Physical biology最新文献

{"title":"Bayesian filtering for model predictive control of stochastic gene expression in single cells.","authors":"Zachary Fox,&nbsp;Gregory Batt,&nbsp;Jakob Ruess","doi":"10.1088/1478-3975/ace094","DOIUrl":"https://doi.org/10.1088/1478-3975/ace094","url":null,"abstract":"<p><p>This study describes a method for controlling the production of protein in individual cells using stochastic models of gene expression. By combining modern microscopy platforms with optogenetic gene expression, experimentalists are able to accurately apply light to individual cells, which can induce protein production. Here we use a finite state projection based stochastic model of gene expression, along with Bayesian state estimation to control protein copy numbers within individual cells. We compare this method to previous methods that use population based approaches. We also demonstrate the ability of this control strategy to ameliorate discrepancies between the predictions of a deterministic model and stochastic switching system.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10156988","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":"Correlation, response and entropy approaches to allosteric behaviors: a critical comparison on the ubiquitin case.","authors":"Fabio Cecconi,&nbsp;Giulio Costantini,&nbsp;Carlo Guardiani,&nbsp;Marco Baldovin,&nbsp;Angelo Vulpiani","doi":"10.1088/1478-3975/ace1c5","DOIUrl":"https://doi.org/10.1088/1478-3975/ace1c5","url":null,"abstract":"<p><p>Correlation analysis and its close variant principal component analysis are tools widely applied to predict the biological functions of macromolecules in terms of the relationship between fluctuation dynamics and structural properties. However, since this kind of analysis does not necessarily imply causation links among the elements of the system, its results run the risk of being biologically misinterpreted. By using as a benchmark the structure of ubiquitin, we report a critical comparison of correlation-based analysis with the analysis performed using two other indicators, response function and transfer entropy, that quantify the causal dependence. The use of ubiquitin stems from its simple structure and from recent experimental evidence of an allosteric control of its binding to target substrates. We discuss the ability of correlation, response and transfer-entropy analysis in detecting the role of the residues involved in the allosteric mechanism of ubiquitin as deduced by experiments. To maintain the comparison as much as free from the complexity of the modeling approach and the quality of time series, we describe the fluctuations of ubiquitin native state by the Gaussian network model which, being fully solvable, allows one to derive analytical expressions of the observables of interest. Our comparison suggests that a good strategy consists in combining correlation, response and transfer entropy, such that the preliminary information extracted from correlation analysis is validated by the two other indicators in order to discard those spurious correlations not associated with true causal dependencies.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9878066","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":"Approximate simulation of cortical microtubule models using dynamical graph grammars.","authors":"Eric Medwedeff, Eric Mjolsness","doi":"10.1088/1478-3975/acdbfb","DOIUrl":"10.1088/1478-3975/acdbfb","url":null,"abstract":"<p><p>Dynamical graph grammars (DGGs) are capable of modeling and simulating the dynamics of the cortical microtubule array (CMA) in plant cells by using an exact simulation algorithm derived from a master equation; however, the exact method is slow for large systems. We present preliminary work on an approximate simulation algorithm that is compatible with the DGG formalism. The approximate simulation algorithm uses a spatial decomposition of the domain at the level of the system's time-evolution operator, to gain efficiency at the cost of some reactions firing out of order, which may introduce errors. The decomposition is more coarsely partitioned by effective dimension (<i>d</i>= 0 to 2 or 0 to 3), to promote exact parallelism between different subdomains within a dimension, where most computing will happen, and to confine errors to the interactions between adjacent subdomains of different effective dimensions. To demonstrate these principles we implement a prototype simulator, and run three simple experiments using a DGG for testing the viability of simulating the CMA. We find evidence indicating the initial formulation of the approximate algorithm is substantially faster than the exact algorithm, and one experiment leads to network formation in the long-time behavior, whereas another leads to a long-time behavior of local alignment.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9908222","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":"Infiltration of tumor spheroids by activated immune cells.","authors":"Mrinmoy Mukherjee,&nbsp;Oleksandr Chepizhko,&nbsp;Maria Chiara Lionetti,&nbsp;Stefano Zapperi,&nbsp;Caterina A M La Porta,&nbsp;Herbert Levine","doi":"10.1088/1478-3975/ace0ee","DOIUrl":"https://doi.org/10.1088/1478-3975/ace0ee","url":null,"abstract":"<p><p>Recent years have seen a tremendous growth of interest in understanding the role that the adaptive immune system could play in interdicting tumor progression. In this context, it has been shown that the density of adaptive immune cells inside a solid tumor serves as a favorable prognostic marker across different types of cancer. The exact mechanisms underlying the degree of immune cell infiltration is largely unknown. Here, we quantify the temporal dynamics of the density profile of activated immune cells around a solid tumor spheroid. We propose a computational model incorporating immune cells with active, persistent movement and a proliferation rate that depends on the presence of cancer cells, and show that the model able to reproduce semi-quantitatively the experimentally measured infiltration profile. Studying the density distribution of immune cells inside a solid tumor can help us better understand immune trafficking in the tumor micro-environment, hopefully leading towards novel immunotherapeutic strategies.