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Physical Biology

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https://www.readbyqxmd.com/read/28914615/apoptosis-generates-mechanical-forces-that-close-the-lens-vesicle-in-the-chick-embryo
#1
Alina Oltean, Larry A Taber
During the initial stages of eye development, optic vesicles grow laterally outward from both sides of the forebrain and come into contact with the surrounding surface ectoderm (SE). Within the region of contact, these layers then thicken locally to create placodes and invaginate to form the optic cup (primitive retina) and lens vesicle (LV), respectively. This paper examines the biophysical mechanisms involved in LV formation, which consists of three phases: (1) lens placode formation; (2) invagination to create the lens pit (LP); and (3) closure to form a complete ellipsoidally shaped LV...
September 15, 2017: Physical Biology
https://www.readbyqxmd.com/read/28862157/modelling-the-collective-response-of-heterogeneous-cell-populations-to-stationary-gradients-and-chemical-signal-relay
#2
Miguel Pineda, Raluca Eftimie
The directed motion of cell aggregates toward a chemical source occurs in many relevant biological processes. Understanding the mechanisms that control this complex behavior is of great relevance for our understanding of developmental biological processes and many diseases. In this paper, we consider a self-propelled particle model for the movement of heterogeneous subpopulations of chemically interacting cells towards an imposed stable chemical gradient. Our simulations show explicitly how self-organisation of cell populations (which could lead to engulfment or complete cell segregation) can arise from the heterogeneity of chemotactic responses alone...
September 1, 2017: Physical Biology
https://www.readbyqxmd.com/read/28862154/stalk-length-dependence-of-the-contractility-of-i-vorticella-convallaria-i
#3
Eun Gul Chung, Sangjin Ryu
<i>Vorticella convallaria</i> is a sessile protozoan of which the spasmoneme contracts on a millisecond timescale. Because this contraction is induced and powered by the binding of calcium ions (Ca<sup>2+</sup>), the spasmoneme showcases Ca<sup>2+</sup>-powered cellular motility. Because the isometric tension of <i>V. convallaria</i> increases linearly with its stalk length, it is hypothesized that the contractility of <i>V. convallaria</i> during unhindered contraction depends on the stalk length...
September 1, 2017: Physical Biology
https://www.readbyqxmd.com/read/28809162/statistical-signatures-of-a-targeted-search-by-bacteria
#4
Hossein Jashnsaz, Gregory G Anderson, Steve Pressé
Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium's natural habitat, striking phenomena -- such as the volcano effect or banding -- have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources...
August 15, 2017: Physical Biology
https://www.readbyqxmd.com/read/28714461/predicting-the-dynamics-of-bacterial-growth-inhibition-by-ribosome-targeting-antibiotics
#5
Philip Greulich, Jakub Dolezal, Matthew Scott, Martin R Evans, Rosalind J Allen
Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance - yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment regimen. In particular, in the clinic, antibiotic treatment is time-dependent. Here, we use a theoretical model, previously applied to steady-state bacterial growth, to predict the dynamical response of a bacterial cell to a time-dependent dose of ribosome-targeting antibiotic...
July 17, 2017: Physical Biology
https://www.readbyqxmd.com/read/28699625/mutation-supply-and-the-repeatability-of-selection-for-antibiotic-resistance
#6
Thomas van Dijk, Sungmin Hwang, Joachim Krug, Arjan Gm de Visser, Mark Peter Zwart
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR, were subjected to different antibiotic concentrations...
July 12, 2017: Physical Biology
https://www.readbyqxmd.com/read/28825411/luria-delbr%C3%A3-ck-revisited-the-classic-experiment-does-not-rule-out-lamarckian-evolution
#7
Caroline M Holmes, Mahan Ghafari, Anzar Abbas, Varun Saravanan, Ilya Nemenman
We re-examined data from the classic Luria-Delbrück fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms (as would happen for bacteria with CRISPR-Cas immunity). Analysis of the combined model was not performed in the original 1943 paper...
