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https://www.readbyqxmd.com/read/28328543/challenges-in-describing-ribosome-dynamics
#1
Kien Nguyen, Paul Charles Whitford
For decades, protein folding and functional dynamics have been described in terms of diffusive motion across an underlying energy landscape. With continued advances in structural biology and high-performance computing, the field is positioned to extend these approaches to large biomolecular assemblies. Through the application of energy landscape techniques to the ribosome, one may work towards establishing a comprehensive description of the dynamics, which will bridge theoretical concepts and experimental observations...
March 22, 2017: Physical Biology
https://www.readbyqxmd.com/read/28324865/biomaterials-for-intervertebral-disc-regeneration-and-repair
#2
REVIEW
Robert D Bowles, Lori A Setton
The intervertebral disc contributes to motion, weight bearing, and flexibility of the spine, but is susceptible to damage and morphological changes that contribute to pathology with age and injury. Engineering strategies that rely upon synthetic materials or composite implants that do not interface with the biological components of the disc have not met with widespread use or desirable outcomes in the treatment of intervertebral disc pathology. Here we review bioengineering advances to treat disc disorders, using cell-supplemented materials, or acellular, biologically based materials, that provide opportunity for cell-material interactions and remodeling in the treatment of intervertebral disc disorders...
March 15, 2017: Biomaterials
https://www.readbyqxmd.com/read/28321914/a-compact-0-5%C3%A2-t-mr-elastography-device-and-its-application-for-studying-viscoelasticity-changes-in-biological-tissues-during-progressive-formalin-fixation
#3
Jürgen Braun, Heiko Tzschätzsch, Clara Körting, Angela Ariza de Schellenberger, Marika Jenderka, Toni Drießle, Michael Ledwig, Ingolf Sack
PURPOSE: To develop a method of compact tabletop magnetic resonance elastography (MRE) for rheological tests of tissue samples and to measure changes in viscoelastic powerlaw constants of liver and brain tissue during progressive fixation. METHODS: A 10-mm bore, 0.5-T permanent-magnet-based MRI system was equipped with a gradient-amplifier-controlled piezo-actuator and motion-sensitive spin echo sequence for inducing and measuring harmonic shear vibrations in cylindrical samples...
March 20, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28317993/capturing-the-multiscale-dynamics-of-membrane-protein-complexes-with-all-atom-mixed-resolution-and-coarse-grained-models
#4
Chenyi Liao, Xiaochuan Zhao, Jiyuan Liu, Severin T Schneebeli, John C Shelley, Jianing Li
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28306551/master-equations-and-the-theory-of-stochastic-path-integrals
#5
Markus F Weber, Erwin Frey
This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations...
April 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28304019/probing-the-structure-and-in-silico-stability-of-cargo-loaded-dna-icosahedra-using-md-simulations
#6
Himanshu Joshi, Dhiraj Bhatia, Yamuna Krishnan, Prabal K Maiti
Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems...
March 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/28303197/heterogeneous-tempo-and-mode-of-evolutionary-diversification-of-compounds-in-lizard-chemical-signals
#7
Roberto García-Roa, Manuel Jara, Pilar López, José Martín, Daniel Pincheira-Donoso
Important part of the multivariate selection shaping social and interspecific interactions among and within animal species emerges from communication. Therefore, understanding the diversification of signals for animal communication is a central endeavor in evolutionary biology. Over the last decade, the rapid development of phylogenetic approaches has promoted a stream of studies investigating evolution of communication signals. However, comparative research has primarily focused on visual and acoustic signals, while the evolution of chemical signals remains largely unstudied...
February 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28302571/alpha-9-nicotinic-acetylcholine-receptors-mediate-hypothermic-responses-elicited-by-provocative-motion-in-mice
#8
Longlong Tu, Lauren Poppi, John Rudd, Ethan T Cresswell, Doug W Smith, Alan Brichta, Eugene Nalivaiko
Hypothermic responses accompany motion sickness in humans and can be elicited by provocative motion in rats. We aimed to determine the potential role in these responses of the efferent cholinergic vestibular innervation. To this end, we used knockout (KO) mice lacking α9 cholinoreceptor subunit predominantly expressed in the vestibular hair cells and CBA strain as a wild-type (WT) control. In WT mice, circular horizontal motion (1Hz, 4cm radius, 20min) caused rapid and dramatic falls in core body temperature and surface head temperature associated with a transient rise in the tail temperature; these responses were substantially attenuated in KO mice; changes were (WT vs...
