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Biological motion

Samuel Lenton, Marco Grimaldo, Felix Roosen-Runge, Frank Schreiber, Tommy Nylander, Roger Clegg, Carl Holt, Michael Härtlein, Victoria García Sakai, Tilo Seydel, Susana C Marujo Teixeira
The last decade established that the dynamic properties of the phosphoproteome are central to function and its modulation. The temporal dimension of phosphorylation effects remains nonetheless poorly understood, particularly for intrinsically disordered proteins. Osteopontin, selected for this study due to its key role in biomineralization, is expressed in many species and tissues to play a range of distinct roles. A notable property of highly phosphorylated isoforms of osteopontin is their ability to sequester nanoclusters of calcium phosphate to form a core-shell structure, in a fluid that is supersaturated but stable...
April 25, 2017: Biophysical Journal
Binbin Luo, John W Smith, Zihao Ou, Qian Chen
For decades, one of the overarching objectives of self-assembly science has been to define the rules necessary to build functional, artificial materials with rich and adaptive phase behavior from the bottom-up. To this end, the computational and experimental efforts of chemists, physicists, materials scientists, and biologists alike have built a body of knowledge that spans both disciplines and length scales. Indeed, today control of self-assembly is extending even to supramolecular and molecular levels, where crystal engineering and design of porous materials are becoming exciting areas of exploration...
April 26, 2017: Accounts of Chemical Research
Serim Ilday, Ghaith Makey, Gursoy B Akguc, Özgün Yavuz, Onur Tokel, Ihor Pavlov, Oguz Gülseren, F Ömer Ilday
A profoundly fundamental question at the interface between physics and biology remains open: what are the minimum requirements for emergence of complex behaviour from nonliving systems? Here, we address this question and report complex behaviour of tens to thousands of colloidal nanoparticles in a system designed to be as plain as possible: the system is driven far from equilibrium by ultrafast laser pulses that create spatiotemporal temperature gradients, inducing Marangoni flow that drags particles towards aggregation; strong Brownian motion, used as source of fluctuations, opposes aggregation...
April 26, 2017: Nature Communications
Alexander Pastukhov
Our visual system combines sensory evidence with prior knowledge to produce a representation of an outside world. Here, we explored the limits of the feedforward computation using an ambiguously rotating human biological motion. Specifically, we investigated whether an overall rotation, which was added to all the displays used in the study, would be perceived when the point-light walker was presented upside-down, a condition that typically obliterates perception of a human Gestalt. We report that inversion of the point-light walker or the absence of an identifiable Gestalt abolished the perception of an overall rotation...
April 25, 2017: Scientific Reports
Aifeng Ren, Zhenxing Du, Juan Li, Fangming Hu, Xiaodong Yang, Haider Abbas
As an important biological signal, electrocardiogram (ECG) signals provide a valuable basis for the clinical diagnosis and treatment of several diseases. However, its reference significance is based on the effective acquisition and correct recognition of ECG signals. In fact, this mV-level weak signal can be easily affected by various interferences caused by the power of magnetic field, patient respiratory motion or contraction, and so on from the sampling terminal to the receiving and display end. The overlapping interference affects the quality of ECG waveform, leading to the false detection and recognition of wave groups, and thus causing misdiagnosis or faulty treatment...
April 25, 2017: Sensors
Qing Zhe Ni, Evgeny Markhasin, Thach V Can, Björn Corzilius, Kong O Tan, Alexander B Barnes, Eugenio Daviso, Yongchao Su, Judith Herzfeld, Robert G Griffin
In DNP MAS NMR experiments at ~80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H decoupling. Here we investigate the effect of these dynamic processes on the NMR lineshapes and signal intensities in several typical systems: (1) microcrystalline APG, (2) membrane protein bR, (3) amyloid fibrils PI3-SH3, (4) monomeric alanine-CD3 and (5) the pro-tonated and deuterated dipeptide N-Ac-VL over 78-300 K...
April 24, 2017: Journal of Physical Chemistry. B
Sebastien C Wong, Victor Stamatescu, Adam Gatt, David Kearney, Ivan Lee, Mark D McDonnell
This paper addresses the problem of online tracking and classification of multiple objects in an image sequence. Our proposed solution is to first track all objects in the scene without relying on object-specific prior knowledge, which in other systems can take the form of hand-crafted features or user-based track initialization. We then classify the tracked objects with a fastlearning image classifier that is based on a shallow convolutional neural network architecture and demonstrate that object recognition improves when this is combined with object state information from the tracking algorithm...
April 24, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Eugene Kim, Martin D Baaske, Isabel Schuldes, Peter S Wilsch, Frank Vollmer
Monitoring the kinetics and conformational dynamics of single enzymes is crucial to better understand their biological functions because these motions and structural dynamics are usually unsynchronized among the molecules. However, detecting the enzyme-reactant interactions and associated conformational changes of the enzyme on a single-molecule basis remains as a challenge to established optical techniques because of the commonly required labeling of the reactants or the enzyme itself. The labeling process is usually nontrivial, and the labels themselves might skew the physical properties of the enzyme...
March 2017: Science Advances
Matthew J Langton, Flore Keymeulen, Maria Ciaccia, Nicholas H Williams, Christopher A Hunter
Transmission and amplification of chemical signals across lipid bilayer membranes is of profound significance in many biological processes, from the development of multicellular organisms to information processing in the nervous system. In biology, membrane-spanning proteins are responsible for the transmission of chemical signals across membranes, and signal transduction is often associated with an amplified signalling cascade. The ability to reproduce such processes in artificial systems has potential applications in sensing, controlled drug delivery and communication between compartments in tissue-like constructs of synthetic vesicles...
