of extrinsic noise in a biological system is still an open question. This work considers a general stochastic model of gene expression with extrinsic noise represented as fluctuations of the different model rates, and focuses on the out-of-equilibrium expression dynamics. Combining analytical calculations with stochastic simulations, we characterize how extrinsic noise shapes the protein variability during gene activation or inactivation, depending on the prevailing source of extrinsic variability, on its intensity and timescale. In particular, we show that qualitatively different noise profiles can be identified depending on which are the fluctuating parameters. This indicates an experimentally accessible way to pinpoint the dominant sources of extrinsic noise using time-coarse experiments.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10680095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10020854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fundamental insights into the correlation between chromosome configuration and transcription.","authors":"Swayamshree Senapati,&nbsp;Inayat Ullah Irshad,&nbsp;Ajeet K Sharma,&nbsp;Hemant Kumar","doi":"10.1088/1478-3975/ace8e5","DOIUrl":"https://doi.org/10.1088/1478-3975/ace8e5","url":null,"abstract":"<p><p>Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9969063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emergent dynamics in an astrocyte-neuronal network coupled<i>via</i>nitric oxide.","authors":"Bhanu Sharma,&nbsp;Spandan Kumar,&nbsp;Subhendu Ghosh,&nbsp;Vikram Singh","doi":"10.1088/1478-3975/ace8e6","DOIUrl":"https://doi.org/10.1088/1478-3975/ace8e6","url":null,"abstract":"<p><p>In the brain, both neurons and glial cells work in conjunction with each other during information processing. Stimulation of neurons can induce calcium oscillations in astrocytes which in turn can affect neuronal calcium dynamics. The 'glissandi' effect is one such phenomenon, associated with a decrease in infraslow fluctuations, in which synchronized calcium oscillations propagate as a wave in hundreds of astrocytes. Nitric oxide molecules released from the astrocytes contribute to synaptic functions based on the underlying astrocyte-neuron interaction network. In this study, by defining an astrocyte-neuronal (A-N) calcium unit as an integrated circuit of one neuron and one astrocyte, we developed a minimal model of neuronal stimulus-dependent and NO-mediated emergence of calcium waves in astrocytes. Incorporating inter-unit communication<i>via</i>NO molecules, a coupled network of 1000 such A-N calcium units is developed in which multiple stable regimes were found to emerge in astrocytes. We examined the ranges of neuronal stimulus strength and the coupling strength between A-N calcium units that give rise to such dynamical behaviors. We also report that there exists a range of coupling strength, wherein units not receiving stimulus also start showing oscillations and become synchronized. Our results support the hypothesis that glissandi-like phenomena exhibiting synchronized calcium oscillations in astrocytes help in efficient synaptic transmission by reducing the energy demand of the process.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10318244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum: Correlation, response and entropy approaches to allosteric behaviors: a critical comparison on the ubiquitin case (2023<i>Phys. Biol.</i>20056002).","authors":"Fabio Cecconi,&nbsp;Giulio Costantini,&nbsp;Carlo Guardiani,&nbsp;Marco Baldovin,&nbsp;Angelo Vulpiani","doi":"10.1088/1478-3975/ace8e7","DOIUrl":"https://doi.org/10.1088/1478-3975/ace8e7","url":null,"abstract":"Fabio Cecconi1,2,∗, Giulio Costantini, Carlo Guardiani, Marco Baldovin and Angelo Vulpiani 1 CNR-Istituto dei Sistemi Complessi, Via dei Taurini 19, 00185 Rome, Italy 2 INFN-Sezione di Roma1, P.le Aldo Moro, 2, 00185 Rome, Italy 3 CNR-Istituto dei Sistemi Complessi, Piazzale A. Moro 5, 00185 Rome, Italy 4 Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Universit̀a di Roma, Via Eudossiana 18, 00184 Rome, Italy 5 CNRS, LPTMS, Université Paris-Saclay, 530 Rue André Riviére, 91405 Orsay, France 6 Dipartimento di Fisica, Universit̀a di Roma Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy ∗ Author to whom any correspondence should be addressed.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9874249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced germination and electrotactic behaviour of<i>Phytophthora palmivora</i>zoospores in weak electric fields.","authors":"Eleonora Moratto,&nbsp;Stephen Rothery,&nbsp;Tolga O Bozkurt,&nbsp;Giovanni Sena","doi":"10.1088/1478-3975/ace751","DOIUrl":"https://doi.org/10.1088/1478-3975/ace751","url":null,"abstract":"<p><p>Soil-dwelling microorganisms use a variety of chemical and physical signals to navigate their environment. Plant roots produce endogenous electric fields which result in characteristic current profiles. Such electrical signatures are hypothesised to be used by pathogens and symbionts to track and colonise plant roots. The oomycete pathogen<i>Phytophthora palmivora</i>generates motile zoospores which swim towards the positive pole when exposed to an external electric field<i>in vitro</i>. Here, we provide a quantitative characterization of their electrotactic behaviour in 3D. We found that a weak electric field (0.7-1.0 V cm^-1) is sufficient to induce an accumulation of zoospore at the positive pole, without affecting their encystment rate. We also show that the same external electric field increases the zoospore germination rate and orients the germ tube's growth. We conclude that several early stages of the<i>P. palmivora</i>infection cycle are affected by external electric fields. Taken together, our results are compatible with the hypothesis that pathogens use plant endogenous electric fields for host targeting.