Evolution of DNA Double-Strand Break Repair by Gene Conversion: Coevolution Between a Phage and Restriction-Modification System

The necessity to repair genome damage has been considered to be an immediate factor responsible for the origin of sex. Indeed, attack by a cellular restriction enzyme of invading DNA from several bacteriophages initiates recombinational repair by gene conversion if there is homologous DNA. In the present work, we modeled the interaction between a bacteriophage and a bacterium carrying a restriction enzyme as antagonistic coevolution. We assume a locus on the bacteriophage genome has either a restriction-sensitive or a -resistant allele, and another locus determines whether it is recombination/repair-proficient or -defective. A restriction break can be repaired by a co-infecting phage genome if one of them is recombination/repair-proficient. We define the fitness of phage (resistant/sensitive and repair-positive/-negative) genotypes and bacterial (restriction-positive/-negative) genotypes by assuming random encounter of the genotypes, with a given probabilities of single and double infections, and the costs of resistance, repair and restriction. Our results show the evolution of the repair allele depends on b1 / b0 , the ratio of the burst size b1 under damage to host cell physiology induced by an unrepaired double-strand break to the default burst size b0 . It was not until this effect was taken into account that the evolutionary advantage of DNA repair became apparent

The Effective Particle-Hole Interaction and the Optical Response of Simple Metal Clusters

Following Sham and Rice [L. J. Sham, T. M. Rice, Phys. Rev. 144 (1966) 708] the correlated motion of particle-hole pairs is studied, starting from the general two-particle Greens function. In this way we derive a matrix equation for eigenvalues and wave functions, respectively, of the general type of collective excitation of a N-particle system. The interplay between excitons and plasmons is fully described by this new set of equations. As a by-product we obtain - at least a-posteriori - a justification for the use of the TDLDA for simple-metal clusters.Comment: RevTeX, 15 pages, 5 figures in uufiles format, 1 figure avaible from [email protected]

AtHKT1;1 Mediates Nernstian Sodium Channel Transport Properties in Arabidopsis Root Stelar Cells

The Arabidopsis AtHKT1;1 protein was identified as a sodium (Na+) transporter by heterologous expression in Xenopus laevis oocytes and Saccharomyces cerevisiae. However, direct comparative in vivo electrophysiological analyses of a plant HKT transporter in wild-type and hkt loss-of-function mutants has not yet been reported and it has been recently argued that heterologous expression systems may alter properties of plant transporters, including HKT transporters. In this report, we analyze several key functions of AtHKT1;1-mediated ion currents in their native root stelar cells, including Na+ and K+ conductances, AtHKT1;1-mediated outward currents, and shifts in reversal potentials in the presence of defined intracellular and extracellular salt concentrations. Enhancer trap Arabidopsis plants with GFP-labeled root stelar cells were used to investigate AtHKT1;1-dependent ion transport properties using patch clamp electrophysiology in wild-type and athkt1;1 mutant plants. AtHKT1;1-dependent currents were carried by sodium ions and these currents were not observed in athkt1;1 mutant stelar cells. However, K+ currents in wild-type and athkt1;1 root stelar cell protoplasts were indistinguishable correlating with the Na+ over K+ selectivity of AtHKT1;1-mediated transport. Moreover, AtHKT1;1-mediated currents did not show a strong voltage dependence in vivo. Unexpectedly, removal of extracellular Na+ caused a reduction in AtHKT1;1-mediated outward currents in Columbia root stelar cells and Xenopus oocytes, indicating a role for external Na+ in regulation of AtHKT1;1 activity. Shifting the NaCl gradient in root stelar cells showed a Nernstian shift in the reversal potential providing biophysical evidence for the model that AtHKT1;1 mediates passive Na+ channel transport properties

A new limit of T-violating transverse muon polarization in the K+→π0μ+νK^{+}\to\pi^{0}\mu^{+} \nu decay

A search for T-violating transverse muon polarization ($P_T$) in the $K^{+}\to \pi^{0}\mu^{+}\nu$ decay was performed using kaon decays at rest. A new improved value, $P_T= -0.0017\pm 0.0023 (stat)\pm 0.0011 (syst)$, was obtained giving an upper limit, $| P_T | < 0.0050$. The T-violation parameter was determined to be Im$\xi = -0.0053 \pm 0.0071(stat)\pm 0.0036(syst)$ giving an upper limit, $|$Im$\xi| <0.016$.Comment: 5 pages, 4 figure

