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Directed Evolution

Nobuhiko Muramoto, Arisa Oda, Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa, Kunihiro Ohta
DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages...
May 18, 2018: Nature Communications
Javier Martin-Diaz, Carmen Paret, Eva García-Ruiz, Patricia Molina-Espeja, Miguel Alcalde
Unspecific peroxygenase (UPO) is a highly promiscuous biocatalyst and its selective mono(per)oxygenase activity makes it useful for many synthetic chemistry applications. Among the broad repertory of library creation methods for directed enzyme evolution, genetic drift allows neutral mutations to be accumulated gradually within a polymorphic network of variants. In this study, we conducted a campaign of genetic drift with UPO in Saccharomyces cerevisiae so that neutral mutations were simply added and recombined in vivo With low mutational loading and an activity threshold of 45% of the parent's native function, mutant libraries enriched in folded and active UPO variants were generated...
May 18, 2018: Applied and Environmental Microbiology
Carlos Bonazzola, Alejandro Hnilo, Marcelo Kovalsky, Jorge Tredicce
The passively Q-switched, self-pulsing all-solid-state laser is a device of widespread use in many applications. Depending on the condition of saturation of the absorber, which is easy to adjust, different dynamical regimes are observed: continuous-wave emission, stable oscillations, period doubling bifurcations, chaos, and, within some chaotic regimes, extreme events (EEs) in the form of pulses of extraordinary intensity. These pulses are sometimes called "dissipative optical rogue waves." The mechanism of their formation in this laser is unknown...
March 2018: Physical Review. E
V M Malkin, N J Fisch
Multiscale turbulence naturally develops and plays an important role in many fluid, gas, and plasma phenomena. Statistical models of multiscale turbulence usually employ Kolmogorov hypotheses of spectral locality of interactions (meaning that interactions primarily occur between pulsations of comparable scales) and scale-invariance of turbulent pulsations. However, optical turbulence described by the nonlinear Schrodinger equation exhibits breaking of both the Kolmogorov locality and scale-invariance. A weaker form of spectral locality that holds for multi-scale optical turbulence enables a derivation of simplified evolution equations that reduce the problem to a single scale modeling...
March 2018: Physical Review. E
Kumari Priti Sinha, Rochish M Thaokar
Vesicles or biological cells under simultaneous shear and electric field can be encountered in dielectrophoretic devices or designs used for continuous flow electrofusion or electroporation. In this work, the dynamics of a vesicle subjected to simultaneous shear and uniform alternating current (ac) electric field is investigated in the small deformation limit. The coupled equations for vesicle orientation and shape evolution are derived theoretically, and the resulting nonlinear equations are handled numerically to generate relevant phase diagrams that demonstrate the effect of electrical parameters on the different dynamical regimes such as tank treading (TT), vacillating breathing (VB) [called trembling (TR) in this work], and tumbling (TU)...
March 2018: Physical Review. E
K M Schoeffler, N F Loureiro, L O Silva
The dynamical evolution of a fully kinetic, collisionless system with imposed background density and temperature gradients is investigated analytically. The temperature gradient leads to the generation of temperature anisotropy, with the temperature along the gradient becoming larger than that in the direction perpendicular to it. This causes the system to become unstable to pressure anisotropy driven instabilities, dominantly to the electron Weibel instability. When both density and temperature gradients are present and nonparallel to each other, we obtain a Biermann-like linear-in-time magnetic field growth...
March 2018: Physical Review. E
Norihiro Oyama, Kosuke Teshigawara, John Jairo Molina, Ryoichi Yamamoto, Takashi Taniguchi
The collective dynamics of externally driven N_{p}-colloidal systems (1≤N_{p}≤4) in a confined viscous fluid have been investigated using three-dimensional direct numerical simulations with fully resolved hydrodynamics. The dynamical modes of collective particle motion are studied by changing the particle Reynolds number as determined by the strength of the external driving force and the confining wall distance. For a system with N_{p}=3, we found that at a critical Reynolds number a dynamical mode transition occurs from the doublet-singlet mode to the triplet mode, which has not been reported experimentally...