May 2017: Nature Chemistry
Sneha Paul, Tasnim Ahmed, Anunay Samanta
Dynamics in DNA to which water, counterions and DNA motions contribute is a topic of considerable interest as it is closely related to the efficiency of biological functions performed by it. Simulation studies and experiments suggest that counterion dynamics in DNA probed by a minor groove binder is similar for various monovalent counterions. As the influence of higher valent counterions, which are also present around DNA and known to bind more strongly to it compared to the monovalent ions, on the dynamics in DNA has not been studied so far, we investigate in this work the dynamics in presence of Mg2+ and Ca2+, chosen for their relative abundance in the cell, using 4', 6-diamidino-2-phenylindole (DAPI), a minor groove-binder, as fluorescence probe...
April 18, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Elsen Tjhung, Michael E Cates, Davide Marenduzzo
Active fluids are a class of nonequilibrium systems where energy is injected into the system continuously by the constituent particles themselves. Many examples, such as bacterial suspensions and actomyosin networks, are intrinsically chiral at a local scale, so that their activity involves torque dipoles alongside the force dipoles usually considered. Although many aspects of active fluids have been studied, the effects of chirality on them are much less known. Here, we study by computer simulation the dynamics of an unstructured droplet of chiral active fluid in three dimensions...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
John Hartman, Brian Kirby
Nanoparticle tracking analysis, a multiprobe single particle tracking technique, is a widely used method to quickly determine the concentration and size distribution of colloidal particle suspensions. Many popular tools remove non-Brownian components of particle motion by subtracting the ensemble-average displacement at each time step, which is termed dedrifting. Though critical for accurate size measurements, dedrifting is shown here to introduce significant biasing error and can fundamentally limit the dynamic range of particle size that can be measured for dilute heterogeneous suspensions such as biological extracellular vesicles...
March 2017: Physical Review. E
C Charalambous, G Muñoz-Gil, A Celi, M F Garcia-Parajo, M Lewenstein, C Manzo, M A García-March
Spatiotemporal disorder has been recently associated to the occurrence of anomalous nonergodic diffusion of molecular components in biological systems, but the underlying microscopic mechanism is still unclear. We introduce a model in which a particle performs continuous Brownian motion with changes of diffusion coefficients induced by transient molecular interactions with diffusive binding partners. In spite of the exponential distribution of waiting times, the model shows subdiffusion and nonergodicity similar to the heavy-tailed continuous time random walk...
March 2017: Physical Review. E
Aboutaleb Amiri, Cameron Harvey, Amy Buchmann, Scott Christley, Joshua D Shrout, Igor S Aranson, Mark Alber
Swarming groups of bacteria coordinate their behavior by self-organizing as a population to move over surfaces in search of nutrients and optimal niches for colonization. Many open questions remain about the cues used by swarming bacteria to achieve this self-organization. While chemical cue signaling known as quorum sensing is well-described, swarming bacteria often act and coordinate on time scales that could not be achieved via these extracellular quorum sensing cues. Here, cell-cell contact-dependent protein exchange is explored as a mechanism of intercellular signaling for the bacterium Myxococcus xanthus...
March 2017: Physical Review. E
J Rydzewski, W Nowak
Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes...
April 1, 2017: Physics of Life Reviews
T Gopinath, Sarah E D Nelson, Kailey J Soller, Gianluigi Veglia
Proteins exist in ensembles of conformational states that interconvert on various motional time scales. High-energy states of proteins, often referred to as conformationally excited states, are sparsely populated and have been found to play an essential role in many biological functions. However, detecting these states is quite difficult for conventional structural techniques. Recent progress in solution NMR spectroscopy made it possible to detect conformationally excited states in soluble proteins and characterize them at high resolution...
April 20, 2017: Journal of Physical Chemistry. B
Martina Franchini, Hillary Wood de Wilde, Bronwyn Glaser, Edouard Gentaz, Stephan Eliez, Marie Schaer
[This corrects the article on p. 143 in vol. 7, PMID: 27605914.].
2017: Frontiers in Psychiatry
Kyogo Kawaguchi, Ryoichiro Kageyama, Masaki Sano
Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and macroscopic patterns resulting from cell-to-cell interactions remain largely qualitative. Here we report the collective motion of cultured neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system[1]. At low densities, NPCs moved in an amoeba-like fashion and with random motion...
April 12, 2017: Nature
Peng Cheng, Junhui Peng, Zhiyong Zhang
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well...
April 11, 2017: Biophysical Journal
Zachary Estlack, Devasier Bennet, Ted Reid, Jungkyu Kim
Current ophthalmological drug discovery and testing methods have limitations and concerns regarding reliability, ethicality, and applicability. These drawbacks can be mitigated by developing biomimetic eye models through mathematical and experimental methods which are often referred to as "eye-on-a-chip" or "eye chip". These eye chip technologies emulate ocular physiology, anatomy, and microenvironmental conditions. Such models enable understanding of the fundamental biology, pharmacology, and toxicology mechanisms by investigating the pharmacokinetics and pharmacodynamics of various candidate drugs under ocular anatomical and physiological conditions without animal models...
April 12, 2017: Lab on a Chip
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