Phylogenetics and Biogeography of the Phalaenopsis violacea (Orchidaceae) Species Complex Based on Nuclear and Plastid DNA

The Phalaenopsis violacea complex includes two species P violacea Witte and Phalaenopsis bellina (Rchb f) E A Christ However three forms of P violacea have been found in different areas including Sumatra the Malay Peninsula and Mentawai Island The phylogenetic tree inferred from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) the trnL intron and the atpB rbcL spacer of plastid DNA were used to clarify the phylogenetics and biogeography of the P violacea complex Analyses of the trnL intron sequences and of the atpB rbcL spacer did not allow for apparent discrimination among these three species of the P violacea complex Based on the phylogenetic tree inferred from th

Impact of Subleading Corrections on Hadronic B Decays

We study the subleading corrections originating from the 3-parton (q\bar q g) Fock states of final-state mesons in B decays. The corrections could give significant contributions to decays involving an \omega or \eta^{(\prime)} in the final states. Our results indicate the similarity of \omega K and \omega \pi^- rates, of order 5\times 10^{-6}, consistent with the recent measurements. We obtain a_2(B\to J/\psi K)\approx 0.27+0.05i, in good agreement with data. Without resorting to the unknown singlet annihilation effects, 3-parton Fock state contributions can enhance the branching ratios of K\eta' to the level above 50\times 10^{-6}.Comment: 5 pages, 5 figures, revtex4; some typos corrected, a new figure and a reference added, more explanations for the calculation provided, to appear in Phys. Rev.

High-throughput avian molecular sexing by SYBR green-based real-time PCR combined with melting curve analysis

<p>Abstract</p> <p>Background</p> <p>Combination of <it>CHD </it>(chromo-helicase-DNA binding protein)-specific polymerase chain reaction (PCR) with electrophoresis (PCR/electrophoresis) is the most common avian molecular sexing technique but it is lab-intensive and gel-required. Gender determination often fails when the difference in length between the PCR products of <it>CHD-Z </it>and <it>CHD-W </it>genes is too short to be resolved.</p> <p>Results</p> <p>Here, we are the first to introduce a PCR-melting curve analysis (PCR/MCA) to identify the gender of birds by genomic DNA, which is gel-free, quick, and inexpensive. <it>Spilornis cheela hoya </it>(<it>S. c. hoya</it>) and <it>Pycnonotus sinensis </it>(<it>P. sinensis</it>) were used to illustrate this novel molecular sexing technique. The difference in the length of <it>CHD </it>genes in <it>S. c. hoya </it>and <it>P. sinensis </it>is 13-, and 52-bp, respectively. Using Griffiths' P2/P8 primers, molecular sexing failed both in PCR/electrophoresis of <it>S. c. hoya </it>and in PCR/MCA of <it>S. c. hoya </it>and <it>P. sinensis</it>. In contrast, we redesigned sex-specific primers to yield 185- and 112-bp PCR products for the <it>CHD-Z </it>and <it>CHD-W </it>genes of <it>S. c. hoya</it>, respectively, using PCR/MCA. Using this specific primer set, at least 13 samples of <it>S. c. hoya </it>were examined simultaneously and the Tm peaks of <it>CHD-Z </it>and <it>CHD-W </it>PCR products were distinguished.</p> <p>Conclusion</p> <p>In this study, we introduced a high-throughput avian molecular sexing technique and successfully applied it to two species. This new method holds a great potential for use in high throughput sexing of other avian species, as well.</p

Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

<p>Abstract</p> <p>Background</p> <p>Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as <it>Arabidopsis thaliana </it>do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied.</p> <p>Results</p> <p>Several molecular biology tools were used to isolate flower-specific gene promoters from <it>Oncidium </it>'Gower Ramsey' (<it>Onc</it>. GR). A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in <it>Onc</it>. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (<it>TI</it>) genes (<it>OnTI1</it>, <it>OnTI2 </it>and <it>OnTI3</it>), which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable <it>A. thaliana </it>transformation analyses.</p> <p>Conclusions</p> <p>By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.</p

Exact Master Equation and Non-Markovian Decoherence for Quantum Dot Quantum Computing

