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https://www.readbyqxmd.com/read/28110274/c4-photosynthesis-50-years-of-discovery-and-innovation
#1
EDITORIAL
Susanne von Caemmerer, Oula Ghannoum, Robert T Furbank
It is now over half a century since the biochemical characterization of the C4 photosynthetic pathway, and this special issue highlights the sheer breadth of current knowledge. New genomic and transcriptomic information shows that multi-level regulation of gene expression is required for the pathway to function, yet we know it to be one of the most dynamic examples of convergent evolution. Now, a focus on the molecular transition from C3-C4 intermediates, together with improved mathematical models, experimental tools and transformation systems, holds great promise for improving C4 photosynthesis in crops...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110185/computational-analysis-of-amsacrine-resistance-in-human-topoisomerase-ii-alpha-mutants-r487k-and-e571k-using-homology-modeling-docking-and-all-atom-molecular-dynamics-simulation-in-explicit-solvent
#2
Safaa Sader, Chun Wu
Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28109815/a-novel-biocompatible-drug-delivery-system-of-chitosan-temozolomide-nanoparticles-loaded-pcl-pu-nanofibers-for-sustained-delivery-of-temozolomide
#3
Mohammad Irani, Gity Mir Mohamad Sadeghi, Ismaeil Haririan
In the present study, the anticancer drug temozolomide (TMZ) was initially loaded into the chitosan (CS) nanoparticles and synthesized CS/TMZ nanoparticles were incorporated into the synthesized poly (ε-caprolactone diol) based polyurethane (PCL-Diol-b-PU) nanofibers. The synthesized nanoparticles and nanofibers were characterized using dynamic light scattering, transmission electron microscopy, X-ray powder diffraction and scanning electron microscopy. The obtained results revealed that the CS/TMZ nanoparticles were successfully embedded into the PCL-Diol-b-PU nanofibers...
January 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28109305/medical-pluralism-and-livestock-health-ethnomedical-and-biomedical-veterinary-knowledge-among-east-african-agropastoralists
#4
Mark A Caudell, Marsha B Quinlan, Robert J Quinlan, Douglas R Call
BACKGROUND: Human and animal health are deeply intertwined in livestock dependent areas. Livestock health contributes to food security and can influence human health through the transmission of zoonotic diseases. In low-income countries diagnosis and treatment of livestock diseases is often carried out by household members who draw upon both ethnoveterinary medicine (EVM) and contemporary veterinary biomedicine (VB). Expertise in these knowledge bases, along with their coexistence, informs treatment and thus ultimately impacts animal and human health...
January 21, 2017: Journal of Ethnobiology and Ethnomedicine
https://www.readbyqxmd.com/read/28109249/parameter-estimation-in-large-scale-systems-biology-models-a-parallel-and-self-adaptive-cooperative-strategy
#5
David R Penas, Patricia González, Jose A Egea, Ramón Doallo, Julio R Banga
BACKGROUND: The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic models. Global optimization methods can be used to solve this type of problems but the associated computational cost is very large. Moreover, many of these methods need the tuning of a number of adjustable search parameters, requiring a number of initial exploratory runs and therefore further increasing the computation times...
