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TEM study of chronic alcoholism effects on early carcinogenesis by probing the nanoscale structural alterations of cell nuclei Phys. Biol. (IF 2.0) Pub Date : 2021-01-12 Prakash Adhikari, Pradeep K Shukla, Hemendra M Ghimire, Mehedi Hasan, Peeyush Sahay, Huda Almabadi, Vibha Tripathi, Omar Skalli, Radhakrishna Rao and Prabhakar Pradhan
Nanoscale structural alteration in the nuclei of cells with the progression of carcinogenesis is due to the rearrangements of the basic building blocks in the cell such as DNA, RNA, lipids, etc. Although epigenetic modifications underlie the development of cancer, exposure to carcinogenic chemicals such as alcohol also enhances the development of cancer. We report the effects of chronic alcoholism
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Neuronal growth from a volume perspective Phys. Biol. (IF 2.0) Pub Date : 2021-01-12 Céline Braïni, Ghislain Bugnicourt and Catherine Villard
Microfluidic-based fluorescent exclusion method allows to tackle the issue of neuronal growth from a volume perspective. Based on this technology, we studied the two main actin-rich structures accompanying the early stages of neuron development, i.e. growth cones, located at the tip of growing neuronal processes, and propagative actin waves. Our work reveals that growth cones tend to loose volume during
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Noise and the molecular processes underlying cell fate decision-making Phys. Biol. (IF 2.0) Pub Date : 2021-01-07 Anissa Guillemin and Michael P H Stumpf
Cell fate decision-making events involve the interplay of many molecular processes, ranging from signal transduction to genetic regulation, as well as a set of molecular and physiological feedback loops. Each aspect offers a rich field of investigation in its own right, but to understand the whole process, even in simple terms, we need to consider them together. Here we attempt to characterise this
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Theoretical modelling of competitive microbial range expansion with heterogeneous mechanical interactions Phys. Biol. (IF 2.0) Pub Date : 2021-01-07 E Maikranz and L Santen
Microbial range expansion experiments provide insight into the complex link between dynamic structure, pattern formation and evolutionary dynamics of growing populations. In this work, we develop a theoretical model in order to investigate the interplay of growth statistics and mechanical interactions which are implemented as division driven pushing and swapping of cells. For the case of the competitive
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Liquid–liquid phase separation driven compartmentalization of reactive nucleoplasm Phys. Biol. (IF 2.0) Pub Date : 2021-01-07 Rabia Laghmach and Davit A Potoyan
The nucleus of eukaryotic cells harbors active and out of equilibrium environments conducive to diverse gene regulatory processes. On a molecular scale, gene regulatory processes take place within hierarchically compartmentalized sub-nuclear bodies. While the impact of nuclear structure on gene regulation is widely appreciated, it has remained much less clear whether and how gene regulation is impacting
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Microtubule catastrophe under force: mathematical and computational results from a Brownian ratchet model Phys. Biol. (IF 2.0) Pub Date : 2020-12-11 Vandana Yadav, Balaramamahanti Srinivas and Manoj Gopalakrishnan
In the intracellular environment, the intrinsic dynamics of microtubule filaments is often hindered by the presence of barriers of various kind, such as kinetochore complexes and cell cortex, which impact their polymerisation force and dynamical properties such as catastrophe frequency. We present a theoretical study of the effect of a forced barrier, also subjected to thermal noise, on the statistics
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Uncovering the release mechanism of nucleotide import by HIV-1 capsid Phys. Biol. (IF 2.0) Pub Date : 2020-12-01 Guang Song
Efficient nucleotide import is critical to fuel the reverse DNA synthesis that takes place within the HIV-1 capsid. However, the mechanism by which the HIV-1 capsid imports nucleotides is presently unclear. In this work, we carry out a series of Brownian diffusion simulations to elucidate the nucleotide import process through the hexamer pores of the HIV-1 capsid. Our simulations reveal a significant
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O-GlcNAcylation inhibits the oligomerization of alpha-synuclein by declining intermolecular hydrogen bonds through a steric effect. Phys. Biol. (IF 2.0) Pub Date : 2020-12-01 Kai Wu,Dechang Li,Peng Xiu,Baohua Ji,Jiajie Diao
Toxic abnormal aggregation of α-synuclein (α-Syn) is a feature of Parkinson’s disease. Several biochemical and biophysical studies have demonstrated that many post-translational modifications (PTM) of α-Syn could distinctly alleviate its oligomerization-mediated toxicity. Recently, a compelling link is emerging between the PTM O-GlcNAcylation (O-GlcNAc) and protein aggregation, yet the underlying molecular
