RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip

Supplementary_Material. This docx file contains all supplementary tables and supplementary figures. (DOCX 424 kb

Comet assay to measure DNA repair: approach and applications

Cellular repair enzymes remove virtually all DNA damage before it is fixed; repair therefore plays a crucial role in preventing cancer. Repair studied at the level of transcription correlates poorly with enzyme activity, and so assays of phenotype are needed. In a biochemical approach, substrate nucleoids containing specific DNA lesions are incubated with cell extract; repair enzymes in the extract induce breaks at damage sites and the breaks are measured with the comet assay. The nature of the substrate lesions defines the repair pathway to be studied. This in vitro DNA repair assay has been modified for use in animal tissues, specifically to study the effects of aging and nutritional intervention on repair. Recently, the assay was applied to different strains of Drosophila melanogaster proficient and deficient in DNA repair. Most applications of the repair assay have been in human biomonitoring. Individual DNA repair activity may be a marker of cancer susceptibility; alternatively, high repair activity may result from induction of repair enzymes by exposure to DNA-damaging agents. Studies to date have examined effects of environment, nutrition, lifestyle and occupation, in addition to clinical investigations

Anomalous Diffusion in Aperiodic Environments

We study the Brownian motion of a classical particle in one-dimensional inhomogeneous environments where the transition probabilities follow quasiperiodic or aperiodic distributions. Exploiting an exact correspondence with the transverse-field Ising model with inhomogeneous couplings we obtain many new analytical results for the random walk problem. In the absence of global bias the qualitative behavior of the diffusive motion of the particle and the corresponding persistence probability strongly depend on the fluctuation properties of the environment. In environments with bounded fluctuations the particle shows normal diffusive motion and the diffusion constant is simply related to the persistence probability. On the other hand in a medium with unbounded fluctuations the diffusion is ultra-slow, the displacement of the particle grows on logarithmic time scales. For the borderline situation with marginal fluctuations both the diffusion exponent and the persistence exponent are continuously varying functions of the aperiodicity. Extensions of the results to disordered media and to higher dimensions are also discussed.Comment: 11 pages, RevTe

An ECVAG† trial on assessment of oxidative damage to DNA measured by the comet assay

The increasing use of single cell gel electrophoresis (the comet assay) highlights its popularity as a method for detecting DNA damage, including the use of enzymes for assessment of oxidatively damaged DNA. However, comparison of DNA damage levels between laboratories can be difficult due to differences in assay protocols (e.g. lysis conditions, enzyme treatment, the duration of the alkaline treatment and electrophoresis) and in the end points used for reporting results (e.g. %DNA in tail, arbitrary units, tail moment and tail length). One way to facilitate comparisons is to convert primary comet assay end points to number of lesions/106 bp by calibration with ionizing radiation. The aim of this study was to investigate the inter-laboratory variation in assessment of oxidatively damaged DNA by the comet assay in terms of oxidized purines converted to strand breaks with formamidopyrimidine DNA glycosylase (FPG). Coded samples with DNA oxidation damage induced by treatment with different concentrations of photosensitizer (Ro 19-8022) plus light and calibration samples irradiated with ionizing radiation were distributed to the 10 participating laboratories to measure DNA damage using their own comet assay protocols. Nine of 10 laboratories reported the same ranking of the level of damage in the coded samples. The variation in assessment of oxidatively damaged DNA was largely due to differences in protocols. After conversion of the data to lesions/106 bp using laboratory-specific calibration curves, the variation between the laboratories was reduced. The contribution of the concentration of photosensitizer to the variation in net FPG-sensitive sites increased from 49 to 73%, whereas the inter-laboratory variation decreased. The participating laboratories were successful in finding a dose–response of oxidatively damaged DNA in coded samples, but there remains a need to standardize the protocols to enable direct comparisons between laboratories

Local critical behaviour at aperiodic surface extended perturbation in the Ising quantum chain

The surface critical behaviour of the semi--infinite one--dimensional quantum Ising model in a transverse field is studied in the presence of an aperiodic surface extended modulation. The perturbed couplings are distributed according to a generalized Fredholm sequence, leading to a marginal perturbation and varying surface exponents. The surface magnetic exponents are calculated exactly whereas the expression of the surface energy density exponent is conjectured from a finite--size scaling study. The system displays surface order at the bulk critical point, above a critical value of the modulation amplitude. It may be considered as a discrete realization of the Hilhorst--van Leeuwen model.Comment: 13 pages, TeX file + 6 figures, epsf neede

Surface Magnetization of Aperiodic Ising Systems: a Comparative Study of the Bond and Site Problems