August 21, 2017: Physical Biology
https://www.readbyqxmd.com/read/28698411/estimation-of-turgor-pressure-through-comparison-between-single-plant-cell-and-pressurized-shell-mechanics
#8
P Durand-Smet, E Gauquelin, N Chastrette, A Boudaoud, A Asnacios
While plant growth is well known to rely on turgor pressure, it is challenging to quantify the contribution of turgor pressure to plant cell rheology. Here we used a custom-made micro-rheometer to quantify the viscoelastic behavior of isolated plant cells while varying their internal turgor pressure. To get insight into how plant cells adapt their internal pressure to the osmolarity of their medium, we compared the mechanical behavior of single plant cells to that of a simple, passive, pressurized shell: a soccer ball...
August 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28675379/non-steady-state-mass-action-dynamics-without-rate-constants-dynamics-of-coupled-reactions-using-chemical-potentials
#9
William R Cannon, Scott E Baker
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants...
August 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28649958/modeling-mechanical-interactions-in-growing-populations-of-rod-shaped-bacteria
#10
James J Winkle, Oleg A Igoshin, Matthew R Bennett, Krešimir Josić, William Ott
Advances in synthetic biology allow us to engineer bacterial collectives with pre-specified characteristics. However, the behavior of these collectives is difficult to understand, as cellular growth and division as well as extra-cellular fluid flow lead to complex, changing arrangements of cells within the population. To rationally engineer and control the behavior of cell collectives we need theoretical and computational tools to understand their emergent spatiotemporal dynamics. Here, we present an agent-based model that allows growing cells to detect and respond to mechanical interactions...
July 28, 2017: Physical Biology
https://www.readbyqxmd.com/read/28443826/rebinding-in-biochemical-reactions-on-membranes
#11
Sean D Lawley, James P Keener
The behavior of many biochemical processes depends crucially on molecules rapidly rebinding after dissociating. In the case of multisite protein modification, the importance of rebinding has been demonstrated both experimentally and through several recent computational studies involving stochastic spatial simulations. As rebinding stems from spatio-temporal correlations, theorists have resorted to models that explicitly include space to properly account for the effects of rebinding. However, for reactions in three space dimensions it was recently shown that well-mixed ordinary differential equation (ODE) models can incorporate rebinding by adding connections to the reaction network...
July 28, 2017: Physical Biology
https://www.readbyqxmd.com/read/28350301/sub-cellular-mrna-localization-modulates-the-regulation-of-gene-expression-by-small-rnas-in-bacteria
#12
Hamid Teimouri, Elgin Korkmazhan, Joel Stavans, Erel Levine
Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that demonstrate that families of mRNAs show non-trivial sub-cellular distributions raise the question of how localization may affect the regulatory activity of sRNAs. Here we address this question within a simple mathematical model. We show that the non-uniform spatial distributions of mRNA can alter the threshold-linear response that characterizes sRNAs that act stoichiometrically, and modulate the hierarchy among targets co-regulated by the same sRNA...
July 28, 2017: Physical Biology
https://www.readbyqxmd.com/read/28656904/mapping-quorum-sensing-onto-neural-networks-to-understand-collective-decision-making-in-heterogeneous-microbial-communities
#13
Tahir I Yusufaly, James Q Boedicker
Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. AI molecules bind to 'cognate' receptors, but also to 'non-cognate' receptors found in other strains, resulting in inter-strain crosstalk...
July 19, 2017: Physical Biology
https://www.readbyqxmd.com/read/28649977/convection-shapes-the-trade-off-between-antibiotic-efficacy-and-the-selection-for-resistance-in-spatial-gradients
#14
Matti Gralka, Diana Fusco, Stephen Martis, Oskar Hallatschek
Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for mutant types that survive the drug attack. A crucial question therefore is how one could eradicate as many cells as possible for a given acceptable risk of drug resistance evolution. We address this general question in a model of drug resistance evolution in spatial drug gradients, which recent experiments and theories have suggested as key drivers of drug resistance...