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Identifying potential gene biomarkers for Parkinson’s disease through an information entropy based approach Phys. Biol. (IF 2.0) Pub Date : 2020-12-01 A Monaco, E Pantaleo, N Amoroso, L Bellantuono, A Lombardi, A Tateo, S Tangaro and R Bellotti
Parkinson’s disease (PD) is a chronic, progressive neurodegenerative disease and represents the most common disease of this type, after Alzheimer’s dementia. It is characterized by motor and nonmotor features and by a long prodromal stage that lasts many years. Genetic research has shown that PD is a complex and multisystem disorder. To capture the molecular complexity of this disease we used a complex
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The vimentin cytoskeleton: when polymer physics meets cell biology Phys. Biol. (IF 2.0) Pub Date : 2020-12-01 Alison E Patteson, Robert J Carroll, Daniel V Iwamoto and Paul A Janmey
The proper functions of tissues depend on the ability of cells to withstand stress and maintain shape. Central to this process is the cytoskeleton, comprised of three polymeric networks: F-actin, microtubules, and intermediate filaments (IFs). IF proteins are among the most abundant cytoskeletal proteins in cells; yet they remain some of the least understood. Their structure and function deviate from
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A lattice model on the rate of in vivo site-specific DNA-protein interactions Phys. Biol. (IF 2.0) Pub Date : 2020-12-01 R Murugan
We develop a lattice model of site-specific DNA-protein interactions under in vivo conditions where DNA is modelled as a self-avoiding random walk that is embedded in a cubic lattice box resembling the living cell. The protein molecule searches for its cognate site on DNA via a combination of three dimensional (3D) and one dimensional (1D) random walks. Hopping and intersegmental transfers occur depending
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Integrating transcriptomics and bulk time course data into a mathematical framework to describe and predict therapeutic resistance in cancer Phys. Biol. (IF 2.0) Pub Date : 2020-11-20 Kaitlyn E Johnson, Grant R Howard, Daylin Morgan, Eric A Brenner, Andrea L Gardner, Russell E Durrett, William Mo, Aziz Al’Khafaji, Eduardo D Sontag, Angela M Jarrett, Thomas E Yankeelov and Amy Brock
A significant challenge in the field of biomedicine is the development of methods to integrate the multitude of dispersed data sets into comprehensive frameworks to be used to generate optimal clinical decisions. Recent technological advances in single cell analysis allow for high-dimensional molecular characterization of cells and populations, but to date, few mathematical models have attempted to
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Self-organized multicellular structures from simple cell signaling: a computational model Phys. Biol. (IF 2.0) Pub Date : 2020-11-19 Nicola Mulberry and Leah Edelstein-Keshet
Recent synthetic biology experiments reveal that signaling modules designed to target cell–cell adhesion enable self-organization of multicellular structures Toda et al (2018 Science 361 156–162). Changes in homotypic adhesion that arise through contact-dependent signaling networks result in sorting of an aggregate into two- or three-layered structures. Here we investigate the formation, maintenance
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Shape of population interfaces as an indicator of mutational instability in coexisting cell populations Phys. Biol. (IF 2.0) Pub Date : 2020-11-19 Daniel Castillo and Maxim O Lavrentovich
Cellular populations such as avascular tumors and microbial biofilms may ‘invade’ or grow into surrounding populations. The invading population is often comprised of a heterogeneous mixture of cells with varying growth rates. The population may also exhibit mutational instabilities, such as a heavy deleterious mutation load in a cancerous growth. We study the dynamics of a heterogeneous, mutating population
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Heterogeneity and ‘memory’ in stem cell populations Phys. Biol. (IF 2.0) Pub Date : 2020-11-19 Patrick S Stumpf, Fumio Arai and Ben D MacArthur
Modern single cell experiments have revealed unexpected heterogeneity in apparently functionally ‘pure’ cell populations. However, we are still lacking a conceptual framework to understand this heterogeneity. Here, we propose that cellular memories—changes in the molecular status of a cell in response to a stimulus, that modify the ability of the cell to respond to future stimuli—are an essential ingredient
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Emerging algebraic growth trends in SARS-CoV-2 pandemic data. Phys. Biol. (IF 2.0) Pub Date : 2020-11-19 Katarina Bodova,Richard Kollar
