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Physical Biology

Michael W Deem, Melia Elizabeth Bonomo
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology...
March 15, 2018: Physical Biology
Ivan Junier, Paul Frémont, Olivier Rivoire
In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes...
March 7, 2018: Physical Biology
Yuriy Ivanovich Glazachev, Darya Orlova, Petra Řezníčková, Eva Bártová
We proposed an effective kinetics scheme of photolysis of GFP observed in live cell with commercial confocal fluorescence microscope. At present work, we investigated GFP tagged heterochromatin protein, HP1β-GFP, and applied pulse position modulation approach, which has several advantages over classical pump-and-probe method. In the basis of proposed scheme is a process of photoswitching from native fluorescence state to intermediate fluorescence state, which has a lower fluorescence yield and recovers back in the dark...
March 1, 2018: Physical Biology
Ton Viet Ta, Linh Thi Hoai Nguyen
Constructing models for locating the source of food of living organizing has important implications for the understanding of animal behavior and for the development of distributed technologies. 
 This paper presents a novel simple model of stochastic differential equations (SDEs) for foraging behavior of fish schools in space including obstacles. The model is studied numerically. Three configurations of space with different locations of food resource are considered. In the first configuration, fish swim in free but limited space...
February 27, 2018: Physical Biology
Cole Zmurchok, Dhananjay Bhaskar, Leah Edelstein-Keshet
Regulators of the actin cytoskeleton such Rho GTPases can modulate forces developed in cells by promoting actomyosin contraction. At the same time, through mechanosensing, tension is known to affect the activity of Rho GTPases. What happens when these effects act in concert? Using a minimal model (1 GTPase coupled to a Kelvin-Voigt element), we show that two-way feedback between signaling ("RhoA") and mechanical tension (stretching) leads to a spectrum of cell behaviors, including contracted or relaxed cells, and cells that oscillate between these extremes...
February 23, 2018: Physical Biology
Nash Delta Rochman, Dan M Popescu, Sean Sun
Many single-cell observables are highly heterogeneous. A part of this heterogeneity stems from
 age-related phenomena: the fact that there is a nonuniform distribution of cells with different ages.
 This has led to a renewed interest in analytic methodologies including use of the "von Foerster
 equation" for predicting population growth and cell age distributions. Here we discuss how some of
 the most popular implementations of this machinery assume a strong condition on the ergodicity of
 the cell cycle duration ensemble...
February 20, 2018: Physical Biology
Brian M Kobylkevich, Anyesha Sarkar, Brady R Carlberg, Ling Huang, Suman Ranjit, David M Graham, Mark A Messerli
Weak external electric fields (EFs) polarize cellular structure and direct most migrating cells (galvanotaxis) toward the cathode, making it a useful tool during tissue engineering and healing of epidermal wounds. However, the biophysical mechanisms for sensing weak EFs remain elusive. We have reinvestigated the mechanism of cathode-directed water flow (electro-osmosis) in the boundary layer of cells, by reducing it with neutral, viscous polymers. We report that increasing viscosity with low molecular weight polymers decreases cathodal migration and promotes anodal migration in a concentration dependent manner...
February 7, 2018: Physical Biology
Valeria Hernandez, Rafael A Barrio, Mariana Benítez, Naomi Nakayama, José Roberto Romero-Arias, Carlos Villarreal Lujan
Intracellular polarisation of auxin efflux carriers is crucial for understanding how auxin gradients form in plants. The polarisation dynamics of auxin efflux carriers PIN-FORMED (PIN) depends on both biomechanical forces as well as chemical, molecular and genetic factors. Biomechanical forces have shown to affect the localisation of PIN transporters to the plasma membrane. We propose a physico-genetic module of PIN polarisation that integrates biomechanical, molecular, and cellular processes as well as their non-linear interactions...
February 2, 2018: Physical Biology
Ranjit Ranbhor, Anil Kumar, Kirti Patel, Vibin Ramakrishnan, Susheel Durani
Diversification of chain stereochemistry opens up the possibilities of 'in principle' increase in the design space of proteins. This huge increase in the sequence and consequent structural variation is aimed at the generation of smart materials of biological origin. For diversifying protein structure stereochemically, we introduced L- and D--amino acids as the design alphabet. With an inverse design algorithm, we now explore the usage of specific variables such as stereochemistry and sequence of this alphabet in independent steps...
February 2, 2018: Physical Biology
Alejandro Jose Fendrik, Lilia Romanelli, Ernesto Rotondo
The self renewal process in colonic crypts is the object of several studies. We present here a new compartment model with the following characteristics: a) We distinguish different classes of cells: stem cells, 6 generations of transit amplifying cells and the differentiated cells. b) In order to take into account the monoclonal character of the crypts in homeostatic regime we include symmetric divisions of the stem cells. We first consider the dynamic differential equations that describe the evolution of the mean values of the populations but the small observed value of the total number of cells involved plus the huge dispersion of experimental data found in the literature leads us to study the stochastic discrete process...
