Genetic markers in s. Paratyphi c reveal primary adaptation to pigs

Salmonella enterica with the identical antigenic formula 6,7:c:1,5 can be differentiated biochemically and by disease syndrome. One grouping, Salmonella Paratyphi C, is currently considered a typhoidal serovar, responsible for enteric fever in humans. The human-restricted typhoidal serovars (S. Typhi and Paratyphi A, B and C) typically display high levels of genome degradation and are cited as an example of convergent evolution for host adaptation in humans. However, S. Paratyphi C presents a different clinical picture to S. Typhi/Paratyphi A, in a patient group with predisposition, raising the possibility that its natural history is different, and that infection is invasive salmonellosis rather than enteric fever. Using whole genome sequencing and metabolic pathway analysis, we compared the genomes of 17 S. Paratyphi C strains to other members of the 6,7:c:1,5 group and to two typhoidal serovars: S. Typhi and Paratyphi A. The genome degradation observed in S. Paratyphi C was much lower than S. Typhi/Paratyphi A, but similar to the other 6,7:c:1,5 strains. Genomic and metabolic comparisons revealed little to no overlap between S. Paratyphi C and the other typhoidal serovars, arguing against convergent evolution and instead providing evidence of a primary adaptation to pigs in accordance with the 6,7:c:1.5 strains

The malleability of uranium: manipulating the charge-density wave in epitaxial films

We report x-ray synchrotron experiments on epitaxial films of uranium, deposited on niobium and tungsten seed layers. Despite similar lattice parameters for these refractory metals, the uranium epitaxial arrangements are different and the strains propagated along the a-axis of the uranium layers are of opposite sign. At low temperatures these changes in epitaxy result in dramatic modifications to the behavior of the charge-density wave in uranium. The differences are explained with the current theory for the electron-phonon coupling in the uranium lattice. Our results emphasize the intriguing possibilities of producing epitaxial films of elements that have complex structures like the light actinides uranium to plutonium.Comment: 6 pages, 6 figure

Late Holocene landscape change history related to the Alpine Fault determined from drowned forests in Lake Poerua, Westland, New Zealand

Lake Poerua is a small, shallow lake that abuts the scarp of the Alpine Fault on the West Coast of New Zealand’s South Island. Radiocarbon dates from drowned podocarp trees on the lake floor, a sediment core from a rangefront alluvial fan, and living tree ring ages have been used to deduce the late Holocene history of the lake. Remnant drowned stumps of kahikatea (Dacrycarpus dacrydioides) at 1.7–1.9m water depth yield a preferred time-ofdeath age at 1766–1807 AD, while a dryland podocarp and kahikatea stumps at 2.4–2.6m yield preferred time-of-death ages of ca. 1459–1626 AD. These age ranges are matched to, but offset from, the timings of Alpine Fault rupture events at ca. 1717 AD, and either ca. 1615 or 1430 AD. Alluvial fan detritus dated from a core into the toe of a rangefront alluvial fan, at an equivalent depth to the maximum depth of the modern lake (6.7 m), yields a calibrated age of AD 1223–1413. This age is similar to the timing of an earlier Alpine Fault rupture event at ca. 1230AD±50 yr. Kahikatea trees growing on rangefront fans give ages of up to 270 yr, which is consistent with alluvial fan aggradation following the 1717AD earthquake. The elevation levels of the lake and fan imply a causal and chronological link between lake-level rise and Alpine Fault rupture. The results of this study suggest that the growth of large, coalescing alluvial fans (Dry and Evans Creek fans) originating from landslides within the rangefront of the Alpine Fault and the rise in the level of Lake Poerua may occur within a decade or so of large Alpine Fault earthquakes that rupture adjacent to this area. These rises have in turn drowned lowland forests that fringed the lake. Radiocarbon chronologies built using OxCal show that a series of massive landscape changes beginning with fault rupture, followed by landsliding, fan sedimentation and lake expansion. However, drowned Kahikatea trees may be poor candidates for intimately dating these events, as they may be able to tolerate water for several decades after metre-scale lake level rises have occurred

Positional, Reorientational and Bond Orientational Order in DNA Mesophases

We investigate the orientational order of transverse polarization vectors of long, stiff polymer molecules and their coupling to bond orientational and positional order in high density mesophases. Homogeneous ordering of transverse polarization vector promotes distortions in the hexatic phase, whereas inhomogeneous ordering precipitates crystalization of the 2D sections with different orientations of the transverse polarization vector on each molecule in the unit cell. We propose possible scenarios for going from the hexatic phase, through the distorted hexatic phase to the crystalline phase with an orthorhombic unit cell observed experimentally for the case of DNA.Comment: 4 pages, 2 figure

Conformational stability in dinucleoside phosphate crystals. Semiempirical potential energy calculations for uridylyl-3'-5'-adenosine monophosphate (UpA) and guanylyl-3',5'-cytidine monophosphate (GpC)

Classical potential energy calculations were performed for the dinucleoside phosphates UpA and GpC. Two widely accessible low-energy regions of conformation space were found for the w', w pair. That of lowest energy contains conformations similar to helical RNA, with w' and w in the vicinity of 300° and 280°, respectively. All five experimental observations of crystalline GpC, two of ApU, and the helical fragment of ApApA fall in this range. The second lowest region has w' and w at about 20° and 80°, respectively, which is in the general region of one experimentally observed crystalline conformer of UpA, and the nonhelical region of ApApA. It is concluded that GpC and ApU, which were crystallized as either sodium or calcium salts, are shielded from each other in the crystal by the water of hydration and are therefore free to adopt their predicted in vacuo minimum energy helical conformations. By contrast, crystalline UpA had only 1/2 water per molecule, and was forced into higher energy conformations in order to maximize intermolecular hydrogen bonding