Physical biology最新文献_第2页

Theory of epigenetic switching due to stochastic histone mark loss during DNA replication. DNA 复制过程中随机组蛋白标记丢失导致表观遗传学转换的理论。

IF 2 4区生物学

Physical biology Pub Date : 2024-11-29 DOI: 10.1088/1478-3975/ad942c

Ander Movilla Miangolarra, Martin Howard

{"title":"Theory of epigenetic switching due to stochastic histone mark loss during DNA replication.","authors":"Ander Movilla Miangolarra, Martin Howard","doi":"10.1088/1478-3975/ad942c","DOIUrl":"10.1088/1478-3975/ad942c","url":null,"abstract":"How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell cycle is still not fully understood. Often, epigenetic marks can display bistable behaviour and their bistable state is transmitted to daughter cells through the cell cycle, providing the cell with a form of memory. However, loss-of-memory events also take place, where a daughter cell switches epigenetic state (with respect to the mother cell). Here, we develop a framework to compute these epigenetic switching rates, for the case when they are driven by DNA replication, i.e. the frequency of loss-of-memory events due to replication. We consider the dynamics of histone modifications during the cell cycle deterministically, except at DNA replication, where nucleosomes are randomly distributed between the two daughter DNA strands, which is therefore implemented stochastically. This hybrid stochastic-deterministic approach enables an analytic derivation of the replication-driven switching rate. While retaining great simplicity, this framework can explain experimental switching rate data, establishing its biological importance as a framework to quantitatively study epigenetic inheritance.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11605279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668868","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

A role of fear on diseased food web model with multiple functional response. 恐惧对具有多重功能反应的病态食物网模型的作用

IF 2 4区生物学

Physical biology Pub Date : 2024-11-26 DOI: 10.1088/1478-3975/ad9261

Thangavel Megala, Manickasundaram Siva Pradeep, Mehmet Yavuz, Thangaraj Nandha Gopal, Muthuradhinam Sivabalan

{"title":"A role of fear on diseased food web model with multiple functional response.","authors":"Thangavel Megala, Manickasundaram Siva Pradeep, Mehmet Yavuz, Thangaraj Nandha Gopal, Muthuradhinam Sivabalan","doi":"10.1088/1478-3975/ad9261","DOIUrl":"10.1088/1478-3975/ad9261","url":null,"abstract":"In this paper, we analyze the role of fear in a three-species non-delayed ecological model that examines the interactions among susceptible prey, infectious (diseased) prey, and predators within a food web. The prey population grows in a logistic manner until it achieves a carrying capacity, reflecting common population dynamics in the absence of predators. Diseased prey is assumed to transmit infection to healthful prey by the use of a Holling type II reaction. Predators, alternatively, are modeled to consume their prey using Beddington-DeAngelis and Crowley-Martin response features. This evaluation specializes in ensuring the non-negativity of solutions, practical constraints on population dynamics, and long-term stability of the system. Each biologically possible equilibrium point is tested to understand the environmental stable states. Local stability is assessed through eigenvalue analysis, while global stability of positive equilibria is evaluated by the use of Lyapunov features to determine the overall stability of the model. Furthermore, Hopf bifurcation is explored primarily based on infection rateɛ. Numerical simulations are carried out to validate the theoretical effects and offer practical insights into the model behaviour under specific conditions.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625959","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

Two fitness inference schemes compared using allele frequencies from 1068 391 sequences sampled in the UK during the COVID-19 pandemic. 利用 COVID-19 大流行期间在英国采样的 1,068,391 个序列中的等位基因频率，比较了两种适应性推断方案。

