Investigations into the molecular effects of single nucleotide polymorphism

Objectives: DNA sequences are very rich in short repeats and their pattern can be altered by point mutations. We wanted to investigate the effect of single nucleotide polymorphism (SNP) on the pattern of short DNA repeats and its biological consequences. Methods: Analysis of the pattern of short DNA repeats of the Thy-1 sequence with and without SNP. Searching for DNA-binding factors in any region of significance. Results: Comparing the pattern of short repeats in the Thy-1 gene sequences of Turkish patients with ataxia telangiectasia (AT) with the `wild type' sequence from the DNA database, we identified a missing 8-bp repeat element due to an SNP in position 1271 (intron II) in AT-DNA sequences. Only the mutated sequence had the potential for the formation of a stem loop in DNA or pre-mRNA. In super-shift experiments we found that DNA oligomers covering the area of this SNP formed a complex with proteins amongst which we identified the proliferating cell nuclear antigen (PCNA) protein. Conclusion: SNPs have the potential to alter DNA or pre-mRNA conformation. Although no SNP-depeding formation of the DNA-protein complex was evident, future investigations could reveal differential molecular mechanisms of cellular regulation. Copyright (C) 2001 S. Karger AG, Basel

Reply to Comment on "Critical analysis of a variational method used to describe molecular electron transport"

We show that the failure of the Delaney-Greer (DG) variational ansatz for transport demonstrated by us in Phys.\ Rev.\ B {\bf 80}, 165301 (2009) (I) is not related to an unsuitable constraint that prevents a broken time-reversal symmetry or to real orbitals, as DG incorrectly claim. The complex orbitals suggested by them as a way-out solution merely represent a particular case of the general case considered by us in I, which do not in the least affect our conclusion.Comment: Manuscript as submitted to Phys. Rev. B on 30 November 2010. Sections VII, VIII, and IX present significant details, which enlarge the analysis of the published versio

An Account of the Loss of the Country Ship Forbes and Frazer Sinclair, Her Late Commander

This paper reports on the life of the English Country trader Captain Frazer Sinclair leading up to and following the loss of the Forbes in the Karimata Strait in 1806. It examines the adventure and tenuous times of trading around the Indonesian archipelago after the fall of the VOC and subsequent transfer to the British. Included are the details of Captain Sinclair\u27s trading history, multiple prizes as a privateer, and shipwrecks

Chemical freezeout in relativistic A+A collisions: is it close to the QGP?

Preliminary experimental data for particle number ratios in the collisions of Au+Au at the BNL AGS (11A GeV/c) and Pb+Pb at the CERN SPS (160A GeV/c) are analyzed in a thermodynamically consistent hadron gas model with excluded volume. Large values of temperature, T = 140 185 MeV, and baryonic chemical potential, µb = 590 270 MeV, close to the boundary of the quark-gluon plasma phase are found from fitting the data. This seems to indicate that the energy density at the chemical freezeout is tremendous which would be indeed the case for the point-like hadrons. However, a self-consistent treatment of the van der Waals excluded volume reveals much smaller energy densities which are very far below a lowest limit estimate of the quark-gluon plasma energy density. PACS number(s): 25.75.-q, 24.10.P

Rapidity dependence of entropy production in proton- and nucleus-induced reactions on heavy nuclei

The entropy of hot nuclear systems is deduced from the mass distribution of fragments emitted from high energy proton- and nucleus-induced reactions via a quantum statistical model. It is found that the entropy per baryon, S/A, of intermediate rapidity ("participant") fragments is higher than the entropy of target rapidity ("spectator") fragments. The spectator fragments exhibit S/A values of ≅ 1.8 independent of the projectile energy from 30 MeV/nucleon up to 350 GeV. This value of the entropy coincides with the entropy at which nuclear matter becomes unbound

On a method to calculate conductance by means of the Wigner function: two critical tests

We have implemented the linear response approximation of a method proposed to compute the electron transport through correlated molecules based on the time-independent Wigner function [P. Delaney and J. C. Greer, \prl {\bf 93}, 36805 (2004)]. The results thus obtained for the zero-bias conductance through quantum dot both without and with correlations demonstrate that this method is either quantitatively nor qualitatively able to provide a correct physical escription of the electric transport through nanosystems. We present an analysis indicating that the failure is due to the manner of imposing the boundary conditions, and that it cannot be simply remedied.Comment: 22 pages, 7 figur

Mach Cones and Hydrodynamic Flow: Probing Big Bang Matter in the Laboratory

A critical discussion of the present signals for the phase transition to quark-gluon plasma (QGP) is given. Since hadronic rescattering models predict much larger flow than observed from 1 to 50 A GeV laboratory bombarding energies, this observation is interpreted as potential evidence for a first-order phase transition at high baryon density. A detailed discussion of the collective flow as a barometer for the equation of state (EoS) of hot dense matter at RHIC follows. Here, hadronic rescattering models can explain < 30 % of the observed elliptic flow v_2 for $p_T > 2$ GeV/c. This is interpreted as an evidence for the production of superdense matter at RHIC. The connection of v_2 to jet suppression is examined. A study of Mach shocks generated by fast partonic jets propagating through the QGP is given. The main goal is to take into account different types of collective motion during the formation and evolution of this matter. A significant deformation of Mach shocks in central Au+Au collisions at RHIC and LHC energies as compared to the case of jet propagation in a static medium is predicted. A new hydrodynamical study of jet energy loss is presented.Comment: 18 pages, 12 figures, presented at the IWCF 2006, Nov. 21-24, Hangzhou, Chin