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Directed Evolution

Gordon Y C Cheung, Emilie L Fisher, Joshua W McCausland, Justin Choi, John W M Collins, Seth W Dickey, Michael Otto
Antimicrobial peptides (AMPs) constitute an important part of innate host defense. Possibly limiting the therapeutic potential of AMPs is the fact that bacteria have developed AMP resistance mechanisms during their co-evolution with humans. However, there is no direct evidence that AMP resistance per se is important during an infection. Here we show that the Staphylococcus aureus Pmt ABC transporter defends the bacteria from killing by important human AMPs and elimination by human neutrophils. By showing that Pmt contributes to virulence during skin infection in an AMP-dependent manner, we provide evidence that AMP resistance plays a key role in bacterial infection...
January 17, 2018: Journal of Infectious Diseases
Simon K Emms, Alisa A Hove, Leah S Dudley, Susan J Mazer, Amy S Verhoeven
Background and Aims: The evolution of selfing from outcrossing may be the most common transition in plant reproductive systems and is associated with a variety of ecological circumstances and life history strategies. The most widely discussed explanation for these associations is the reproductive assurance hypothesis - the proposition that selfing is favoured because it increases female fitness when outcross pollen receipt is limited. Here an alternative explanation, the time limitation hypothesis, is addressed, one scenario of which proposes that selfing may evolve as a correlated response to selection for a faster life cycle in seasonally deteriorating environments...
January 17, 2018: Annals of Botany
Jingzhou Xin, Jianting Zhou, Simon X Yang, Xiaoqing Li, Yu Wang
Bridges are an essential part of the ground transportation system. Health monitoring is fundamentally important for the safety and service life of bridges. A large amount of structural information is obtained from various sensors using sensing technology, and the data processing has become a challenging issue. To improve the prediction accuracy of bridge structure deformation based on data mining and to accurately evaluate the time-varying characteristics of bridge structure performance evolution, this paper proposes a new method for bridge structure deformation prediction, which integrates the Kalman filter, autoregressive integrated moving average model (ARIMA), and generalized autoregressive conditional heteroskedasticity (GARCH)...
January 19, 2018: Sensors
Adriano Angelucci, Simona Delle Monache, Alessio Cortellini, Monica Di Padova, Ficorella Corrado
High expectations are placed upon anti-angiogenic compounds for metastatic colorectal cancer (mCRC), the first malignancy for which such type of treatment has been approved. Indeed, clinical trials have confirmed that targeting the formation of new vessels can improve in many cases clinical outcomes of mCRC patients. However, current anti-angiogenic drugs are far from obtaining the desirable or expected curative results. Many are the factors probably involved in such disappointing results, but particular attention is currently focused on the validation of biomarkers able to improve the direction of treatment protocols...
January 19, 2018: International Journal of Molecular Sciences
S L Zuo, Y Zhang, L C Peng, X Zhao, R Li, H Li, J F Xiong, M He, T Y Zhao, J R Sun, F X Hu, B G Shen
The evolution of topological magnetic domains microscopically correlates the dynamic behavior of memory units in spintronic application. Nanometric bubbles with variation of spin configurations have been directly observed in a centrosymmetric hexagonal magnet (Mn0.5Ni0.5)65(Ga1-yYy)35 (y = 0.01) using Lorentz transmission electron microscopy. Magnetic bubbles instead of biskyrmions are generated due to the enhancement of quality factor Q caused by the substitution of rare-earth element Y. Furthermore, the bubble density and diversified spin configurations are systematically manipulated via combining the electric current with perpendicular magnetic fields...
January 19, 2018: Nanoscale
Andrea Lombardi, Federico Palazzetti
Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies...
January 19, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Zhifeng Jiang, Weiming Wan, Huaming Li, Shouqi Yuan, Huijun Zhao, Po Keung Wong
The challenge in the artificial photosynthesis of fossil resources from CO2 by utilizing solar energy is to achieve stable photocatalysts with effective CO2 adsorption capacity and high charge-separation efficiency. A hierarchical direct Z-scheme system consisting of urchin-like hematite and carbon nitride provides an enhanced photocatalytic activity of reduction of CO2 to CO, yielding a CO evolution rate of 27.2 µmol g-1 h-1 without cocatalyst and sacrifice reagent, which is >2.2 times higher than that produced by g-C3 N4 alone (10...
