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

A multiscale coarse grained model for simulating mechanical responses of plant food tissues

Plant food materials are highly sensitive to the external mechanical responses. Simulation of the material behaviour under mechanical loading is important in many engineering applications. Several researchers have used tissue based (macroscale) and cellular based (microscale) numerical models to assess the plant material behaviour. In doing so, generally, finite element modelling and meshfree based discretization strategies are commonly used and the latter has been proven to be more flexible, accurate and more robust in numerical simulations. This study aims to develop a coarse grained (CG) model for a cellular system of plant food tissue in microscale. The basic idea here is to maintain the accuracy given by the cellular scale while minimizing the computational cost for the simulations. The developed model accounts for the deformation of a coarse grained system under an external mechanical load. In order to represent the viscoelastic behaviour of a plant food material, we use a spring damper system connected to coarse grained beads. The model predictions show a satisfactory agreement with the morphological changes given by the cellular model. This developed CG model has laid a solid foundation for the further development of the multiscale model for the plant tissue

Ferromagnetic phase transition and Bose-Einstein condensation in spinor Bose gases

Phase transitions in spinor Bose gases with ferromagnetic (FM) couplings are studied via mean-field theory. We show that an infinitesimal value of the coupling can induce a FM phase transition at a finite temperature always above the critical temperature of Bose-Einstein condensation. This contrasts sharply with the case of Fermi gases, in which the Stoner coupling $I_s$ can not lead to a FM phase transition unless it is larger than a threshold value $I_0$. The FM coupling also increases the critical temperatures of both the ferromagnetic transition and the Bose-Einstein condensation.Comment: 4 pages, 4 figure

Electron-phonon anomaly related to charge stripes: static stripe phase versus optimally-doped superconducting La1.85Sr0.15CuO4

Inelastic neutron scattering was used to study the Cu-O bond-stretching vibrations in optimally doped La1.85Sr0.15CuO4 (Tc = 35 K) and in two other cuprates showing static stripe order at low temperatures, i.e. La1.48Nd0.4Sr0.12CuO4 and La1.875Ba0.125CuO4. All three compounds exhibit a very similar phonon anomaly, which is not predicted by conventional band theory. It is argued that the phonon anomaly reflects a coupling to charge inhomogeneities in the form of stripes, which remain dynamic in superconducting La1.85Sr0.15CuO4 down to the lowest temperatures. These results show that the phonon effect indicating stripe formation is not restricted to a narrow region of the phase diagram around the so-called 1/8 anomaly but occurs in optimally doped samples as well.Comment: to appear in J. Low Temp. Phy

Marginal Fermi liquid analysis of 300 K reflectance of Bi2Sr2CaCu2O8+x

We use 300 K reflectance data to investigate the normal-state electrodynamics of the high temperature superconductor Bi$_{2}$Sr$_{2}$CaCu$_{2}$O$_{8+\delta}$ over a wide range of doping levels. The data show that at this temperature the free carriers are coupled to a continuous spectrum of fluctuations. Assuming the Marginal Fermi Liquid (MFL) form as a first approximation for the fluctuation spectrum, the doping-dependent coupling constant $\lambda (p)$ can be estimated directly from the slope of the reflectance spectrum. We find that $\lambda (p)$ decreases smoothly with the hole doping level, from underdoped samples with $p=0.103$ ($T_c = 67$ K) where $\lambda (p)= 0.93$ to overdoped samples with $p=0.226$, ($T_c= 60$ K) where $\lambda(p)= 0.53$. An analysis of the intercept and curvature of the reflectance spectrum shows deviations from the MFL spectrum symmetrically placed at the optimal doping point $p=0.16$. The Kubo formula for the conductivity gives a better fit to the experiments with the MFL spectrum up to 2000 cm$^{-1}$ and with an additional Drude component or an additional Lorentz component up to 7000 cm$^{-1}$. By comparing three different model fits we conclude that the MFL channel is necessary for a good fit to the reflectance data. Finally, we note that the monotonic variation of the reflectance slope with doping provides us with an independent measure of the doping level for the Bi-2212 system.Comment: 11 pages, 11 figure

Charge order and low frequency spin dynamics in lanthanum cuprates revealed by Nuclear Magnetic Resonance

We report detailed 17O, 139La, and 63Cu Nuclear Magnetic Resonance (NMR) and Nuclear Quadrupole Resonance (NQR) measurements in a stripe ordered La1.875Ba0.125CuO4 single crystal and in oriented powder samples of La1.8-xEu0.2SrxCuO4. We observe a partial wipeout of the 17O NMR intensity and a simultaneous drop of the 17O electric field gradient (EFG) at low temperatures where the spin stripe order sets in. In contrast, the 63Cu intensity is completely wiped out at the same temperature. The drop of the 17O quadrupole frequency is compatible with a charge stripe order. The 17O spin lattice relaxation rate shows a peak similar to that of the 139La, which is of magnetic origin. This peak is doping dependent and is maximal at x ~ 1/8.Comment: submitted to European Physical Journal Special Topic

Five blood pressure loci identified by an updated genome-wide linkage scan: meta-analysis of the Family Blood Pressure Program.

