Tracking bacterial pathogens with genetically-encoded reporters

AbstractDuring the infectious process, bacterial pathogens are subject to changes in environmental conditions such as nutrient availability, immune response challenges, bacterial density and physical contacts with targeted host cells. These conditions occur in the colonized organs, in diverse regions within infected tissues or even at the subcellular level for intracellular pathogens. Integration of environmental cues leads to measurable biological responses in the bacterium required for adaptation. Recent progress in technology enabled the study of bacterial adaptation in situ using genetically encoded reporters that allow single cell analysis or whole body imaging based on fluorescent proteins, alternative fluorescent assays or luciferases. This review presents a historical perspective and technical details on the methods used to develop transcriptional reporters, protein–protein interaction assays and secretion detection assays to study pathogenic bacteria adaptation in situ. Finally, studies published in the last 5years on gram positive and gram negative bacterial adaptation to the host during infection are discussed. However, the methods described here could easily be extended to study complex microbial communities within host tissue and in the environment

Detection of positron-atom bound states through resonant annihilation

A method is proposed for detecting positron-atom bound states by observing enhanced positron annihilation due to electronic Feshbach resonances at electron-volt energies. The method is applicable to a range of open-shell transition metal atoms which are likely to bind the positron: Fe, Co, Ni, Tc, Ru, Rh, Sn, Sb, Ta, W, Os, Ir, and Pt. Estimates of their binding energies are provided.Comment: 5 pages, 1 figure; estimates of binding energies have been adde

Spin gaps and spin-flip energies in density-functional theory

Energy gaps are crucial aspects of the electronic structure of finite and extended systems. Whereas much is known about how to define and calculate charge gaps in density-functional theory (DFT), and about the relation between these gaps and derivative discontinuities of the exchange-correlation functional, much less is know about spin gaps. In this paper we give density-functional definitions of spin-conserving gaps, spin-flip gaps and the spin stiffness in terms of many-body energies and in terms of single-particle (Kohn-Sham) energies. Our definitions are as analogous as possible to those commonly made in the charge case, but important differences between spin and charge gaps emerge already on the single-particle level because unlike the fundamental charge gap spin gaps involve excited-state energies. Kohn-Sham and many-body spin gaps are predicted to differ, and the difference is related to derivative discontinuities that are similar to, but distinct from, those usually considered in the case of charge gaps. Both ensemble DFT and time-dependent DFT (TDDFT) can be used to calculate these spin discontinuities from a suitable functional. We illustrate our findings by evaluating our definitions for the Lithium atom, for which we calculate spin gaps and spin discontinuities by making use of near-exact Kohn-Sham eigenvalues and, independently, from the single-pole approximation to TDDFT. The many-body corrections to the Kohn-Sham spin gaps are found to be negative, i.e., single particle calculations tend to overestimate spin gaps while they underestimate charge gaps.Comment: 11 pages, 1 figure, 3 table

Controlled spontaneous emission

The problem of spontaneous emission is studied by a direct computer simulation of the dynamics of a combined system: atom + radiation field. The parameters of the discrete finite model, including up to 20k field oscillators, have been optimized by a comparison with the exact solution for the case when the oscillators have equidistant frequencies and equal coupling constants. Simulation of the effect of multi-pulse sequence of phase kicks and emission by a pair of atoms shows that both the frequency and the linewidth of the emitted spectrum could be controlled.Comment: 25 pages including 11 figure

HD 65949: Rosetta Stone or Red Herring

HD 65949 is a late B star with exceptionally strong Hg II at 3984[A], but it is not a typical HgMn star. The Re II spectrum is of extraordinary strength. Abundances, or upper limits are derived here for 58 elements based on a model with Teff = 13100K, and log(g) = 4.0. Even-Z elements through nickel show minor deviations from solar abundances. Anomalies among the odd-Z elements through copper are mostly small. Beyond the iron peak, a huge scatter is found. The abundance pattern of the heaviest elements resembles the N=126 r-process peak of solar material, though not in detail. We find a significant correlation of the abundance excesses with second ionization potentials for elements with Z > 30. This indicates the relevance of photospheric or near-photospheric processes. We explore a model with mass accretion of exotic material followed by the more commonly accepted differentiation by diffusion. That model leads to a number of predictions which challenge future work. Likely primary and secondary masses are near 3.3 and 1.6 M(solar), with a separation of ca. 0.25 AU. New atomic structure calculations are presented in two appendices.Comment: Accepted by MNRAS: 16 pages, 5 figure

