Physical biology最新文献

{"title":"Anisotropic 3D confinement of MCF-7 cells induces directed cell-migration and viscoelastic anisotropy of cell-membrane.","authors":"Privita Edwina Rayappan George Edwin,&nbsp;Sumeet Kumar,&nbsp;Srestha Roy,&nbsp;Basudev Roy,&nbsp;Saumendra Kumar Bajpai","doi":"10.1088/1478-3975/ac9bc1","DOIUrl":"https://doi.org/10.1088/1478-3975/ac9bc1","url":null,"abstract":"<p><p>Tumor-associated collagen signature-3 (TACS-3) is a prognostic indicator for breast cancer survival. It is characterized by highly organized, parallel bundles of collagen fibers oriented perpendicular to the tumor boundary, serving as directional, confining channels for cancer cell invasion. Here we design a TACS-3-mimetic anisotropic, confined collagen I matrix and examine the relation between anisotropy of matrix, directed cellular migration, and anisotropy of cell membrane-the first direct contact between TACS-3 and cell-using Michigan Cancer Foundation-7 (MCF-7) cells as cancer-model. Using unidirectional freezing, we generated ∼50<i>μ</i>m-wide channels filled with collagen I. Optical tweezer (OT) microrheology shows that anisotropic confinement increases collagen viscoelasticity by two orders of magnitude, and the elastic modulus is significantly greater along the direction of anisotropic confinement compared to that along the orthogonal direction, thus establishing matrix anisotropy. Furthermore, MCF-7 cells embedded in anisotropic collagen I, exhibit directionality in cellular morphology and migration. Finally, using customized OT to trap polystyrene probes bound to cell-membrane (and not to ECM) of either free cells or cells under anisotropic confinement, we quantified the effect of matrix anisotropy on membrane viscoelasticity, both in-plane and out-of-plane, vis-à-vis the membrane. Both bulk and viscous modulus of cell-membrane of MCF-7 cells exhibit significant anisotropy under anisotropic confinement. Moreover, the cell membrane of MCF-7 cells under anisotropic confinement is significantly softer (both in-plane and out-of-plane moduli) despite their local environment being five times stiffer than free cells. In order to test if the coupling between anisotropy of extracellular matrix and anisotropy of cell-membrane is regulated by cell-cytoskeleton, actin cytoskeleton was depolymerized for both free and confined cells. Results show that cell membrane viscoelasticity of confined MCF-7 cells is unaffected by actin de-polymerization, in contrast to free cells. Together, these findings suggest that anisotropy of ECM induces directed migration and correlates with anisotropy of cell-membrane viscoelasticity of the MCF-7 cells in an actin-independent manner.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10343827","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":"Sliding of motor tails on cargo surface due to drift and diffusion affects their team arrangement and collective transport.","authors":"Saumya Yadav,&nbsp;Ambarish Kunwar","doi":"10.1088/1478-3975/ac99b2","DOIUrl":"https://doi.org/10.1088/1478-3975/ac99b2","url":null,"abstract":"<p><p>Kinesin is a microtubule-associated motor protein which works in teams to carry the cellular cargo transport. Lipid rafts on membranous cargos reorganize, causing the motors present in these areas to physically cluster. Unregulated clustering of motors leads to diseases such as Leishmaniasis, Newmann-Pick disease, etc. Various<i>in-vitro</i>and computational studies have reported improved cargo velocity and travel distance of a fluid cargo as compared to a rigid cargo. However, only cargo velocity increases with increase in membrane fluidity of a fluid cargo. Thermal and motor forces acting tangentially on a cargo generate random torque and motor torque respectively, leading to cargo rotation and motor tail sliding on cargo surface. However, it is unknown which of these forces/torques play a crucial role in improving the transport properties. Here, we use computational models that incorporate random torque, motor torque, and combination of both random and motor torques to understand how they influence the clustering of Kinesin motors on cargo surface due to drift and diffusion of their tails. These studies were performed at varying tail diffusivity to understand their effect on clustering of tails in dispersed and clustered arrangement. We find that in dispersed arrangement, random torque does not cause clustering, whereas motor torque is crucial for clustering of tails on cargo surface, and tails sliding due to both random and motor torques have fastest cargo transport and maximum cooperativity. In clustered arrangement, tails slide to form a broad and steady cluster whose size increases with tail diffusivity resulting in decreased cargo runlength, velocity and cooperativity. These findings suggest that increased tail diffusivity negatively impacts the cluster and cargo transport of tails in the clustered arrangement, whereas it aids physical clustering of tails and cargo transport in dispersed arrangement.