March 14, 2017: Physiology & Behavior
https://www.readbyqxmd.com/read/28301074/high-throughput-inclusion-body-sizing-nano-particle-tracking-analysis
#9
Wieland N Reichelt, Andreas Kaineder, Markus Brillmann, Lukas Neutsch, Alexander Taschauer, Hans Lohninger, Christoph Herwig
The expression of pharmaceutical relevant proteins in E. coli frequently triggers inclusion body (IB) formation caused by protein aggregation. In literature, substantial effort has been invested into the quantification of IB size. But up to this date particle based methods to analyze physical IB properties of representative numbers of IBs lack sensitivity and/or lack orthogonal verification. Using high pressure freezing and automated freeze substitution for transmission electron microscopy (TEM) the cytosolic inclusion body structure was preserved within the cells...
March 16, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28299891/biohybrid-microtube-swimmers-driven-by-single-captured-bacteria
#10
Morgan M Stanton, Byung-Wook Park, Albert Miguel-López, Xing Ma, Metin Sitti, Samuel Sánchez
Bacteria biohybrids employ the motility and power of swimming bacteria to carry and maneuver microscale particles. They have the potential to perform microdrug and cargo delivery in vivo, but have been limited by poor design, reduced swimming capabilities, and impeded functionality. To address these challenge, motile Escherichia coli are captured inside electropolymerized microtubes, exhibiting the first report of a bacteria microswimmer that does not utilize a spherical particle chassis. Single bacterium becomes partially trapped within the tube and becomes a bioengine to push the microtube though biological media...
March 16, 2017: Small
https://www.readbyqxmd.com/read/28298006/nuclear-magnetic-resonance-diffusion-pore-imaging-experimental-phase-detection-by-double-diffusion-encoding
#11
Kerstin Demberg, Frederik Bernd Laun, Johannes Windschuh, Reiner Umathum, Peter Bachert, Tristan Anselm Kuder
Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of spin-bearing particles. Examples of such pores comprise cells in biological tissue or oil containing cavities in porous rocks. All pores contained in the measurement volume contribute to one reconstructed image, which reduces the problem of vanishing signal at increasing resolution present in conventional magnetic resonance imaging...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297979/brownian-motion-of-a-circle-swimmer-in-a-harmonic-trap
#12
Soudeh Jahanshahi, Hartmut Löwen, Borge Ten Hagen
We study the dynamics of a Brownian circle swimmer with a time-dependent self-propulsion velocity in an external temporally varying harmonic potential. For several situations, the noise-free swimming paths, the noise-averaged mean trajectories, and the mean-square displacements are calculated analytically or by computer simulation. Based on our results, we discuss optimal swimming strategies in order to explore a maximum spatial range around the trap center. In particular, we find a resonance situation for the maximum escape distance as a function of the various frequencies in the system...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297652/moving-in-the-right-direction-protein-vibrational-steering-function
#13
Katherine A Niessen, Mengyang Xu, Alessandro Paciaroni, Andrea Orecchini, Edward H Snell, Andrea G Markelz
Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28293182/visual-field-map-clusters-in-high-order-visual-processing-organization-of-v3a-v3b-and-a-new-cloverleaf-cluster-in-the-posterior-superior-temporal-sulcus
#14
Brian Barton, Alyssa A Brewer
The cortical hierarchy of the human visual system has been shown to be organized around retinal spatial coordinates throughout much of low- and mid-level visual processing. These regions contain visual field maps (VFMs) that each follows the organization of the retina, with neighboring aspects of the visual field processed in neighboring cortical locations. On a larger, macrostructural scale, groups of such sensory cortical field maps (CFMs) in both the visual and auditory systems are organized into roughly circular cloverleaf clusters...