IF 2 4区生物学

Physical biology Pub Date : 2024-11-21 DOI: 10.1088/1478-3975/ad9213

Hong-Li Zeng, Cheng-Long Yang, Bo Jing, John Barton, Erik Aurell

{"title":"Two fitness inference schemes compared using allele frequencies from 1068 391 sequences sampled in the UK during the COVID-19 pandemic.","authors":"Hong-Li Zeng, Cheng-Long Yang, Bo Jing, John Barton, Erik Aurell","doi":"10.1088/1478-3975/ad9213","DOIUrl":"10.1088/1478-3975/ad9213","url":null,"abstract":"Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more strongly to the receptors that it uses to enter human cells. Here, we compared two methods that estimate the fitness effects of viral mutations using the abundant sequence data gathered over the course of the pandemic. Both approaches are grounded in population genetics theory but with different assumptions. One approach, tQLE, features an epistatic fitness landscape and assumes that alleles are nearly in linkage equilibrium. Another approach, MPL, assumes a simple, additive fitness landscape, but allows for any level of correlation between alleles. We characterized differences in the distributions of fitness values inferred by each approach and in the ranks of fitness values that they assign to sequences across time. We find that in a large fraction of weeks the two methods are in good agreement as to their top-ranked sequences, i.e. as to which sequences observed that week are most fit. We also find that agreement between the ranking of sequences varies with genetic unimodality in the population in a given week.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142626021","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

Unraveling the role of exercise in cancer suppression: insights from a mathematical model. 揭示运动在抑制癌症中的作用：数学模型的启示

IF 2 4区生物学

Physical biology Pub Date : 2024-11-07 DOI: 10.1088/1478-3975/ad899d

Jay Taylor, T Bagarti, Niraj Kumar

引用次数: 0

An exactly solvable model for RNA polymerase during the elongation stage. 延伸阶段 RNA 聚合酶的精确可解模型

IF 2 4区生物学

Physical biology Pub Date : 2024-11-06 DOI: 10.1088/1478-3975/ad899e

Ngo P N Ngoc, Vladimir Belitsky, Gunter M Schütz

引用次数: 0

A theoretical framework for predicting the heterogeneous stiffness map of brain white matter tissue. 预测大脑白质组织异质硬度图的理论框架

IF 2 4区生物学

Physical biology Pub Date : 2024-10-30 DOI: 10.1088/1478-3975/ad88e4

Poorya Chavoshnejad, Guangfa Li, Akbar Solhtalab, Dehao Liu, Mir Jalil Razavi

{"title":"A theoretical framework for predicting the heterogeneous stiffness map of brain white matter tissue.","authors":"Poorya Chavoshnejad, Guangfa Li, Akbar Solhtalab, Dehao Liu, Mir Jalil Razavi","doi":"10.1088/1478-3975/ad88e4","DOIUrl":"10.1088/1478-3975/ad88e4","url":null,"abstract":"Finding the stiffness map of biological tissues is of great importance in evaluating their healthy or pathological conditions. However, due to the heterogeneity and anisotropy of biological fibrous tissues, this task presents challenges and significant uncertainty when characterized only by single-mode loading experiments. In this study, we propose a new theoretical framework to map the stiffness landscape of fibrous tissues, specifically focusing on brain white matter tissue. Initially, a finite element (FE) model of the fibrous tissue was subjected to six loading cases, and their corresponding stress-strain curves were characterized. By employing multiobjective optimization, the material constants of an equivalent anisotropic material model were inversely extracted to best fit all six loading modes simultaneously. Subsequently, large-scale FE simulations were conducted, incorporating various fiber volume fractions and orientations, to train a convolutional neural network capable of predicting the equivalent anisotropic material properties solely based on the fibrous architecture of any given tissue. The proposed method, leveraging brain fiber tractography, was applied to a localized volume of white matter, demonstrating its effectiveness in precisely mapping the anisotropic behavior of fibrous tissue. In the long-term, the proposed method may find applications in traumatic brain injury, brain folding studies, and neurodegenerative diseases, where accurately capturing the material behavior of the tissue is crucial for simulations and experiments.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142472872","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