Apparatus for a Search for T-violating Muon Polarization in Stopped-Kaon Decays

The detector built at KEK to search for T-violating transverse muon polarization in K+ --> pi0 mu+ nu (Kmu3) decay of stopped kaons is described. Sensitivity to the transverse polarization component is obtained from reconstruction of the decay plane by tracking the mu+ through a toroidal spectrometer and detecting the pi0 in a segmented CsI(Tl) photon calorimeter. The muon polarization was obtained from the decay positron asymmetry of muons stopped in a polarimeter. The detector included features which minimized systematic errors while maintaining high acceptance.Comment: 56 pages, 30 figures, submitted to NI

Homogenization of weakly coupled systems of Hamilton--Jacobi equations with fast switching rates

We consider homogenization for weakly coupled systems of Hamilton--Jacobi equations with fast switching rates. The fast switching rate terms force the solutions converge to the same limit, which is a solution of the effective equation. We discover the appearance of the initial layers, which appear naturally when we consider the systems with different initial data and analyze them rigorously. In particular, we obtain matched asymptotic solutions of the systems and rate of convergence. We also investigate properties of the effective Hamiltonian of weakly coupled systems and show some examples which do not appear in the context of single equations.Comment: final version, to appear in Arch. Ration. Mech. Ana

Cytotoxicity and ion release of alloy nanoparticles

It is well-known that nanoparticles could cause toxic effects in cells. Alloy nanoparticles with yet unknown health risk may be released from cardiovascular implants made of Nickel–Titanium or Cobalt–Chromium due to abrasion or production failure. We show the bio-response of human primary endothelial and smooth muscle cells exposed to different concentrations of metal and alloy nanoparticles. Nanoparticles having primary particle sizes in the range of 5–250 nm were generated using laser ablation in three different solutions avoiding artificial chemical additives, and giving access to formulations containing nanoparticles only stabilized by biological ligands. Endothelial cells are found to be more sensitive to nanoparticle exposure than smooth muscle cells. Cobalt and Nickel nanoparticles caused the highest cytotoxicity. In contrast, Titanium, Nickel–Iron, and Nickel–Titanium nanoparticles had almost no influence on cells below a nanoparticle concentration of 10 μM. Nanoparticles in cysteine dissolved almost completely, whereas less ions are released when nanoparticles were stabilized in water or citrate solution. Nanoparticles stabilized by cysteine caused less inhibitory effects on cells suggesting cysteine to form metal complexes with bioactive ions in media

Test of exotic scalar and tensor interactions in K_e3 decay using stopped positive kaons

The form factors of the decay K+ --> pi0 e+ nu (K_e3) have been determined from the comparison of the experimental and Monte Carlo Dalitz distributions containing about 10^5 K_e3 events. The following values of the parameters were obtained: lambda_+ = 0.0278 +- 0.0017(stat) +- 0.0015(syst), f_S/f_+(0) = 0.0040 +- 0.0160(stat) +- 0.0067(syst) and f_T/f_+(0) = 0.019 +- 0.080(stat) +- 0.038(syst). Both scalar f_S and tensor f_T form factors are consistent with the Standard Model predictions of zero values.Comment: 10 pages, 5 figures, contributed to the proceedings of NANP Conference, Dubna, June 19-23, 200

No Evidence for Natural Selection on Endogenous Borna-Like Nucleoprotein Elements after the Divergence of Old World and New World Monkeys

Endogenous Borna-like nucleoprotein (EBLNs) elements were recently discovered as non-retroviral RNA virus elements derived from bornavirus in the genomes of various animals. Most of EBLNs appeared to be defective, but some of primate EBLN-1 to -4, which appeared to be originated from four independent integrations of bornavirus nucleoprotein (N) gene, have retained an open reading frame (ORF) for more than 40 million years. It was therefore possible that primate EBLNs have encoded functional proteins during evolution. To examine this possibility, natural selection operating on all ORFs of primate EBLN-1 to -4 was examined by comparing the rates of synonymous and nonsynonymous substitutions. The expected number of premature termination codons in EBLN-1 generated after the divergence of Old World and New World monkeys under the selective neutrality was also examined by the Monte Carlo simulation. As a result, natural selection was not identified for the entire region as well as parts of ORFs in the pairwise analysis of primate EBLN-1 to -4 and for any branch of the phylogenetic trees for EBLN-1 to -4 after the divergence of Old World and New World monkeys. Computer simulation also indicated that the absence of premature termination codon in the present-day EBLN-1 does not necessarily support the maintenance of function after the divergence of Old World and New World monkeys. These results suggest that EBLNs have not generally encoded functional proteins after the divergence of Old World and New World monkeys