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

Helical magnetic structure and the anomalous and topological Hall effects in epitaxial B20 Fe1−y_{1-y}Coy_yGe films

Epitaxial films of the B20-structure alloy Fe$_{1-y}$Co$_y$Ge were grown by molecular beam epitaxy on Si (111) substrates. The magnetization varied smoothly from the bulk-like values of one Bohr magneton per Fe atom for FeGe to zero for non-magnetic CoGe. The chiral lattice structure leads to a Dzyaloshinskii-Moriya interaction (DMI), and the films' helical magnetic ground state was confirmed using polarized neutron reflectometry measurements. The pitch of the spin helix, measured by this method, varies with Co content $y$ and diverges at $y \sim 0.45$. This indicates a zero-crossing of the DMI, which we reproduced in calculations using first principle methods. We also measured the longitudinal and Hall resistivity of our films as a function of magnetic field, temperature, and Co content $y$. The Hall resistivity is expected to contain contributions from the ordinary, anomalous, and topological Hall effects. Both the anomalous and topological Hall resistivities show peaks around $y \sim 0.5$. Our first principles calculations show a peak in the topological Hall constant at this value of $y$, related to the strong spin-polarisation predicted for intermediate values of $y$. Half-metallicity is predicted for $y = 0.6$, consistent with the experimentally observed linear magnetoresistance at this composition. Whilst it is possible to reconcile theory with experiment for the various Hall effects for FeGe, the large topological Hall resistivities for $y \sim 0.5$ are much larger then expected when the very small emergent fields associated with the divergence in the DMI are taken into account

The elevated Curie temperature and half-metallicity in the ferromagnetic semiconductor Lax_{x}Eu1−x_{1-x}O

Here we study the effect of La doping in EuO thin films using SQUID magnetometry, muon spin rotation ($\mu$SR), polarized neutron reflectivity (PNR), and density functional theory (DFT). The $\mu$SR data shows that the La$_{0.15}$Eu$_{0.85}$O is homogeneously magnetically ordered up to its elevated $T_{\rm C}$. It is concluded that bound magnetic polaron behavior does not explain the increase in $T_{\rm C}$ and an RKKY-like interaction is consistent with the $\mu$SR data. The estimation of the magnetic moment by DFT simulations concurs with the results obtained by PNR, showing a reduction of the magnetic moment per La$_{x}$Eu$_{1-x}$O for increasing lanthanum doping. This reduction of the magnetic moment is explained by the reduction of the number of Eu-4$f$ electrons present in all the magnetic interactions in EuO films. Finally, we show that an upwards shift of the Fermi energy with La or Gd doping gives rise to half-metallicity for doping levels as high as 3.2 %.Comment: 7 pages, 11 figure

Small mammal responses to long-term large-scale woodland creation: the influence of local and landscape-level attributes

Habitat loss and fragmentation greatly affect biological diversity. Actions to counteract their negative effects include increasing the quality, amount and connectivity of semi-natural habitats at the landscape scale. However, much of the scientific evidence underpinning landscape restoration comes from studies of habitat loss and fragmentation, and it is unclear whether the ecological principles derived from habitat removal investigations are applicable to habitat creation. In addition, the relative importance of local- (e.g. improving habitat quality) vs. landscape-level (e.g. increasing habitat connectivity) actions to restore species is largely unknown, partly because studying species responses over sufficiently large spatial and temporal scales is challenging. We studied small mammal responses to large scale woodland creation spanning 150 years, and assessed the influence of local- and landscape-level characteristics on three small mammal species of varying woodland affinity. Woodland specialists, generalists and grassland specialists were present in woodlands across a range of ages from 10 to 160 years, demonstrating that these species can quickly colonize newly created woodlands. However, we found evidence that woodlands become gradually better over time for some species. The responses of individual species corresponded to their habitat specificity. A grassland specialist (Microtus agrestis) was influenced only by landscape attributes; a woodland generalist (Apodemus sylvaticus) and specialist (Myodes glareolus) were primarily influenced by local habitat attributes, and partially by landscape characteristics. At the local scale, high structural heterogeneity, large amounts of deadwood and a relatively open understory positively influenced woodland species (both generalists and specialists); livestock grazing had strong negative effects on woodland species abundance. Actions to enhance habitat quality at the patch scale focusing on these attributes would benefit these species. Woodland creation in agricultural landscapes is also likely to benefit larger mammals and birds of prey feeding on small mammals and increase ecosystem processes such as seed dispersal

