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Physical Biology

Anwesha Sarkar, Yuanchang Zhao, Yongliang Wang, Xuefeng Wang
Integrin-transmitted cellular forces are crucial mechanical signals regulating a vast range of cell functions. Although various methods have been developed to visualize and quantify cellular forces at the cell-matrix interface, a method with high performance and low technical barrier is still in demand. Here we developed force-activatable coating (FAC) which can be simply coated on regular cell culture apparatus's surfaces by physical adsorption, and turn these surfaces to force reporting platforms that enable cellular force mapping directly by fluorescence imaging...
May 22, 2018: Physical Biology
Marta Marty-Roda, Oda Dahlen, Titus Sebastiaan van Erp, Santiago Cuesta-López
Although previously developed mesoscopic DNA models have successfully
 reproduced thermodynamic denaturation data, recent studies show that these
 overestimate the rate of denaturation by orders of magnitude. Using adapted PeyrardBishop-Dauxois (PBD) models, we calculated the denaturation rates of several DNA
 hairpins and made comparison with experimental data. We show that the addition of
 a barrier at the onsite potential of the PBD model gives a more accurate description
 of the unzipping dynamics of short DNA sequences...
May 18, 2018: Physical Biology
Mohammad Tehrani, Zahra Ghalamzan, Alireza Sarvestani
The classical theory of polymer elasticity is built upon the assumption of network monodispersity, the premise that polymer networks are comprised from sub-chains of equal length. The crosslinking of biopolymers, however, is a random process and the resultant networks are likely to be polydisperse. The effect of structural polydispersity on mechanical behavior of biopolymer networks is not well understood. The purpose of this contribution is to show how network polydispersity controls the mechanical behavior and ultimate properties of crosslinked semi-flexible filaments at finite deformations...
May 17, 2018: Physical Biology
Hong-Yan Shih, Harry Mickalide, David T Fraebel, Nigel D Goldenfeld, Seppe Kuehn
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in populations from microbes to higher animals. Phenotypic fluctuations can provide a basis for adaptation and be the target of selection. Here we present a theoretical and experimental investigation of the fate of phenotypic fluctuations in directed evolution experiments where phenotypes are subject to constraints...
May 15, 2018: Physical Biology
Shiliang Feng, Lvwen Zhou, ShouQin Lü, Yan Zhang
Directed movement of eukaryotic cells toward spatiotemporally varied chemotactic stimuli enables rapid intracellular signaling responses. While macroscopic cellular manifestation is shaped by balancing external stimuli strength with finite internal delays, the organizing principles of the underlying molecular mechanisms remain to be clarified. Here, we developed a novel modeling framework based on a simple seesaw mechanism to elucidate how cells repeatedly reverse polarity. As a key feature of the modeling, the bottom module of bidirectional molecular transport is successively controlled by three upstream modules of signal reception, initial signal processing, and Rho GTPase regulation...
May 14, 2018: Physical Biology
Benedikt von Bronk, Alexandra Götz, Madeleine Opitz
Complex biological systems offer a variety of interesting phenomena at the different physical scales. With increasing abstraction, details of the microscopic scales can often be extrapolated to average or typical macroscopic properties. However, emergent properties and cross-scale interactions can impede naïve abstractions and necessitate comprehensive investigations of these complex systems.
 In this review paper, we focus on microbial communities, and first, summarize a general hierarchy of relevant scales and description levels to understand these complex systems: (1) genetic networks, (2) single cells, (3) populations, and (4) emergent multi-cellular properties...
May 14, 2018: Physical Biology
Ankur Kulkarni, Aritra Chatterjee, Paturu Kondaiah, Namrata Gundiah
Mechanical properties of cells regulate cell behaviors which lead to phenotypic changes that may aid in the development and progression of disease. In this study, we used atomic force microscopy (AFM) indentation with a spherical probe to characterize the elastic and viscoelastic properties of invasive (MDA-MB-231) and noninvasive (MCF-7) breast cancer cells treated with transforming growth factor-β (TGF-β). We also used confocal fluorescence imaging to investigate the sub-membrane cytoskeletal structure of the cells...