2017: Frontiers in Integrative Neuroscience
https://www.readbyqxmd.com/read/28292904/optimal-run-and-tumble-based-transportation-of-a-janus-particle-with-active-steering
#15
Tomoyuki Mano, Jean-Baptiste Delfau, Junichiro Iwasawa, Masaki Sano
Although making artificial micrometric swimmers has been made possible by using various propulsion mechanisms, guiding their motion in the presence of thermal fluctuations still remains a great challenge. Such a task is essential in biological systems, which present a number of intriguing solutions that are robust against noisy environmental conditions as well as variability in individual genetic makeup. Using synthetic Janus particles driven by an electric field, we present a feedback-based particle-guiding method quite analogous to the "run-and-tumbling" behavior of Escherichia coli but with a deterministic steering in the tumbling phase: the particle is set to the run state when its orientation vector aligns with the target, whereas the transition to the "steering" state is triggered when it exceeds a tolerance angle [Formula: see text] The active and deterministic reorientation of the particle is achieved by a characteristic rotational motion that can be switched on and off by modulating the ac frequency of the electric field, which is reported in this work...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28290511/action-observation-activates-neurons-of-the-monkey-ventrolateral-prefrontal-cortex
#16
Luciano Simone, Marco Bimbi, Francesca Rodà, Leonardo Fogassi, Stefano Rozzi
Prefrontal cortex is crucial for exploiting contextual information for the planning and guidance of behavioral responses. Among contextual cues, those provided by others' behavior are particularly important, in primates, for selecting appropriate reactions and suppressing the inappropriate ones. These latter functions deeply rely on the ability to understand others' actions. However, it is largely unknown whether prefrontal neurons are activated by action observation. To address this issue, we recorded the activity of ventrolateral prefrontal (VLPF) neurons of macaque monkeys during the observation of videos depicting biological movements performed by a monkey or a human agent, and object motion...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28286893/rearrangement-of-vinyl-allene-oxide-geometric-isomers-to-cyclopentenones-further-computational-insights-with-biologically-relevant-model-systems
#17
Adán B González-Pérez, Alexander Grechkin, Ángel R de Lera
Pathways for the rearrangement of the E and Z isomers of allyl- and methyl-substituted vinyl allene oxides to stereodefined cyclopentenones have been studied by DFT computations. Regardless of the reactant geometry, cis-configured cyclopentenones are found to be formed in a stepwise cascade comprising as key steps the ring opening of the oxirane to give an oxidopentadienyl diradical, its isomerization, and electrocyclization. An allyl substituent at the Csp(3) atom of the starting vinyl allene oxide induces opposite effects on the activation energies for ring opening: a decrease owing to assistance by homoconjugation for the out motion and an increase due to the stereoelectronic stabilization of the reactant...
March 13, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28285029/biological-motion-processing-in-schizophrenia-systematic-review-and-meta-analysis
#18
Łukasz Okruszek, Izabela Pilecka
CONTEXT: Patients with schizophrenia show impairments in processing of biological motion. This is especially important since deficits in domains of social cognition has been associated with functional outcome and everyday functioning in this population. OBJECTIVES: We conducted a systematic review and meta-analysis of studies which have used point-light displays to present whole-body motion to patients with schizophrenia and healthy controls, to evaluate the magnitude of differences between these groups in biological motion processing...
March 9, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28282194/electron-dynamics-upon-ionization-of-polyatomic-molecules-coupling-to-quantum-nuclear-motion-and-decoherence
#19
Morgane Vacher, Michael J Bearpark, Michael A Robb, João Pedro Malhado
Knowledge about the electronic motion in molecules is essential for our understanding of chemical reactions and biological processes. The advent of attosecond techniques opens up the possibility to induce electronic motion, observe it in real time, and potentially steer it. A fundamental question remains the factors influencing electronic decoherence and the role played by nuclear motion in this process. Here, we simulate the dynamics upon ionization of the polyatomic molecules paraxylene and modified bismethylene-adamantane, with a quantum mechanical treatment of both electron and nuclear dynamics using the direct dynamics variational multiconfigurational Gaussian method...
February 24, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28282168/critical-fluctuations-in-the-native-state-of-proteins
#20
Qian-Yuan Tang, Yang-Yang Zhang, Jun Wang, Wei Wang, Dante R Chialvo
Based on protein structural ensembles determined by nuclear magnetic resonance, we study the position fluctuations of residues by calculating distance-dependent correlations and conducting finite-size scaling analysis. The fluctuations exhibit high susceptibility and long-range correlations up to the protein sizes. The scaling relations between the correlations or susceptibility and protein sizes resemble those in other physical and biological systems near their critical points. These results indicate that, at the native states, motions of each residue are felt by every other one in the protein...
February 24, 2017: Physical Review Letters
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