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10293624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization.","authors":"Jarosław Paturej, Aykut Erbaş","doi":"10.1088/1478-3975/ace750","DOIUrl":"10.1088/1478-3975/ace750","url":null,"abstract":"<p><p>Interphase chromosomes are known to organize non-randomly in the micron-sized eukaryotic cell nucleus and occupy certain fraction of nuclear volume, often without mixing. Using extensive coarse-grained simulations, we model such chromosome structures as colloidal particles whose surfaces are grafted by cyclic polymers. This model system is known as Rosetta. The cyclic polymers, with varying polymerization degrees, mimic chromatin loops present in interphase chromosomes, while the rigid core models the chromocenter section of the chromosome. Our simulations show that the colloidal chromosome model provides a well-separated particle distribution without specific attraction between the chain monomers. As the polymerization degree of the grafted cyclic chains decreases while maintaining the total chromosomal length (e.g. the more potent activity of condensin-family proteins), the average chromosomal volume becomes smaller, inter-chromosomal contacts decrease, and chromocenters organize in a quasi-crystalline order reminiscent of a glassy state. This order weakens for polymer chains with a characteristic size on the order of the confinement radius. Notably, linear-polymer grafted particles also provide the same chromocenter organization scheme. However, unlike linear chains, cyclic chains result in less contact between the polymer layers of neighboring chromosome particles, demonstrating the effect of DNA breaks in altering genome-wide contacts. Our simulations show that polymer-grafted colloidal systems could help decipher 3D genome architecture along with the fractal globular and loop-extrusion models.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9876494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Data-driven discovery of stochastic dynamical equations of collective motion.","authors":"Arshed Nabeel, Vivek Jadhav, Danny Raj M, Clément Sire, Guy Theraulaz, Ramón Escobedo, Srikanth K Iyer, Vishwesha Guttal","doi":"10.1088/1478-3975/ace22d","DOIUrl":"10.1088/1478-3975/ace22d","url":null,"abstract":"<p><p>Coarse-grained descriptions of collective motion of flocking systems are often derived for the macroscopic or the thermodynamic limit. However, the size of many real flocks falls within 'mesoscopic' scales (10 to 100 individuals), where stochasticity arising from the finite flock sizes is important. Previous studies on mesoscopic models have typically focused on non-spatial models. Developing mesoscopic scale equations, typically in the form of stochastic differential equations, can be challenging even for the simplest of the collective motion models that explicitly account for space. To address this gap, here, we take a novel data-driven equation learning approach to construct the stochastic mesoscopic descriptions of a simple, spatial, self-propelled particle (SPP) model of collective motion. In the spatial model, a focal individual can interact with<i>k</i>randomly chosen neighbours within an interaction radius. We consider<i>k</i> = 1 (called stochastic pairwise interactions),<i>k</i> = 2 (stochastic ternary interactions), and<i>k</i>equalling all available neighbours within the interaction radius (equivalent to Vicsek-like local averaging). For the stochastic pairwise interaction model, the data-driven mesoscopic equations reveal that the collective order is driven by a multiplicative noise term (hence termed, noise-induced flocking). In contrast, for higher order interactions (<i>k</i> > 1), including Vicsek-like averaging interactions, models yield collective order driven by a combination of deterministic and stochastic forces. We find that the relation between the parameters of the mesoscopic equations describing the dynamics and the population size are sensitive to the density and to the interaction radius, exhibiting deviations from mean-field theoretical expectations. We provide semi-analytic arguments potentially explaining these observed deviations. In summary, our study emphasises the importance of mesoscopic descriptions of flocking systems and demonstrates the potential of the data-driven equation discovery methods for complex systems studies.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9835059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial networks through the lens of mathematics.","authors":"Greyson R Lewis, Wallace F Marshall","doi":"10.1088/1478-3975/acdcdb","DOIUrl":"10.1088/1478-3975/acdcdb","url":null,"abstract":"<p><p>Mitochondria serve a wide range of functions within cells, most notably via their production of ATP. Although their morphology is commonly described as bean-like, mitochondria often form interconnected networks within cells that exhibit dynamic restructuring through a variety of physical changes. Further, though relationships between form and function in biology are well established, the extant toolkit for understanding mitochondrial morphology is limited. Here, we emphasize new and established methods for quantitatively describing mitochondrial networks, ranging from unweighted graph-theoretic representations to multi-scale approaches from applied topology, in particular persistent homology. We also show fundamental relationships between mitochondrial networks, mathematics, and physics, using ideas of graph planarity and statistical mechanics to better understand the full possible morphological space of mitochondrial network structures. Lastly, we provide suggestions for how examination of mitochondrial network form through the language of mathematics can inform biological understanding, and vice versa.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10347554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9797316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}