The largest reservoir of mitochondrial introns is a relic of an ancestral split gene

In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms (ref. 1-4). Large introns (0.1 to 5 kbp) are frequent in mitochondrial genomes of plant and fungi (ref. 1,5) but scarce in Metazoa, despite these organisms are grouped with fungi among Opisthokonts. Introns are classified in two main groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism (ref. 5,6). Most of the group I introns carry a "Homing Endonuclease Gene" (ref. 7-9) encoding a DNA endonuclease acting in the transfer and site specific integration "homing") and allowing the intron spreading and gain after lateral transfer even between species from different kingdoms (ref. 10,11). Opposite to this "late intron" paradigm, the "early intron" theory indicates that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss (ref. 12,13).

Here we report the sequence of the cox1 gene of the button mushroom _Agaricus bisporus_, the most worldwide cultivated mushroom. This gene is both the longest mitochondrial gene (29,902 nt) and the largest Group I intron reservoir reported to date. An analysis of the group I introns available in _cox1_ genes shows that they are ancestral mobile genetic elements, whose frequent events of loss (according to the "late theory") and gain by lateral transfer ("early theory") must be combined to explain their wide and patchy distribution extending on several kingdoms. This allows the conciliation of the "early" and "late intron" paradigms, which are still matters of much debate (ref. 14,15). The overview of the intron distribution indicates that they evolve towards elimination. In such a landscape of eroded and lost intron sequences, the _A. bisporus_ largest intron reservoir, by its singular dynamics of intron keeping and catching, constitutes the most fitted relic of an early split gene

Giant Optical Non-linearity induced by a Single Two-Level System interacting with a Cavity in the Purcell Regime

A two-level system that is coupled to a high-finesse cavity in the Purcell regime exhibits a giant optical non-linearity due to the saturation of the two-level system at very low intensities, of the order of one photon per lifetime. We perform a detailed analysis of this effect, taking into account the most important practical imperfections. Our conclusion is that an experimental demonstration of the giant non-linearity should be feasible using semiconductor micropillar cavities containing a single quantum dot in resonance with the cavity mode.Comment: 40 pages, 16 figures, accepted in Phys. Rev.

Exciton photon strong-coupling regime for a single quantum dot in a microcavity

We report on the observation of the strong coupling regime between a single GaAs quantum dot and a microdisk optical mode. Photoluminescence is performed at various temperatures to tune the quantum dot exciton with respect to the optical mode. At resonance, we observe an anticrossing, signature of the strong coupling regime with a well resolved doublet. The Vacuum Rabi splitting amounts to 400 μeV and is twice as large as the individual linewidths.Comment: submitted on November 7th 200

Dynamical ultrafast all-optical switching of planar GaAs/AlAs photonic microcavities

The authors study the ultrafast switching-on and -off of planar GaAs/AlAs microcavities. Up to 0.8% refractive index changes are achieved by optically exciting free carriers at 1720 nm and a pulse energy of 1.8 micro Joules. The cavity resonance is dynamically tracked by measuring reflectivity versus time delay with tunable laser pulses, and is found to shift by as much as 3.3 linewidths within a few picoseconds. The switching-off occurs with a decay time of around 50 ps. The authors derive the dynamic behavior of the carrier density and of the complex refractive index. They propose that the inferred 10 GHz switching rate may be tenfold improved by optimized sample growth.Comment: 1.) Replaced figure 1 (linear reflectivity) with a more recent and improved measurement 2.) Included a Figure of Merit for switching and compared to other recent contributions 3.) Explained more precisely the effect of embedded Quantum Dots (namely no effect on measurement) 4.) Changed wording in a few place