May 10, 2018: Physical Biology
Ramakanth Neeli-Venkata, Samuel Oliveira, Leonardo Martins, Sofia Startceva, Mohamed Bahrudeen, Jose Manuel Fonseca, Marco Minoia, Andre Sanches Ribeiro
Cell division in Escherichia coli is morphologically symmetric due to, among other, these cells' ability to place the Z-ring at midcell. Studies have reported that, at sub-optimal temperatures, this symmetry decreases at the single-cell level, but the causes remain unclear. Using fluorescence microscopy, we observe FtsZ-GFP and DAPI-stained nucleoids to assess the robustness of the symmetry of Z-ring formation and positioning in individual cells under sub-optimal and critical temperatures. We find the Z-ring formation and positioning to be robust at sub-optimal temperatures, as the Z-ring's mean width, density and displacement from midcell maintain similar levels of correlation to one another as in optimal temperatures...
May 2, 2018: Physical Biology
Nicholas Brunk, Lye Siang Lee, James A Glazier, William D Butske, Adam Zlotnick
Virus capsids are polymeric protein shells that protect the viral cargo. About half of known virus families have icosahedral capsids that self-assemble from tens to thousands of subunits. Capsid disassembly is critical to the lifecycles of many viruses yet is poorly understood. Here, we apply a graph and percolation theory to examine the effect of removing capsid subunits on capsid stability and fragmentation. Based on the structure of the icosahedral capsid of Hepatitis B Virus (HBV), we constructed a graph of rhombic subunits arranged with icosahedral symmetry...
May 1, 2018: Physical Biology
Ramon Grima, Sebastian Sonntag, Filippo Venezia, Stefan Kircher, Robert W Smith, Christian Fleck
Spatial relocalization of proteins is crucial for the correct functioning of living cells. An interesting example of spatial ordering is the light-induced clustering of plant photoreceptor proteins. Upon irradiation by white or red light, the red light-active phytochrome, phytochrome B, enters the nucleus and accumulates in large nuclear bodies. The underlying physical process of nuclear body formation remains unclear, but phytochrome B is thought to coagulate via a simple protein-protein binding process. We measure, for the first time, the distribution of the number of phytochrome B-containing nuclear bodies as well as their volume distribution...
May 1, 2018: Physical Biology
Pooja Sharma, Parth Pratim Pandey, Sanjay Jain
Escherichia coli cells differentially regulate the production of metabolic and ribosomal proteins
 in order to stay close to an optimal growth rate in different environments, and exhibit the bacterial growth
 laws as a consequence. We present a simple mathematical model of a growing-dividing cell in which an
 internal dynamical mechanism regulates the allocation of proteomic resources between different protein sectors.
 The model allows an endogenous determination of the growth rate of the cell as a function of cellular and
 environmental parameters, and reproduces the bacterial growth laws...
April 16, 2018: Physical Biology
Amit Pathak
Motile cells sense the stiffness of their extracellular matrix (ECM) through adhesions and respond by modulating the generated forces, which in turn lead to varying mechanosensitive migration phenotypes. Through modeling and experiments, cell migration speed is known to vary with matrix stiffness in a biphasic manner, with optimal motility at an intermediate stiffness. Here, we present a two-dimensional cell model defined by nodes and elements, integrated with subcellular modeling components corresponding to mechanotransductive adhesion formation, force generation, protrusions and node displacement...