March 2018: Physical Review. E
Natsuko Ota, Ryo Kurahashi, Satoshi Sano, Kazufumi Takano
Protein evolution is potentially governed by protein stability. Here, we investigated the relationship between protein evolution and stability through the random mutational drift of a thermophilic bacterial protein, an esterase of Alicyclobacillus acidocaldarius (Aac-Est), at high and low temperatures. In the first random mutation of Aac-Est, few proteins exhibit increased activity at 65°C, indicating that the wild-type (WT) Aac-Est is located on the peak of a mountain in a fitness landscape for activity at high temperature...
May 15, 2018: Biochimie
Kaiwen Tian, David L Goldsby, Robert W Carpick
Rate and state friction (RSF) laws are widely used empirical relationships that describe macroscale to microscale frictional behavior. They entail a linear combination of the direct effect (the increase of friction with sliding velocity due to the reduced influence of thermal excitations) and the evolution effect (the change in friction with changes in contact "state," such as the real contact area or the degree of interfacial chemical bonds). Recent atomic force microscope (AFM) experiments and simulations found that nanoscale single-asperity amorphous silica-silica contacts exhibit logarithmic aging (increasing friction with time) over several decades of contact time, due to the formation of interfacial chemical bonds...
May 4, 2018: Physical Review Letters
Ming Tang, Monica Erdman, Graham Eldridge, Cin-Ty A Lee
The two most important magmatic differentiation series on Earth are the Fe-enriching tholeiitic series, which dominates the oceanic crust and island arcs, and the Fe-depleting calc-alkaline series, which dominates the continental crust and continental arcs. It is well known that calc-alkaline magmas are more oxidized when they erupt and are preferentially found in regions of thick crust, but why these quantities should be related remains unexplained. We use the redox-sensitive behavior of europium (Eu) in deep-seated, plagioclase-free arc cumulates to directly constrain the redox evolution of arc magmas at depth...
May 2018: Science Advances
Ming Wang, Haoqing Li, Yujing Tian, Hong Guo, Xiaoying Fang, Yuebin Guo
Changes in various grain interfaces, including the grain boundary and phase boundary, are a strong indication of microstructural changes, particularly ultra-fined grains achieved by large strain deformation and subsequent annealing. After direct rolling and cross rolling with the same strain of ε = 2, the distributions of the interfaces in annealed UNS S32304 duplex stainless steel were investigated using electron backscatter diffraction (EBSD) in this study. The ferrite experienced continued recovery, and a high density of low-angle grain boundaries (LAGBs) was produced...
May 16, 2018: Materials
Jingfeng Wang, Weiyan Jiang, Shengfeng Guo, Yang Li, Yao Ma
The morphology evolution of long-period stacking ordered (LPSO) phases on corrosion behavior of Mg95.33 Zn₂Y2.67 alloy is investigated systematically during as-cast, pre-extrusion heat-treated, as-extruded and post-extrusion heat-treated conditions. The second phases in the as-cast alloy are only LPSO phases with a few Y particles. The pre-extrusion heat treatment changed LPSO phases from blocks into a rudimentary rod shape with lamellar structure, subsequently into fine fragments by extrusion, and then into a regular rod shape with lamellar structure followed by post-extrusion heat treatment...
May 16, 2018: Materials
Xuewei Fang, Lijuan Zhang, Hui Li, Chaolong Li, Ke Huang, Bingheng Lu
In this research, four different welding arc modes including conventional cold metal transfer (CMT), CMT-Pulse (CMT-P), CMT-Advanced (CMT-ADV), and CMT pulse advanced (CMT-PADV) were used to deposit 2219-Al wire. The effects of different arc modes on porosity, pore size distribution, microstructure evolution, and mechanical properties were thoroughly investigated. The statistical analysis of the porosity and its size distribution indicated that the CMT-PADV process gave the smallest pore area percentage and pore aspect ratio, and had almost no larger pores...
May 16, 2018: Materials
Tereza Králová, Tomáš Albrecht, Josef Bryja, David Hořák, Arild Johnsen, Jan T Lifjeld, Marian Novotný, Ondřej Sedláček, Hana Velová, Michal Vinkler
Positive selection acting on Toll-like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host-pathogen molecular co-adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study we provide evidence of phenotypic variability in the avian TLR4 ligand-binding region (LBR), the direct interface between host and pathogen molecular structures...