January 19, 2018: Advanced Materials
Nilan T Jacob
Over the years, the pharmaceutical industry has been at the forefront of research and innovation in drug discovery and development. The process of drug discovery extending from pre-clinical studies to multi-centric clinical trials and post-marketing phase is a costly affair running into billions of dollars. On the flip side, not all investigational molecules clear the trial phases and get approved; which puts pressure on the manufacturers to maximise the profit from approved drugs. It is in this key area, the practice of drug promotion plays its role...
January 18, 2018: British Journal of Clinical Pharmacology
Danqing Feng, Tesfaye Biftu, F Anthony Romero, Ahmet Kekec, James Dropinski, Andrew Kassick, Shiyao Xu, Marc M Kurtz, Anantha Gollapudi, Qing Shao, Xiaodong Yang, Ku Lu, Gaochao Zhou, Daniel Kemp, Robert W Myers, Hong-Ping Guan, Maria E Trujillo, Cai Li, Ann Weber, Iyassu K Sebhat
5'-Adenosine monophosphate-activated protein kinase (AMPK) is a key regulator of mammalian energy homeostasis and has been implicated in mediating many of the beneficial effects of exercise and weight loss including lipid and glucose trafficking. As such, the enzyme has long been of interest as a target for the treatment of Type 2 Diabetes Mellitus. We describe the optimization of β1-selective, liver-targeted AMPK activators and their evolution into systemic pan-activators capable of acutely lowering glucose in mouse models...
January 11, 2018: ACS Medicinal Chemistry Letters
João Neiva, Cristina Paulino, Mette M Nielsen, Dorte Krause-Jensen, Gary W Saunders, Jorge Assis, Ignacio Bárbara, Éric Tamigneaux, Licínia Gouveia, Tânia Aires, Núria Marbà, Annette Bruhn, Gareth A Pearson, Ester A Serrão
Glacial vicariance is regarded as one of the most prevalent drivers of phylogeographic structure and speciation among high-latitude organisms, but direct links between ice advances and range fragmentation have been more difficult to establish in marine than in terrestrial systems. Here we investigate the evolution of largely disjunct (and potentially reproductively isolated) phylogeographic lineages within the amphi-boreal kelp Saccharina latissima s. l. Using molecular data (COI, microsatellites) we confirm that S...
January 18, 2018: Scientific Reports
Martin Qvarnström, Piotr Szrek, Per E Ahlberg, Grzegorz Niedźwiedzki
Opinions differ on whether the evolution of tetrapods (limbed vertebrates) from lobe-finned fishes was directly linked to terrestrialization. The earliest known tetrapod fossils, from the Middle Devonian (approximately 390 million years old) of Zachełmie Quarry in Poland, are trackways made by limbs with digits; they document a direct environmental association and thus have the potential to help answer this question. However, the tetrapod identity of the tracks has recently been challenged, despite their well-preserved morphology, on account of their great age and supposedly shallow marine (intertidal or lagoonal) depositional environment...
January 18, 2018: Scientific Reports
César Huete, Tai Jin, Daniel Martínez-Ruiz, Kun Luo
Linear interaction analysis (LIA) is employed to investigate the interaction of reactive and nonreactive shock waves with isotropic vortical turbulence. The analysis is carried out, through Laplace-transform technique, accounting for long-time effects of vortical disturbances on the burnt-gas flow in the fast-reaction limit, where the reaction-region thickness is significantly small in comparison with the most representative turbulent length scales. Results provided by the opposite slow-reaction limit are also recollected...
November 2017: Physical Review. E
Niurka R Quintero, Franz G Mertens, Fred Cooper, Avadh Saxena, A R Bishop
We consider the massless nonlinear Dirac (NLD) equation in 1+1 dimension with scalar-scalar self-interaction g^{2}/2(Ψ[over ¯]Ψ)^{2} in the presence of three external electromagnetic real potentials V(x), a potential barrier, a constant potential, and a potential well. By solving numerically the NLD equation, we find different scenarios depending on initial conditions, namely, propagation of the initial pulse along one direction, splitting of the initial pulse into two pulses traveling in opposite directions, and focusing of two initial pulses followed by a splitting...