Variability in individual native fibrin fiber mechanics. 单个原生纤维蛋白纤维力学的变异性

IF 2 4区生物学

Physical biology Pub Date : 2024-10-30 DOI: 10.1088/1478-3975/ad899f

Christine C Helms

{"title":"Variability in individual native fibrin fiber mechanics.","authors":"Christine C Helms","doi":"10.1088/1478-3975/ad899f","DOIUrl":"10.1088/1478-3975/ad899f","url":null,"abstract":"Fibrin fibers are important structural elements in blood coagulation. They form a mesh network that acts as a scaffold and imparts mechanical strength to the clot. A review of published work measuring the mechanics of fibrin fibers reveals a range of values for fiber extensibility. This study investigates fibrinogen concentration as a variable responsible for variability in fibrin mechanics. It expands previous work to describe the modulus, strain hardening, extensibility, and the force required for fiber failure when fibers are formed with different fibrinogen concentrations using lateral force atomic force microscopy. Analysis of the mechanical properties showed fibers formed from 1 mg ml-1and 2 mg ml-1fibrinogen had significantly different mechanical properties. To help clarify our findings we developed two behavior profiles to describe individual fiber mechanics. The first describes a fiber with low initial modulus and high extensible, that undergoes significant strain hardening, and has moderate strength. Most fibers formed with 1 mg ml-1fibrinogen had this behavior profile. The second profile describes a fiber with a high initial modulus, minimal strain hardening, high strength, and low extensibility. Most fibrin fibers formed with 2 mg ml-1fibrinogen were described by this second profile. In conclusion, we see a range of behaviors from fibers formed from native fibrinogen molecules but various fibrinogen concentrations. Potential differences in fiber formation are investigated with SEM. It is likely this range of behaviors also occursin vivo. Understanding the variability in mechanical properties could contribute to a deeper understanding of pathophysiology of coagulative disorders.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142472875","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

Low shear-induced fibrillar fibronectin: comparative analyses of morphologies and cellular effects on bovine aortic endothelial cell adhesion and proliferation. 低剪切力诱导的纤连蛋白：对牛主动脉内皮细胞粘附和增殖的形态和细胞效应的比较分析。

IF 2 4区生物学

Physical biology Pub Date : 2024-10-18 DOI: 10.1088/1478-3975/ad838c

Hoang-Nghi Mai-Thi, Dang Phu-Hai Nguyen, Phong Le, Ngoc Quyen Tran, Cam Tu Tran, Volker R Stoldt, Khon Huynh

{"title":"Low shear-induced fibrillar fibronectin: comparative analyses of morphologies and cellular effects on bovine aortic endothelial cell adhesion and proliferation.","authors":"Hoang-Nghi Mai-Thi, Dang Phu-Hai Nguyen, Phong Le, Ngoc Quyen Tran, Cam Tu Tran, Volker R Stoldt, Khon Huynh","doi":"10.1088/1478-3975/ad838c","DOIUrl":"10.1088/1478-3975/ad838c","url":null,"abstract":"Wall shear stress (WSS) is a critical factor in vascular biology, and both high and low WSS are implicated in atherosclerosis. Fibronectin (FN) is a key extracellular matrix protein that plays an important role in cell activities. Under high shear stress, plasma FN undergoes fibrillogenesis; however, its behavior under low shear stress remains unclear. This study aimed to investigate the formation ofin vitrocell-free fibrillar FN (FFN) under low shear rate conditions and its effect on bovine aortic endothelial cell behavior. FN (500µg ml-1) was perfused through slide chambers at three flow rates (0.16 ml h-1, 0.25 ml h-1, and 0.48 ml h-1), corresponding to low shear rates of 0.35 s-1, 0.55 s-1, and 1.05 s-1, respectively, for 4 h at room temperature. The formed FN matrices were observed using fluorescence microscopy and scanning electron microscopy. Under low shear rates, distinct FN matrix structures were observed. FFN0.48 formed immense fibrils with smooth surfaces, FFN0.25 formed a matrix with a rough surface, and FFN16 exhibited nodular structures. FFN0.25 supported cell activities to a greater extent than native FN and other FFN surfaces. Our study suggests that abnormally low shear conditions impact FN structure and function and enhance the understanding of FN fibrillogenesis in vascular biology, particularly in atherosclerosis.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375818","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