May 17, 2018: Molecular Ecology
Yujie Bai, Gaixia Luo, Lijuan Meng, Qinfang Zhang, Ning Xu, Haiyang Zhang, Xiuqiang Wu, Fanjie Kong, Baolin Wang
Searching for two-dimensional semiconductor materials that are suitable for visible-light photocatalytic water splitting provides a sustainable solution to deal with the future energy crisis and environmental problems. Herein, based on first-principles calculations, single-layer ZnMN2 (M = Si, Ge, Sn) zinc nitrides are proposed as efficient photocatalysts for water splitting. Stability analyses show that the single-layer ZnMN2 zinc nitrides exhibit energetic and dynamical stability. The electronic properties reveal that all of the single-layer ZnMN2 zinc nitrides are semiconductors...
May 17, 2018: Physical Chemistry Chemical Physics: PCCP
Roger A Sheldon, Dean Brady
In the period 1985 to 1995 applications of biocatalysis, driven by the need for more sustainable manufacture of chemicals and catalytic, (enantio)selective methods for the synthesis of pharmaceutical intermediates, largely involved the available hydrolases. This was followed, in the next two decades, by revolutionary developments in protein engineering and directed evolution for the optimisation of enzyme function and performance that totally changed the biocatalysis landscape. In the same period, metabolic engineering and synthetic biology revolutionised the use of whole cell biocatalysis in the synthesis of commodity chemicals by fermentation...
May 17, 2018: Chemical Communications: Chem Comm
Melissa Oddie, Ralph Büchler, Bjørn Dahle, Marin Kovacic, Yves Le Conte, Barbara Locke, Joachim R de Miranda, Fanny Mondet, Peter Neumann
In eusocial insect colonies nestmates cooperate to combat parasites, a trait called social immunity. However, social immunity failed for Western honey bees (Apis mellifera) when the ectoparasitic mite Varroa destructor switched hosts from Eastern honey bees (Apis cerana). This mite has since become the most severe threat to A. mellifera world-wide. Despite this, some isolated A. mellifera populations are known to survive infestations by means of natural selection, largely by supressing mite reproduction, but the underlying mechanisms of this are poorly understood...
May 16, 2018: Scientific Reports
Roxanne S Beltran, Jennifer M Burns, Greg A Breed
Birds and mammals have developed numerous strategies for replacing worn feathers and hair. Moulting usually occurs on an annual basis; however, moults that take place twice per year (biannual moults) also occur. Here, we review the forces driving the evolution of various moult strategies, focusing on the special case of the complete biannual moult as a convergence of selection pressures across birds and mammals. Current evidence suggests that harsh environmental conditions or seasonality (e.g. larger variation in temperatures) drive evolution of a biannual moult...
May 16, 2018: Proceedings. Biological Sciences
Yu-Ching Huang, Viet Dai Dang, Ni-Chen Chang, John Wang
Supergenes consist of co-adapted loci that segregate together and are associated with adaptive traits. In the fire ant Solenopsis invicta , two 'social' supergene variants regulate differences in colony queen number and other traits. Suppressed recombination in this system is maintained, in part, by a greater than 9 Mb inversion, but the supergene is larger. Has the supergene in S. invicta undergone multiple large inversions? The initial gene content of the inverted allele of a supergene would be the same as that of the wild-type allele...
May 16, 2018: Proceedings. Biological Sciences
Simone Lanini, Paola Scognamiglio, Alessandra Mecozzi, Lorella Lombardozzi, Vincenzo Vullo, Mario Angelico, Antonio Gasbarrini, Gloria Taliani, Adolfo Francesco Attili, Carlo Federico Perno, Adriano De Santis, Vincenzo Puro, Fabio Cerqua, Gianpiero D'Offizi, Adriano Pellicelli, Orlando Armignacco, Francesco Saverio Mennini, Massimo Siciliano, Enrico Girardi, Vincenzo Panella, Giuseppe Ippolito
BACKGROUND: Management of chronic hepatitis C (CHC) has significantly accelerated in the last few years. Currently, second generation direct acting antivirals (DAAs) promise clearance of infection in most of patients. Here we present the results of the first analysis carried out on data of Lazio clinical network for DAAs. METHODS: The study was designed as a multicenter cohort: a) to assess the evolution of treatment during the first 24 months of the activity of the Clinical Network; b) to report overall efficacy of treatments; c) to analyze potential factors associated with lack of virological response at 12 weeks after therapy (SVR12); d) to evaluate the variation of ALT at baseline and 12 weeks after therapy in those who achieved SVR12 in comparison to those who did not...
May 16, 2018: BMC Infectious Diseases
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