MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering.

Untargeted plasmid integration into mammalian cell genomes remains a poorly understood and inefficient process. The formation of plasmid concatemers and their genomic integration has been ascribed either to non-homologous end-joining (NHEJ) or homologous recombination (HR) DNA repair pathways. However, a direct involvement of these pathways has remained unclear. Here, we show that the silencing of many HR factors enhanced plasmid concatemer formation and stable expression of the gene of interest in Chinese hamster ovary (CHO) cells, while the inhibition of NHEJ had no effect. However, genomic integration was decreased by the silencing of specific HR components, such as Rad51, and DNA synthesis-dependent microhomology-mediated end-joining (SD-MMEJ) activities. Genome-wide analysis of the integration loci and junction sequences validated the prevalent use of the SD-MMEJ pathway for transgene integration close to cellular genes, an effect shared with matrix attachment region (MAR) DNA elements that stimulate plasmid integration and expression. Overall, we conclude that SD-MMEJ is the main mechanism driving the illegitimate genomic integration of foreign DNA in CHO cells, and we provide a recombination engineering approach that increases transgene integration and recombinant protein expression in these cells. Biotechnol. Bioeng. 2017;114: 384-396. © 2016 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals, Inc

The Phonon Drag Effect in Single-Walled Carbon Nanotubes

A variational solution of the coupled electron-phonon Boltzmann equations is used to calculate the phonon drag contribution to the thermopower in a 1-D system. A simple formula is derived for the temperature dependence of the phonon drag in metallic, single-walled carbon nanotubes. Scattering between different electronic bands yields nonzero values for the phonon drag as the Fermi level varies.Comment: 8 pages, 4 figure

Berezinskii-Kosterlitz-Thouless transition and BCS-Bose crossover in the two-dimensional attractive Hubbard model

We study the two-dimensional attractive Hubbard model using the mapping onto the half-filled repulsive Hubbard model in a uniform magnetic field coupled to the fermion spins. The low-energy effective action for charge and pairing fluctuations is obtained in the hydrodynamic regime. We recover the action of a Bose superfluid where half the fermion density is identified as the conjugate variable of the phase of the superconducting order parameter. By integrating out charge fluctuations, we obtain a phase-only action. In the zero-temperature superconducting state, this action describes a collective phase mode smoothly evolving from the Anderson-Bogoliubov mode at weak coupling to the Bogoliubov mode of a Bose superfluid at strong coupling. At finite temperature, the phase-only action can be used to extract an effective XY model and thus obtain the Berezinskii-Kosterlitz-Thouless (BKT) phase transition temperature. We also identify a renormalized classical regime of superconducting fluctuations above the BKT phase transition, and a regime of incoherent pairs at higher temperature. Special care is devoted to the nearly half-filled case where the symmetry of the order parameter is enlarged to SO(3) due to strong ${\bf q}=(\pi,\pi)$ charge fluctuations. The low-energy effective action is then an SO(3) non-linear sigma model with a (symmetry breaking) magnetic field proportional to the doping. In the strong-coupling limit, the attractive Hubbard model can be mapped onto the Heisenberg model, from which we recover the Gross-Pitaevskii equation in the low-density limit.Comment: 31 pages, 12 figures, RevTex4; (v2) changes following referees' comments, references adde

Effective action for Superconductors and BCS-Bose crossover

A standard perturbative expansion around the mean-field solution is used to derive the low-energy effective action for superconductors at T=0. Taking into account the density fluctuations at the outset we get the effective action where the density $\rho$ is the conjugated momentum to the phase $\theta$ of the order parameter. In the hydrodynamic regime, the dynamics of the superconductor is described by a time dependent non-linear Schr\"odinger equation (TDNLS) for the field $\Psi(x)=\sqrt{\rho/2} e^{i\theta}$. The evolution of the density fluctuations in the crossover from weak-coupling (BCS) to strong-coupling (Bose condensation of localized pairs) superconductivity is discussed for the attractive Hubbard model. In the bosonic limit, the TDNLS equation reduces to the the Gross-Pitaevskii equation for the order parameter, as in the standard description of superfluidity. The conditions under which a phase-only action can be derived in the presence of a long-range interaction to describe the physics of the superconductivity of ``bad metals'' are discussed.Comment: 13 pages, accepted for publication on Phys. Rev.

Upward curvature of the upper critical field in the Boson--Fermion model

We report on a non-conventional temperature behavior of the upper critical field ($H_{c2}(T)$) which is found for the Boson-Fermion (BF) model. We show that the BF model properly reproduces two crucial features of the experimental data obtained for high-$T_c$ superconductors: $H_{c2}(T)$ does not saturate at low temperatures and has an upward curvature. Moreover, the calculated upper critical field fits very well the experimental results. This agreement holds also for overdoped compounds, where a purely bosonic approach is not applicable.Comment: 4 pages, 3 figures, revte

Density functional calculations of nanoscale conductance

Density functional calculations for the electronic conductance of single molecules are now common. We examine the methodology from a rigorous point of view, discussing where it can be expected to work, and where it should fail. When molecules are weakly coupled to leads, local and gradient-corrected approximations fail, as the Kohn-Sham levels are misaligned. In the weak bias regime, XC corrections to the current are missed by the standard methodology. For finite bias, a new methodology for performing calculations can be rigorously derived using an extension of time-dependent current density functional theory from the Schroedinger equation to a Master equation.Comment: topical review, 28 pages, updated version with some revision