Physical biology最新文献_第9页

GIFT: new method for the genetic analysis of small gene effects involving small sample sizes. GIFT:涉及小样本量的小基因效应遗传分析的新方法。

IF 2 4区生物学

Physical biology Pub Date : 2022-11-03 DOI: 10.1088/1478-3975/ac99b3

Cyril Rauch, Panagiota Kyratzi, Sarah Blott, Sian Bray, Jonathan Wattis

{"title":"GIFT: new method for the genetic analysis of small gene effects involving small sample sizes.","authors":"Cyril Rauch, Panagiota Kyratzi, Sarah Blott, Sian Bray, Jonathan Wattis","doi":"10.1088/1478-3975/ac99b3","DOIUrl":"https://doi.org/10.1088/1478-3975/ac99b3","url":null,"abstract":"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.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"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}

引用次数: 1

Corrigendum: Coordination of size-control, reproduction and generational memory in freshwater planarians (2021Phys. Biol.14 036003). 淡水涡虫体型控制、繁殖和世代记忆的协调(20121)。Biol.14 036003)。

IF 2 4区生物学

Physical biology Pub Date : 2022-11-01 DOI: 10.1088/1478-3975/ac97d6

Xingbo Yang, Kelson J Kaj, David J Schwab, Eva-Maria S Collins

引用次数: 0

Corrigendum: Let it rip: the mechanics of self-bisection in asexual planarians determines their population reproductive strategies (2022Phys. Biol.19 016002). 更正:让它撕下来:无性涡虫的自我一分为二机制决定了它们的种群繁殖策略。Biol.19 016002)。

IF 2 4区生物学

Physical biology Pub Date : 2022-10-26 DOI: 10.1088/1478-3975/ac97d7

Tapan Goel, Danielle Ireland, Vir Shetty, Christina Rabeler, Patrick H Diamond, Eva-Maria S Collins

引用次数: 0

Morphogen gradient formation in partially absorbing media. 部分吸收介质中形态形成梯度的形成。

IF 2 4区生物学

Physical biology Pub Date : 2022-10-25 DOI: 10.1088/1478-3975/ac95ea

Paul C Bressloff

{"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":"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 thresholda; 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(a) 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.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"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}

引用次数: 1

Learning feedback molecular network models using integer linear programming. 利用整数线性规划学习反馈分子网络模型。

IF 2 4区生物学

Physical biology Pub Date : 2022-10-04 DOI: 10.1088/1478-3975/ac920d

Mustafa Ozen, Effat S Emamian, Ali Abdi

{"title":"Learning feedback molecular network models using integer linear programming.","authors":"Mustafa Ozen, Effat S Emamian, Ali Abdi","doi":"10.1088/1478-3975/ac920d","DOIUrl":"https://doi.org/10.1088/1478-3975/ac920d","url":null,"abstract":"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.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"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}

引用次数: 0

Comment on 'A physics perspective on collective animal behavior' 2022Phys. Biol.19 021004. 评论“集体动物行为的物理学视角”2022Phys。Biol.19 021004。

IF 2 4区生物学

Physical biology Pub Date : 2022-09-19 DOI: 10.1088/1478-3975/ac8fd5

Andy M Reynolds

引用次数: 2

A compressed logistic equation on bacteria growth: inferring time-dependent growth rate. 细菌生长的压缩逻辑方程:推断随时间变化的生长速率。

IF 2 4区生物学

Physical biology Pub Date : 2022-09-15 DOI: 10.1088/1478-3975/ac8c15

Carlito Pinto, Koichi Shimakawa

引用次数: 3

Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology. 重构细胞表型转换的数据驱动管理方程：数据科学与系统生物学的整合。

IF 2 4区生物学

Physical biology Pub Date : 2022-09-09 DOI: 10.1088/1478-3975/ac8c16

Jianhua Xing

{"title":"Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology.","authors":"Jianhua Xing","doi":"10.1088/1478-3975/ac8c16","DOIUrl":"10.1088/1478-3975/ac8c16","url":null,"abstract":"Cells with the same genome can exist in different phenotypes and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming for induced pluripotent stem cells and transdifferentiation, cancer metastasis and fibrosis progression. The regulation and dynamics of cell phenotypic conversion is a fundamental problem in biology, and has a long history of being studied within the formalism of dynamical systems. A main challenge for mechanism-driven modeling studies is acquiring sufficient amount of quantitative information for constraining model parameters. Advances in quantitative experimental approaches, especially high throughput single-cell techniques, have accelerated the emergence of a new direction for reconstructing the governing dynamical equations of a cellular system from quantitative single-cell data, beyond the dominant statistical approaches. Here I review a selected number of recent studies using live- and fixed-cell data and provide my perspective on future development.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9585661/pdf/nihms-1835862.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10557945","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}

引用次数: 0

Non-genetic resistance facilitates survival while hindering the evolution of drug resistance due to intraspecific competition. 非遗传抗性促进了生存，同时由于种内竞争阻碍了耐药性的进化。

IF 2 4区生物学

Physical biology Pub Date : 2022-09-08 DOI: 10.1088/1478-3975/ac8c17

Joshua D Guthrie, Daniel A Charlebois

{"title":"Non-genetic resistance facilitates survival while hindering the evolution of drug resistance due to intraspecific competition.","authors":"Joshua D Guthrie, Daniel A Charlebois","doi":"10.1088/1478-3975/ac8c17","DOIUrl":"https://doi.org/10.1088/1478-3975/ac8c17","url":null,"abstract":"Rising rates of resistance to antimicrobial drugs threaten the effective treatment of infections across the globe. Drug resistance has been established to emerge from non-genetic mechanisms as well as from genetic mechanisms. However, it is still unclear how non-genetic resistance affects the evolution of genetic drug resistance. We develop deterministic and stochastic population models that incorporate resource competition to quantitatively investigate the transition from non-genetic to genetic resistance during the exposure to static and cidal drugs. We find that non-genetic resistance facilitates the survival of cell populations during drug treatment while hindering the development of genetic resistance due to competition between the non-genetically and genetically resistant subpopulations. Non-genetic resistance in the presence of subpopulation competition increases the fixation times of drug resistance mutations, while increasing the probability of mutation before population extinction during cidal drug treatment. Intense intraspecific competition during drug treatment leads to extinction of susceptible and non-genetically resistant subpopulations. Alternating between drug and no drug conditions results in oscillatory population dynamics, increased resistance mutation fixation timescales, and reduced population survival. These findings advance our fundamental understanding of the evolution of resistance and may guide novel treatment strategies for patients with drug-resistant infections.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40436958","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}

引用次数: 3

Long-range morphogen gradient formation by cell-to-cell signal propagation. 细胞间信号传播形成的远距离形态形成梯度。

IF 2 4区生物学

Physical biology Pub Date : 2022-09-07 DOI: 10.1088/1478-3975/ac86b4

Johanna E M Dickmann, Jochen C Rink, Frank Jülicher

{"title":"Long-range morphogen gradient formation by cell-to-cell signal propagation.","authors":"Johanna E M Dickmann, Jochen C Rink, Frank Jülicher","doi":"10.1088/1478-3975/ac86b4","DOIUrl":"https://doi.org/10.1088/1478-3975/ac86b4","url":null,"abstract":"Morphogen gradients are a central concept in developmental biology. Their formation often involves the secretion of morphogens from a local source, that spread by diffusion in the cell field, where molecules eventually get degraded. This implies limits to both the time and length scales over which morphogen gradients can form which are set by diffusion coefficients and degradation rates. Towards the goal of identifying plausible mechanisms capable of extending the gradient range, we here use theory to explore properties of a cell-to-cell signaling relay. Inspired by the millimeter-scalewnt-expression and signaling gradients in flatworms, we consider morphogen-mediated morphogen production in the cell field. We show that such a relay can generate stable morphogen and signaling gradients that are oriented by a local, morphogen-independent source of morphogen at a boundary. This gradient formation can be related to an effective diffusion and an effective degradation that result from morphogen production due to signaling relay. If the secretion of morphogen produced in response to the relay is polarized, it further gives rise to an effective drift. We find that signaling relay can generate long-range gradients in relevant times without relying on extreme choices of diffusion coefficients or degradation rates, thus exceeding the limits set by physiological diffusion coefficients and degradation rates. A signaling relay is hence an attractive principle to conceptualize long-range gradient formation by slowly diffusing morphogens that are relevant for patterning in adult contexts such as regeneration and tissue turn-over.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2022-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40580475","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}

引用次数: 6