November 2017: Physical Review. E
Beth Jelfs, Rosa H M Chan
Directionality indices can be used as an indicator of the asymmetry in coupling between systems and have found particular application in relation to neurological systems. The directionality index between two systems is a function of measures of information transfer in both directions. Here we illustrate that before inferring the directionality of coupling it is first necessary to consider the use of appropriate tests of significance. We propose a surrogate corrected directionality index which incorporates such testing...
November 2017: Physical Review. E
Luca Lanotte, Didier Laux, Benoît Charlot, Manouk Abkarian
The morphology of dried blood droplets derives from the deposition of red cells, the main components of their solute phase. Up to now, evaporation-induced convective flows were supposed to be at the base of red cell distribution in blood samples. Here, we present a direct visualization by videomicroscopy of the internal dynamics in desiccating blood droplets, focusing on the role of cell concentration and plasma composition. We show that in diluted suspensions, the convection is promoted by the rich molecular composition of plasma, whereas it is replaced by an outward red blood cell displacement front at higher hematocrits...
November 2017: Physical Review. E
Pierre Le Doussal
We obtain several exact results for universal distributions involving the maximum of the Airy_{2} process minus a parabola and plus a Brownian motion, with applications to the one-dimensional Kardar-Parisi-Zhang (KPZ) stochastic growth universality class. This allows one to obtain (i) the universal limit, for large time separation, of the two-time height correlation for droplet initial conditions, e.g., C_{∞}=lim_{t_{2}/t_{1}→+∞}h(t_{1})h(t_{2})[over ¯]^{c}/h(t_{1})^{2}[over ¯]^{c}, with C_{∞}≈0...
December 2017: Physical Review. E
Daeseong Yong, Jaeup U Kim
For the purpose of checking material conservation of various numerical algorithms used in the self-consistent-field theory (SCFT) of polymeric systems, we develop an algebraic method using matrix and bra-ket notation, which traces the Hermiticity of the product of the volume and evolution matrices. Algebraic tests for material conservation reveal that the popular pseudospectral method in the Cartesian grid conserves material perfectly, while the finite-volume method (FVM) is the proper tool when real-space SCFT with the Crank-Nicolson method is adopted in orthogonal coordinate systems...
December 2017: Physical Review. E
Diego Frezzato
This work deals with thermostated fluctuating systems subjected to driven transformations of the internal energetics. The main focus is on generally multidimensional systems with continuous configurational degrees of freedom over which overdamped Markovian fluctuations take place (diffusive regime of the motion). Mutual bounds are established between the average energy dissipation, the deviation between nonequilibrium probability density and underlying equilibrium distribution due to the system's lag, and the statistical properties of the components of the directed flow induced by the transformation itself...
December 2017: Physical Review. E
Oleg Schilling, Nicholas J Mueschke
Data from a 1152×760×1280 direct numerical simulation [N. J. Mueschke and O. Schilling, Phys. Fluids 21, 014106 (2009)PHFLE61070-663110.1063/1.3064120] of a Rayleigh-Taylor mixing layer modeled after a small-Atwood-number water-channel experiment is used to investigate the validity of gradient diffusion and similarity closures a priori. The budgets of the mean flow, turbulent kinetic energy, turbulent kinetic energy dissipation rate, heavy-fluid mass fraction variance, and heavy-fluid mass fraction variance dissipation rate transport equations across the mixing layer were previously analyzed [O...
December 2017: Physical Review. E
Roland Lauter, Aditi Mitra, Florian Marquardt
Phase oscillator lattices subject to noise are one of the most fundamental systems in nonequilibrium physics. We have discovered a dynamical transition which has a significant impact on the synchronization dynamics in such lattices, as it leads to an explosive increase of the phase diffusion rate by orders of magnitude. Our analysis is based on the widely applicable Kuramoto-Sakaguchi model, with local couplings between oscillators. For one-dimensional lattices, we observe the universal evolution of the phase spread that is suggested by a connection to the theory of surface growth, as described by the Kardar-Parisi-Zhang (KPZ) model...
July 2017: Physical Review. E
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