We study the reported data from the SARS-CoV-2 pandemic outbreak in January–May 2020 in 119 countries. We observe that the time series of active cases in individual countries (the difference of the total number of confirmed infections and the sum of the total number of reported deaths and recovered cases) display a strong agreement with algebraic growth and at a later epidemic stage also with a combined
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An adaptive solution to the chemical master equation using quantized tensor trains with sliding windows. Phys. Biol. (IF 2.0) Pub Date : 2020-11-19 Trang Dinh,Roger B Sidje
To cope with an extremely large or even infinite state space when solving the chemical master equation in biological problems, a potent strategy is to restrict to a finite state projection (FSP) and represent the transition matrix and probability vector in quantized tensor train (QTT) format, leading to savings in storage while retaining accuracy. In an earlier adaptive FSP–QTT algorithm, the multidimensional
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Coupled differentiation and division of embryonic stem cells inferred from clonal snapshots. Phys. Biol. (IF 2.0) Pub Date : 2020-10-20 Liam J Ruske,Jochen Kursawe,Anestis Tsakiridis,Valerie Wilson,Alex Fletcher,Richard A Blythe,Linus J Schumacher
The deluge of single-cell data obtained by sequencing, imaging and epigenetic markers has led to an increasingly detailed description of cell state. However, it remains challenging to identify how cells transition between different states, in part because data are typically limited to snapshots in time. A prerequisite for inferring cell state transitions from such snapshots is to distinguish whether
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Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding Phys. Biol. (IF 2.0) Pub Date : 2020-10-20 Kevin Tsai, Samuel Britton, Ali Nematbakhsh, Roya Zandi, Weitao Chen and Mark Alber
Budding yeast, Saccharomyces cerevisiae, serves as a prime biological model to study mechanisms underlying asymmetric growth. Previous studies have shown that prior to bud emergence, polarization of a conserved small GTPase Cdc42 must be established on the cell membrane of a budding yeast. Additionally, such polarization contributes to the delivery of cell wall remodeling enzymes and hydrolase from
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A minimal model for household effects in epidemics Phys. Biol. (IF 2.0) Pub Date : 2020-10-20 Greg Huber, Mason Kamb, Kyle Kawagoe, Lucy M Li, Boris Veytsman, David Yllanes and Dan Zigmond
Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. We introduce a minimal model that incorporates these household effects in the framework
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Why COVID-19 models should incorporate the network of social interactions. Phys. Biol. (IF 2.0) Pub Date : 2020-10-12 Helena A Herrmann,Jean-Marc Schwartz
The global spread of coronavirus disease 2019 (COVID-19) is overwhelming many health-care systems. As a result, epidemiological models are being used to inform policy on how to effectively deal with this pandemic. The majority of existing models assume random diffusion but do not take into account differences in the amount of interactions between individuals, i.e. the underlying human interaction network
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Testing of asymptomatic individuals for fast feedback-control of COVID-19 pandemics. Phys. Biol. (IF 2.0) Pub Date : 2020-10-12 Markus Müller,Peter M Derlet,Christopher Mudry,Gabriel Aeppli
We argue that frequent sampling of the fraction of a priori non-symptomatic but infectious humans (either by random or cohort testing) significantly improves the management of the COVID-19 pandemic, when compared to intervention strategies relying on data from symptomatic cases only. This is because such sampling measures the incidence of the disease, the key variable controlled by restrictive measures
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Getting around the cell: physical transport in the intracellular world. Phys. Biol. (IF 2.0) Pub Date : 2020-10-12 Saurabh Mogre,Aidan Ivar Brown,Elena F Koslover
Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We
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Computation in bacterial communities Phys. Biol. (IF 2.0) Pub Date : 2020-10-08 Ghazaleh Ostovar, Kyle L Naughton and James Q Boedicker
Bacteria across many scales are involved in a dynamic process of information exchange to coordinate activity and community structure within large and diverse populations. The molecular components bacteria use to communicate have been discovered and characterized, and recent efforts have begun to understand the potential for bacterial signal exchange to gather information from the environment and coordinate
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Efficiency of Covid-19 mobile contact tracing containment by measuring time dependent doubling time. Phys. Biol. (IF 2.0) Pub Date : 2020-10-08 Antonio Bianconi,Augusto Marcelli,Gaetano Campi,Andrea Perali