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10700160","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":"Dynamical adaptation in photoreceptors with gain control.","authors":"Miguel Castillo García,&nbsp;Eugenio Urdapilleta","doi":"10.1088/1478-3975/ac9947","DOIUrl":"https://doi.org/10.1088/1478-3975/ac9947","url":null,"abstract":"<p><p>The retina hosts all processes needed to convert external visual stimuli into a neural code. Light phototransduction and its conversion into an electrical signal involve biochemical cascades, ionic regulations, and different kinds of coupling, among other relevant processes. These create a nonlinear processing scheme and light-dependent adaptive responses. The dynamical adaptation model formulated in recent years is an excellent phenomenological candidate to resume all these phenomena into a single feedforward processing scheme. In this work, we analyze this description in highly nonlinear conditions and find that responses do not match those resulting from a very detailed microscopic model, developed to reproduce electrophysiological recordings on horizontal cells. When a delayed light-dependent gain factor incorporates into the description, responses are in excellent agreement, even when spanning several orders of magnitude in light intensity, contrast, and duration, for simple and complex stimuli. This extended model may be instrumental for studies of the retinal function, enabling the linking of the microscopic domain to the understanding of signal processing properties, and further incorporated in spatially extended retinal networks.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"19 6","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10355123","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":"GIFT: new method for the genetic analysis of small gene effects involving small sample sizes.","authors":"Cyril Rauch,&nbsp;Panagiota Kyratzi,&nbsp;Sarah Blott,&nbsp;Sian Bray,&nbsp;Jonathan Wattis","doi":"10.1088/1478-3975/ac99b3","DOIUrl":"https://doi.org/10.1088/1478-3975/ac99b3","url":null,"abstract":"<p><p>Small gene effects involved in complex/omnigenic traits remain costly to analyse using current genome-wide association studies (GWAS) because of the number of individuals required to return meaningful association(s), a.k.a. study power. Inspired by field theory in physics, we provide a different method called genomic informational field theory (GIFT). In contrast to GWAS, GIFT assumes that the phenotype is measured precisely enough and/or the number of individuals in the population is too small to permit the creation of categories. To extract information, GIFT uses the information contained in the cumulative sums difference of gene microstates between two configurations: (i) when the individuals are taken at random without information on phenotype values, and (ii) when individuals are ranked as a function of their phenotypic value. The difference in the cumulative sum is then attributed to the emergence of phenotypic fields. We demonstrate that GIFT recovers GWAS, that is, Fisher's theory, when the phenotypic fields are linear (first order). However, unlike GWAS, GIFT demonstrates how the variance of microstate distribution density functions can also be involved in genotype-phenotype associations when the phenotypic fields are quadratic (second order). Using genotype-phenotype simulations based on Fisher's theory as a toy model, we illustrate the application of the method with a small sample size of 1000 individuals.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10411408","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: Coordination of size-control, reproduction and generational memory in freshwater planarians (2021<i>Phys. Biol.</i>14 036003).","authors":"Xingbo Yang,&nbsp;Kelson J Kaj,&nbsp;David J Schwab,&nbsp;Eva-Maria S Collins","doi":"10.1088/1478-3975/ac97d6","DOIUrl":"https://doi.org/10.1088/1478-3975/ac97d6","url":null,"abstract":"Xingbo Yang1, Kelson J Kaj2, David J Schwab1 and Eva-Maria S Collins2,3,4,∗ 1 Department of Physics and Astronomy, Northwestern University, Evanston, IL, United States of America 2 Department of Physics, University of California San Diego, La Jolla, CA, United States of America 3 Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America 4 Department of Biology, Swarthmore College, Swarthmore, PA, United States of America ∗ Author to whom any correspondence should be addressed. E-mail: ecollin3@swarthmore.edu","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"19 6","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10639893","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: Let it rip: the mechanics of self-bisection in asexual planarians determines their population reproductive strategies (2022<i>Phys. Biol.</i>19 016002).","authors":"Tapan Goel,&nbsp;Danielle Ireland,&nbsp;Vir Shetty,&nbsp;Christina Rabeler,&nbsp;Patrick H Diamond,&nbsp;Eva-Maria S Collins","doi":"10.1088/1478-3975/ac97d7","DOIUrl":"https://doi.org/10.1088/1478-3975/ac97d7","url":null,"abstract":"Tapan Goel1 , Danielle Ireland2 , Vir Shetty3, Christina Rabeler2, Patrick H Diamond1 and Eva-Maria S Collins1,2,3,∗ 1 Physics Department, UC San Diego, La Jolla, CA, United States of America 2 Biology Department, Swarthmore College, Swarthmore, PA, United States of America 3 Physics and Astronomy Department, Swarthmore College, Swarthmore, PA, United States of America ∗ Author to whom any correspondence should be addressed.