Pyrimido[1,2-a]-purin-10(3H)-one, M(1)G, is less prone to artifact than base oxidation

Pyrimido[1,2-a]-purin-10(3H)-one (M(1)G) is a secondary DNA damage product arising from primary reactive oxygen species (ROS) damage to membrane lipids or deoxyribose. The present study investigated conditions that might lead to artifactual formation or loss of M(1)G during DNA isolation. The addition of antioxidants, DNA isolation at low temperature or non-phenol extraction methods had no statistically significant effect on the number of M(1)G adducts measured in either control or positive control tissue samples. The number of M(1)G adducts in nuclear DNA isolated from brain, liver, kidney, pancreas, lung and heart of control male rats were 0.8, 1.1, 1.1, 1.1, 1.8 and 4.2 M(1)G/10(8) nt, respectively. In rat liver tissue, the mitochondrial DNA contained a 2-fold greater number of M(1)G adducts compared with nuclear DNA. Overall, the results from this study demonstrated that measuring M(1)G is a reliable way to assess oxidative DNA damage because the number of M(1)G adducts is significantly affected by the amount of ROS production, but not by DNA isolation procedures. In addition, this study confirmed that the background number of M(1)G adducts reported in genomic DNA could have been overestimated by one to three orders of magnitude in previous reports

tRNA modification profiles in obligate and moderate thermophilic bacilli

Transfer RNAs (tRNAs) are the most ancient RNA molecules in the cell, modification pattern of which is linked to phylogeny. The aim of this study was to determine the tRNA modification profiles of obligate (Anoxybacillus, Geobacillus, Paragebacillus) and moderate (Bacillus, Brevibacillus, Ureibacillus, Paenibacillus) thermophilic aerobic bacilli strains to find out its linkage to phylogenetic variations between species. LC-MS was applied for the quantification of modified nucleosides using both natural and isotopically labeled standards. The presence of m(2)A and m(7)G modifications at high levels was determined in all species. Relatively high level of i(6)A and m(5)C modification was observed for Paenibacillus and Ureibacillus, respectively. The lowest level of Cm modification was found in Bacillus. The modification ms(2)i(6)A and m(1)G were absent in Brevibacillus and Ureibacillus, respectively, while modifications Am and m(2)(2)G were observed only for Ureibacillus. While both obligate and moderate thermophilic species contain Gm, m(1)G and ms(2)i(6)A modifications, large quantities of them (especially Gm and ms(2)i(6)A modification) were detected in obligate thermophilic ones (Geobacillus, Paragebacillus and Anoxybacillus). The collective set of modified tRNA bases is genus-specific and linked to the phylogeny of bacilli. In addition, the dataset could be applied to distinguish obligate thermophilic bacilli from moderate ones

The Virtual Element Method with curved edges

In this paper we initiate the investigation of Virtual Elements with curved faces. We consider the case of a fixed curved boundary in two dimensions, as it happens in the approximation of problems posed on a curved domain or with a curved interface. While an approximation of the domain with polygons leads, for degree of accuracy $k \geq 2$, to a sub-optimal rate of convergence, we show (both theoretically and numerically) that the proposed curved VEM lead to an optimal rate of convergence

Finite Order BFFT Method

We have proposed a method in the context of BFFT approach that leads to truncation of the infinite series regarded to constraints in the extended phase space, as well as other physical quantities (such as Hamiltonian). This has been done for cases where the matrix of Poisson brackets among the constraints is symplectic or constant. The method is applied to Proca model, single self dual chiral bosons and chiral Schwinger models as examples.Comment: 14 pages, no figure to appear in Int. J. of Mod. Phys.

Learning the dynamics of articulated tracked vehicles

In this work, we present a Bayesian non-parametric approach to model the motion control of ATVs. The motion control model is based on a Dirichlet Process-Gaussian Process (DP-GP) mixture model. The DP-GP mixture model provides a flexible representation of patterns of control manoeuvres along trajectories of different lengths and discretizations. The model also estimates the number of patterns, sufficient for modeling the dynamics of the ATV

Linking and causality in globally hyperbolic spacetimes

The linking number $lk$ is defined if link components are zero homologous. Our affine linking invariant $alk$ generalizes $lk$ to the case of linked submanifolds with arbitrary homology classes. We apply $alk$ to the study of causality in Lorentz manifolds. Let $M^m$ be a spacelike Cauchy surface in a globally hyperbolic spacetime $(X^{m+1}, g)$. The spherical cotangent bundle $ST^*M$ is identified with the space $N$ of all null geodesics in $(X,g).$ Hence the set of null geodesics passing through a point $x\in X$ gives an embedded $(m-1)$-sphere $S_x$ in $N=ST^*M$ called the sky of $x.$ Low observed that if the link $(S_x, S_y)$ is nontrivial, then $x,y\in X$ are causally related. This motivated the problem (communicated by Penrose) on the Arnold's 1998 problem list to apply link theory to the study of causality. The spheres $S_x$ are isotopic to fibers of $(ST^*M)^{2m-1}\to M^m.$ They are nonzero homologous and $lk(S_x,S_y)$ is undefined when $M$ is closed, while $alk(S_x, S_y)$ is well defined. Moreover, $alk(S_x, S_y)\in Z$ if $M$ is not an odd-dimensional rational homology sphere. We give a formula for the increment of \alk under passages through Arnold dangerous tangencies. If $(X,g)$ is such that $alk$ takes values in $\Z$ and $g$ is conformal to $g'$ having all the timelike sectional curvatures nonnegative, then $x, y\in X$ are causally related if and only if $alk(S_x,S_y)\neq 0$. We show that $x,y$ in nonrefocussing $(X, g)$ are causally unrelated iff $(S_x, S_y)$ can be deformed to a pair of $S^{m-1}$-fibers of $ST^*M\to M$ by an isotopy through skies. Low showed that if (\ss, g) is refocussing, then $M$ is compact. We show that the universal cover of $M$ is also compact.Comment: We added: Theorem 11.5 saying that a Cauchy surface in a refocussing space time has finite pi_1; changed Theorem 7.5 to be in terms of conformal classes of Lorentz metrics and did a few more changes. 45 pages, 3 figures. A part of the paper (several results of sections 4,5,6,9,10) is an extension and development of our work math.GT/0207219 in the context of Lorentzian geometry. The results of sections 7,8,11,12 and Appendix B are ne

Multidimensional replica-exchange method for free-energy calculations

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.Comment: 13 pages, (ReVTeX), 9 figures. J. Chem. Phys. 113 (2000), in pres