The COVID-19 epidemic of the novel coronavirus (severe acute respiratory syndrome SARS-CoV-2) has spread around the world. While different containment policies using non-pharmaceutical interventions have been applied, their efficiencies are not known quantitatively. We show that the doubling time T d ( t ) with the success s factor , the characteristic time of the exponential growth of T d ( t ) in
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Non-random distribution of vacuoles inSchizosaccharomyces pombe. Phys. Biol. (IF 2.0) Pub Date : 2020-10-08 William Chadwick,Sujoy Biswas,Simone Bianco,Yee-Hung Mark Chan
A central question in eukaryotic cell biology asks, during cell division, how is the growth and distribution of organelles regulated to ensure each daughter cell receives an appropriate amount. For vacuoles in budding yeast, there are well described organelle-to-cell size scaling trends as well as inheritance mechanisms involving highly coordinated movements. It is unclear whether such mechanisms are
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Urn models for stochastic gene expression yield intuitive insights into the probability distributions of single-cell mRNA and protein counts. Phys. Biol. (IF 2.0) Pub Date : 2020-09-27 Krishna Choudhary,Atul Narang
Fitting the probability mass functions from analytical solutions of stochastic models of gene expression to the single-cell count distributions of mRNA and protein molecules can yield valuable insights into mechanisms underlying gene expression. Solutions of chemical master equations are available for various kinetic schemes but, even for the basic ON–OFF genetic switch, they take complex forms with
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The physical basis and practical consequences of biological promiscuity Phys. Biol. (IF 2.0) Pub Date : 2020-09-23 Shelley D Copley
Proteins interact with metabolites, nucleic acids, and other proteins to orchestrate the myriad catalytic, structural and regulatory functions that support life, from the simplest microbes to the most complex multicellular organisms. These molecular interactions are often exquisitely specific, but never perfectly so. Adventitious ‘promiscuous’ interactions are ubiquitous due to the thousands of macromolecules
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Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Phys. Biol. (IF 2.0) Pub Date : 2020-09-22 Jack Merrin
Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described
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Why case fatality ratios can be misleading: individual- and population-based mortality estimates and factors influencing them. Phys. Biol. (IF 2.0) Pub Date : 2020-09-22 Lucas Böttcher,Mingtao Xia,Tom Chou
Different ways of calculating mortality during epidemics have yielded very different results, particularly during the current COVID-19 pandemic. For example, the ‘CFR’ has been interchangeably called the case fatality ratio, case fatality rate, and case fatality risk, often without standard mathematical definitions. The most commonly used CFR is the case fatality ratio , typically constructed using
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Using posterior predictive distributions to analyse epidemic models: COVID-19 in Mexico City. Phys. Biol. (IF 2.0) Pub Date : 2020-09-21 Ramsés H Mena,Jorge X Velasco-Hernandez,Natalia B Mantilla-Beniers,Gabriel A Carranco-Sapiéns,Luis Benet,Denis Boyer,Isaac Pérez Castillo
Epidemiological models usually contain a set of parameters that must be adjusted based on available observations. Once a model has been calibrated, it can be used as a forecasting tool to make predictions and to evaluate contingency plans. It is customary to employ only point estimators of model parameters for such predictions. However, some models may fit the same data reasonably well for a broad
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Forecasting the outcome and estimating the epidemic model parameters from the fatality time series in COVID-19 outbreaks. Phys. Biol. (IF 2.0) Pub Date : 2020-09-21 Gabor Vattay
In the absence of other tools, monitoring the effects of protective measures, including social distancing and forecasting the outcome of outbreaks is of immense interest. Real-time data is noisy and very often hampered by systematic errors in reporting. Detailed epidemic models may contain a large number of empirical parameters, which cannot be determined with sufficient accuracy. In this paper, we
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Computational modelling in single-cell cancer genomics: methods and future directions. Phys. Biol. (IF 2.0) Pub Date : 2020-09-18 Allen Zhang,Kieran Campbell
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, proteome, and epigenome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays offer new insights into tumour heterogeneity, which underlies cancer initiation, progression, and relapse. However, the large quantities of high-dimensional