We investigate the influence of aperiodic perturbations on the critical behaviour at a second order phase transition. The bond and site problems are compared for layered systems and aperiodic sequences generated through substitution. In the bond problem, the interactions between the layers are distributed according to an aperiodic sequence whereas in the site problem, the layers themselves follow the sequence. A relevance-irrelevance criterion introduced by Luck for the bond problem is extended to discuss the site problem. It involves a wandering exponent for pairs, which can be larger than the one considered before in the bond problem. The surface magnetization of the layered two-dimensional Ising model is obtained, in the extreme anisotropic limit, for the period-doubling and Thue-Morse sequences.Comment: 19 pages, Plain TeX, IOP macros + epsf, 6 postscript figures, minor correction

Surface Magnetization and Critical Behavior of Aperiodic Ising Quantum Chains

We consider semi-infinite two-dimensional layered Ising models in the extreme anisotropic limit with an aperiodic modulation of the couplings. Using substitution rules to generate the aperiodic sequences, we derive functional equations for the surface magnetization. These equations are solved by iteration and the surface magnetic exponent can be determined exactly. The method is applied to three specific aperiodic sequences, which represent different types of perturbation, according to a relevance-irrelevance criterion. On the Thue-Morse lattice, for which the modulation is an irrelevant perturbation, the surface magnetization vanishes with a square root singularity, like in the homogeneous lattice. For the period-doubling sequence, the perturbation is marginal and the surface magnetic exponent varies continuously with the modulation amplitude. Finally, the Rudin-Shapiro sequence, which corresponds to the relevant case, displays an anomalous surface critical behavior which is analyzed via scaling considerations: Depending on the value of the modulation, the surface magnetization either vanishes with an essential singularity or remains finite at the bulk critical point, i.e., the surface phase transition is of first order.Comment: 8 pages, 7 eps-figures, uses RevTex and epsf, minor correction

DNA damage in circulating leukocytes measured with the comet assay may predict the risk of death

The comet assay or single cell gel electrophoresis, is the most common method used to measure strand breaks and a variety of other DNA lesions in human populations. To estimate the risk of overall mortality, mortality by cause, and cancer incidence associated to DNA damage, a cohort of 2,403 healthy individuals (25,978 person-years) screened in 16 laboratories using the comet assay between 1996 and 2016 was followed-up. Kaplan-Meier analysis indicated a worse overall survival in the medium and high tertile of DNA damage (p < 0.001). The effect of DNA damage on survival was modelled according to Cox proportional hazard regression model. The adjusted hazard ratio (HR) was 1.42 (1.06-1.90) for overall mortality, and 1.94 (1.04-3.59) for diseases of the circulatory system in subjects with the highest tertile of DNA damage. The findings of this study provide epidemiological evidence encouraging the implementation of the comet assay in preventive strategies for non-communicable diseases

hMMS2 serves a redundant role in human PCNA polyubiquitination

<p>Abstract</p> <p>Background</p> <p>In yeast, DNA damage leads to the mono and polyubiquitination of the sliding clamp PCNA. Monoubiquitination of PCNA is controlled by RAD18 (E3 ligase) and RAD6 (E2 conjugating enzyme), while the extension of the monoubiquitinated PCNA into a polyubiquitinated substrate is governed by RAD5, and the heterodimer of UBC13/MMS2. Each modification directs a different branch of the DNA damage tolerance pathway (DDT). While PCNA monoubiquitination leads to error-prone bypass via TLS, biochemical studies have identified MMS2 along with its heteromeric partner UBC13 to govern the error-free repair of DNA lesions by catalyzing the formation of lysine 63-linked polyubiquitin chains (K63-polyUb). Recently, it was shown that PCNA polyubiquitination is conserved in human cells and that this modification is dependent on RAD18, UBC13 and SHPRH. However, the role of hMMS2 in this process was not specifically addressed.</p> <p>Results</p> <p>In this report we show that mammalian cells in which MMS2 was reduced by siRNA-mediated knockdown maintains PCNA polyubiquitination while a knockdown of RAD18 or UBC13 abrogates PCNA ubiquitination. Moreover, the additional knockdown of a UEV1A (MMS2 homolog) does not deplete PCNA polyubiquitination. Finally, mouse embryonic stem cells null for MMS2 with or without the additional depletion of mUEV1A continue to polyubiquitinated PCNA with normal kinetics.</p> <p>Conclusion</p> <p>Our results point to a high level of redundancy in the DDT pathway and suggest the existence of another hMMS2 variant (hMMSv) or complex that can compensate for its loss.</p