Stress testing the ELBA water model

© 2015 © 2015 The Author(s). Published by Taylor & Francis. The ELBA coarse-grained model describes a water molecule as a single-site Lennard-Jones particle embedded with a point dipole. ELBA was previously reported to capture several properties of real water with relatively high accuracy, while being up to two orders of magnitude more computationally efficient than atomistic models. Here, we stress test the ELBA model by investigating the temperature and pressure dependences of two most important water properties, the liquid density and the self-diffusion coefficient. In particular, molecular dynamics simulations are performed spanning temperatures from 268 K up to 378 K and pressures from 1 atm up to 4000 atm. Comparisons are made with literature data from experiments and from simulations of traditional three-site atomistic models. Remarkably, the ELBA results show an overall similar (and sometimes higher) accuracy with respect to the atomistic data. We also calculate a number of additional thermodynamic properties at ambient conditions, namely isothermal compressibility, shear viscosity, isobaric heat capacity, thermal expansion coefficient and melting point. The accuracy of ELBA is relatively good compared to atomistic and other coarse-grained models

Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes

<p>Abstract</p> <p>Background</p> <p>The genus <it>Listeria </it>includes two closely related pathogenic and non-pathogenic species, <it>L. monocytogenes </it>and <it>L. innocua</it>. <it>L. monocytogenes </it>is an opportunistic human foodborne and animal pathogen that includes two common lineages. While lineage I is more commonly found among human listeriosis cases, lineage II appears to be overrepresented among isolates from foods and environmental sources. This study used the genome sequences for one <it>L. innocua </it>strain and four <it>L. monocytogenes </it>strains representing lineages I and II, to characterize the contributions of positive selection and recombination to the evolution of the <it>L. innocua</it>/<it>L. monocytogenes </it>core genome.</p> <p>Results</p> <p>Among the 2267 genes in the <it>L. monocytogenes/L. innocua </it>core genome, 1097 genes showed evidence for recombination and 36 genes showed evidence for positive selection. Positive selection was strongly associated with recombination. Specifically, 29 of the 36 genes under positive selection also showed evidence for recombination. Recombination was more common among isolates in lineage II than lineage I; this trend was confirmed by sequencing five genes in a larger isolate set. Positive selection was more abundant in the ancestral branch of lineage II (20 genes) as compared to the ancestral branch of lineage I (9 genes). Additional genes under positive selection were identified in the branch separating the two species; for this branch, genes in the role category "Cell wall and membrane biogenesis" were significantly more likely to have evidence for positive selection. Positive selection of three genes was confirmed in a larger isolate set, which also revealed occurrence of multiple premature stop codons in one positively selected gene involved in flagellar motility (<it>flaR</it>).</p> <p>Conclusion</p> <p>While recombination and positive selection both contribute to evolution of <it>L. monocytogenes</it>, the relative contributions of these evolutionary forces seem to differ by <it>L. monocytogenes </it>lineages and appear to be more important in the evolution of lineage II, which seems to be found in a broader range of environments, as compared to the apparently more host adapted lineage I. Diversification of cell wall and membrane biogenesis and motility-related genes may play a particularly important role in the evolution of <it>L. monocytogenes</it>.</p

Homopolymeric tracts represent a general regulatory mechanism in prokaryotes

<p>Abstract</p> <p>Background</p> <p>While, traditionally, regulation of gene expression can be grouped into transcriptional, translational, and post-translational mechanisms, some mechanisms of rapid genetic variation can also contribute to regulation of gene expression, e.g., phase variation.</p> <p>Results</p> <p>We show here that prokaryotes evolved to include homopolymeric tracts (HTs) within coding genes as a system that allows for efficient gene inactivation. Analyses of 81 bacterial and 18 archaeal genomes showed that poly(A) and poly(T) HTs are overrepresented in these genomes and preferentially located at the 5' end of coding genes. Location of HTs at the 5' end is not driven by a preferential placement of aminoacids encoded by the AAA and TTT codons at the N-terminal of proteins. The <it>inlA </it>gene of the pathogen <it>L. monocytogenes </it>was used as a model to further study the role of HTs in reversible gene inactivation. In a number of <it>L. monocytogenes </it>strains, <it>inlA </it>harbors a 5' poly(A) HT, which regularly shows frameshift mutation leading to expression of a truncated 8 aa InlA protein. Translational fusions of the <it>inlA </it>5' end allowed us to estimate that the frequency of variation in this HT is about 1,000 fold higher than the estimated average point mutation frequency.</p> <p>Conclusions</p> <p>As frameshift mutations in HTs can occur at high frequencies and enable efficient gene inactivation, hypermutable HTs appear to represent a universal system for regulation of gene expression in prokaryotes. Combined with other studies indicating that HTs also enable rapid diversification of both coding and regulatory genetic sequences in eukaryotes, our data suggest that hypermutable HTs represent a general and rapid evolutionary mechanism facilitating adaptation and gene regulation across diverse organisms.</p

