DNA Rereplication Is Susceptible to Nucleotide-Level Mutagenesis.

The sources of genome instability, a hallmark of cancer, remain incompletely understood. One potential source is DNA rereplication, which arises when the mechanisms that prevent the reinitiation of replication origins within a single cell cycle are compromised. Using the budding yeast Saccharomyces cerevisiae, we previously showed that DNA rereplication is extremely potent at inducing gross chromosomal alterations and that this arises in part because of the susceptibility of rereplication forks to break. Here, we examine the ability of DNA rereplication to induce nucleotide-level mutations. During normal replication these mutations are restricted by three overlapping error-avoidance mechanisms: the nucleotide selectivity of replicative polymerases, their proofreading activity, and mismatch repair. Using lys2InsEA14 , a frameshift reporter that is poorly proofread, we show that rereplication induces up to a 30× higher rate of frameshift mutations and that this mutagenesis is due to passage of the rereplication fork, not secondary to rereplication fork breakage. Rereplication can also induce comparable rates of frameshift and base-substitution mutations in a more general mutagenesis reporter CAN1, when the proofreading activity of DNA polymerase ε is inactivated. Finally, we show that the rereplication-induced mutagenesis of both lys2InsEA14 and CAN1 disappears in the absence of mismatch repair. These results suggest that mismatch repair is attenuated during rereplication, although at most sequences DNA polymerase proofreading provides enough error correction to mitigate the mutagenic consequences. Thus, rereplication can facilitate nucleotide-level mutagenesis in addition to inducing gross chromosomal alterations, broadening its potential role in genome instability

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104}, 527 (2006) and J. Chem.\Phys. {\bf 124}, 084905 (2006)). In the level-set method, a possible solute-solvent interface is represented by the zero level-set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy {\it functional} that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerene $C_{60}$. The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system

High Performance P3M N-body code: CUBEP3M

This paper presents CUBEP3M, a publicly-available high performance cosmological N-body code and describes many utilities and extensions that have been added to the standard package. These include a memory-light runtime SO halo finder, a non-Gaussian initial conditions generator, and a system of unique particle identification. CUBEP3M is fast, its accuracy is tuneable to optimize speed or memory, and has been run on more than 27,000 cores, achieving within a factor of two of ideal weak scaling even at this problem size. The code can be run in an extra-lean mode where the peak memory imprint for large runs is as low as 37 bytes per particles, which is almost two times leaner than other widely used N-body codes. However, load imbalances can increase this requirement by a factor of two, such that fast configurations with all the utilities enabled and load imbalances factored in require between 70 and 120 bytes per particles. CUBEP3M is well designed to study large scales cosmological systems, where imbalances are not too large and adaptive time-stepping not essential. It has already been used for a broad number of science applications that require either large samples of non-linear realizations or very large dark matter N-body simulations, including cosmological reionization, halo formation, baryonic acoustic oscillations, weak lensing or non-Gaussian statistics. We discuss the structure, the accuracy, known systematic effects and the scaling performance of the code and its utilities, when applicable.Comment: 20 pages, 17 figures, added halo profiles, updated to match MNRAS accepted versio

Electron transport through dipyrimidinyl-diphenyl diblock molecular wire: protonation effect

Recently, rectifying direction inversion has been observed in dipyrimidinyl-diphenyl (PMPH) diblock molecular wire [J. Am. Chem. Soc. (2005) 127, 10456], and a protonation mechanism was suggested to explain this interesting phenomena. In this paper, we study the protonation effect on transport properties of PMPH molecule by first principles calculations. No significant rectification is found for the pristine diblock molecular wire. Protonation leads to conductance enhancement and rectification. However, for all considered junctions with rectifying effect, the preferential current directions are samely from dipyrimidinyl side to diphenyl side. Effect of molecule-electrode anchoring geometry is studied, and it is not responsible for the discrepancy between experiment and theory.Comment: 17 pages, 8 figure

Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics

Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge theoretical descriptions. Here, we devise a holistic, implicit-solvent, multi-method approach to predict the (un)binding kinetics for a generic ligand-pocket model. We use the variational implicit-solvent model (VISM) to calculate the solute-solvent interfacial structures and the corresponding free energies, and combine the VISM with the string method to obtain the minimum energy paths and transition states between the various metastable ('dry' and 'wet') hydration states. The resulting dry-wet transition rates are then used in a spatially-dependent multi-state continuous-time Markov chain Brownian dynamics simulations, and the related Fokker-Planck equation calculations, of the ligand stochastic motion, providing the mean first-passage times for binding and unbinding. We find the hydration transitions to significantly slow down the binding process, in semi-quantitative agreement with existing explicit-water simulations, but significantly accelerate the unbinding process. Moreover, our methods allow the characterization of non-equilibrium hydration states of pocket and ligand during the ligand movement, for which we find substantial memory and hysteresis effects for binding versus unbinding. Our study thus provides a significant step forward towards efficient, physics-based interpretation and predictions of the complex kinetics in realistic ligand-receptor systems.Comment: 6 pages, 5 figures, accepted for publication in Proc. Natl. Acad. Sci. (PNAS

Orbital Interaction Mechanisms of Conductance Enhancement and Rectification by Dithiocarboxylate Anchoring Group

We study computationally the electron transport properties of dithiocarboxylate terminated molecular junctions. Transport properties are computed self-consistently within density functional theory and nonequilibrium Green's functions formalism. A microscopic origin of the experimentally observed current amplification by dithiocarboxylate anchoring groups is established. For the 4,4'-biphenyl bis(dithiocarboxylate) junction, we find that the interaction of the lowest unoccupied molecular orbital (LUMO) of the dithiocarboxylate anchoring group with LUMO and highest occupied molecular orbital (HOMO) of the biphenyl part results in bonding and antibonding resonances in the transmission spectrum in the vicinity of the electrode Fermi energy. A new microscopic mechanism of rectification is predicted based on the electronic structure of asymmetrical anchoring groups. We show that the peaks in the transmission spectra of 4'-thiolato-biphenyl-4-dithiocarboxylate junction respond differently to the applied voltage. Depending upon the origin of a transmission resonance in the orbital interaction picture, its energy can be shifted along with the chemical potential of the electrode to which the molecule is more strongly or more weakly coupled

Assessment of retinal vascular calibres as a biomarker of disease activity in birdshot chorioretinopathy

Purpose Birdshot chorioretinopathy (BCR) is a potentially blinding ocular disorder involving the retinal vasculature and choroid without any systemic manifestations. The objective of the study was to describe vascular calibre changes in BCR and analyse the possibility of this optical biomarker for staging and monitoring disease activity in BCR. Methods This retrospective case–control study at a tertiary referral eye centre in the UK included 33 eyes from 21 patients with BCR and equal number of eyes from control subjects. Diagnosis of BCR was confirmed on fundus fluorescein and indocyanine green angiography. Vascular calibres were measured using validated semiautomated software. Results Patients with BCR had smaller retinal venular calibres central retinal venular equivalent (CRVE) than controls (211.3 versus 227.9 μm, p = 0.008). After adjusting for variables, the difference between the two groups for CRVE at baseline was statistically significant based on two different analysis methods. Central retinal venular equivalent (CRVE) was lower at the 6-month follow-up visit (206.2 versus 213.8 μm, p-value = 0.03), and arteriole-to-venule ratio was larger (0.74 versus 0.71, p = 0.04) in subjects with BCR. Arteriolar calibre (CRAE) remained the same. Conclusion This study provides novel insight into the pattern of vascular involvement in BCR. There was significant difference in the CRVE in patients with BCR. More studies are needed to correlate this data with visual function and treatment outcome and to validate the findings