Exploring sperm cell rheotaxis in microfluidic channel: the role of flow and viscosity. 探索微流控通道中精子细胞的流变性：流动和粘度的作用

IF 2 4区生物学

Physical biology Pub Date : 2024-09-24 DOI: 10.1088/1478-3975/ad7b1a

Dhiraj B Puri, Paul Jacob, Vadiraj Hemadri, Arnab Banerjee, Siddhartha Tripathi

{"title":"Exploring sperm cell rheotaxis in microfluidic channel: the role of flow and viscosity.","authors":"Dhiraj B Puri, Paul Jacob, Vadiraj Hemadri, Arnab Banerjee, Siddhartha Tripathi","doi":"10.1088/1478-3975/ad7b1a","DOIUrl":"10.1088/1478-3975/ad7b1a","url":null,"abstract":"Rheotaxis is a fundamental mechanism of sperm cells that guides them in navigating towards the oocyte. The present study investigates the phenomenon of sperm rheotaxis in Newtonian and non-Newtonian fluid media, which for the first time explores a viscosity range equivalent to that of the oviductal fluid of the female reproductive tract in rectilinear microfluidic channels. Three parameters, the progressive velocity while performing rheotaxis, the radius of rotation during rheotaxis, and the percentage of rheotactic sperm cells in the bulk and near-wall regions of the microfluidic channel were measured. Numerical simulations of the flow were conducted to estimate the shear rate, flow velocity, and the drag force acting on the sperm head at specific locations where the sperms undergo rheotaxis. Increasing the flow velocity resulted in a change in the position of rheotactic sperm from the bulk center to the near wall region, an increase and subsequent decrease in the sperm's upstream progressive velocity, and a decrease in the radius of rotation. We observed that with an increase in viscosity, rheotactic sperms migrate to the near wall regions at lower flow rates, the upstream progressive velocity of the sperm decreases for Newtonian and increases for non-Newtonian media, and the radius of rotation increases for Newtonian and decreases for non-Newtonian media. These results quantify the effects of fluid properties such as viscosity and flow rate on sperm rheotaxis and navigation, thereby paving the way for manipulating sperm behavior in microfluidic devices, potentially leading to advancements in assisted reproduction techniques.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293605","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

Application of coincidence index in the discovery of co-expressed metabolic pathways. 共现指数在发现共表达代谢途径中的应用

IF 2 4区生物学

Physical biology Pub Date : 2024-08-29 DOI: 10.1088/1478-3975/ad68b6

João Paulo Cassucci Dos Santos, Odemir Martinez Bruno

{"title":"Application of coincidence index in the discovery of co-expressed metabolic pathways.","authors":"João Paulo Cassucci Dos Santos, Odemir Martinez Bruno","doi":"10.1088/1478-3975/ad68b6","DOIUrl":"10.1088/1478-3975/ad68b6","url":null,"abstract":"Analyzing transcription data requires intensive statistical analysis to obtain useful biological information and knowledge. A significant portion of this data is affected by random noise or even noise intrinsic to the modeling of the experiment. Without robust treatment, the data might not be explored thoroughly, and incorrect conclusions could be drawn. Examining the correlation between gene expression profiles is one way bioinformaticians extract information from transcriptomic experiments. However, the correlation measurements traditionally used have worrisome shortcomings that need to be addressed. This paper compares five already published and experimented-with correlation measurements to the newly developed coincidence index, a similarity measurement that combines Jaccard and interiority indexes and generalizes them to be applied to vectors containing real values. We used microarray and RNA-Seq data from the archaeonHalobacterium salinarumand the bacteriumEscherichia coli, respectively, to evaluate the capacity of each correlation/similarity measurement. The utilized method explores the co-expressed metabolic pathways by measuring the correlations between the expression levels of enzymes that share metabolites, represented in the form of a weighted graph. It then searches for local maxima in this graph using a simulated annealing algorithm. We demonstrate that the coincidence index extracts larger, more comprehensive, and more statistically significant pathways for microarray experiments. In RNA-Seq experiments, the results are more limited, but the coincidence index managed the largest percentage of significant components in the graph.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793171","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