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

<p>Abstract</p> <p>Background</p> <p>Of the > 2000 serovars of <it>Salmonella enterica </it>subspecies I, most cause self-limiting gastrointestinal disease in a wide range of mammalian hosts. However, <it>S. enterica </it>serovars Typhi and Paratyphi A are restricted to the human host and cause the similar systemic diseases typhoid and paratyphoid fever. Genome sequence similarity between Paratyphi A and Typhi has been attributed to convergent evolution via relatively recent recombination of a quarter of their genomes. The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi.</p> <p>Results</p> <p>We report the 4.5 Mbp genome of a clinical isolate of Paratyphi A, strain AKU_12601, completely sequenced using capillary techniques and subsequently checked using Illumina/Solexa resequencing. Comparison with the published genome of Paratyphi A ATCC9150 revealed the two are collinear and highly similar, with 188 single nucleotide polymorphisms and 39 insertions/deletions. A comparative analysis of pseudogene complements of these and two finished Typhi genomes (CT18, Ty2) identified several pseudogenes that had been overlooked in prior genome annotations of one or both serovars, and identified 66 pseudogenes shared between serovars. By determining whether each shared and serovar-specific pseudogene had been recombined between Paratyphi A and Typhi, we found evidence that most pseudogenes have accumulated after the recombination between serovars. We also divided pseudogenes into relative-time groups: ancestral pseudogenes inherited from a common ancestor, pseudogenes recombined between serovars which likely arose between initial divergence and later recombination, serovar-specific pseudogenes arising after recombination but prior to the last evolutionary bottlenecks in each population, and more recent strain-specific pseudogenes.</p> <p>Conclusion</p> <p>Recombination and pseudogene-formation have been important mechanisms of genetic convergence between Paratyphi A and Typhi, with most pseudogenes arising independently after extensive recombination between the serovars. The recombination events, along with divergence of and within each serovar, provide a relative time scale for pseudogene-forming mutations, affording rare insights into the progression of functional gene loss associated with host adaptation in <it>Salmonella</it>.</p

Data for Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica: date estimation 1

Salmonella enterica serovar Paratyphi C is the causative agent of enteric (paratyphoid) fever. While today a potentially lethal infection of humans that occurs in Africa and Asia, early 20th century observations in Eastern Europe suggest it may once have had a wider-ranging impact on human societies. We recovered a draft Paratyphi C genome from the 800-year-old skeleton of a young woman in Trondheim, Norway, who likely died of enteric fever. Analysis of this genome against a new, significantly expanded database of related modern genomes demonstrated that Paratyphi C is descended from the ancestors of swine pathogens, serovars Choleraesuis and Typhisuis, together forming the Para C Lineage. Our results indicate that Paratyphi C has been a pathogen of humans for at least 1,000 years, and may have evolved after zoonotic transfer from swine during the Neolithic period

The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource.

Studies of historical isolates inform on the evolution and emergence of important pathogens and phenotypes, including antimicrobial resistance. Crucial to studying antimicrobial resistance are isolates that predate the widespread clinical use of antimicrobials. The Murray collection of several hundred bacterial strains of pre-antibiotic era Enterobacteriaceae is an invaluable resource of historical strains from important pathogen groups. Studies performed on the Collection to date merely exemplify its potential, which will only be realised through the continued effort of many scientific groups. To enable that aim, we announce the public availability of the Murray collection through the National Collection of Type Cultures, and present associated metadata with whole genome sequence data for over half of the strains. Using this information we verify the metadata for the collection with regard to subgroup designations, equivalence groupings and plasmid content. We also present genomic analyses of population structure and determinants of mobilisable antimicrobial resistance to aid strain selection in future studies. This represents an invaluable public resource for the study of these important pathogen groups and the emergence and evolution of antimicrobial resistance