Lineage specific recombination rates and microevolution in Listeria monocytogenes

Background: The bacterium Listeria monocytogenes is a saprotroph as well as an opportunistic human foodborne pathogen, which has previously been shown to consist of at least two widespread lineages (termed lineages I and II) and an uncommon lineage (lineage III). While some L. monocytogenes strains show evidence for considerable diversification by homologous recombination, our understanding of the contribution of recombination to L. monocytogenes evolution is still limited. We therefore used STRUCTURE and ClonalFrame, two programs that model the effect of recombination, to make inferences about the population structure and different aspects of the recombination process in L. monocytogenes. Analyses were performed using sequences for seven loci (including the house-keeping genes gap, prs, purM and ribC, the stress response gene sigB, and the virulence genes actA and inlA) for 195 L. monocytogenes isolates. Results: Sequence analyses with ClonalFrame and the Sawyer's test showed that recombination is more prevalent in lineage II than lineage I and is most frequent in two house-keeping genes (ribC and purM) and the two virulence genes (actA and inlA). The relative occurrence of recombination versus point mutation is about six times higher in lineage II than in lineage I, which causes a higher genetic variability in lineage II. Unlike lineage I, lineage II represents a genetically heterogeneous population with a relatively high proportion (30% average) of genetic material imported from external sources. Phylograms, constructed with correcting for recombination, as well as Tajima's D data suggest that both lineages I and II have suffered a population bottleneck. Conclusion: Our study shows that evolutionary lineages within a single bacterial species can differ considerably in the relative contributions of recombination to genetic diversification. Accounting for recombination in phylogenetic studies is critical, and new evolutionary models that account for the possibility of changes in the rate of recombination would be required. While previous studies suggested that only L. monocytogenes lineage I has experienced a recent bottleneck, our analyses clearly show that lineage II experienced a bottleneck at about the same time, which was subsequently obscured by abundant homologous recombination after the lineage II bottleneck. While lineage I and lineage II should be considered separate species from an evolutionary viewpoint, maintaining single species name may be warranted since both lineages cause the same type of human disease

Field-induced insulating states in a graphene superlattice

We report on high-field magnetotransport (B up to 35 T) on a gated superlattice based on single-layer graphene aligned on top of hexagonal boron nitride. The large-period moir\'e modulation (15 nm) enables us to access the Hofstadter spectrum in the vicinity of and above one flux quantum per superlattice unit cell (Phi/Phi_0 = 1 at B = 22 T). We thereby reveal, in addition to the spin-valley antiferromagnet at nu = 0, two insulating states developing in positive and negative effective magnetic fields from the main nu = 1 and nu = -2 quantum Hall states respectively. We investigate the field dependence of the energy gaps associated with these insulating states, which we quantify from the temperature-activated peak resistance. Referring to a simple model of local Landau quantization of third generation Dirac fermions arising at Phi/Phi_0 = 1, we describe the different microscopic origins of the insulating states and experimentally determine the energy-momentum dispersion of the emergent gapped Dirac quasi-particles

Thermally activated intersubband scattering and oscillating magnetoresistance in quantum wells

Experimental studies of magnetoresistance in high-mobility wide quantum wells reveal oscillations which appear with an increase in temperature to 10 K and whose period is close to that of Shubnikov-de Haas oscillations. The observed phenomenon is identified as magnetointersubband oscillations caused by the scattering of electrons between two occupied subbands and the third subband which becomes occupied as a result of thermal activation. These small-period oscillations are less sensitive to thermal suppression than the largeperiod magnetointersubband oscillations caused by the scattering between the first and the second subbands. Theoretical study, based on consideration of electron scattering near the edge of the third subband, gives a reasonable explanation of our experimental findings.Comment: 9 pages, 5 figure

Structural and calorimetric studies demonstrate that the hepatocyte nuclear factor 1β (HNF1β) transcription factor is imported into the nucleus via a monopartite NLS sequence.

The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in ovarian clear cell carcinoma (CCC) and is a potential therapeutic target. To explore potential approaches that block HNF1β transcription we have identified and characterised extensively the nuclear localisation signal (NLS) for HNF1β and its interactions with the nuclear protein import receptor, Importin-α. Pull-down assays demonstrated that the DNA binding domain of HNF1β interacted with a spectrum of Importin-α isoforms and deletion constructs tagged with eGFP confirmed that the HNF1β (229)KKMRRNR(235) sequence was essential for nuclear localisation. We further characterised the interaction between the NLS and Importin-α using complementary biophysical techniques and have determined the 2.4Å resolution crystal structure of the HNF1β NLS peptide bound to Importin-α. The functional, biochemical, and structural characterisation of the nuclear localisation signal present on HNF1β and its interaction with the nuclear import protein Importin-α provide the basis for the development of compounds targeting transcription factor HNF1β via its nuclear import pathway.We thank our colleagues in Cambridge for their assistance, comments and criticisms. M.W. is funded by Cancer Research UK, Department of Chemistry at the University of Cambridge, School of the Physical Sciences and the Cambridge Cancer Centre. Funding in part was also provided by Medical Research Council Grant U105178939 to M.S. We would like to thank the Biorepository, Research Instrumentation, and Microscopy facilities at the Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK for assistance and Matthew Maggiolini for proofreading. We are grateful for the use of the Diamond Light Source Synchrotron (Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK) for data collection.This is the author accepted manuscript. The final version is available from Elsevier at http://dx.doi.org/10.1016/j.jsb.2016.06.018

Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

<p>Abstract</p> <p>Background</p> <p>The bacterium <it>Salmonella enterica </it>includes a diversity of serotypes that cause disease in humans and different animal species. Some <it>Salmonella </it>serotypes show a broad host range, some are host restricted and exclusively associated with one particular host, and some are associated with one particular host species, but able to cause disease in other host species and are thus considered "host adapted". Five <it>Salmonella </it>genome sequences, representing a broad host range serotype (Typhimurium), two host restricted serotypes (Typhi [two genomes] and Paratyphi) and one host adapted serotype (Choleraesuis) were used to identify core genome genes that show evidence for recombination and positive selection.</p> <p>Results</p> <p>Overall, 3323 orthologous genes were identified in all 5 <it>Salmonella </it>genomes analyzed. Use of four different methods to assess homologous recombination identified 270 genes that showed evidence for recombination with at least one of these methods (false discovery rate [FDR] <10%). After exclusion of genes with evidence for recombination, site and branch specific models identified 41 genes as showing evidence for positive selection (FDR <20%), including a number of genes with confirmed or likely roles in virulence and <it>ompC</it>, a gene encoding an outer membrane protein, which has also been found to be under positive selection in other bacteria. A total of 8, 16, 7, and 5 genes showed evidence for positive selection in Choleraesuis, Typhi, Typhimurium, and Paratyphi branch analyses, respectively. Sequencing and evolutionary analyses of four genes in an additional 42 isolates representing 23 serotypes confirmed branch specific positive selection and recombination patterns.</p> <p>Conclusion</p> <p>Our data show that, among the four serotypes analyzed, (i) less than 10% of <it>Salmonella </it>genes in the core genome show evidence for homologous recombination, (ii) a number of <it>Salmonella </it>genes are under positive selection, including genes that appear to contribute to virulence, and (iii) branch specific positive selection contributes to the evolution of host restricted <it>Salmonella </it>serotypes.</p

Validation of flank-to-flank allometric equations in predicting weight of lactating sows and lactation weight change

The objectives of this study were to validate the use of flank-to-flank measurement in predicting weight of lactating sows and to determine the accuracy of the developed models in estimating lactation weight change. A total of 70 lactating sows (PIC Line 1050) were used in this study. Flank-to-flank measurement and body weight were measured on each individual sow after farrowing and at weaning. Flank-to-flank measurement and weight of lactating sows was positively correlated (R2 = 0.61; P<.0001) with the following equation: BW0.33, kg = 0.0371 x Flank-to-flank (cm) + 2.161. Weights of sows post-farrowing and at weaning were lower (P<0.03) when predicted with the previous allometric model developed from growing pigs and sows than their actual weights or weights predicted using the lactating sow model. Likewise, absolute residuals for post-farrowing and weaning weights using a previous allometric model developed from growing pigs and gestating sows were greater (P<0.02) than those of the lactating sow model. There were no differences (P<0.89) between the predicted weights using the lactating sow model and their actual weights. There also were no differences between the actual average weight loss (P<0.14) and the predicted loss using the lactating sow model. Using the model previously developed with growing pigs and gestating sows resulted in 15.5 lb (P<0.007) greater than the actual average weight loss. In conclusion, flank-to-flank measurement can be used as a predictor of weight of lactating sows, with the relationship having less accuracy than those used for growing-finishing pigs, gestating sows, and boars. The pig allometric equation cannot be used to estimate weights of lactating sows and lactation weight change. The developed lactating sow model was more appropriate in estimating weights and weight loss at the herd level, but needs to be validated on other sows before use can be recommended

Shedding New Light on Kaon-Nucleon/Nuclei Interaction and Its Astrophysical Implications with the AMADEUS Experiment at DAFNE

The AMADEUS experiment deals with the investigation of the low-energy kaon-nuclei hadronic interaction at the DA{\Phi}NE collider at LNF-INFN, which is fundamental to respond longstanding questions in the non-perturbative QCD strangeness sector. The antikaon-nucleon potential is investigated searching for signals from possible bound kaonic clusters, which would open the possibility for the formation of cold dense baryonic matter. The confirmation of this scenario may imply a fundamental role of strangeness in astrophysics. AMADEUS step 0 consisted in the reanalysis of 2004/2005 KLOE dataset, exploiting K- absorptions in H, 4He, 9Be and 12C in the setup materials. In this paper, together with a review on the multi-nucleon K- absorption and the particle identification procedure, the first results on the {\Sigma}0-p channel will be presented including a statistical analysis on the possible accomodation of a deeply bound stateComment: 6 pages, 2 figure, 1 table, HADRON 2015 conferenc

Estimating CO₂ emissions for 108000 European cities

City-level CO₂ emissions inventories are foundational for supporting the EU's decarbonization goals. Inventories are essential for priority setting and for estimating impacts from the decarbonization transition. Here we present a new CO₂ emissions inventory for all 116572 municipal and local-government units in Europe, containing 108000 cities at the smallest scale used. The inventory spatially disaggregates the national reported emissions, using nine spatialization methods to distribute the 167 line items detailed in the National Inventory Reports (NIRs) using the UNFCCC (United Nations Framework Convention on Climate Change) Common Reporting Framework (CRF). The novel contribution of this model is that results are provided per administrative jurisdiction at multiple administrative levels, following the region boundaries defined OpenStreetMap, using a new spatialization approach