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9753121","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":"The emergence of lines of hierarchy in collective motion of biological systems.","authors":"James M Greene,&nbsp;Eitan Tadmor,&nbsp;Ming Zhong","doi":"10.1088/1478-3975/acdc79","DOIUrl":"https://doi.org/10.1088/1478-3975/acdc79","url":null,"abstract":"<p><p>The emergence of large-scale structures in biological systems, and in particular the formation of lines of hierarchy, is observed at many scales, from collections of cells to groups of insects to herds of animals. Motivated by phenomena in chemotaxis and phototaxis, we present a new class of alignment models that exhibit alignment into lines. The spontaneous formation of such 'fingers' can be interpreted as the emergence of leaders and followers in a system of identically interacting agents. Various numerical examples are provided, which demonstrate emergent behaviors similar to the 'fingering' phenomenon observed in some phototaxis and chemotaxis experiments; this phenomenon is generally known to be a challenging pattern for existing models to capture. A novel protocol for pairwise interactions provides a fundamental alignment mechanism by which agents may form lines of hierarchy across a wide range of biological systems.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10094918","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":"Allometry of<i>Escherichia coli</i>surface area with volume: effect of size variability, filamentation and division dynamics.","authors":"Tanvi Kale,&nbsp;Dhruv Khatri,&nbsp;Chaitanya A Athale","doi":"10.1088/1478-3975/acdcda","DOIUrl":"https://doi.org/10.1088/1478-3975/acdcda","url":null,"abstract":"<p><p>The cell surface area (SA) increase with volume (V) is determined by growth and regulation of size and shape. Most studies of the rod-shaped model bacterium<i>Escherichia coli</i>have focussed on the phenomenology or molecular mechanisms governing such scaling. Here, we proceed to examine the role of population statistics and cell division dynamics in such scaling by a combination of microscopy, image analysis and statistical simulations. We find that while the SA of cells sampled from mid-log cultures scales with V by a scaling exponent 2/3, i.e. the geometric law SA ∼V2/3, filamentous cells have higher exponent values. We modulate the growth rate to change the proportion of filamentous cells, and find SA-V scales with an exponent>2/3, exceeding that predicted by the geometric scaling law. However, since increasing growth rates alter the mean and spread of population cell size distributions, we use statistical modeling to disambiguate between the effect of the mean size and variability. Simulating (i) increasing mean cell length with a constant standard deviation (s.d.), (ii) a constant mean length with increasing s.d. and (iii) varying both simultaneously, results in scaling exponents that exceed the 2/3 geometric law, when population variability is included, with the s.d. having a stronger effect. In order to overcome possible effects of statistical sampling of unsynchronized cell populations, we 'virtually synchronized' time-series of cells by using the frames between birth and division identified by the image-analysis pipeline and divided them into four equally spaced phases-B, C1, C2 and D. Phase-specific scaling exponents estimated from these time series and the cell length variability were both found to decrease with the successive stages of birth (B), C1, C2 and division (D). These results point to a need to consider population statistics and a role for cell growth and division when estimating SA-V scaling of bacterial cells.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9688316","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":"Individual bias and fluctuations in collective decision making: from algorithms to Hamiltonians.","authors":"Petro Sarkanych,&nbsp;Mariana Krasnytska,&nbsp;Luis Gómez-Nava,&nbsp;Pawel Romanczuk,&nbsp;Yurij Holovatch","doi":"10.1088/1478-3975/acd6ce","DOIUrl":"https://doi.org/10.1088/1478-3975/acd6ce","url":null,"abstract":"<p><p>In this paper, we reconsider the spin model suggested recently to understand some features of collective decision making among higher organisms (Hartnett<i>et al</i>2016<i>Phys. Rev. Lett.</i><b>116</b>038701). Within the model, the state of an agent<i>i</i>is described by the pair of variables corresponding to its opinionSi=±1and a bias<i>ω</i>_<i>i</i>toward any of the opposing values of<i>S</i>_<i>i</i>. Collective decision making is interpreted as an approach to the equilibrium state within the nonlinear voter model subject to a social pressure and a probabilistic algorithm. Here, we push such a physical analogy further and give the statistical physics interpretation of the model, describing it in terms of the Hamiltonian of interaction and looking for the equilibrium state via explicit calculation of its partition function. We show that, depending on the assumptions about the nature of social interactions, two different Hamiltonians can be formulated, which can be solved using different methods. In such an interpretation the temperature serves as a measure of fluctuations, not considered before in the original model. We find exact solutions for the thermodynamics of the model on the complete graph. The general analytical predictions are confirmed using individual-based simulations. The simulations also allow us to study the impact of system size and initial conditions on the collective decision making in finite-sized systems, in particular, with respect to convergence to metastable states.