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40659095","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":"Morphogen gradient formation in partially absorbing media.","authors":"Paul C Bressloff","doi":"10.1088/1478-3975/ac95ea","DOIUrl":"https://doi.org/10.1088/1478-3975/ac95ea","url":null,"abstract":"<p><p>Morphogen gradients play an essential role in the spatial regulation of cell patterning during early development. The classical mechanism of morphogen gradient formation involves the diffusion of morphogens away from a localized source combined with some form of bulk absorption. Morphogen gradient formation plays a crucial role during early development, whereby a spatially varying concentration of morphogen protein drives a corresponding spatial variation in gene expression during embryogenesis. In most models, the absorption rate is taken to be a constant multiple of the local concentration. In this paper, we explore a more general class of diffusion-based model in which absorption is formulated probabilistically in terms of a stopping time condition. Absorption of each particle occurs when its time spent within the bulk domain (occupation time) exceeds a randomly distributed threshold<i>a</i>; the classical model with a constant rate of absorption is recovered by taking the threshold distributionΨ(a)=e-κ0a. We explore how the choice of Ψ(<i>a</i>) affects the steady-state concentration gradient, and the relaxation to steady-state as determined by the accumulation time. In particular, we show that the more general model can generate similar concentration profiles to the classical case, while significantly reducing the accumulation time.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"19 6","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10354077","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":"Learning feedback molecular network models using integer linear programming.","authors":"Mustafa Ozen,&nbsp;Effat S Emamian,&nbsp;Ali Abdi","doi":"10.1088/1478-3975/ac920d","DOIUrl":"https://doi.org/10.1088/1478-3975/ac920d","url":null,"abstract":"<p><p>Analysis of intracellular molecular networks has many applications in understanding of the molecular bases of some complex diseases and finding effective therapeutic targets for drug development. To perform such analyses, the molecular networks need to be converted into computational models. In general, network models constructed using literature and pathway databases may not accurately predict experimental network data. This can be due to the incompleteness of literature on molecular pathways, the resources used to construct the networks, or some conflicting information in the resources. In this paper, we propose a network learning approach via an integer linear programming formulation that can systematically incorporate biological dynamics and regulatory mechanisms of molecular networks in the learning process. Moreover, we present a method to properly consider the feedback paths, while learning the network from data. Examples are also provided to show how one can apply the proposed learning approach to a network of interest. In particular, we apply the framework to the ERBB signaling network, to learn it from some experimental data. Overall, the proposed methods are useful for reducing the gap between the curated networks and experimental data, and result in calibrated networks that are more reliable for making biologically meaningful predictions.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40357335","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":"Comment on 'A physics perspective on collective animal behavior' 2022<i>Phys. Biol.</i>19 021004.","authors":"Andy M Reynolds","doi":"10.1088/1478-3975/ac8fd5","DOIUrl":"https://doi.org/10.1088/1478-3975/ac8fd5","url":null,"abstract":"<p><p>In his insightful and timely review Ouellette (2022<i>Phys. Biol.</i><b>19</b>021004) noted three theoretical impediments to progress in understanding and modelling collective animal behavior. Here through novel analyses and by drawing on the latest research I show how these obstacles can be either overcome or negated. I suggest ways in which recent advances in the physics of collective behavior provide significant biological information.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40353055","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":"A compressed logistic equation on bacteria growth: inferring time-dependent growth rate.","authors":"Carlito Pinto,&nbsp;Koichi Shimakawa","doi":"10.1088/1478-3975/ac8c15","DOIUrl":"https://doi.org/10.1088/1478-3975/ac8c15","url":null,"abstract":"We propose a compressed logistic model for bacterial growth by invoking a time-dependent rate instead of the intrinsic growth rate (constant), which was adopted in traditional logistic models. The new model may have a better physiological basis than the traditional ones, and it replicates experimental observations, such as the case example for E. coli, Salmonella, and Staphylococcus aureus. Stochastic colonial growth at a different rate may have a fractal-like nature, which should be an origin of the time-dependent reaction rate. The present model, from a stochastic viewpoint, is approximated as a Gaussian time evolution of bacteria (error function).","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40436956","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}