Re II and Other Exotic Spectra in HD 65949

Powerful astronomical spectra reveal an urgent need for additional work on atomic lines, levels, and oscillator strengths. The star HD 65949 provides some excellent examples of species rarely identified in stellar spectra. For example, the Re II spectrum is well developed, with 17 lines between 3731 and 4904 [A], attributed wholly or partially to Re II. Classifications and oscillator strengths are lacking for a number of these lines. The spectrum of Os II is well identified. Of 14 lines attributed wholly or partially to Os II, only one has an entry in the VALD database. We find strong evidence that Te II is present. There are NO Te II lines in the VALD database. Ru II is clearly present, but oscillator strengths for lines in the visual are lacking. There is excellent to marginal evidence for a number of less commonly identified species, including Kr II, Nb II, Sb II, Xe II, Pr III, Ho III, Au II, and Pt II (probably Pt-198), to be present in the spectrum of HD 65949. The line Hg II at 3984 [A] is of outstanding strength, and all three lines of Multiplet 1 of Hg I are present, even though the surface temperature of HD 65949 is relatively high. Finally, we present the case of an unidentified, 24 [mA], line at 3859.63 [A], which could be the same feature seen in magnetic CP stars. It is typically blended with a putative U II line used in cosmochronology.Comment: ASOS9 Poster (Lund, Sweden, August 2007), to be published in Journal of Physics: Conference Series (JPCS), 6 pages 1 figur

Counting Oceanians of Non-European, Non-Asian Descent (ONENA) in the South Pacific to make them count in global health

Several diseases and vulnerabilities associated with genetic or microbial factors are more frequent among populations of Oceanian, Non-European, Non-Asian descent (ONENA). ONENA are specific and have long been isolated geographically. To our knowledge, there are no published official, quantitative, aggregated data on the populations impacted by these excess vulnerabilities in Oceania. We searched official census reports for updated estimates of the total population for each of the Pacific Island Countries and Territories (including Australia) and the US State of Hawaii, privileging local official statistical or censual sources. We multiplied the most recent total population estimate by the cumulative percentage of the ONENA population as determined in official reports. Including Australia and the US State of Hawaii, Oceania counts 27 countries and territories, populated in 2016 by approximately 41 M inhabitants (17 M not counting Australia) among which approximately 12.5 M (11.6 M not counting Australia) consider themselves of entire or partial ONENA ancestry. Specific genetic and microbiome traits of ONENA may be unique and need further investigation to adjust risk estimates, risk prevention, diagnostic and therapeutic strategies, to the benefit of populations in the Pacific and beyond

Electron affinity of Li: A state-selective measurement

We have investigated the threshold of photodetachment of Li^- leading to the formation of the residual Li atom in the $2p ^2P$ state. The excited residual atom was selectively photoionized via an intermediate Rydberg state and the resulting Li^+ ion was detected. A collinear laser-ion beam geometry enabled both high resolution and sensitivity to be attained. We have demonstrated the potential of this state selective photodetachment spectroscopic method by improving the accuracy of Li electron affinity measurements an order of magnitude. From a fit to the Wigner law in the threshold region, we obtained a Li electron affinity of 0.618 049(20) eV.Comment: 5 pages,6 figures,22 reference

A layering model for superconductivity in the borocarbides

We propose a superlattice model to describe superconductivity in layered materials, such as the borocarbide families with the chemical formul\ae\ $RT_2$B$_2$C and $RT$BC, with $R$ being (essentially) a rare earth, and $T$ a transition metal. We assume a single band in which electrons feel a local attractive interaction (negative Hubbard-$U$) on sites representing the $T$B layers, while U=0 on sites representing the $R$C layers; the multi-band structure is taken into account minimally through a band offset $\epsilon$. The one-dimensional model is studied numerically through the calculation of the charge gap, the Drude weight, and of the pairing correlation function. A comparison with the available information on the nature of the electronic ground state (metallic or superconducting) indicates that the model provides a systematic parametrization of the whole borocarbide family.Comment: 4 figure