In this article, we report the recent progress on decoherence dynamics of electrons in quantum dot quantum computing systems using the exact master equation we derived recently based on the Feynman-Vernon influence functional approach. The exact master equation is valid for general nanostructure systems coupled to multi-reservoirs with arbitrary spectral densities, temperatures and biases. We take the double quantum dot charge qubit system as a specific example, and discuss in details the decoherence dynamics of the charge qubit under coherence controls. The decoherence dynamics risen from the entanglement between the system and the environment is mainly non-Markovian. We further discuss the decoherence of the double-dot charge qubit induced by quantum point contact (QPC) measurement where the master equation is re-derived using the Keldysh non-equilibrium Green function technique due to the non-linear coupling between the charge qubit and the QPC. The non-Markovian decoherence dynamics in the measurement processes is extensively discussed as well.Comment: 15 pages, Invited article for the special issue "Quantum Decoherence and Entanglement" in Quantum Inf. Proces

Generating oxidation-resistant variants of Bacillus kaustophilus leucine aminopeptidase by substitution of the critical methionine residues with leucine

Bacillus kaustophilus leucine aminopeptidase (bkLAP) was sensitive to oxidative damage by hydrogen peroxide. To improve its oxidative stability, the oxidation-sensitive methionine residues in the enzyme were replaced with leucine by site-directed mutagenesis. The variants, each with an apparent molecular mass of approximately 54 kDa, were overexpressed in recombinant Escherichia coli M15 cells and purified to homogeneity by nickel-chelate chromatography. The specific activity for M282L, M285L, M289L and M321L decreased by more than 43%, while M400L, M426L, M445L, and M485L showed 191, 79, 313, and 103%, respectively, higher activity than the wild-type enzyme. Although the mutations did not cause significant changes in the K-m value, more than 67.8% increase in the value of k(cat)/K-m was observed in the M400L, M426L, M445L and M485L. In the presence of 50 mM H2O2 most variants were more stable with respect to the wild-type enzyme, indicating that the oxidative stability of the enzyme can be improved by engineering the methionine residues

Exact analytical solutions to the master equation of quantum Brownian motion for a general environment

We revisit the model of a quantum Brownian oscillator linearly coupled to an environment of quantum oscillators at finite temperature. By introducing a compact and particularly well-suited formulation, we give a rather quick and direct derivation of the master equation and its solutions for general spectral functions and arbitrary temperatures. The flexibility of our approach allows for an immediate generalization to cases with an external force and with an arbitrary number of Brownian oscillators. More importantly, we point out an important mathematical subtlety concerning boundary-value problems for integro-differential equations which led to incorrect master equation coefficients and impacts on the description of nonlocal dissipation effects in all earlier derivations. Furthermore, we provide explicit, exact analytical results for the master equation coefficients and its solutions in a wide variety of cases, including ohmic, sub-ohmic and supra-ohmic environments with a finite cut-off.Comment: 37 pages (26 + appendices), 14 figures; this paper is an evolution of arXiv:0705.2766v1, but contains far more general and significant results; v2 minor changes, double column, improved Appendix

Infrared optical properties of the spin-1/2 quantum magnet TiOClTiOCl

We report results on the electrodynamic response of $TiOCl$, a low-dimensional spin-1/2 quantum magnet that shows a spin gap formation for T$<T_{c1}$= 67 $K$. The Fano-like shape of a few selected infrared active phonons suggests an interaction between lattice vibrations and a continuum of low frequency (spin) excitations. The temperature dependence of the phonon mode parameters extends over a broad temperature range well above $T_{c1}$, indicating the presence of an extended fluctuation regime. In the temperature interval between 200 $K$ and $T_{c1}$ there is a progressive dimensionality crossover (from two to one), as well as a spectral weight shift from low towards high frequencies. This allows us to identify a characteristic energy scale of about 430 $K$, ascribed to a pseudo spin-gap

Quantum teleportation of light beams

We experimentally demonstrate quantum teleportation for continuous variables using squeezed-state entanglement. The teleportation fidelity for a real experimental system is calculated explicitly, including relevant imperfection factors such as propagation losses, detection inefficiencies and phase fluctuations. The inferred fidelity for input coherent states is F = 0.61 +- 0.02, which when corrected for the efficiency of detection by the output observer, gives a fidelity of 0.62. By contrast, the projected result based on the independently measured entanglement and efficiencies is 0.69. The teleportation protocol is explained in detail, including a discussion of discrepancy between experiment and theory, as well as of the limitations of the current apparatus.Comment: 17 pages, 19 figures, submitted to PR