Trends of the major porin gene (ompF) evolution

OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species

Experimental studies and nuclear model calculations on (p,xn) and (p,pxn) reactions on 85Rb from their threshold up to 100 MeV

Excitation functions were measured by the stacked-foil technique for the reactions Rb-85(p, pxn)Rb-89m,Rb-g83,Rb-82m.81 from their thresholds up to 100MeV. Nuclear model calculations were performed using the code ALICE-IPPE both on (p, xn) reactions reported earlier and (p, pxn) reactions described here. The experimental excitation curves and the results of nuclear model calculations were found to be qualitatively in agreement. With the exception of the (p, n) reaction above 40MeV, the theory appears to reproduce all the experimental data within deviations of about 50%. The cross section ratios for the isomeric pairs Sr-85m,Sr-g and Rb-84m,Rb-g are discussed qualitatively in terms of the spins of the states involved and the increasing projectile energy

Quantum Graphs II: Some spectral properties of quantum and combinatorial graphs

The paper deals with some spectral properties of (mostly infinite) quantum and combinatorial graphs. Quantum graphs have been intensively studied lately due to their numerous applications to mesoscopic physics, nanotechnology, optics, and other areas. A Schnol type theorem is proven that allows one to detect that a point belongs to the spectrum when a generalized eigenfunction with an subexponential growth integral estimate is available. A theorem on spectral gap opening for ``decorated'' quantum graphs is established (its analog is known for the combinatorial case). It is also shown that if a periodic combinatorial or quantum graph has a point spectrum, it is generated by compactly supported eigenfunctions (``scars'').Comment: 4 eps figures, LATEX file, 21 pages Revised form: a cut-and-paste blooper fixe

Hydrodynamic limit for weakly asymmetric simple exclusion processes in crystal lattices

We investigate the hydrodynamic limit for weakly asymmetric simple exclusion processes in crystal lattices. We construct a suitable scaling limit by using a discrete harmonic map. As we shall observe, the quasi-linear parabolic equation in the limit is defined on a flat torus and depends on both the local structure of the crystal lattice and the discrete harmonic map. We formulate the local ergodic theorem on the crystal lattice by introducing the notion of local function bundle, which is a family of local functions on the configuration space. The ideas and methods are taken from the discrete geometric analysis to these problems. Results we obtain are extensions of ones by Kipnis, Olla and Varadhan to crystal lattices.Comment: 41 pages, 7 figure