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9993454","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":"PyEcoLib: a python library for simulating stochastic cell size dynamics.","authors":"César Nieto, Sergio Camilo Blanco, César Vargas-García, Abhyudai Singh, Pedraza Juan Manuel","doi":"10.1088/1478-3975/acd897","DOIUrl":"10.1088/1478-3975/acd897","url":null,"abstract":"<p><p>Recently, there has been an increasing need for tools to simulate cell size regulation due to important applications in cell proliferation and gene expression. However, implementing the simulation usually presents some difficulties, as the division has a cycle-dependent occurrence rate. In this article, we gather a recent theoretical framework in<i>PyEcoLib</i>, a python-based library to simulate the stochastic dynamics of the size of bacterial cells. This library can simulate cell size trajectories with an arbitrarily small sampling period. In addition, this simulator can include stochastic variables, such as the cell size at the beginning of the experiment, the cycle duration timing, the growth rate, and the splitting position. Furthermore, from a population perspective, the user can choose between tracking a single lineage or all cells in a colony. They can also simulate the most common division strategies (adder, timer, and sizer) using the division rate formalism and numerical methods. As an example of PyecoLib applications, we explain how to couple size dynamics with gene expression predicting, from simulations, how the noise in protein levels increases by increasing the noise in division timing, the noise in growth rate and the noise in cell splitting position. The simplicity of this library and its transparency about the underlying theoretical framework yield the inclusion of cell size stochasticity in complex models of gene expression.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10665115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10218943","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":"Fractal dimension to characterize interactions between blood and lymphatic endothelial cells.","authors":"Donghyun Paul Jeong, Daniel Montes, Hsueh-Chia Chang, Donny Hanjaya-Putra","doi":"10.1088/1478-3975/acd898","DOIUrl":"10.1088/1478-3975/acd898","url":null,"abstract":"<p><p>Spatial patterning of different cell types is crucial for tissue engineering and is characterized by the formation of sharp boundary between segregated groups of cells of different lineages. The cell-cell boundary layers, depending on the relative adhesion forces, can result in kinks in the border, similar to fingering patterns between two viscous partially miscible fluids which can be characterized by its fractal dimension. This suggests that mathematical models used to analyze the fingering patterns can be applied to cell migration data as a metric for intercellular adhesion forces. In this study, we develop a novel computational analysis method to characterize the interactions between blood endothelial cells (BECs) and lymphatic endothelial cells (LECs), which form segregated vasculature by recognizing each other through podoplanin. We observed indiscriminate mixing with LEC-LEC and BEC-BEC pairs and a sharp boundary between LEC-BEC pair, and fingering-like patterns with pseudo-LEC-BEC pairs. We found that the box counting method yields fractal dimension between 1 for sharp boundaries and 1.3 for indiscriminate mixing, and intermediate values for fingering-like boundaries. We further verify that these results are due to differential affinity by performing random walk simulations with differential attraction to nearby cells and generate similar migration pattern, confirming that higher differential attraction between different cell types result in lower fractal dimensions. We estimate the characteristic velocity and interfacial tension for our simulated and experimental data to show that the fractal dimension negatively correlates with capillary number (<i>Ca</i>), further indicating that the mathematical models used to study viscous fingering pattern can be used to characterize cell-cell mixing. Taken together, these results indicate that the fractal analysis of segregation boundaries can be used as a simple metric to estimate relative cell-cell adhesion forces between different cell types.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10258918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9628804","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":"Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens.","authors":"Sheryl Le Chang,&nbsp;Carl J E Suster,&nbsp;Rebecca Rockett,&nbsp;Adam Svahn,&nbsp;Oliver Cliff,&nbsp;Alicia Arnott,&nbsp;Qinning Wang,&nbsp;Rady Kim,&nbsp;Basel Suliman,&nbsp;Mailie Gall,&nbsp;Tania Sorrell,&nbsp;Vitali Sintchenko,&nbsp;Mikhail Prokopenko","doi":"10.1088/1478-3975/acd899","DOIUrl":"https://doi.org/10.1088/1478-3975/acd899","url":null,"abstract":"<p><p>Modelling evolution of foodborne pathogens is crucial for mitigation and prevention of outbreaks. We apply network-theoretic and information-theoretic methods to trace evolutionary pathways of<i>Salmonella</i>Typhimurium in New South Wales, Australia, by studying whole genome sequencing surveillance data over a five-year period which included several outbreaks. The study derives both undirected and directed genotype networks based on genetic proximity, and relates the network's structural property (centrality) to its functional property (prevalence). The centrality-prevalence space derived for the undirected network reveals a salient exploration-exploitation distinction across the pathogens, further quantified by the normalised Shannon entropy and the Fisher information of the corresponding shell genome. This distinction is also analysed by tracing the probability density along evolutionary paths in the centrality-prevalence space. We quantify the evolutionary pathways, and show that pathogens exploring the evolutionary search-space during the considered period begin to exploit their environment (their prevalence increases resulting in outbreaks), but eventually encounter a bottleneck formed by epidemic containment measures.</p>","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9628807","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}