Synthetic biology for evolutionary engineering: from perturbation of genotype to acquisition of desired phenotype

With the increased attention on bio-based industry, demands for techniques that enable fast and effective strain improvement have been dramatically increased. Evolutionary engineering, which is less dependent on biological information, has been applied to strain improvement. Currently, synthetic biology has made great innovations in evolutionary engineering, particularly in the development of synthetic tools for phenotypic perturbation. Furthermore, discovering biological parts with regulatory roles and devising novel genetic circuits have promoted high-throughput screening and selection. In this review, we first briefly explain basics of synthetic biology tools for mutagenesis and screening of improved variants, and then describe how these strategies have been improved and applied to phenotypic engineering. Evolutionary engineering using advanced synthetic biology tools will enable further innovation in phenotypic engineering through the development of novel genetic parts and assembly into well-designed logic circuits that perform complex tasks.11Ysciescopu

Absence of First-order Transition and Tri-critical Point in the Dynamic Phase Diagram of a Spatially Extended Bistable System in an Oscillating Field

It has been well established that spatially extended, bistable systems that are driven by an oscillating field exhibit a nonequilibrium dynamic phase transition (DPT). The DPT occurs when the field frequency is on the order of the inverse of an intrinsic lifetime associated with the transitions between the two stable states in a static field of the same magnitude as the amplitude of the oscillating field. The DPT is continuous and belongs to the same universality class as the equilibrium phase transition of the Ising model in zero field [G. Korniss et al., Phys. Rev. E 63, 016120 (2001); H. Fujisaka et al., Phys. Rev. E 63, 036109 (2001)]. However, it has previously been claimed that the DPT becomes discontinuous at temperatures below a tricritical point [M. Acharyya, Phys. Rev. E 59, 218 (1999)]. This claim was based on observations in dynamic Monte Carlo simulations of a multipeaked probability density for the dynamic order parameter and negative values of the fourth-order cumulant ratio. Both phenomena can be characteristic of discontinuous phase transitions. Here we use classical nucleation theory for the decay of metastable phases, together with data from large-scale dynamic Monte Carlo simulations of a two-dimensional kinetic Ising ferromagnet, to show that these observations in this case are merely finite-size effects. For sufficiently small systems and low temperatures, the continuous DPT is replaced, not by a discontinuous phase transition, but by a crossover to stochastic resonance. In the infinite-system limit the stochastic-resonance regime vanishes, and the continuous DPT should persist for all nonzero temperatures

Uniform Strain Elements for Three-Node Triangular and Four-Node Tetrahedral Meshes

A family of uniform strain elements is presented for three-node triangular and four-node tetrahedral meshes. The elements use the linear interpolation functions of the original mesh, but each element is associated with a single node. As a result, a favorable constraint ratio for the volumetric response is obtained for problems in solid mechanics. The uniform strain elements do not require the introduction of additional degrees of freedom and their performance is shown to be significantly better than that of three-node triangular or four-node tetrahedral elements. In addition, nodes inside the boundary of the mesh are observed to exhibit superconvergent behavior for a set of example problems

Brane decay of a (4+n)-dimensional rotating black hole: spin-0 particles

In this work, we study the `scalar channel' of the emission of Hawking radiation from a (4+n)-dimensional, rotating black hole on the brane. We numerically solve both the radial and angular part of the equation of motion for the scalar field, and determine the exact values of the absorption probability and of the spheroidal harmonics, respectively. With these, we calculate the particle, energy and angular momentum emission rates, as well as the angular variation in the flux and power spectra -- a distinctive feature of emission during the spin-down phase of the life of the produced black hole. Our analysis is free from any approximations, with our results being valid for arbitrarily large values of the energy of the emitted particle, angular momentum of the black hole and dimensionality of spacetime. We finally compute the total emissivities for the number of particles, energy and angular momentum and compare their relative behaviour for different values of the parameters of the theory.Comment: 24 pages, 13 figure

Magnetization steps in Zn_(1-x)Mn_xO: Four largest exchange constants and single-ion anisotropy

Magnetization steps (MST's) from Mn pairs in several single crystals of Zn_(1-x)Mn_xO (0.0056<=x<=0.030, and in one powder (x=0.029), were observed. The largest two exchange constants, J1/kB=-18.2+/-0.5K and J1'/kB=-24.3+/-0.6K, were obtained from large peaks in the differential susceptibility, dM/dH, measured in pulsed magnetic fields, H, up to 500 kOe. These two largest J's are associated with the two inequivalent classes of nearest neighbors (NN's) in the wurtzite structure. The 29% difference between J1 and J1' is substantially larger than 13% in CdS:Mn, and 15% in CdSe:Mn. The pulsed-field data also indicate that, despite the direct contact between the samples and a superfluid-helium bath, substantial departures from thermal equilibrium occurred during the 7.4 ms pulse. The third- and fourth-largest J's were determined from the magnetization M at 20 mK, measured in dc magnetic fields H up to 90 kOe. Both field orientations H||c and H||[10-10] were studied. (The [10-10] direction is perpendicular to the c-axis, [0001].) By definition, neighbors which are not NN's are distant neighbors (DN's). The largest DN exchange constant (third-largest overall), has the value J/kB=-0.543+/-0.005K, and is associated with the DN at r=c. Because this is not the closest DN, this result implies that the J's do not decrease monotonically with the distance r. The second-largest DN exchange constant (fourth-largest overall), has the value J/kB=-0.080 K. It is associated with one of the two classes of neighbors that have a coordination number z=12, but the evidence is insufficient for a definite unique choice. The dependence of M on the direction of H gives D/kB=-0.039+/-0.008K, in fair agreement with -0.031 K from earlier EPR work.Comment: 12 pages, 10 figures. Submitted to PR