January 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28109242/local-spin-dynamics-of-iron-oxide-magnetic-nanoparticles-dispersed-in-different-solvents-with-variable-size-and-shape-a-1-h-nmr-study
#6
M Basini, T Orlando, P Arosio, M F Casula, D Espa, S Murgia, C Sangregorio, C Innocenti, A Lascialfari
Colloidal magnetic nanoparticles (MNPs) based on a nearly monodisperse iron oxide core and capped by oleic acid have been used as model systems for investigating the superparamagnetic spin dynamics by means of magnetometry measurements and nuclear magnetic resonance ((1)H NMR) relaxometry. The key magnetic properties (saturation magnetization, coercive field, and frequency dependent "blocking" temperature) of MNPs with different core size (3.5 nm, 8.5 nm, and 17.5 nm), shape (spherical and cubic), and dispersant (hexane and water-based formulation) have been determined...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28109228/vibronic-eigenstates-and-the-geometric-phase-effect-in-the-2-e%C3%A2-state-of-no3
#7
Wolfgang Eisfeld, Alexandra Viel
The (2)E″ state of NO3, a prototype for the Jahn-Teller effect, has been an enigma and a challenge for a long time for both experiment and theory. We present a detailed theoretical study of the vibronic quantum dynamics in this electronic state, uncovering the effects of tunnelling, geometric phase, and symmetry. To this end, 45 vibronic levels of NO3 in the (2)E″ state are determined accurately and analyzed thoroughly. The computation is based on a high quality diabatic potential representation of the two-sheeted surface of the (2)E″ state developed by us [W...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28108450/netland-quantitative-modeling-and-visualization-of-waddington-s-epigenetic-landscape-using-probabilistic-potential
#8
Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng
: Waddington's epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks. Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington's landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of gene regulatory networks (GRNs), and visualizing the corresponding Waddington's epigenetic landscape in three dimensions without restriction on the number of genes in a GRN...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108306/bone-remodeling-as-a-spatial-evolutionary-game
#9
Marc D Ryser, Kevin A Murgas
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location in the bone. Several spatial extensions of these models have been proposed, but they generally suffer from two limitations: first, they are not amenable to analysis and are computationally expensive, and second, they neglect the role played by bone-embedded osteocytes. To address these issues, we developed a novel model of spatial remodeling based on the principles of evolutionary game theory...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28108173/broach-handle-design-changes-force-distribution-in-the-femur-during-total-hip-arthroplasty
#10
Dustin A Greenhill, Pooyan Abbasi, Kurosh Darvish, Andrew M Star
BACKGROUND: Curved broach handles were developed to overcome limited surgical exposures during total hip arthroplasty. Some authors report increased intraoperative fracture rates during limited exposures. This study evaluates mechanical force ratios transmitted to the bone while broaching with curved vs straight handles. METHODS: An experimental model utilized a 6-axis load cell to measure force distributions produced by 4 different broach handles, each with increasing offset and curvature...
December 29, 2016: Journal of Arthroplasty
https://www.readbyqxmd.com/read/28108002/reduced-order-model-based-active-disturbance-rejection-control-of-hydraulic-servo-system-with-singular-value-perturbation-theory
#11
Chengwen Wang, Long Quan, Shijie Zhang, Hongjun Meng, Yuan Lan
Hydraulic servomechanism is the typical mechanical/hydraulic double-dynamics coupling system with the high stiffness control and mismatched uncertainties input problems, which hinder direct applications of many advanced control approaches in the hydraulic servo fields. In this paper, by introducing the singular value perturbation theory, the original double-dynamics coupling model of the hydraulic servomechanism was reduced to a integral chain system. So that, the popular ADRC (active disturbance rejection control) technology could be directly applied to the reduced system...
January 17, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28107591/the-role-of-autonomic-dysfunction-in-predicting-one-year-mortality-after-liver-transplantation
#12
Kuang-Cheng Chan, Jia-Rong Yeh, Wei-Zen Sun
BACKGROUND & AIMS: Model for end-stage liver disease (MELD) score has been extensively used to prioritize patients for liver transplantation and determine their prognosis, but with limited predictive value. Autonomic dysfunction may correlate with increased mortality after liver transplant. In this study, two autonomic biomarkers, complexity and deceleration capacity, were added to the predicting model for one-year mortality after liver transplantation. METHODS: Thirty patients with end-stage liver diseases awaiting liver transplantation were included...
January 20, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28107510/effect-of-the-crystal-environment-on-side-chain-conformational-dynamics-in-cyanovirin-n-investigated-through-crystal-and-solution-molecular-dynamics-simulations
#13
Logan S Ahlstrom, Ivan I Vorontsov, Jun Shi, Osamu Miyashita
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure...