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Rate-dependent force-extension models for single-molecule force spectroscopy experiments. Phys. Biol. (IF 2.0) Pub Date : 2020-08-26 Manon Benedito,Fabio Manca,Pier Luca Palla,Stefano Giordano
Single-molecule force spectroscopy techniques allow for the measurement of several static and dynamic features of macromolecules of biological origin. In particular, atomic force microscopy, used with a variable pulling rate, provides valuable information on the folding/unfolding dynamics of proteins. We propose here two different models able to describe the out-of-equilibrium statistical mechanics
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Replicating landmine blast loading in cellular in vitro models. Phys. Biol. (IF 2.0) Pub Date : 2020-08-11 David R Sory,Harsh D Amin,David J Chapman,William G Proud,Sara M Rankin
Trauma arising from landmines and improvised explosive devices promotes heterotopic ossification, the formation of extra-skeletal bone in non-osseous tissue. To date, experimental platforms that can replicate the loading parameter space relevant to improvised explosive device and landmine blast wave exposure have not been available to study the effects of such non-physiological mechanical loading on
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Guidelines for designing the antithetic feedback motif. Phys. Biol. (IF 2.0) Pub Date : 2020-08-09 Ania-Ariadna Baetica,Yoke Peng Leong,Richard M Murray
Integral feedback control is commonly used in mechanical and electrical systems to achieve zero steady-state error following an external disturbance. Equivalently, in biological systems, a property known as robust perfect adaptation guarantees robustness to environmental perturbations and return to the pre-disturbance state. Previously, Briat et al proposed a biomolecular design for integral feedback
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Nano-bio interactions in drug delivery. Phys. Biol. (IF 2.0) Pub Date : 2020-07-28 Amir M Farnoud
Description unavailable
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The COVID-19 pandemic: growth patterns, power law scaling, and saturation. Phys. Biol. (IF 2.0) Pub Date : 2020-07-28 H M Singer
More and more countries are showing a significant slowdown in the number of new COVID-19 infections due to effective governmentally instituted lockdown and social distancing measures. We have analyzed the growth behavior of the top 25 most affected countries by means of a local slope analysis and found three distinct patterns that individual countries follow depending on the strictness of the lockdown
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Leader-cell-driven epithelial sheet fingering. Phys. Biol. (IF 2.0) Pub Date : 2020-06-30 Yanjun Yang,Herbert Levine
Collective cell migration is crucial in many biological processes such as wound healing, tissue morphogenesis, and tumor progression. The leading front of a collective migrating epithelial cell layer often destabilizes into multicellular finger-like protrusions, each of which is guided by a leader cell at the fingertip. Here, we develop a subcellular-element-based model of this fingering instability
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3 tera-basepairs as a fundamental limit for robust DNA replication. Phys. Biol. (IF 2.0) Pub Date : 2020-06-30 M Al Mamun,L Albergante,J J Blow,T J Newman
In order to maintain functional robustness and species integrity, organisms must ensure high fidelity of the genome duplication process. This is particularly true during early development, where cell division is often occurring both rapidly and coherently. By studying the extreme limits of suppressing DNA replication failure due to double fork stall errors, we uncover a fundamental constant that describes
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Does frequency-dependent cell proliferation exhibit a Fano-type resonance? Phys. Biol. (IF 2.0) Pub Date : 2020-06-29 Zubaidah Ningsih,Andrew H A Clayton
We examined PC12 cell proliferation in environments with temporally varying epidermal growth factor concentrations by means of a microfluidic system. Our measurements revealed frequency-dependent cell behaviour over an observation period of three days. The cell population either increased, decreased or remained constant depending on the frequency of epidermal growth factor applied. A plot of the apparent
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Dynamic catch-bonding generates the large stall forces of cytoplasmic dynein. Phys. Biol. (IF 2.0) Pub Date : 2020-06-18 Christopher M Johnson,J Daniel Fenn,Anthony Brown,P Jung
Cytoplasmic dynein is an important molecular motor involved in the transport of vesicular and macromolecular cargo along microtubules in cells, often in conjunction with kinesin motors. Dynein is larger and more complex than kinesin and the mechanism and regulation of its movement is currently the subject of intense research. While it was believed for a long time that dynein motors are relatively weak