Photon creation in a spherical oscillating cavity

We study the photon creation inside a perfectly conducting, spherical oscillating cavity. The electromagnetic field inside the cavity is described by means of two scalar fields which satisfy Dirichlet and (generalized) Neumann boundary conditions. As a preliminary step, we analyze the dynamical Casimir effect for both scalar fields. We then consider the full electromagnetic case. The conservation of angular momentum of the electromagnetic field is also discussed, showing that photons inside the cavity are created in singlet states.Comment: 14 pages, no figure

Volume of Mixing Effect on Fluid Counter-Diffusion

The counter-current diffusion-driven mixing process of two miscible fluids is studied in the absence of gravity, assuming that the mixture is non regular, that is its volume is smaller than the sum of the initial volumes of the two components. Two competing effects are present in the mixing region: on one hand, the mass flow rate of each species increases, due to the larger density of the fluid; on the other hand, though, the volumetric flux is retarded by the inward convection due to volume disappearance, which opposes the outward velocity field due to diffusion. This intuition is confirmed by the analytical result of a 1D non-ideal mixing process, showing that, in the presence of the convection induced by a volume decrease, a) the process is self-similar; b) the mass flux of each species at the interface increases by approximately 0.8 e, where e is the maximum relative volume decrease; c) the volume flux of each species decreases by approximately a 0.2 e amount. This result is further confirmed by a perturbation analysis for small e

Logical Rules and a Preliminary Prototype for Translating Mortality Coding Rules from ICD-10 to ICD-11

Iris is a system for coding multiple causes of death in ICD-10 and for the selection of the underlying cause of death, based on a knowledge base composed by a large number of rules. With the adoption of ICD-11, those rules need translation to ICD-11. A pre-project has been carried out to evaluate feasibility of transition to ICD-11, which included the analysis of the logical meta-rules needed for rule translation and development of a prototype support system for the expert that will translate the coding rules

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

Cooling and ventilating the abyssal ocean

The abyssal ocean is filled with cold, dense waters that sink along the Antarctic continental slope and overflow sills that lie south of the Nordic Seas. Recent integrations of chlorofluorocarbon‐11 (CFC) measurements are similar in Antarctic Bottom Water (AABW) and in lower North Atlantic Deep Water (NADW), but Antarctic inputs are ≈ 2°C colder than their northern counterparts. This indicates comparable ventilation rates from both polar regions, and accounts for the Southern Ocean dominance over abyssal cooling. The decadal CFC‐based estimates of recent ventilation are consistent with other hydrographic observations and with longer‐term radiocarbon data, but not with hypotheses of a 20th‐century slowdown in the rate of AABW formation. Significant variability is not precluded by the available ocean measurements, however, and interannual to decadal changes are increasingly evident at high latitudes

The Ross Sea: In a Sea of Change

The Ross Sea, the most productive region in the Antarctic, reaches farther south than any body of water in the world. While its food web is relatively intact, its oceanography, biogeochemistry, and sea ice coverage have been changing dramatically, and likely will continue to do so in the future. Sea ice cover and persistence have been increasing, in contrast to the Amundsen-Bellingshausen sector, which has resulted in reduced open water duration for its biota. Models predict that as the ozone hole recovers, ice cover will begin to diminish. Currents on the continental shelf will likely change in the coming century, with a projected intensification of flow leading to altered deep ocean ventilation. Such changes in ice and circulation will lead to altered plankton distributions and composition, but it is difficult at present to predict the nature of these changes. Iron and irradiance play central roles in regulating phytoplankton production in the Ross Sea, but the impacts of oceanographic changes on the biogeochemistry of iron are unclear. Unlike other Southern Ocean regions, where continental shelves are very narrow and Antarctic krill dominates the herbivorous fauna, the broad shelf of the Ross Sea is dominated by crystal krill and silverfish, which are the major prey items for higher trophic levels. At present, the Ross Sea is considered to be one of the most species-rich areas of the Southern Ocean and a biodiversity hotspot due to its heterogeneous habitats. Despite being among the best-studied regions in the entire Southern Ocean, accurate predictions of the impacts of climate change on the oceanography and ecology of the Ross Sea remain fraught with uncertainty