2017: PloS One
https://www.readbyqxmd.com/read/28107341/complex-dynamics-of-virus-spread-from-low-infection-multiplicities-implications-for-the-spread-of-oncolytic-viruses
#14
Ignacio A Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz
While virus growth dynamics have been well-characterized in several infections, data are typically collected once the virus population becomes easily detectable. Earlier dynamics, however, remain less understood. We recently reported unusual early dynamics in an experimental system using adenovirus infection of human embryonic kidney (293) cells. Under identical experimental conditions, inoculation at low infection multiplicities resulted in either robust spread, or in limited spread that eventually stalled, with both outcomes occurring with approximately equal frequencies...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28107053/diversity-and-coevolutionary-dynamics-in-high-dimensional-phenotype-spaces
#15
Michael Doebeli, Iaroslav Ispolatov
We study macroevolutionary dynamics by extending microevolutionary competition models to long timescales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be nonstationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along nonequilibrium trajectories in phenotype space. We combine these lines of thinking by studying long-term coevolutionary dynamics of emerging lineages in multidimensional phenotype spaces...
February 2017: American Naturalist
https://www.readbyqxmd.com/read/28106441/loschmidt-echo-revivals-critical-and-noncritical
#16
R Jafari, Henrik Johannesson
A quantum phase transition is generally thought to imprint distinctive characteristics on the nonequilibrium dynamics of a closed quantum system. Specifically, the Loschmidt echo after a sudden quench to a quantum critical point-measuring the time dependence of the overlap between initial and time-evolved states-is expected to exhibit an accelerated relaxation followed by periodic revivals. We here introduce a new exactly solvable model, the extended Su-Schrieffer-Heeger model, the Loschmidt echo of which provides a counterexample...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106436/transient-casimir-forces-from-quenches-in-thermal-and-active-matter
#17
Christian M Rohwer, Mehran Kardar, Matthias Krüger
We compute fluctuation-induced (Casimir) forces for classical systems after a temperature quench. Using a generic coarse-grained model for fluctuations of a conserved density, we find that transient forces arise even if the initial and final states are force free. In setups reminiscent of Casimir (planar walls) and van der Waals (small inclusions) interactions, we find comparable exact universal expressions for the force. Dynamical details only scale the time axis of transient force curves. We propose that such quenches can be achieved, for instance, in experiments on active matter, employing tunable activity or interaction protocols...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106417/chaos-and-regularity-in-the-doubly-magic-nucleus-208-pb
#18
B Dietz, A Heusler, K H Maier, A Richter, B A Brown
High-resolution experiments have recently lead to a complete identification (energy, spin, and parity) of 151 nuclear levels up to an excitation energy of E_{x}=6.20  MeV in ^{208}Pb [Heusler et al., Phys. Rev. C 93, 054321 (2016)PRVCAN2469-998510.1103/PhysRevC.93.054321]. We present a thorough study of the fluctuation properties in the energy spectra of the unprecedented set of nuclear bound states. In a first approach, we group states with the same spin and parity into 14 subspectra, analyze standard statistical measures for short- and long-range correlations, i...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106223/next-generation-of-network-medicine-interdisciplinary-signaling-approaches
#19
REVIEW
Tamas Korcsmaros, Maria Victoria Schneider, Giulio Superti-Furga
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more...
January 20, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28106047/scale-dependent-diffusion-anisotropy-in-nanoporous-silicon
#20
Daria Kondrashova, Alexander Lauerer, Dirk Mehlhorn, Hervé Jobic, Armin Feldhoff, Matthias Thommes, Dipanjan Chakraborty, Cedric Gommes, Jovana Zecevic, Petra de Jongh, Armin Bunde, Jörg Kärger, Rustem Valiullin
Nanoporous silicon produced by electrochemical etching of highly B-doped p-type silicon wafers can be prepared with tubular pores imbedded in a silicon matrix. Such materials have found many technological applications and provide a useful model system for studying phase transitions under confinement. This paper reports a joint experimental and simulation study of diffusion in such materials, covering displacements from molecular dimensions up to tens of micrometers with carefully selected probe molecules. In addition to mass transfer through the channels, diffusion (at much smaller rates) is also found to occur in directions perpendicular to the channels, thus providing clear evidence of connectivity...
January 20, 2017: Scientific Reports
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