Cross section measurement of N 14 ( p , γ ) O 15 in the CNO cycle

Background: The CNO cycle is the main energy source in stars more massive than our sun; it defines the energy production and the cycle time that lead to the lifetime of massive stars, and it is an important tool for the determination of the age of globular clusters. In our sun about 1.6% of the total solar neutrino flux comes from the CNO cycle. The largest uncertainty in the prediction of this CNO flux from the standard solar model comes from the uncertainty in the ^{14}\mathrm{N}(p,\ensuremath{\gamma})^{15}\mathrm{O} reaction rate; thus, the determination of the cross section at astrophysical temperatures is of great interest.Purpose: The total cross section of the ^{14}\mathrm{N}(p,\ensuremath{\gamma})^{15}\mathrm{O} reaction has large contributions from the transitions to the ${E}_{x}=6.79\phantom{\rule{4pt}{0ex}}\mathrm{MeV}$ excited state and the ground state of $^{15}\mathrm{O}$. The ${E}_{x}=6.79\phantom{\rule{4pt}{0ex}}\mathrm{MeV}$ transition is dominated by radiative direct capture, while the ground state is a complex mixture of direct and resonance capture components and the interferences between them. Recent studies have concentrated on cross-section measurements at very low energies, but broad resonances at higher energy may also play a role. A single measurement has been made that covers a broad higher-energy range but it has large uncertainties stemming from uncorrected summing effects. Furthermore, the extrapolations of the cross section vary significantly depending on the data sets considered. Thus, new direct measurements have been made to improve the previous high-energy studies and to better constrain the extrapolation.Methods: Measurements were performed at the low-energy accelerator facilities of the nuclear science laboratory at the University of Notre Dame. The cross section was measured over the proton energy range from ${E}_{p}=0.7$ to 3.6 MeV for both the ground state and the ${E}_{x}=6.79\phantom{\rule{4.pt}{0ex}}\mathrm{MeV}$ transitions at {\ensuremath{\theta}}_{\text{lab}}={0}^{\ensuremath{\circ}}, {45}^{\ensuremath{\circ}}, {90}^{\ensuremath{\circ}}, {135}^{\ensuremath{\circ}}, and {150}^{\ensuremath{\circ}}. Both TiN and implanted-$^{14}\mathrm{N}$ targets were utilized. \ensuremath{\gamma} rays were detected by using an array of high-purity germanium detectors.Results: The excitation function as well as angular distributions of the two transitions were measured. A multichannel $R$-matrix analysis was performed with the present data and is compared with previous measurements. The analysis covers a wide energy range so that the contributions from broad resonances and direct capture can be better constrained.Conclusion: The astrophysical $S$ factors of the ${E}_{x}=6.79\phantom{\rule{4.pt}{0ex}}\mathrm{MeV}$ and the ground-state transitions were extrapolated to low energies with the newly measured differential-cross-section data. Based on the present work, the extrapolations yield {S}_{6.79}(0)=1.29\ifmmode\pm\else\textpm\fi{}0.04(\mathrm{stat})\ifmmode\pm\else\textpm\fi{}0.09(\mathrm{syst})\phantom{\rule{4pt}{0ex}}\mathrm{keV}\phantom{\rule{0.16em}{0ex}}\mathrm{b} and {S}_{\text{g.s.}}(0)=0.42\ifmmode\pm\else\textpm\fi{}0.04(\mathrm{stat})\phantom{\rule{4pt}{0ex}}\mathrm{keV}\phantom{\rule{0.16em}{0ex}}\mathrm{b}. While significant improvement and consistency is found in modeling the ${E}_{x}=6.79\phantom{\rule{4.pt}{0ex}}\mathrm{MeV}$ transition, large inconsistencies in both the $R$-matrix fitting and the low-energy data are reaffirmed for the ground-state transition. Reflecting this, a systematic uncertainty of {}_{\ensuremath{-}0.19}^{+0.09}\phantom{\rule{4pt}{0ex}}\mathrm{keV}\phantom{\rule{0.16em}{0ex}}\mathrm{b} is recommended for the ground-state transition

Temperature dependence of polaronic transport through single molecules and quantum dots

Motivated by recent experiments on electric transport through single molecules and quantum dots, we investigate a model for transport that allows for significant coupling between the electrons and a boson mode isolated on the molecule or dot. We focus our attention on the temperature dependent properties of the transport. In the Holstein picture for polaronic transport in molecular crystals the temperature dependence of the conductivity exhibits a crossover from coherent (band) to incoherent (hopping) transport. Here, the temperature dependence of the differential conductance on resonance does not show such a crossover, but is mostly determined by the lifetime of the resonant level on the molecule or dot.Comment: 8 pages, 7 figure

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism