Physical biology最新文献

{"title":"History-dependent attachment of<i>Pseudomonas aeruginosa</i>to solid-liquid interfaces and the dependence of the bacterial surface density on the residence time distribution.","authors":"A L Ritter,&nbsp;Yow-Ren Chang,&nbsp;Zachary Benmamoun,&nbsp;William A Ducker","doi":"10.1088/1478-3975/aca6c9","DOIUrl":"https://doi.org/10.1088/1478-3975/aca6c9","url":null,"abstract":"<p><p>This study investigates how the recent history of bacteria affects their attachment to a solid-liquid interface. We compare the attachment from a flowing suspension of the bacterium,<i>Pseudomonas aeruginosa</i>PAO1, after one of two histories: (a) passage through a tube packed with glass beads or (b) passage through an empty tube. The glass beads were designed to increase the rate of bacterial interactions with solid-liquid surfaces prior to observation in a flow cell. Analysis of time-lapse microscopy of the bacteria in the flow cells shows that the residence time distribution and surface density of bacteria differ for these two histories. In particular, bacteria exiting the bead-filled tube, in contrast to those bacteria exiting the empty tube, are less likely to attach to the subsequent flow cell window and begin surface growth. In contrast, when we compared two histories defined by different lengths of tubing, there was no difference in either the mean residence time or the surface density. In order to provide a framework for understanding these results, we present a phenomenological model in which the rate of bacterial surface density growth,dN(t)/dt, depends on two terms. One term models the initial attachment of bacteria to a surface, and is proportional to the nonprocessive cumulative residence time distribution for bacteria that attach and detach from the surface without cell division. The second term for the rate is proportional to the bacterial surface density and models surface cell division. The model is in surprisingly good agreement with the data even though the surface growth process is a complex interplay between attachment/detachment at the solid-liquid interface and cell division on the surface.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9079948","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":"How to build an epithelial tree.","authors":"Sarah V Paramore,&nbsp;Katharine Goodwin,&nbsp;Celeste M Nelson","doi":"10.1088/1478-3975/ac9e38","DOIUrl":"https://doi.org/10.1088/1478-3975/ac9e38","url":null,"abstract":"<p><p>Nature has evolved a variety of mechanisms to build epithelial trees of diverse architectures within different organs and across species. Epithelial trees are elaborated through branch initiation and extension, and their morphogenesis ends with branch termination. Each of these steps of the branching process can be driven by the actions of epithelial cells themselves (epithelial-intrinsic mechanisms) or by the cells of their surrounding tissues (epithelial-extrinsic mechanisms). Here, we describe examples of how these mechanisms drive each stage of branching morphogenesis, drawing primarily from studies of the lung, kidney, salivary gland, mammary gland, and pancreas, all of which contain epithelial trees that form through collective cell behaviors. Much of our understanding of epithelial branching comes from experiments using mice, but we also include examples here from avian and reptilian models. Throughout, we highlight how distinct mechanisms are employed in different organs and species to build epithelial trees. We also highlight how similar morphogenetic motifs are used to carry out conserved developmental programs or repurposed to support novel ones. Understanding the unique strategies used by nature to build branched epithelia from across the tree of life can help to inspire creative solutions to problems in tissue engineering and regenerative medicine.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"19 6","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10700711","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":"Proteolytic and mechanical remodeling of the extracellular matrix by invadopodia in cancer.","authors":"L Perrin, B Gligorijevic","doi":"10.1088/1478-3975/aca0d8","DOIUrl":"10.1088/1478-3975/aca0d8","url":null,"abstract":"<p><p>Cancer invasion and metastasis require remodeling of the adjacent extracellular matrix (ECM). In this mini review, we will cover the mechanisms of proteolytic degradation and the mechanical remodeling of the ECM by cancer cells, with a focus on invadopodia. Invadopodia are membrane protrusions unique to cancer cells, characterized by an actin core and by the focal degradation of ECM via matrix metalloproteases (MMPs). While ECM can also be remodeled, at lower levels, by focal adhesions, or internal collagen digestion, invadopodia are now recognized as the major mechanism for MMP-dependent pericellular ECM degradation by cancer cells. Recent evidence suggests that the completion of epithelial-mesenchymal transition may be dispensable for invadopodia and metastasis, and that invadopodia are required not only for mesenchymal, single cell invasion, but also for collective invasion. During collective invasion, invadopodia was then shown to be located in leader cells, allowing follower cells to move via cooperation. Collectively, this suggests that invadopodia function may be a requirement not only for later steps of metastasis, but also for early invasion of epithelial cells into the stromal tissue. Over the last decade, invadopodia studies have transitioned into in 3D and<i>in vivo</i>settings, leading to the confirmation of their essential role in metastasis in preclinical animal models. In summary, invadopodia may hold a great potential for individual risk assessment as a prognostic marker for metastasis, as well as a therapeutic target.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"20 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2022-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9942491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10751581","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":"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}