Learning Tolerance while Fighting Ignorance

Research on microbe-host interactions focuses principally on pathogens, yet our immune system must deal with the huge number of beneficial commensal bacteria in our gut. It is becoming clear that the host immune system must reach a delicate balance between destroying dangerous bacterial pathogens while preserving the beneficial gut microbiota

State-insensitive bichromatic optical trapping

We propose a scheme for state-insensitive trapping of neutral atoms by using light with two independent wavelengths. In particular, we describe the use of trapping and control lasers to minimize the variance of the potential experienced by a trapped Rb atom in ground and excited states. We present calculated values of wavelength pairs for which the 5s and 5p_{3/2} levels have the same ac Stark shifts in the presence of two laser fields.Comment: 5 pages, 4 figure

Shigellosis: An Old Disease in New Clothes?

Sansonetti discusses a "landmark" study of the epidemiology of shigellosis, involving over 600,000 people of all ages in six Asian countries

Helium 2 3S - 2 1S metrology at 1557 nm

An experiment is proposed to excite the 'forbidden' 1s2s 3S1 - 1s2s 1S0 magnetic dipole (M1) transition at 1557 nm in a collimated and slow atomic beam of metastable helium atoms. It is demonstrated that an excitation rate of 5000 /s can be realised with the beam of a 2W narrowband telecom fiber laser intersecting the atomic beam perpendicularly. A Doppler-limited sub-MHz spectroscopic linewidth is anticipated. Doppler-free excitation of 2% of trapped and cooled atoms may be realised in a one-dimensional optical lattice geometry, using the 2W laser both for trapping and spectroscopy. The very small (8 Hz) natural linewidth of this transition presents an opportunity for accurate tests of atomic structure calculations of the helium atom. A measurement of the 3He - 4He isotope shift allows for accurate determination of the difference in nuclear charge radius of both isotopes.Comment: accepted for publication in Europhysics Letter

Electric Quadrupole Moments of Metastable States of Ca+, Sr+, and Ba+

Electric quadrupole moments of the metastable nd3/2 and nd5/2 states of Ca+, Sr+, and Ba+ are calculated using the relativistic all-order method including all single, double, and partial triple excitations of the Dirac-Hartree-Fock wave function to provide recommended values for the cases where no experimental data are available. The contributions of all non-linear single and double terms are also calculated for the case of Ca+ for comparison of our approach with the CCSD(T) results. The third-order many body perturbation theory is used to evaluate contributions of high partial waves and the Breit interaction. The remaining omitted correlation corrections are estimated as well. Extensive study of the uncertainty of our calculations is carried out to establish accuracy of our recommended values to be 0.5% - 1% depending on the particular ion. Comprehensive comparison of our results with other theoretical values and experiment is carried out. Our result for the quadrupole moment of the 3d5/2 state of Ca+ ion, 1.849(17)ea_0^2, is in agreement with the most precise recent measurement 1.83(1)ea_0^2 by Roos et al. [Nature 443, 316 (2006)].Comment: 7 page

Resolving all-order method convergence problems for atomic physics applications

The development of the relativistic all-order method where all single, double, and partial triple excitations of the Dirac-Hartree-Fock wave function are included to all orders of perturbation theory led to many important results for study of fundamental symmetries, development of atomic clocks, ultracold atom physics, and others, as well as provided recommended values of many atomic properties critically evaluated for their accuracy for large number of monovalent systems. This approach requires iterative solutions of the linearized coupled-cluster equations leading to convergence issues in some cases where correlation corrections are particularly large or lead to an oscillating pattern. Moreover, these issues also lead to similar problems in the CI+all-order method for many-particle systems. In this work, we have resolved most of the known convergence problems by applying two different convergence stabilizer methods, reduced linear equation (RLE) and direct inversion of iterative subspace (DIIS). Examples are presented for B, Al, Zn$^+$, and Yb$^+$. Solving these convergence problems greatly expands the number of atomic species that can be treated with the all-order methods and is anticipated to facilitate many interesting future applications

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

Innate immune receptor NOD2 mediates LGR5+ intestinal stem cell protection against ROS cytotoxicity via mitophagy stimulation

International audienceThe nucleotide-binding oligomerization domain-containing protein 2 (NOD2) agonist muramyl dipeptide (MDP), a peptidoglycan motif common to all bacteria, supports leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5)+ intestinal stem cell (ISC) survival through NOD2 activation upon an otherwise lethal oxidative stress-mediated signal. However, the underlying protective mechanisms remain unknown. Here, using irradiation as stressor and primarily murine-derived intestinal organoids as a model system, we show that MDP induced a significant reduction of total and mitochondrial reactive oxygen species (ROS) within ISCs, which was associated with mitophagy induction. ATG16L1 knockout (KO) and NOD2 KO organoids did not benefit from the MDP-induced cytoprotection. We confirmed the MDP-dependent induction of ISC mitophagy upon stress in vivo. These findings elucidate the NOD2-mediated mechanism of cytoprotection involving the clearance of the lethal excess of ROS molecules through mitophagy, triggered by the coordinated activation of NOD2 and ATG16L1 by a nuclear factor κB (NF-κB)-independent pathway

Wavelengths of the 3d6(5D)4s a6D - 3d6(5D)4p y6P Multiplet of Fe II (UV 8)

We investigate the wavenumber scale of Fe I and Fe II lines using new spectra recorded with Fourier transform spectroscopy and using a re-analysis of archival spectra. We find that standards in Ar II, Mg I, Mg II and Ge I give a consistent wavenumber calibration. We use the recalibrated spectra to derive accurate wavelengths for the a6D-y6P multiplet of Fe II (UV 8) using both directly measured lines and Ritz wavelengths. Lines from this multiplet are important for astronomical tests of the invariance of the fine structure constant on a cosmological time scale. We recommend a wavelength of 1608.45081 {\AA} with a one standard deviation uncertainty of 0.00007 {\AA} for the a6D9/2-y6P7/2 transition.Comment: 29 pages, 7 figures, 8 tables. Accepted for publication in J. Opt. Soc. Am