Intestinal spirochaetes of the genus Brachyspira share a partially conserved 26 kilobase genomic region with Enterococcus faecalis and Escherichia coli

Anaerobic intestinal spirochaetes of the genus Brachyspira include both pathogenic and commensal species. The two best-studied members are the pathogenic species B. hyodysenteriae (the aetiological agent of swine dysentery) and B. pilosicoli (a cause of intestinal spirochaetosis in humans and other species). Analysis of near-complete genome sequences of these two species identifi ed a highly conserved 26 kilobase (kb) region that was shared, against a background of otherwise very little sequence conservation between the two species. PCR amplification was used to identify sets of contiguous genes from this region in the related Brachyspira species B. intermedia, B. innocens, B. murdochii, B. alvinipulli, and B. aalborgi, and demonstrated the presence of at least part of this region in species from throughout the genus. Comparative genomic analysis with other sequenced bacterial species revealed that none of the completely sequenced spirochaete species from different genera contained this conserved cluster of coding sequences. In contrast, Enterococcus faecalis and Escherichia coli contained high gene cluster conservation across the 26 kb region, against an expected background of little sequence conservation between these phylogenetically distinct species. The conserved region in B. hyodysenteriae contained five genes predicted to be associated with amino acid transport and metabolism, four with energy production and conversion, two with nucleotide transport and metabolism, one with ion transport and metabolism, and four with poorly characterised or uncertain function, including an ankyrin repeat unit at the 5’ end. The most likely explanation for the presence of this 26 kb region in the Brachyspira species and in two unrelated enteric bacterial species is that the region has been involved in horizontal gene transfer

Change in the distribution of a member of the strand line community: the seaweed fly (Diptera: Coelopidae)

1. Coastal organisms are predicted to be particularly susceptible to the impact of global warming. In this study the distribution and relative abundance of two coastal invertebrates, Coelopa frigida (Fabricius) and C. pilipes are investigated. 2. Coelopa pilipes has a more southerly distribution than C. frigida , and prefers a warmer climate. Coelopa pilipes is less resistant to sub-zero temperatures than C. frigida and its northerly distribution is probably limited by cold winter days. 3. The most recent distribution map of C. frigida and C. pilipes in northern Europe was published a decade ago and showed the northerly extent of the distribution of C. pilipes reaching the north coast of mainland Scotland but its complete absence from the Western and Northern Isles. 4. C. pilipes has now spread throughout the Western Isles and the Orkney Islands but is still absent from Shetland. There has also been an increase in the relative frequency of C. pilipes at sites harbouring coelopids on the British mainland. A similar pattern of distribution change along the west coast of Sweden is reported. 5. It is proposed that these changes have occurred primarily as a result of global warming and in particular due to the recent increase in winter temperatures. A number of other indirect effects may have also contributed to these changes, including a probable change in macroalgae distribution. The implications of these changes for the wrack bed ecosystem and at higher trophic levels are considered

Local Dynamics and Strong Correlation Physics I: 1D and 2D Half-filled Hubbard Models

We report on a non-perturbative approach to the 1D and 2D Hubbard models that is capable of recovering both strong and weak-coupling limits. We first show that even when the on-site Coulomb repulsion, U, is much smaller than the bandwith, the Mott-Hubbard gap never closes at half-filling in both 1D and 2D. Consequently, the Hubbard model at half-filling is always in the strong-coupling non-perturbative regime. For both large and small U, we find that the population of nearest-neighbour singlet states approaches a value of order unity as $T\to 0$ as would be expected for antiferromagnetic order. We also find that the double occupancy is a smooth monotonic function of U and approaches the anticipated non-interacting limit and large U limits. Finally, in our results for the heat capacity in 1D differ by no more than 1% from the Bethe ansatz predictions. In addition, we find that in 2D, the heat capacity vs T for different values of U exhibits a universal crossing point at two characteristic temperatures as is seen experimentally in a wide range of strongly-correlated systems such as $^3He$, $UBe_3$, and $CeCu_{6-x}Al_x$. The success of this method in recovering well-established results that stem fundamentally from the Coulomb interaction suggests that local dynamics are at the heart of the physics of strongly correlated systems.Comment: 10 pages, 16 figures included in text, Final version for publication with a reference added and minor corrections. Phys. Rev. B, in pres

Asymptotic Expansions for Stationary Distributions of Perturbed Semi-Markov Processes

New algorithms for computing of asymptotic expansions for stationary distributions of nonlinearly perturbed semi-Markov processes are presented. The algorithms are based on special techniques of sequential phase space reduction, which can be applied to processes with asymptotically coupled and uncoupled finite phase spaces.Comment: 83 page

Is weak temperature dependence of electron dephasing possible?

