Molecular Evolution of the Substrate Utilization Strategies and Putative Virulence Factors in Mosquito-Associated Spiroplasma Species

Comparative genomics provides a powerful tool to characterize the genetic differences among species that may be linked to their phenotypic variations. In the case of mosquito-associated Spiroplasma species, such approach is useful for the investigation of their differentiations in substrate utilization strategies and putative virulence factors. Among the four species that have been assessed for pathogenicity by artificial infection experiments, Spiroplasma culicicola and S. taiwanense were found to be pathogenic, whereas S. diminutum and S. sabaudiense were not. Intriguingly, based on the species phylogeny, the association with mosquito hosts and the gain or loss of pathogenicity in these species appears to have evolved independently. Through comparison of their complete genome sequences, we identified the genes and pathways that are shared by all or specific to one of these four species. Notably, we found that a glycerol-3-phosphate oxidase gene (glpO) is present in S. culicicola and S. taiwanense but not in S. diminutum or S. sabaudiense. Because this gene is involved in the production of reactive oxygen species and has been demonstrated as a major virulence factor in Mycoplasma, this distribution pattern suggests that it may be linked to the observed differences in pathogenicity among these species as well. Moreover, through comparative analysis with other Spiroplasma, Mycoplasma, and Mesoplasma species, we found that the absence of glpO in S. diminutum and S. sabaudiense is best explained by independent losses. Finally, our phylogenetic analyses revealed possible recombination of glpO between distantly related lineages and local rearrangements of adjacent genes

Decoherence of a Josephson qubit due to coupling to two level systems

Noise and decoherence are major obstacles to the implementation of Josephson junction qubits in quantum computing. Recent experiments suggest that two level systems (TLS) in the oxide tunnel barrier are a source of decoherence. We explore two decoherence mechanisms in which these two level systems lead to the decay of Rabi oscillations that result when Josephson junction qubits are subjected to strong microwave driving. (A) We consider a Josephson qubit coupled resonantly to a two level system, i.e., the qubit and TLS have equal energy splittings. As a result of this resonant interaction, the occupation probability of the excited state of the qubit exhibits beating. Decoherence of the qubit results when the two level system decays from its excited state by emitting a phonon. (B) Fluctuations of the two level systems in the oxide barrier produce fluctuations and 1/f noise in the Josephson junction critical current I_o. This in turn leads to fluctuations in the qubit energy splitting that degrades the qubit coherence. We compare our results with experiments on Josephson junction phase qubits.Comment: 23 pages, Latex, 6 encapsulated postscript figure

Low-Energy Charge-Density Excitations in MgB2_{2}: Striking Interplay between Single-Particle and Collective Behavior for Large Momenta

A sharp feature in the charge-density excitation spectra of single-crystal MgB$_{2}$, displaying a remarkable cosine-like, periodic energy dispersion with momentum transfer ($q$) along the $c^{*}$-axis, has been observed for the first time by high-resolution non-resonant inelastic x-ray scattering (NIXS). Time-dependent density-functional theory calculations show that the physics underlying the NIXS data is strong coupling between single-particle and collective degrees of freedom, mediated by large crystal local-field effects. As a result, the small-$q$ collective mode residing in the single-particle excitation gap of the B $\pi$ bands reappears periodically in higher Brillouin zones. The NIXS data thus embody a novel signature of the layered electronic structure of MgB$_{2}$.Comment: 5 pages, 4 figures, submitted to PR

Coupling of spin and orbital excitations in the iron-based superconductor FeSe(0.5)Te(0.5)

We present a combined analysis of neutron scattering and photoemission measurements on superconducting FeSe(0.5)Te(0.5). The low-energy magnetic excitations disperse only in the direction transverse to the characteristic wave vector (1/2,0,0), whereas the electronic Fermi surface near (1/2,0,0) appears to consist of four incommensurate pockets. While the spin resonance occurs at an incommensurate wave vector compatible with nesting, neither spin-wave nor Fermi-surface-nesting models can describe the magnetic dispersion. We propose that a coupling of spin and orbital correlations is key to explaining this behavior. If correct, it follows that these nematic fluctuations are involved in the resonance and could be relevant to the pairing mechanism.Comment: 4 pages, 4 figures; accepted versio

Language control and parallel recovery of language in individuals with aphasia

Background: The causal basis of the different patterns of language recovery following stroke in bilingual speakers is not well understood. Our approach distinguishes the representation of language from the mechanisms involved in its control. Previous studies have suggested that difficulties in language control can explain selective aphasia in one language as well as pathological switching between languages. Here we test the hypothesis that difficulties in managing and resolving competition will also be observed in those who are equally impaired in both their languages even in the absence of pathological switching. Aims: To examine difficulties in language control in bilingual individuals with parallel recovery in aphasia and to compare their performance on different types of conflict task. Methods & procedures: Two right-handed, non-native English-speaking participants who showed parallel recovery of two languages after stroke and a group of non-native English-speaking, bilingual controls described a scene in English and in their first language and completed three explicit conflict tasks. Two of these were verbal conflict tasks: a lexical decision task in English, in which individuals distinguished English words from non-words, and a Stroop task, in English and in their first language. The third conflict task was a non-verbal flanker task. Outcomes & Results: Both participants with aphasia were impaired in the picture description task in English and in their first language but showed different patterns of impairment on the conflict tasks. For the participant with left subcortical damage, conflict was abnormally high during the verbal tasks (lexical decision and Stroop) but not during the non-verbal flanker task. In contrast, for the participant with extensive left parietal damage, conflict was less abnormal during the Stroop task than the flanker or lexical decision task. Conclusions: Our data reveal two distinct control impairments associated with parallel recovery. We stress the need to explore the precise nature of control problems and how control is implemented in order to develop fuller causal accounts of language recovery patterns in bilingual aphasia

Exchange Biasing of the Ferromagnetic Semiconductor (Ga,Mn)As by MnO

We provide an overview of progress on the exchange biasing of a ferromagnetic semiconductor (Ga1-xMnxAs) by proximity to an antiferromagnetic oxide layer (MnO). We present a detailed characterization study of the antiferromagnetic layer using Rutherford backscattering spectrometry, x-ray photoelectron spectroscopy, transmission electron microscopy, and x-ray reflection. In addition, we describe the variation of the exchange and coercive fields with temperature and cooling field for multiple samples.Comment: To appear in J. Appl. Phys. (invited paper in Proceedings of the 49th Annual Conference on Magnetism & Magnetic Materials); pdf file onl