Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia

The current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SSU) rRNA molecular phylogeny, but such single-gene phylogenies may not reflect the evolution of the genome as a whole. To test this, parts of the atpD and recA genes have been sequenced for 25 type strains within the alpha -Proteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Agrobacterium, Phyllobacterium, Mycoplana and Brevundimonas. The current genera Sinorhizobium and Mesorhizobium are well supported by these genes, each forming a distinct phylogenetic clade with unequivocal bootstrap support. There is good support for a Rhizobium clade that includes Agrobacterium tumefaciens, and the very close relationship between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. There is evidence for recombination within the genera Mesorhizobium and Sinorhizobium, but the congruence of the phylogenies at higher levels indicates that the genera are genetically isolated. rRNA provides a reliable distinction between genera, but genetic relationships within a genus may be disturbed by recombination

Identifying heterogeneity in rates of morphological evolution:Discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi)

Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as living fossils due to an apparent slowdown in rates since the Devonian. We find that morphological rates are highly heterogeneous across the phylogeny and recover a general pattern of decreasing rates along the phylogenetic backbone toward living taxa, from the Devonian until the present. Compared with previous work, we are able to report a more nuanced picture of lungfish evolution using these new methods

Quantum information processing using Josephson junctions coupled through cavities

Josephson junctions have been shown to be a promising solid-state system for implementation of quantum computation. The significant two-qubit gates are generally realized by the capacitive coupling between the nearest neighbour qubits. We propose an effective Hamiltonian to describe charge qubits coupled through the cavity. We find that nontrivial two-qubit gates may be achieved by this coupling. The ability to interconvert localized charge qubits and flying qubits in the proposed scheme implies that quantum network can be constructed using this large scalable solid-state system.Comment: 5 pages, to appear in Phys Rev A; typos corrected, solutions in last eqs. correcte

Effect of Host Plant on Parasitism of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) by Hyposoter didymator Thunberg (Hymenoptera: Ichneumonidae) and Cotesia kazak (Telenga) (Hymenoptera: Braconidae)

The effect of host plant on parasitism of second-instar Helicoverpa armigera by two introduced larval parasitoids, Hyposoter didymator and Cotesia kazak, was investigated in glasshouse experiments. Parasitism was lowest on chickpea (5.4% for H. didymator and 11.8% for C. kazak). Higher levels of parasitism (50.1-85.0% for H. didymator and 25.7-55.3% for C. kazak) were recorded on sorghum, sunflower, cotton, soybean and pigeonpea. This suggests that the parasitoids should be released against Helicoverpa spp. infestations on the major summer crops—sorghum, sunflower, cotton and soybean—rather than against the first spring generation infesting chickpea. Sorghum and sunflower are preferred release crops because parasitism levels are high and disruption by insecticide sprays is less likely

Protecting Quantum Information with Entanglement and Noisy Optical Modes

We incorporate active and passive quantum error-correcting techniques to protect a set of optical information modes of a continuous-variable quantum information system. Our method uses ancilla modes, entangled modes, and gauge modes (modes in a mixed state) to help correct errors on a set of information modes. A linear-optical encoding circuit consisting of offline squeezers, passive optical devices, feedforward control, conditional modulation, and homodyne measurements performs the encoding. The result is that we extend the entanglement-assisted operator stabilizer formalism for discrete variables to continuous-variable quantum information processing.Comment: 7 pages, 1 figur

Universal quantum gates based on a pair of orthogonal cyclic states: Application to NMR systems

We propose an experimentally feasible scheme to achieve quantum computation based on a pair of orthogonal cyclic states. In this scheme, quantum gates can be implemented based on the total phase accumulated in cyclic evolutions. In particular, geometric quantum computation may be achieved by eliminating the dynamic phase accumulated in the whole evolution. Therefore, both dynamic and geometric operations for quantum computation are workable in the present theory. Physical implementation of this set of gates is designed for NMR systems. Also interestingly, we show that a set of universal geometric quantum gates in NMR systems may be realized in one cycle by simply choosing specific parameters of the external rotating magnetic fields. In addition, we demonstrate explicitly a multiloop method to remove the dynamic phase in geometric quantum gates. Our results may provide useful information for the experimental implementation of quantum logical gates.Comment: 9 pages, language revised, the publication versio

Continuous variable quantum cryptography

We propose a quantum cryptographic scheme in which small phase and amplitude modulations of CW light beams carry the key information. The presence of EPR type correlations provides the quantum protection.Comment: 8 pages, 3 figure

Experimental Vacuum Squeezing in Rubidium Vapor via Self-Rotation

We report the generation of optical squeezed vacuum states by means of polarization self-rotation in rubidium vapor following a proposal by Matsko et al. [Phys. Rev. A 66, 043815 (2002)]. The experimental setup, involving in essence just a diode laser and a heated rubidium gas cell, is simple and easily scalable. A squeezing of 0.85+-0.05 dB was achieved

Entanglement concentration of continuous variable quantum states

We propose two probabilistic entanglement concentration schemes for a single copy of two-mode squeezed vacuum state. The first scheme is based on the off-resonant interaction of a Rydberg atom with the cavity field while the second setup involves the cross Kerr interaction, auxiliary mode prepared in a strong coherent state and a homodyne detection. We show that the continuous-variable entanglement concentration allows us to improve the fidelity of teleportation of coherent states.Comment: 7 pages, 7 figure

Geometric Strategy for the Optimal Quantum Search

We explore quantum search from the geometric viewpoint of a complex projective space $CP$, a space of rays. First, we show that the optimal quantum search can be geometrically identified with the shortest path along the geodesic joining a target state, an element of the computational basis, and such an initial state as overlaps equally, up to phases, with all the elements of the computational basis. Second, we calculate the entanglement through the algorithm for any number of qubits $n$ as the minimum Fubini-Study distance to the submanifold formed by separable states in Segre embedding, and find that entanglement is used almost maximally for large $n$. The computational time seems to be optimized by the dynamics as the geodesic, running across entangled states away from the submanifold of separable states, rather than the amount of entanglement itself.Comment: revtex, 10 pages, 7 eps figures, uses psfrag packag