CPD damage recognition by transcribing RNA polymerase II.

Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light–induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5′-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II

Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region

The design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing Bradyrhizobium japonicum is reported here. The custom-synthesized chip (Affymetrix GeneChip®) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. RNA was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regR mutant and microaerobically grown nifA mutant. Comparative microarray analyses thus revealed genes that are transcribed in either a RegR- or a NifA-dependent manner plus genes whose expression depends on the cellular oxygen status. Several genes were newly identified as members of the RegR and NifA regulons, beyond genes, which had been known from previous work. A comprehensive transcription analysis was performed with one of the new RegR-controlled genes (id880). Expression levels determined by microarray analysis of selected NifA- and RegR-controlled genes corresponded well with quantitative real-time PCR data, demonstrating the high complementarity of microarray analysis to classical methods of gene expression analysis in B. japonicum. Nevertheless, several previously established members of the NifA regulon were not detected as transcribed genes by microarray analysis, confirming the potential pitfalls of this approach also observed by other authors. By and large, this pilot study has paved the way towards the genome-wide transcriptome analysis of the 9.1-Mb B. japonicum genom

Drawing Graphs within Restricted Area

We study the problem of selecting a maximum-weight subgraph of a given graph such that the subgraph can be drawn within a prescribed drawing area subject to given non-uniform vertex sizes. We develop and analyze heuristics both for the general (undirected) case and for the use case of (directed) calculation graphs which are used to analyze the typical mistakes that high school students make when transforming mathematical expressions in the process of calculating, for example, sums of fractions

Self-Averaging, Distribution of Pseudo-Critical Temperatures and Finite Size Scaling in Critical Disordered Systems

The distributions $P(X)$ of singular thermodynamic quantities in an ensemble of quenched random samples of linear size $l$ at the critical point $T_c$ are studied by Monte Carlo in two models. Our results confirm predictions of Aharony and Harris based on Renormalization group considerations. For an Ashkin-Teller model with strong but irrelevant bond randomness we find that the relative squared width, $R_X$, of $P(X)$ is weakly self averaging. $R_X\sim l^{\alpha/\nu}$, where $\alpha$ is the specific heat exponent and $\nu$ is the correlation length exponent of the pure model fixed point governing the transition. For the site dilute Ising model on a cubic lattice, known to be governed by a random fixed point, we find that $R_X$ tends to a universal constant independent of the amount of dilution (no self averaging). However this constant is different for canonical and grand canonical disorder. We study the distribution of the pseudo-critical temperatures $T_c(i,l)$ of the ensemble defined as the temperatures of the maximum susceptibility of each sample. We find that its variance scales as $(\delta T_c(l))^2 \sim l^{-2/\nu}$ and NOT as $\sim l^{-d}. We find that$R_\chi$is reduced by a factor of$\sim 70$with respect to$R_\chi (T_c)$by measuring$\chi$of each sample at$T_c(i,l)$. We analyze correlations between the magnetization at criticality$m_i(T_c,l)$and the pseudo-critical temperature$T_c(i,l)$in terms of a sample independent finite size scaling function of a sample dependent reduced temperature$(T-T_c(i,l))/T_c$. This function is found to be universal and to behave similarly to pure systems.Comment: 31 pages, 17 figures, submitted to Phys. Rev.

Computer simulation of the critical behavior of 3D disordered Ising model

The critical behavior of the disordered ferromagnetic Ising model is studied numerically by the Monte Carlo method in a wide range of variation of concentration of nonmagnetic impurity atoms. The temperature dependences of correlation length and magnetic susceptibility are determined for samples with various spin concentrations and various linear sizes. The finite-size scaling technique is used for obtaining scaling functions for these quantities, which exhibit a universal behavior in the critical region; the critical temperatures and static critical exponents are also determined using scaling corrections. On the basis of variation of the scaling functions and values of critical exponents upon a change in the concentration, the conclusion is drawn concerning the existence of two universal classes of the critical behavior of the diluted Ising model with different characteristics for weakly and strongly disordered systems.Comment: 14 RevTeX pages, 6 figure

Congested Traffic States in Empirical Observations and Microscopic Simulations

We present data from several German freeways showing different kinds of congested traffic forming near road inhomogeneities, specifically lane closings, intersections, or uphill gradients. The states are localized or extended, homogeneous or oscillating. Combined states are observed as well, like the coexistence of moving localized clusters and clusters pinned at road inhomogeneities, or regions of oscillating congested traffic upstream of nearly homogeneous congested traffic. The experimental findings are consistent with a recently proposed theoretical phase diagram for traffic near on-ramps [D. Helbing, A. Hennecke, and M. Treiber, Phys. Rev. Lett. {\bf 82}, 4360 (1999)]. We simulate these situations with a novel continuous microscopic single-lane model, the ``intelligent driver model'' (IDM), using the empirical boundary conditions. All observations, including the coexistence of states, are qualitatively reproduced by describing inhomogeneities with local variations of one model parameter. We show that the results of the microscopic model can be understood by formulating the theoretical phase diagram for bottlenecks in a more general way. In particular, a local drop of the road capacity induced by parameter variations has practically the same effect as an on-ramp.Comment: Now published in Phys. Rev. E. Minor changes suggested by a referee are incorporated; full bibliographic info added. For related work see http://www.mtreiber.de/ and http://www.helbing.org

Derivation, Properties, and Simulation of a Gas-Kinetic-Based, Non-Local Traffic Model

We derive macroscopic traffic equations from specific gas-kinetic equations, dropping some of the assumptions and approximations made in previous papers. The resulting partial differential equations for the vehicle density and average velocity contain a non-local interaction term which is very favorable for a fast and robust numerical integration, so that several thousand freeway kilometers can be simulated in real-time. The model parameters can be easily calibrated by means of empirical data. They are directly related to the quantities characterizing individual driver-vehicle behavior, and their optimal values have the expected order of magnitude. Therefore, they allow to investigate the influences of varying street and weather conditions or freeway control measures. Simulation results for realistic model parameters are in good agreement with the diverse non-linear dynamical phenomena observed in freeway traffic.Comment: For related work see http://www.theo2.physik.uni-stuttgart.de/helbing.html and http://www.theo2.physik.uni-stuttgart.de/treiber.htm

Wang-Landau study of the 3D Ising model with bond disorder

We implement a two-stage approach of the Wang-Landau algorithm to investigate the critical properties of the 3D Ising model with quenched bond randomness. In particular, we consider the case where disorder couples to the nearest-neighbor ferromagnetic interaction, in terms of a bimodal distribution of strong versus weak bonds. Our simulations are carried out for large ensembles of disorder realizations and lattices with linear sizes $L$ in the range $L=8-64$. We apply well-established finite-size scaling techniques and concepts from the scaling theory of disordered systems to describe the nature of the phase transition of the disordered model, departing gradually from the fixed point of the pure system. Our analysis (based on the determination of the critical exponents) shows that the 3D random-bond Ising model belongs to the same universality class with the site- and bond-dilution models, providing a single universality class for the 3D Ising model with these three types of quenched uncorrelated disorder.Comment: 7 pages, 7 figures, to be published in Eur. Phys. J.