The first-principle theory of electron dephasing by disorder-induced two state fluctuators is developed. There exist two mechanisms of dephasing. First, dephasing occurs due to direct transitions between the defect levels caused by inelastic electron-defect scattering. The second mechanism is due to violation of the time reversal symmetry caused by time-dependent fluctuations of the scattering potential. These fluctuations originate from an interaction between the dynamic defects and conduction electrons forming a thermal bath. The first contribution to the dephasing rate saturates as temperature decreases. The second contribution does not saturate, although its temperature dependence is rather weak, $\propto T^{1/3}$. The quantitative estimates based on the experimental data show that these mechanisms considered can explain the weak temperature dependence of the dephasing rate in some temperature interval. However, below some temperature dependent on the model of dynamic defects the dephasing rate tends rapidly to zero. The relation to earlier studies of the dephasing caused by the dynamical defects is discussed.Comment: 14 pages, 6 figures, submitted to PR

A glassy contribution to the heat capacity of hcp 4^4He solids

We model the low-temperature specific heat of solid $^4$He in the hexagonal closed packed structure by invoking two-level tunneling states in addition to the usual phonon contribution of a Debye crystal for temperatures far below the Debye temperature, $T < \Theta_D/50$. By introducing a cutoff energy in the two-level tunneling density of states, we can describe the excess specific heat observed in solid hcp $^4$He, as well as the low-temperature linear term in the specific heat. Agreement is found with recent measurements of the temperature behavior of both specific heat and pressure. These results suggest the presence of a very small fraction, at the parts-per-million (ppm) level, of two-level tunneling systems in solid $^4$He, irrespective of the existence of supersolidity.Comment: 11 pages, 4 figure

Rings and rigidity transitions in network glasses

Three elastic phases of covalent networks, (I) floppy, (II) isostatically rigid and (III) stressed-rigid have now been identified in glasses at specific degrees of cross-linking (or chemical composition) both in theory and experiments. Here we use size-increasing cluster combinatorics and constraint counting algorithms to study analytically possible consequences of self-organization. In the presence of small rings that can be locally I, II or III, we obtain two transitions instead of the previously reported single percolative transition at the mean coordination number $\bar r=2.4$, one from a floppy to an isostatic rigid phase, and a second one from an isostatic to a stressed rigid phase. The width of the intermediate phase $~ \bar r$ and the order of the phase transitions depend on the nature of medium range order (relative ring fractions). We compare the results to the Group IV chalcogenides, such as Ge-Se and Si-Se, for which evidence of an intermediate phase has been obtained, and for which estimates of ring fractions can be made from structures of high T crystalline phases.Comment: 29 pages, revtex, 7 eps figure

Collective dynamics of internal states in a Bose gas

Theory for the Rabi and internal Josephson effects in an interacting Bose gas in the cold collision regime is presented. By using microscopic transport equation for the density matrix the problem is mapped onto a problem of precession of two coupled classical spins. In the absence of an external excitation field our results agree with the theory for the density induced frequency shifts in atomic clocks. In the presence of the external field, the internal Josephson effect takes place in a condensed Bose gas as well as in a non-condensed gas. The crossover from Rabi oscillations to the Josephson oscillations as a function of interaction strength is studied in detail.Comment: 18 pages, 2 figure

Antiferromagnetic and van Hove Scenarios for the Cuprates: Taking the Best of Both Worlds

A theory for the high temperature superconductors is proposed. Holes are spin-1/2, charge e, quasiparticles strongly dressed by spin fluctuations. Based on their dispersion, it is claimed that the experimentally observed van Hove singularities of the cuprates are likely originated by antiferromagnetic (AF) correlations. From the two carriers problem in the 2D t-J model, an effective Hamiltonian for holes is defined with %no free parameters. This effective model has superconductivity in the ${\rm d_{x^2-y^2}}$ channel, a critical temperature ${\rm T_c \sim 100K}$ at the optimal hole density, ${\rm x=0.15}$, and a quasiparticle lifetime linearly dependent with energy. Other experimental results are also $quantitatively$ reproduced by the theory.Comment: 12 pages, 4 figures (on request), RevTeX (version 3.0), preprint NHMF