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Correlation between protein concentration and bacterial cell size can reveal mechanisms of gene expression. Phys. Biol. (IF 2.0) Pub Date : 2020-05-21 César Nieto-Acuña,Juan Carlos Arias-Castro,César Vargas-García,Carlos Sánchez,Juan Manuel Pedraza
Classically, gene expression is modeled as a chemical process with reaction rates dependent on the concentration of the reactants (typically, DNA loci, plasmids, RNA, enzymes, etc). Other variables like cell size are in general ignored. Size dynamics can become an important variable due to the low number of many of these reactants, imperfectly symmetric cell partitioning and molecule segregation. In
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From reversible to irreversible bistable switches via bifurcations in a gene regulatory network. Phys. Biol. (IF 2.0) Pub Date : 2020-05-21 Lijie Hao,Zhuoqin Yang,Danhong Shen,Miaomiao Xing
The interplay of small, noncoding microRNAs (miRNAs), mRNAs and proteins plays crucial roles in almost all cellular processes. MiR-124, widely known as a memory-related miRNA, can regulate LTM by binding to the mRNA of CREB1 stimulated with 5-HT. In this paper, we establish a regulatory network model of CREB1 and miR-124 stimulated by 5-HT, in which miR-124 inhibits CREB1, which in turn enhances miR-124
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Effects of surfaces and macromolecular crowding on bimolecular reaction rates. Phys. Biol. (IF 2.0) Pub Date : 2020-05-15 Steven S Andrews
Biological cells are complex environments that are densely packed with macromolecules and subdivided by membranes, both of which affect the rates of chemical reactions. It is well known that crowding reduces the volume available to reactants, which increases reaction rates, and also inhibits reactant diffusion, which decreases reaction rates. This work investigates these effects quantitatively using
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Bidirectional interplay between physical and biological approaches on studying the epithelial-to-mesenchymal transition. Phys. Biol. (IF 2.0) Pub Date : 2020-02-28 Jianhua Xing
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Continuous active development of super-resolution fluorescence microscopy. Phys. Biol. (IF 2.0) Pub Date : 2020-04-07 Yong Wang,Jingyi Fei
N/A.
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Membrane potentials, oxidative stress and the dispersal response of bacterial biofilms to 405 nm light. Phys. Biol. (IF 2.0) Pub Date : 2020-03-04 J A Blee,I S Roberts,T A Waigh
The majority of chronic infections are caused by biofilms, which have higher levels of antibiotic resistance than planktonic growth. Violet-blue 405 nm light has recently emerged as a novel bactericide, but limited studies have been conducted on its effectiveness against biofilms. We found that in response to 405 nm light both Pseudomonas aeruginosa and Bacillus subtilis biofilms exhibited cell dispersal
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Advanced fluorescence imaging of in situ protein aggregation. Phys. Biol. (IF 2.0) Pub Date : 2020-02-11 Meng Lu,Clemens F Kaminski,Gabriele S Kaminski Schierle
The aggregation of intrinsically disordered proteins is a hallmark of neurodegenerative diseases, such as Alzheimer's, Parkinson's and Huntington's disease. Although we currently have a good molecular level understanding on how protein aggregation occurs in vitro, the details of its self-assembly in live cells are still mainly unknown. During the last ten years, we have witnessed the rapid development
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Effect of solvent on protein structure and dynamics. Phys. Biol. (IF 2.0) Pub Date : 2020-04-08 Anshuman Bose Majumdar,In Jung Kim,Hyuntae Na
Understanding how much solvents influence the structures and dynamics of proteins is important to understand functional mechanisms of solvated proteins. We propose a solvated potential model that approximates the potential energy of a solvated protein by projecting the solvent information into the protein structure. Using the model, we derive three properties of the solvent. First, the influence of
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A biomechanical model for the transendothelial migration of cancer cells. Phys. Biol. (IF 2.0) Pub Date : 2020-03-19 S M Amin Arefi,Daria Tsvirkun,Claude Verdier,James J Feng
We propose a biomechanical model for the extravasation of a tumor cell (TC) through the endothelium of a blood vessel. Based on prior in vitro observations, we assume that the TC extends a protrusion between adjacent endothelial cells (ECs) that adheres to the basement membrane via focal adhesions (FAs). As the protrusion grows in size and branches out, the actomyosin contraction along the stress fibers
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A Rho-GTPase based model explains group advantage in collective chemotaxis of neural crest cells. Phys. Biol. (IF 2.0) Pub Date : 2020-03-10 Brian Merchant,James J Feng