BACKGROUND: A preliminary genome-wide linkage analysis of blood pressure in the Family Blood Pressure Program (FBPP) was reported previously. We harnessed the power and ethnic diversity of the final pooled FBPP dataset to identify novel loci for blood pressure thereby enhancing localization of genes containing less common variants with large effects on blood pressure levels and hypertension. METHODS: We performed one overall and 4 race-specific meta-analyses of genome-wide blood pressure linkage scans using data on 4,226 African-American, 2,154 Asian, 4,229 Caucasian, and 2,435 Mexican-American participants (total N = 13,044). Variance components models were fit to measured (raw) blood pressure levels and two types of antihypertensive medication adjusted blood pressure phenotypes within each of 10 subgroups defined by race and network. A modified Fisher's method was used to combine the P values for each linkage marker across the 10 subgroups. RESULTS: Five quantitative trait loci (QTLs) were detected on chromosomes 6p22.3, 8q23.1, 20q13.12, 21q21.1, and 21q21.3 based on significant linkage evidence (defined by logarithm of odds (lod) score ≥3) in at least one meta-analysis and lod scores ≥1 in at least 2 subgroups defined by network and race. The chromosome 8q23.1 locus was supported by Asian-, Caucasian-, and Mexican-American-specific meta-analyses. CONCLUSIONS: The new QTLs reported justify new candidate gene studies. They may help support results from genome-wide association studies (GWAS) that fall in these QTL regions but fail to achieve the genome-wide significance

Partial Wave Analysis of J/ψ→γ(K+K−π+π−)J/\psi \to \gamma (K^+K^-\pi^+\pi^-)

BES data on $J/\psi \to \gamma (K^+K^-\pi^+\pi^-)$ are presented. The $K^*\bar K^*$ contribution peaks strongly near threshold. It is fitted with a broad $0^{-+}$ resonance with mass $M = 1800 \pm 100$ MeV, width $\Gamma = 500 \pm 200$ MeV. A broad $2^{++}$ resonance peaking at 2020 MeV is also required with width $\sim 500$ MeV. There is further evidence for a $2^{-+}$ component peaking at 2.55 GeV. The non-$K^*\bar K^*$ contribution is close to phase space; it peaks at 2.6 GeV and is very different from $K^{*}\bar{K^{*}}$.Comment: 15 pages, 6 figures, 1 table, Submitted to PL

Measurements of the observed cross sections for e+e−→e^+e^-\to exclusive light hadrons containing π0π0\pi^0\pi^0 at s=3.773\sqrt s= 3.773, 3.650 and 3.6648 GeV

By analyzing the data sets of 17.3, 6.5 and 1.0 pb$^{-1}$ taken, respectively, at $\sqrt s= 3.773$, 3.650 and 3.6648 GeV with the BES-II detector at the BEPC collider, we measure the observed cross sections for $e^+e^-\to \pi^+\pi^-\pi^0\pi^0$, $K^+K^-\pi^0\pi^0$, $2(\pi^+\pi^-\pi^0)$, $K^+K^-\pi^+\pi^-\pi^0\pi^0$ and $3(\pi^+\pi^-)\pi^0\pi^0$ at the three energy points. Based on these cross sections we set the upper limits on the observed cross sections and the branching fractions for $\psi(3770)$ decay into these final states at 90% C.L..Comment: 7 pages, 2 figure

Partial wave analysis of J/\psi \to \gamma \phi \phi

Using $5.8 \times 10^7 J/\psi$ events collected in the BESII detector, the radiative decay $J/\psi \to \gamma \phi \phi \to \gamma K^+ K^- K^0_S K^0_L$ is studied. The $\phi\phi$ invariant mass distribution exhibits a near-threshold enhancement that peaks around 2.24 GeV/$c^{2}$. A partial wave analysis shows that the structure is dominated by a $0^{-+}$ state ($\eta(2225)$) with a mass of $2.24^{+0.03}_{-0.02}{}^{+0.03}_{-0.02}$ GeV/$c^{2}$ and a width of $0.19 \pm 0.03^{+0.06}_{-0.04}$ GeV/$c^{2}$. The product branching fraction is: $Br(J/\psi \to \gamma \eta(2225))\cdot Br(\eta(2225)\to \phi\phi) = (4.4 \pm 0.4 \pm 0.8)\times 10^{-4}$.Comment: 11 pages, 4 figures. corrected proof for journa