Multiple mitochondrial introgression events and heteroplasmy in trypanosoma cruzi revealed by Maxicircle MLST and next generation sequencing

Background Mitochondrial DNA is a valuable taxonomic marker due to its relatively fast rate of evolution. In Trypanosoma cruzi, the causative agent of Chagas disease, the mitochondrial genome has a unique structural organization consisting of 20–50 maxicircles (∼20 kb) and thousands of minicircles (0.5–10 kb). T. cruzi is an early diverging protist displaying remarkable genetic heterogeneity and is recognized as a complex of six discrete typing units (DTUs). The majority of infected humans are asymptomatic for life while 30–35% develop potentially fatal cardiac and/or digestive syndromes. However, the relationship between specific clinical outcomes and T. cruzi genotype remains elusive. The availability of whole genome sequences has driven advances in high resolution genotyping techniques and re-invigorated interest in exploring the diversity present within the various DTUs. Methodology/Principal Findings To describe intra-DTU diversity, we developed a highly resolutive maxicircle multilocus sequence typing (mtMLST) scheme based on ten gene fragments. A panel of 32 TcI isolates was genotyped using the mtMLST scheme, GPI, mini-exon and 25 microsatellite loci. Comparison of nuclear and mitochondrial data revealed clearly incongruent phylogenetic histories among different geographical populations as well as major DTUs. In parallel, we exploited read depth data, generated by Illumina sequencing of the maxicircle genome from the TcI reference strain Sylvio X10/1, to provide the first evidence of mitochondrial heteroplasmy (heterogeneous mitochondrial genomes in an individual cell) in T. cruzi. Conclusions/Significance mtMLST provides a powerful approach to genotyping at the sub-DTU level. This strategy will facilitate attempts to resolve phenotypic variation in T. cruzi and to address epidemiologically important hypotheses in conjunction with intensive spatio-temporal sampling. The observations of both general and specific incidences of nuclear-mitochondrial phylogenetic incongruence indicate that genetic recombination is geographically widespread and continues to influence the natural population structure of TcI, a conclusion which challenges the traditional paradigm of clonality in T. cruzi

Entanglement preparation using symmetric multiports

We investigate the entanglement produced by a multi-path interferometer that is composed of two symmetric multiports, with phase shifts applied to the output of the first multiport. Particular attention is paid to the case when we have a single photon entering the interferometer. For this situation we derive a simple condition that characterize the types of entanglement that one can generate. We then show how one can use the results from the single photon case to determine what kinds of multi-photon entangled states one can prepare using the interferometer.Comment: 6 pages, 2 figures, accepted for publication in European Journal of Physics

Entanglement preparation using symmetric multiports

We investigate the entanglement produced by a multi-path interferometer that is composed of two symmetric multiports, with phase shifts applied to the output of the first multiport. Particular attention is paid to the case when we have a single photon entering the interferometer. For this situation we derive a simple condition that characterize the types of entanglement that one can generate. We then show how one can use the results from the single photon case to determine what kinds of multi-photon entangled states one can prepare using the interferometer.Comment: 6 pages, 2 figures, accepted for publication in European Journal of Physics

Ferromagnetism in Oriented Graphite Samples

We have studied the magnetization of various, well characterized samples of highly oriented pyrolitic graphite (HOPG), Kish graphite and natural graphite to investigate the recently reported ferromagnetic-like signal and its possible relation to ferromagnetic impurities. The magnetization results obtained for HOPG samples for applied fields parallel to the graphene layers - to minimize the diamagnetic background - show no correlation with the magnetic impurity concentration. Our overall results suggest an intrinsic origin for the ferromagnetism found in graphite. We discuss possible origins of the ferromagnetic signal.Comment: 11 figure