A cluster of neural crest cells (NCCs) may chemotax up a shallow external gradient to which a single cell is unresponsive. To explain this intriguing 'group advantage', we propose a chemo-mechanical model based on the signaling proteins Rac1 and RhoA. We represent each cell as a polygon with nodes connected by elastic membranes. Via reaction-diffusion on the membrane and exchange with their cytosolic
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Widespread non-modular overlapping codes in the coding regions. Phys. Biol. (IF 2.0) Pub Date : 2020-04-08 Shaked Bergman,Tamir Tuller
Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5'UTR and 3'UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic
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Towards computer-aided design of cellular structure. Phys. Biol. (IF 2.0) Pub Date : 2020-02-25 Simone Bianco,Yee-Hung Mark Chan,Wallace F Marshall
Cells are complex machines with tremendous potential for applications in medicine and biotechnology. Although much effort has been devoted to engineering the metabolic, genetic, and signaling pathways of cells, methods for systematically engineering the physical structure of cells are less developed. Here we consider how coarse-grained models for cellular geometry at the organelle level can be used
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Studying nanoscale structural alterations in cancer cells to evaluate ovarian cancer drug treatment, using transmission electron microscopy imaging. Phys. Biol. (IF 2.0) Pub Date : 2020-03-25 Prakash Adhikari,Mehedi Hasan,Vijayalakshmi Sridhar,Debarshi Roy,Prabhakar Pradhan
Understanding nanoscale structural changes can provide information about the physical state of cells/tissues. It has now been shown that increases in nanoscale structural alterations are associated with the progress of carcinogenesis in most cancer cases, including early carcinogenesis. Anti-cancerous therapies are designed to inhibit the growth of cancer cells; however, it is challenging to detect
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A computational approach for detecting micro-domains and confinement domains in cells: a simulation study. Phys. Biol. (IF 2.0) Pub Date : 2020-02-12 Vincent Briane,Antoine Salomon,Myriam Vimond,Charles Kervrann
In this paper, we aim to detect trapping areas (equivalently microdomains or confinement areas) within cells, corresponding to regions where molecules are trapped and thereby undergo subdiffusion. We propose an original computational approach that takes as input a set of molecule trajectories estimated by appropriate tracking methods. The core of the algorithm is based on a combination of clustering
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Pulling-force generation by ensembles of polymerizing actin filaments. Phys. Biol. (IF 2.0) Pub Date : 2019-12-13 F Motahari,A E Carlsson
The process by which actin polymerization generates pulling forces in cellular processes such as endocytosis is less well understood than pushing-force generation. To clarify the basic mechanisms of pulling-force generation, we perform stochastic polymerization simulations for a square array of polymerizing semiflexible actin filaments, having different interactions with the membrane. The filaments
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Cell-based simulations of biased epithelial lung growth. Phys. Biol. (IF 2.0) Pub Date : 2019-12-13 Anna Stopka,Marco Kokic,Dagmar Iber
During morphogenesis, epithelial tubes elongate. In the case of the mammalian lung, biased elongation has been linked to a bias in cell shape and cell division, but it has remained unclear whether a bias in cell shape along the axis of outgrowth is sufficient for biased outgrowth and how it arises. Here, we use our 2D cell-based tissue simulation software [Formula: see text] to investigate the conditions
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Power series method for solving TASEP-based models of mRNA translation. Phys. Biol. (IF 2.0) Pub Date : 2019-12-03 S Scott,J Szavits-Nossan
We develop a method for solving mathematical models of messenger RNA (mRNA) translation based on the totally asymmetric simple exclusion process (TASEP). Our main goal is to demonstrate that the method is versatile and applicable to realistic models of translation. To this end we consider the TASEP with codon-dependent elongation rates, premature termination due to ribosome drop-off and translation
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Role of hydrodynamic interactions in chemotaxis of bacterial populations. Phys. Biol. (IF 2.0) Pub Date : 2019-12-03 Shawn D Ryan
How bacteria sense local chemical gradients and decide to move has been a fascinating area of recent study. Chemotaxis of bacterial populations has been traditionally modeled using either individual-based models describing the motion of a single bacterium as a velocity jump process, or macroscopic PDE models that describe the evolution of the bacterial density. In these models, the hydrodynamic interaction
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