January 30, 2018: Physical Biology
Quentin Marcou, Irit Carmi-Levy, Coline Trichot, Vassili Soumelis, Thierry Mora, Aleksandra Walczak
Cells of the immune system are confronted with opposing pro- and anti- inflammatory signals. Dendritic cells (DC) integrate these cues to make informed decisions whether to initiate an immune response. Confronted with exogenous microbial stimuli, DC endogenously produce both anti- (IL-10) and pro-inflammatory (TNFα) cues whose joint integration controls the cell's final decision. Backed by experimental measurements we present a theoretical model to quantitatively describe the integration mode of these opposing signals...
January 23, 2018: Physical Biology
Paul C Bressloff, Hyunjoong Kim
Morphogen protein gradients play an important role in the spatial regulation of patterning during embryonic development. The most commonly accepted mechanism for gradient formation is diffusion from a source combined with degradation. Recently, there has been growing interest in an alternative mechanism, which is based on the direct delivery of morphogens along thin, actin-rich cellular extensions known as cytonemes. In this paper, we develop a bidirectional motor transport model for the flux of morphogens along cytonemes, linking a source cell to a one-dimensional array of target cells...
January 9, 2018: Physical Biology
Yasemin Bozkurt Varolgunes, Alper Demir
It is widely believed that the interactions of proteins with ligands and other proteins are determined by their dynamic characteristics as opposed to only static, time-invariant processes. We propose a novel computational technique, called ProteinAC (PAC), that can be used to analyze small scale functional protein motions as well as interactions with ligands directly in the frequency domain. PAC was inspired by a frequency domain analysis technique that is widely used in electronic circuit design, and can be applied to both coarse-grained and all-atom models...
January 25, 2018: Physical Biology
Nadia S M Goncalves, Sofia Startceva, Cristina S D Palma, Mohamed N M Bahrudeen, Samuel M D Oliveira, Andre S Ribeiro
From in vivo single-cell, single-RNA measurements of the activation times and subsequent steady-state active transcription kinetics of a single-copy Lac-ara-1 promoter in Escherichia coli, we characterize the intake kinetics of the inducer (IPTG) from the media, following temperature shifts. For this, for temperature shifts of various degrees, we obtain the distributions of transcription activation times as well as the distributions of intervals between consecutive RNA productions following activation in individual cells...
January 24, 2018: Physical Biology
Yunsong Zhang, Jingchen Feng, Shay I Heizler, Herbert Levine
How cells move through the three-dimensional extracellular matrix (ECM) is of increasing interest in attempts to understand important biological processes such as cancer metastasis. Just as in motion on flat surfaces, it is expected that experimental measurements of cell-generated forces will provide valuable information for uncovering the mechanisms of cell migration. However, the recovery of forces in fibrous biopolymer networks may suffer from large errors. Here, within the framework of lattice-based models, we explore possible issues in force recovery by solving the inverse problem: how can one determine the forces cells exert to their surroundings from the deformation of the ECM? Our results indicate that irregular cell traction patterns, the uncertainty of local fiber stiffness, the non-affine nature of ECM deformations and inadequate knowledge of network topology will all prevent the precise force determination...
January 11, 2018: Physical Biology
Monique Tirion, Daniel Ben-Avraham
We have extended our analytically derived PDB-NMA formulation, Atomic Torsional Modal Analysis or ATMAN \cite{tirion14}, to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3\AA~resolution model of a small homodimer, ActVA-ORF6, consisting of two 112-residue subunits identically folded in a compact 50\AA~sphere, reproduces the distinct experimental Debye-Waller motility asymmetry for the two chains, demonstrating that structure sensitively selects vibrational signatures...
December 18, 2017: Physical Biology
Dandan Chen, Lei Yang, Xinjian Chen, Xihui Zhang, Yongming Liu, Zhengqing Guo, Leshuai W Zhang
The morphology of 2D cell colonies has been studied to understand tumor metastasis in the past decades. However, 2D cell cultures are lack of many features of 3D tissues, and their physiological behaviors are quite different from solid tumors in vivo. In this work, we studied the multi-cellular tumor spheroid (MCTS) spreading on the substrate, which keeps parts of 3D tissue characteristics and facilitates cell tracking through 2D imaging. By using high content imaging system (HCS), we tracked multiple spheroids in one single 96-well plate for 36h...
December 18, 2017: Physical Biology
Sai Teja Pusuluri, Alex H Lang, Pankaj Mehta, Horacio E Castillo
Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple 1D reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used...
December 6, 2017: Physical Biology
Bozhi Tian, John A Rogers, Peidong Yang, Zhenan Bao, Nicholas A Melosh, Alon Gorodetsky, Timothy Lu, Polina Anikeeva, Michal Cifra, Stefano Cestellos-Blanco, Joao Carvalho-de-Souza, Francisco Bezanilla, Jia Liu, Martin Hjort, Yuhong Cao, Guglielmo Lanzani, Fabio Benfenati, Giulia Galli, Francois Gygi, Rylan Kautz, Samuel Sungil Kim, Ondrej Krivosudský, Daniel Havelka, Yuanwen Jiang, Shuai Xu
This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world...
December 5, 2017: Physical Biology
Kiyoshi Mizuuchi, Anthony G Vecchiarelli
The MinD and MinE proteins of Escherichia coli self-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, MinD and MinE form a spectrum of patterns on artificial bilayers - static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics recapitulate many features of Min oscillation observed in vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane...
November 30, 2017: Physical Biology
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