April 12, 2018: Physical Biology
Renu Maan, Garima Rani, Gautam I Menon, Pramod A Pullarkat
Changes in cell-substrate adhesion are believed to signal the onset of
 cancer metastasis, but such changes must be quantified against background levels of
 intrinsic heterogeneity between cells. Intrinsic variations in cell-substrate adhesion
 strengths can be probed through biophysical measurements of cell detachment from
 substrates upon the application of an external force. Here, we investigate, theoretically
 and experimentally, the detachment of cells adhered to substrates when these cells are
 subjected to the fluid shear...
April 9, 2018: Physical Biology
Alireza Sayyidmousavi, Katrin Rohlf
In the present study, an off-lattice particle-based method called the Reactive Multi-Particle Collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics...
April 6, 2018: Physical Biology
Nicolás Eduardo Muzzio, Marcos Carballido, Miguel Pasquale, Pedro Horacio González, Omar Azzaroni, Alejandro Jorge Arvia
The epidermal growth factor (EGF) plays a key role in physiological and pathological processes. This work reports on the influence of EGF concentration (<i>c</i><sub>EGF</sub>) on the modulation of individual cell phenotype and cell colony kinetics with the aim of perturbing the colony front roughness fluctuations. For this purpose, HeLa cell colonies that remain confluent along the whole expansion process with initial quasi-radial geometry and different initial cell populations, as well as colonies with initial quasi-linear geometry and large cell population, are employed...
April 6, 2018: Physical Biology
Lisa Weber, William Raymond, Brian Munsky
In quantitative analyses of biological processes, one may use many different scales of models (e.g., spatial or non-spatial, deterministic or stochastic, time-varying or at steady-state) or many different approaches to match models to experimental data (e.g., model fitting or parameter uncertainty/sloppiness quantification with different experiment designs). These different analyses can lead to surprisingly different results, even when applied to the same data and the same model. We use a simplified gene regulation model to illustrate many of these concerns, especially for ODE analyses of deterministic processes, chemical master equation and finite state projection analyses of heterogeneous processes, and stochastic simulations...
April 6, 2018: Physical Biology
Gregory Javens, Hossein Jashnsaz, Steve Pressé
Sharp chemoattractant (CA) gradient variations near food sources may give rise to dramatic behavioral changes of bacteria neighboring these sources. For instance, marine bacteria exhibiting <i>run-reverse</i> motility are known to form distinct bands around patches (large sources) of chemoattractant such as nutrient-soaked beads while <i>run-and-tumble</i> bacteria have been predicted to exhibit a "volcano effect" (spherical shell-shaped density) around a small (point) source of food...
April 4, 2018: Physical Biology
Pavel Brodskiy, Jeremiah Zartman
Decoding how tissue properties emerge across multiple spatial and temporal scales from the integration of local signals is a grand challenge in quantitative biology. For example, the collective behavior of epithelial cells is critical for shaping developing embryos. Understanding how epithelial cells interpret a diverse range of local signals to coordinate tissue-level processes requires a systems-level understanding of development. Integration of multiple signaling pathways that specify cell signaling information requires second messengers such as calcium ions...
April 3, 2018: Physical Biology
Yuval Mulla, Anders Aufderhorst-Roberts, Gijsje Koenderink
How do the cells in our body reconfigure their shape to achieve complex tasks like migration and mitosis, yet maintain their shape in response to the forces exerted by for instance blood flow and muscle action? Cell shape control is defined by a delicate mechanical balance between active force generation and passive material properties of the plasma membrane and the cytoskeleton. The cytoskeleton forms a space-spanning fibrous network comprising three subsystems; actin, microtubules and intermediate filaments...
March 23, 2018: Physical Biology
Hyuntae Na, Guang Song
Increasingly more and larger structural complexes are being determined 
 experimentally. The sizes of these systems pose a formidable computational challenge 
 to the study of their vibrational dynamics by normal mode analysis. To overcome this challenge, this work presents a novel resonance-inspired approach. Tests on large shell structures 
 of protein capsids demonstrate there is a strong
 resonance between the vibrations of a whole capsid and those of individual capsomeres...
March 20, 2018: Physical Biology
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