Impact of Enhanced Staphylococcus DNA Extraction on Microbial Community Measures in Cystic Fibrosis Sputum

Staphylococcus aureus is a common constituent of the bacterial community inhabiting the airways of persons with cystic fibrosis (CF). Culture-independent studies have shown that this species is often present in relatively high abundance and would therefore be expected to exert a pronounced effect on measures of CF airway bacterial community structure. We investigated the impact of DNA extraction method on pyrosequencing-based measures of Staphylococcus abundance and bacterial community structure in 17 sputum samples from five CF patients. Staphylococcus was detected in fewer samples when DNA was extracted using a standard bacterial lysis method compared to when DNA was extracted using a lysis buffer amended with lysostaphin and lysozyme. The standard lysis method resulted in significantly lower measures of Staphylococcus relative abundance and higher levels of community diversity, richness, and evenness compared to the lysostaphin-lysozyme modified method. Measures of community dynamics in serial sputum samples from the same individual were nevertheless highly concordant between the two DNA extraction methods. These results illustrate the impact of DNA preparation method on measures of Staphylococcus abundance and bacterial community structures in studies of the airways microbiota in CF

Quantum tomography of an electron

International audienceThe complete knowledge of a quantum state allows the prediction of the probability of all possible measurement outcomes, a crucial step in quantum mechanics. It can be provided by tomographic methods which have been applied to atomic, molecular, spin and photonic states. For optical or microwave photons, standard tomogra-phy is obtained by mixing the unknown state with a large-amplitude coherent photon field. However, for fermions such as electrons in condensed matter, this approach is not applicable because fermionic fields are limited to small amplitudes (at most one particle per state), and so far no determination of an electron wavefunction has been made. Recent proposals involving quantum conductors suggest that the wavefunction can be obtained by measuring the time-dependent current of electronic wave interferometers or the current noise of electronic Hanbury-Brown/Twiss interferometers. Here we show that such measurements are possible despite the extreme noise sensitivity required, and present the reconstructed wavefunction quasi-probability, or Wigner distribution function, of single electrons injected into a ballistic conductor. Many identical electrons are prepared in well-controlled quantum states called levitons by repeatedly applying Lorentzian voltage pulses to a contact on the conductor. After passing through an electron beam splitter, the levitons are mixed with a weak-amplitude fermionic field formed by a coherent superposition of electron–hole pairs generated by a small alternating current with a frequency that is a multiple of the voltage pulse frequency 16. Antibunching of the electrons and holes with the levi-tons at the beam splitter changes the leviton partition statistics, and the noise variations provide the energy density matrix elements of the levitons. This demonstration of quantum tomography makes the developing field of electron quantum optics with ballistic conductors a new test-bed for quantum information with fermions. These results may find direct application in probing the entanglement of electron flying quantum bits, electron decoherence and electron interactions. They could also be applied to cold fermionic (or spin-1/2) atoms