Slewing Mirror Telescope optics for the early observation of UV/optical photons from Gamma-Ray Bursts

We report on design, manufacture, and testing of a Slewing Mirror Telescope (SMT), the first of its kind and a part of Ultra-Fast Flash Observatory-pathfinder (UFFO-p) for space-based prompt measurement of early UV/optical light curves from Gamma-Ray Bursts (GRBs). Using a fast slewing mirror of 150 mm diameter mounted on a 2 axis gimbal stage, SMT can deliver the images of GRB optical counterparts to the intensified CCD detector within 1.5∼1.8 s over ± 35 degrees in the slewing field of view. Its Ritchey-Chrétien telescope of 100 mm diameter provides a 17 × 17 arcmin2 instantaneous field of view. Technical details of design, construction, the laboratory performance tests in space environments for this unique SMT are described in conjunction with the plan for in-orbit operation onboard the Lomonosov satellite in 2013. © 2013 Optical Society of America.This research was supported by the Korean Creative Research Initiatives (RCMST) of MEST/NRF, the Basic Science Research program of MEST/NRF (2010-0025056), the World Class University program of MEST/NRF (R32-2009-000-10130-0), the Spanish MINECO project AYA-2009-14027-C05-01, AYA-2011-29936-C05-01, AYA-2012-39727-C03-01, and AYA 2009-14000-C03-01/ESP, Taiwan's National Science Council Vanguard Program (100-2119-M-002-025) LeCosPA of National Taiwan University, Program of development of Lomonosov Moscow State University and Korean programs NRF 2012-0006632, 20100029390 and Yonsei-KASI joint research for the Frontiers of Astronomy and Space Science Program 2012Peer Reviewe

Limits on anomalous trilinear gauge boson couplings from WW, WZ and Wgamma production in pp-bar collisions at sqrt{s}=1.96 TeV

We present final searches of the anomalous gammaWW and ZWW trilinear gauge boson couplings from WW and WZ production using lepton plus dijet final states and a combination with results from Wgamma, WW, and WZ production with leptonic final states. The analyzed data correspond to up to 8.6/fb of integrated luminosity collected by the D0 detector in pp-bar collisions at sqrt{s}=1.96 TeV. We set the most stringent limits at a hadron collider to date assuming two different relations between the anomalous coupling parameters Delta\kappa_\gamma, lambda, and Delta g_1^Z for a cutoff energy scale Lambda=2 TeV. The combined 68% C.L. limits are -0.057<Delta\kappa_\gamma<0.154, -0.015<lambda<0.028, and -0.008<Delta g_1^Z<0.054 for the LEP parameterization, and -0.007<Delta\kappa<0.081 and -0.017<lambda<0.028 for the equal couplings parameterization. We also present the most stringent limits of the W boson magnetic dipole and electric quadrupole moments.Comment: 10 pages, 5 figures, submitted to PL

Measurement of the photon+b+b-jet production differential cross section in ppˉp\bar{p} collisions at \sqrt{s}=1.96~\TeV

We present measurements of the differential cross section dsigma/dpT_gamma for the inclusive production of a photon in association with a b-quark jet for photons with rapidities |y_gamma|< 1.0 and 30<pT_gamma <300 GeV, as well as for photons with 1.5<|y_gamma|< 2.5 and 30< pT_gamma <200 GeV, where pT_gamma is the photon transverse momentum. The b-quark jets are required to have pT>15 GeV and rapidity |y_jet| < 1.5. The results are based on data corresponding to an integrated luminosity of 8.7 fb^-1, recorded with the D0 detector at the Fermilab Tevatron $p\bar{p}$ Collider at sqrt(s)=1.96 TeV. The measured cross sections are compared with next-to-leading order perturbative QCD calculations using different sets of parton distribution functions as well as to predictions based on the kT-factorization QCD approach, and those from the Sherpa and Pythia Monte Carlo event generators.Comment: 10 pages, 9 figures, submitted to Phys. Lett.

Search for Higgs bosons decaying to tautau pairs in ppbar collisions at sqrt(s) = 1.96 TeV

We present a search for the production of neutral Higgs bosons decaying into tautau pairs in ppbar collisions at a center-of-mass energy of 1.96 TeV. The data, corresponding to an integrated luminosity of 5.4 fb-1, were collected by the D0 experiment at the Fermilab Tevatron Collider. We set upper limits at the 95% C.L. on the product of production cross section and branching ratio for a scalar resonance decaying into tautau pairs, and we then interpret these limits as limits on the production of Higgs bosons in the minimal supersymmetric standard model (MSSM) and as constraints in the MSSM parameter space.Comment: 7 pages, 5 figures, submitted to PL