July 19, 2017: Physical Biology
https://www.readbyqxmd.com/read/28639563/the-role-of-apical-contractility-in-determining-cell-morphology-in-multilayered-epithelial-sheets-and-tubes
#15
Rui Zhen Tan, Tanny Lai, K-H Chiam
A multilayered epithelium is made up of individual cells that are stratified in an orderly fashion, layer by layer. In such tissues, individual cells can adopt a wide range of shapes ranging from columnar to squamous. From histological images, we observe that, in flat epithelia such as the skin, the cells in the top layer are squamous while those in the middle and bottom layers are columnar, whereas in tubular epithelia, the cells in all layers are columnar. We develop a computational model to understand how individual cell shape is governed by the mechanical forces within multilayered flat and curved epithelia...
July 19, 2017: Physical Biology
https://www.readbyqxmd.com/read/28510539/statistical-physics-approaches-to-subnetwork-dynamics-in-biochemical-systems
#16
B Bravi, P Sollich
We apply a Gaussian variational approximation to model reduction in large biochemical networks of unary and binary reactions. We focus on a small subset of variables (subnetwork) of interest, e.g. because they are accessible experimentally, embedded in a larger network (bulk). The key goal is to write dynamical equations reduced to the subnetwork but still retaining the effects of the bulk. As a result, the subnetwork-reduced dynamics contains a memory term and an extrinsic noise term with non-trivial temporal correlations...
July 19, 2017: Physical Biology
https://www.readbyqxmd.com/read/28661893/exact-lower-and-upper-bounds-on-stationary-moments-in-stochastic-biochemical-systems
#17
Khem Raj Ghusinga, Cesar A Vargas-Garcia, Andrew Lamperski, Abhyudai Singh
In the stochastic description of biochemical reaction systems, the time evolution of statistical moments for species population counts is described by a linear dynamical system. However, except for some ideal cases (such as zero- and first-order reaction kinetics), the moment dynamics is underdetermined as lower-order moments depend upon higher-order moments. Here, we propose a novel method to find exact lower and upper bounds on stationary moments for a given arbitrary system of biochemical reactions. The method exploits the fact that statistical moments of any positive-valued random variable must satisfy some constraints that are compactly represented through the positive semidefiniteness of moment matrices...
June 29, 2017: Physical Biology
https://www.readbyqxmd.com/read/28597848/effects-of-soft-interactions-and-bound-mobility-on-diffusion-in-crowded-environments-a-model-of-sticky-and-slippery-obstacles
#18
Michael W Stefferson, Samantha L Norris, Franck J Vernerey, Meredith D Betterton, Loren E Hough
Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While previous theoretical studies of particle diffusion have typically assumed either impenetrable obstacles or binding interactions that immobilize the particle, in many cellular contexts bound particles remain mobile. Examples include membrane proteins or lipids with some entry and diffusion within lipid domains and proteins that can enter into membraneless organelles or compartments such as the nucleolus...
June 29, 2017: Physical Biology
https://www.readbyqxmd.com/read/28597843/dynamical-predictors-of-an-imminent-phenotypic-switch-in-bacteria
#19
Huijing Wang, J Christian J Ray
Single cells can stochastically switch across thresholds imposed by regulatory networks. Such thresholds can act as a tipping point, drastically changing global phenotypic states. In ecology and economics, imminent transitions across such tipping points can be predicted using dynamical early warning indicators. A typical example is 'flickering' of a fast variable, predicting a longer-lasting switch from a low to a high state or vice versa. Considering the different timescales between metabolite and protein fluctuations in bacteria, we hypothesized that metabolic early warning indicators predict imminent transitions across a network threshold caused by enzyme saturation...
June 29, 2017: Physical Biology
https://www.readbyqxmd.com/read/28585521/structural-evaluation-of-an-amyloid-fibril-model-using-small-angle-x-ray-scattering
#20
Eshan Dahal, Mina Choi, Nadia Alam, Ashwinkumar A Bhirde, Serge L Beaucage, Aldo Badano
Amyloid fibrils are highly structured protein aggregates associated with a wide range of diseases including Alzheimer's and Parkinson's. We report a structural investigation of an amyloid fibril model prepared from a commonly used plasma protein (bovine serum albumin (BSA)) using small-angle x-ray scattering (SAXS) technique. As a reference, the size estimates from SAXS are compared to dynamic light scattering (DLS) data and the presence of amyloid-like fibrils is confirmed using Congo red absorbance assay...
June 29, 2017: Physical Biology
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