Pair creation: back-reactions and damping

We solve the quantum Vlasov equation for fermions and bosons, incorporating spontaneous pair creation in the presence of back-reactions and collisions. Pair creation is initiated by an external impulse field and the source term is non-Markovian. A simultaneous solution of Maxwell's equation in the presence of feedback yields an internal current and electric field that exhibit plasma oscillations with a period tau_pl. Allowing for collisions, these oscillations are damped on a time-scale, tau_r, determined by the collision frequency. Plasma oscillations cannot affect the early stages of the formation of a quark-gluon plasma unless tau_r >> tau_pl and tau_pl approx. 1/Lambda_QCD approx 1 fm/c.Comment: 16 pages, 6 figure, REVTEX, epsfig.st

An Updated Description of Heavy-Hadron Interactions in Geant-4

Exotic stable massive particles (SMP) are proposed in a number of scenarios of physics beyond the Standard Model. It is important that LHC experiments are able both to detect and extract the quantum numbers of any SMP with masses around the TeV scale. To do this, an understanding of the interactions of SMPs in matter is required. In this paper a Regge-based model of R-hadron scattering is extended and implemented in Geant-4. In addition, the implications of $R$-hadron scattering for collider searches are discussed

Preparation and Comparison of Reduced Graphene Oxide and Carbon Nanotubes as Fillers in Conductive Natural Rubber for Flexible Electronics

Conductive natural rubber (NR) nanocomposites were prepared by solvent-casting suspensions of reduced graphene oxide (rGO) or carbon nanotubes (CNTs), followed by vulcanization of the rubber composites. Both rGO and CNT were compatible as fillers in the NR as well as having sufficient intrinsic electrical conductivity for functional applications. Physical (thermal) and chemical reduction of GO were investigated, and the results of the reductions were monitored by X-ray photoelectron spectroscopy for establishing a reduction protocol that was useful for the rGO nanocomposite preparation. Field-emission scanning electron microscopy showed that both nanofillers were adequately dispersed in the main NR phase. The CNT composite displays a marked mechanical hysteresis and higher elongation at break, in comparison to the rGO composites for an equal fraction of the carbon phase. Moreover, the composite conductivity was always ca. 3-4 orders of magnitude higher for the CNT composite than for the rGO composites, the former reaching a maximum conductivity of ca. 10.5 S/m, which was explained by the more favorable geometry of the CNT versus the rGO sheets. For low current density applications though, both composites achieved the necessary percolation and showed the electrical conductivity needed for being applied as flexible conductors for a light-emitting diode

Grain Surface Models and Data for Astrochemistry

AbstractThe cross-disciplinary field of astrochemistry exists to understand the formation, destruction, and survival of molecules in astrophysical environments. Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. A broad consensus has been reached in the astrochemistry community on how to suitably treat gas-phase processes in models, and also on how to present the necessary reaction data in databases; however, no such consensus has yet been reached for grain-surface processes. A team of ∼25 experts covering observational, laboratory and theoretical (astro)chemistry met in summer of 2014 at the Lorentz Center in Leiden with the aim to provide solutions for this problem and to review the current state-of-the-art of grain surface models, both in terms of technical implementation into models as well as the most up-to-date information available from experiments and chemical computations. This review builds on the results of this workshop and gives an outlook for future directions

Genuine Correlations of Like-Sign Particles in Hadronic Z0 Decays

Correlations among hadrons with the same electric charge produced in Z0 decays are studied using the high statistics data collected from 1991 through 1995 with the OPAL detector at LEP. Normalized factorial cumulants up to fourth order are used to measure genuine particle correlations as a function of the size of phase space domains in rapidity, azimuthal angle and transverse momentum. Both all-charge and like-sign particle combinations show strong positive genuine correlations. One-dimensional cumulants initially increase rapidly with decreasing size of the phase space cells but saturate quickly. In contrast, cumulants in two- and three-dimensional domains continue to increase. The strong rise of the cumulants for all-charge multiplets is increasingly driven by that of like-sign multiplets. This points to the likely influence of Bose-Einstein correlations. Some of the recently proposed algorithms to simulate Bose-Einstein effects, implemented in the Monte Carlo model PYTHIA, are found to reproduce reasonably well the measured second- and higher-order correlations between particles with the same charge as well as those in all-charge particle multiplets.Comment: 26 pages, 6 figures, Submitted to Phys. Lett.