Lipopolysaccharide is a frequent contaminant of plasmid DNA preparations and can be toxic to primary cells in the presence of adenovirus

Endotoxin (lipopolysaccharide, LPS) is commonly found as a contaminant in plasmid DNA preparations. We demonstrate here that the quantities of LPS typically contaminating DNA preparations can generate a toxicity to primary cells (primary human skin fibroblasts, primary human melanoma cells) in the presence of entry-competent adenovirus particles. Toxicity can be observed with as little as 100 ng/ml free LPS or 100 pg/ml LPS when the LPS is assembled into polylysine/adenovirus complexes. Simple and effective methods of removing the contaminating LPS using either a polymyxin B resin or Triton X-114 extraction are described. Treatment of DNA samples to remove LPS eliminates the toxicity to primary cells

Time-Dependent Density Functional Theory for Driven Lattice Gas Systems with Interactions

We present a new method to describe the kinetics of driven lattice gases with particle-particle interactions beyond hard-core exclusions. The method is based on the time-dependent density functional theory for lattice systems and allows one to set up closed evolution equations for mean site occupation numbers in a systematic manner. Application of the method to a totally asymmetric site exclusion process with nearest-neighbor interactions yields predictions for the current-density relation in the bulk, the phase diagram of non-equilibrium steady states and the time evolution of density profiles that are in good agreement with results from kinetic Monte Carlo simulations.Comment: 11 pages, 3 figure

Kinetics in one-dimensional lattice gas and Ising models from time-dependent density functional theory

Time-dependent density functional theory, proposed recently in the context of atomic diffusion and non-equilibrium processes in solids, is tested against Monte Carlo simulation. In order to assess the basic approximation of that theory, the representation of non-equilibrium states by a local equilibrium distribution function, we focus on one-dimensional lattice models, where all equilibrium properties can be worked exactly from the known free energy as a functional of the density. This functional determines the thermodynamic driving forces away from equilibrium. In our studies of the interfacial kinetics of atomic hopping and spin relaxation, we find excellent agreement with simulations, suggesting that the method is useful also for treating more complex problems.Comment: 8 pages, 5 figures, submitted to Phys. Rev.

Cluster density functional theory for lattice models based on the theory of Mobius functions

Rosenfeld's fundamental measure theory for lattice models is given a rigorous formulation in terms of the theory of Mobius functions of partially ordered sets. The free-energy density functional is expressed as an expansion in a finite set of lattice clusters. This set is endowed a partial order, so that the coefficients of the cluster expansion are connected to its Mobius function. Because of this, it is rigorously proven that a unique such expansion exists for any lattice model. The low-density analysis of the free-energy functional motivates a redefinition of the basic clusters (zero-dimensional cavities) which guarantees a correct zero-density limit of the pair and triplet direct correlation functions. This new definition extends Rosenfeld's theory to lattice model with any kind of short-range interaction (repulsive or attractive, hard or soft, one- or multi-component...). Finally, a proof is given that these functionals have a consistent dimensional reduction, i.e. the functional for dimension d' can be obtained from that for dimension d (d'<d) if the latter is evaluated at a density profile confined to a d'-dimensional subset.Comment: 21 pages, 2 figures, uses iopart.cls, as well as diagrams.sty (included

Fundamental measure theory for lattice fluids with hard core interactions

We present the extension of Rosenfeld's fundamental measure theory to lattice models by constructing a density functional for d-dimensional mixtures of parallel hard hypercubes on a simple hypercubic lattice. The one-dimensional case is exactly solvable and two cases must be distinguished: all the species with the same lebgth parity (additive mixture), and arbitrary length parity (nonadditive mixture). At the best of our knowledge, this is the first time that the latter case is considered. Based on the one-dimensional exact functional form, we propose the extension to higher dimensions by generalizing the zero-dimensional cavities method to lattice models. This assures the functional to have correct dimensional crossovers to any lower dimension, including the exact zero-dimensional limit. Some applications of the functional to particular systems are also shown.Comment: 22 pages, 7 figures, needs IOPP LaTeX styles file

Highly efficient CRISPR-Cas9-mediated gene knockout in primary human B cells for functional genetic studies of Epstein-Barr virus infection

Gene editing is now routine in all prokaryotic and metazoan cells but has not received much attention in immune cells when the CRISPR-Cas9 technology was introduced in the field of mammalian cell biology less than ten years ago. This versatile technology has been successfully adapted for gene modifications in human myeloid cells and T cells, among others, but applications to human primary B cells have been scarce and limited to activated B cells. This limitation has precluded conclusive studies into cell activation, differentiation or cell cycle control in this cell type. We report on highly efficient, simple and rapid genome engineering in primary resting human B cells using nucleofection of Cas9 ribonucleoprotein complexes, followed by EBV infection or culture on CD40 ligand feeder cells to drive in vitro B cell survival. We provide proof-of-principle of gene editing in quiescent human B cells using two model genes: CD46 and CDKN2A. The latter encodes the cell cycle regulator p16INK4a which is an important target of Epstein-Barr virus (EBV). Infection of B cells carrying a knockout of CDKN2A with wildtype and EBNA3 oncoprotein mutant strains of EBV allowed us to conclude that EBNA3C controls CDKN2A, the only barrier to B cell proliferation in EBV infected cells. Together, this approach enables efficient targeting of specific gene loci in quiescent human B cells supporting basic research as well as immunotherapeutic strategies

BZLF1 interacts with chromatin remodelers promoting escape from latent infections with EBV

A hallmark of EBV infections is its latent phase, when all viral lytic genes are repressed. Repression results from a high nucleosome occupancy and epigenetic silencing by cellular factors such as the Polycomb repressive complex 2 (PRC2) and DNA methyltransferases that, respectively, introduce repressive histone marks and DNA methylation. The viral transcription factor BZLF1 acts as a molecular switch to induce transition from the latent to the lytic or productive phase of EBV’s life cycle. It is unknown how BZLF1 can bind to the epigenetically silenced viral DNA and whether it directly reactivates the viral genome through chromatin remodeling. We addressed these fundamental questions and found that BZLF1 binds to nucleosomal DNA motifs both in vivo and in vitro. BZLF1 co-precipitates with cellular chromatin remodeler ATPases, and the knock-down of one of them, INO80, impaired lytic reactivation and virus synthesis. In Assay for Transposase-Accessible Chromatin-seq experiments, non-accessible chromatin opens up locally when BZLF1 binds to its cognate sequence motifs in viral DNA. We conclude that BZLF1 reactivates the EBV genome by directly binding to silenced chromatin and recruiting cellular chromatin-remodeling enzymes, which implement a permissive state for lytic viral transcription. BZLF1 shares this mode of action with a limited number of cellular pioneer factors, which are instrumental in transcriptional activation, differentiation, and reprogramming in all eukaryotic cells