Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I.

The mechanism by which DNA polymerases achieve their extraordinary accuracy has been intensely studied because of the linkage between this process and mutagenesis and carcinogenesis. Here, we have used single-molecule fluorescence microscopy to study the process of nucleotide selection and exonuclease action. Our results show that the binding of Escherichia coli DNA polymerase I (Klenow fragment) to a primer-template is stabilized by the presence of the next correct dNTP, even in the presence of a large excess of the other dNTPs and rNTPs. These results are consistent with a model where nucleotide selection occurs in the open complex prior to the formation of a closed ternary complex. Our assay can also distinguish between primer binding to the polymerase or exonuclease domain and, contrary to ensemble-averaged studies, we find that stable exonuclease binding only occurs with a mismatched primer terminus

Twisting of Siegel paramodular forms

Let $S_k(\Gamma^{\mathrm{para}}(N))$ be the space of Siegel paramodular forms of level $N$ and weight $k$. Let $p\nmid N$ and let $\chi$ be a nontrivial quadratic Dirichlet character mod $p$. Based on our previous work, we define a linear twisting map $\mathcal{T}_\chi:S_k(\Gamma^{\mathrm{para}}(N))\rightarrow S_k(\Gamma^{\mathrm{para}}(Np^4))$. We calculate an explicit expression for this twist and give the commutation relations of this map with the Hecke operators and Atkin-Lehner involution for primes $\ell\neq p$.Comment: 64 pages. In version 2, the paper has been shortened significantly and lengthy, technical proofs given in a separate appendix. In version 3, two typos are corrected. In version 4, we have included the full details of the proof of the local twisting theorem in the paper and improved the results with the L-function theore

The electron lifetime in Luttinger liquids

We investigate the decoherence of the electron wavepacket in purely ballistic one-dimensional systems described through the Luttinger liquid (LL). At a finite temperature $T$ and long times $t$, we show that the electron Green's function for a fixed wavevector close to one Fermi point decays as $\exp(-t/\tau_F)$, as opposed to the power-law behavior occurring at short times, and the emerging electron lifetime obeys $\tau_F^{-1}\propto T$ for spinful as well as spinless electrons. For strong interactions, $(T\tau_F)\ll 1$, reflecting that the electron is not a good Landau quasiparticle in LLs. We justify that fractionalization is the main source of electron decoherence for spinful as well as spinless electrons clarifying the peculiar electron mass renormalization close to the Fermi points. For spinless electrons and weak interactions, our intuition can be enriched through a diagrammatic approach or Fermi Golden rule and through a Johnson-Nyquist noise picture. We stress that the electron lifetime (and the fractional quasiparticles) can be revealed from Aharonov-Bohm experiments or momentum resolved tunneling. We aim to compare the results with those of spin-incoherent and chiral LLs.Comment: 20 pages, 1 column, 6 figures, 1 Table; expands cond-mat/0110307 and cond-mat/0503652; final version to appear in PR

Official Regulations and the Shadow Economy: A Labour Market Approach

This work revisits the role of regulations in emergence o f the shadow economy. In particular, it supplements the previous theoretical research that mainly ignored the fact that the decision to “go underground” is essentially a result of both employers and employees interacting in the labour market. We adapt a job search approach (see, e.g. Acemoglu 2001) to model a transitional economy with an informal sector. We apply and develop the idea first documented inter alia by Loayaza (1996) that there are two types of regulations that influence the size of the informal labour market through two different channels. Red tape and bureaucratic extortion (bribing) make starting a new business officially a not very attractive option and can lead new firms to the informal sector. On the other hand, taxes and redundancy pay make official firms offer lower wages which drives potential employees away into underground jobs. Depending on various combinations of policy parameters equilibria with different share of the informal economy are possible. The paper draws conclusions regarding the role of unemployment benefits in reducing the size of the informal economy. Policy implications are offered.http://deepblue.lib.umich.edu/bitstream/2027.42/39909/3/wp524.pd

Relationships among fat mass, fat-free mass and height in adults: A new method of statistical analysis applied to NHANES data

Objectives: The positive influence of fat mass (FM) on fat-free mass (FFM) has been quantified previously by various methods involving regression analysis of population data, but some are fundamentally flawed through neglect of the tendency of taller individuals to carry more fat. Differences in FFM due to differences in FM—and not directly related to differences in height—are expressed as ΔFFM/ΔFM, denoted KF. The main aims were to find a sounder regression-based method of quantifying KF and simultaneously of estimating mean BMI0, the BMI of hypothetical fat-free individuals. Other, related, objectives were to check the linearity of FFM-FM relationships and to quantify the correlation between FM and height. Methods: New statistical methods, explored and verified by Monte Carlo simulation, were applied to NHANES data. Regression of height2 on FFM and FM produced estimates of mean KF and indirectly of BMI0. Both were then adjusted to allow for variability in KF around its mean. Its standard deviation was estimated by a novel method. Results: Relationships between FFM and FM were linear, not semilogarithmic as is sometimes assumed. Mean KF is similar in Mexican American men and women, but higher in men than women in non-Hispanic European Americans and African Americans. Mean BMI0 is higher in men than in women. FM correlates more strongly with height than has been found previously. Conclusions: A more accurate way of quantifying mean BMI0 and the dependence of FFM on FM is established that may be easily applied to new and existing population data

Manifestation of important role of nuclear forces in emission of photons in scattering of pions off nuclei

Bremsstrahlung of photons emitted during the scattering of $\pi^{+}$-mesons off nuclei is studied for the first time. Role of interactions between $\pi^{+}$-mesons and nuclei in the formation of the bremsstrahlung emission is analyzed in details. We discover essential contribution of emitted photons from nuclear part of Johnson-Satchler potential to the full spectrum, in contrast to the optical Woods-Saxon potential. We observe unusual essential influence of the nuclear part of both potentials on the spectrum at high photon energies. This phenomenon opens a new experimental way to study and check non-Coulomb and nuclear interactions between pions and nuclei via measurements of the emitted photons. We provide predictions of the bremsstrahlung spectra for pion scattering off $^{44}{\rm Ca}$.Comment: 14 pages, 3 figure

Relativistic Mean-Field Theory Equation of State of Neutron Star Matter and a Maxwellian Phase Transition to Strange Quark Matter

The equation of state of neutron star matter is examined in terms of the relativistic mean-field theory, including a scalar-isovector $\delta$-meson effective field. The constants of the theory are determined numerically so that the empirically known characteristics of symmetric nuclear matter are reproduced at the saturation density. The thermodynamic characteristics of both asymmetric nucleonic matter and $\beta$-equilibrium hadron-electron $npe$-plasmas are studied. Assuming that the transition to strange quark matter is an ordinary first-order phase transition described by Maxwell's rule, a detailed study is made of the variations in the parameters of the phase transition owing to the presence of a $\delta$-meson field. The quark phase is described using an improved version of the bag model, in which interactions between quarks are accounted for in a one-gluon exchange approximation. The characteristics of the phase transition are determined for various values of the bag parameter within the range $B\in[60,120]$ $MeV/fm^{3}$ and it is shown that including a $\delta$-meson field leads to a reduction in the phase transition pressure $P_{0}$ and in the concentrations $n_{N}$ and $n_{Q}$ at the phase transition point.Comment: 17 pages, 8 figure