Routine Fetal Rhd Genotyping with Maternal Plasma: A Four-Year Experience in Belgium

peer reviewedBACKGROUND: The objective was to evaluate the diagnostic value of RHD fetal genotyping from the plasma of D- mothers as soon as 10 weeks' gestation in a routine clinical practice in Belgium. STUDY DESIGN AND METHODS: A prospective study was conducted between November 2002 and December 2006. DNA extraction was performed in an automated closed tube system. Fetal RHD/SRY genotypes were detected in the plasma of 563 pregnant mothers by real-time polymerase chain reaction (PCR) targeting multiple exons 4, 5, and 10 of the RHD gene and targeting an SRY gene sequence. These were compared to the D phenotypes determined in the 581 babies they delivered. RESULTS: By combining amplification of three exons, the concordance rate of fetal RHD genotypes in maternal plasma and newborn D phenotypes at delivery was 100 percent (99.8% including one unusual false-positive). The presence of nonfunctional RHD genes and the absence of a universal fetal marker, irrespective of fetal sex, did not influence the accuracy of fetal RhD status prediction. The RHD genotyping from 18 twin pregnancies was also assessed. Five weak D women were excluded from the RHD fetal genotyping prediction. Three discrepant results (0.5%) between predicted fetal genotype and cord blood phenotype were not confirmed by the baby phenotypes from venipuncture blood. CONCLUSION: Prenatal prediction of fetal RHD by targeting multiple exons from the maternal plasma with real-time PCR is highly sensitive and accurate. Over 4 years, this experience has highly modified our management of D- pregnant women

Widely Tunable Quantum-Dot Source Around 3 μm

We propose a widely tunable parametric source in the 3 μm range, based on intracavity spontaneous parametric down conversion (SPDC) of a quantum-dot (QD) laser emitting at 1.55 μm into signal and idler modes around 3.11 μm. To compensate for material dispersion, we engineer the laser structure to emit in a higher-order transverse mode of the waveguide. The width of the latter is used as a degree of freedom to reach phase matching in narrow, deeply etched ridges, where the in-plane confinement of the QDs avoids non-radiative sidewall electron-hole recombination. Since this design depends critically on the knowledge of the refractive index of In1−xGaxAsyP1−y lattice matched to InP at wavelengths where no data are available in the literature, we have accurately determined them as a function of wavelength (λ = 1.55, 2.12 and 3 μm) and arsenic molar fraction (y = 0.55, 0.7 and 0.72) with a precision of ±4 × 10−3. A pair of dichroic dielectric mirrors on the waveguide facets is shown to result in a continuous-wave optical parametric oscillator (OPO), with a threshold around 60 mW. Emission is tunable over hundreds of nanometers and expected to achieve mW levels

Resonant driving of a single photon emitter embedded in a mechanical oscillator

Coupling a microscopic mechanical resonator to a nanoscale quantum system enables control of the mechanical resonator via the quantum system and vice-versa. The coupling is usually achieved through functionalization of the mechanical resonator, but this results in additional mass and dissipation channels. An alternative is an intrinsic coupling based on strain. Here we employ a monolithic semiconductor system: the nanoscale quantum system is a semiconductor quantum dot (QD) located inside a nanowire. We demonstrate the resonant optical driving of the QD transition in such a structure. The noise spectrum of the resonance fluorescence signal, recorded in the single-photon counting regime, reveals a coupling to mechanical modes of different types. We measure a sensitivity to displacement of 65 fm/root Hz limited by charge noise in the device. Finally, we use thermal excitation of the different modes to determine the location of the QD within the trumpet, and calculate the contribution of the Brownian motion to the dephasing of the emitter

Influence of Plasminogen Activator Inhibitor Type 1 on Choroidal Neovascularization

peer reviewedHigh levels of the plasminogen activators, but also their inhibitor, plasminogen activator inhibitor 1 (PAI-1), have been documented in neovascularization of severe ocular pathologies such as diabetic retinopathy or age-related macular degeneration (AMD). AMD is the primary cause of irreversible photoreceptors loss, and current therapies are limited. PAI-1 has recently been shown to be essential for tumoral angiogenesis. We report here that deficient PAI-1 expression in mice prevented the development of subretinal choroidal angiogenesis induced by laser photocoagulation. When systemic and local PAI-1 expression was achieved by intravenous injection of a replication-defective adenoviral vector expressing human PAI-1 cDNA, the wild-type pattern of choroidal angiogenesis was restored. These observations demonstrate the proangiogenic activity of PAI-1 not only in tumoral models, but also in choroidal experimental neovascularization sharing similarities with human AMD. They identify therefore PAI-1 as a potential target for therapeutic ocular anti-angiogenic strategies