Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses

<p>Abstract</p> <p>Background</p> <p>Housekeeping genes are routinely used as endogenous references to account for experimental differences in gene expression assays. However, recent reports show that they could be de-regulated in different diseases, model animals, or even under varied experimental conditions, which may lead to unreliable results and consequently misinterpretations. This study focused on the selection of suitable reference genes for quantitative PCR in human hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) with different clinical outcomes.</p> <p>Methods</p> <p>We evaluated 6 commonly used housekeeping genes' expression levels in 108 HBV-related HCCs' matched tumor and non-tomor tissue samples with different clinical outcomes and 26 normal liver specimens by real-time PCR. The expression stability of the 6 genes was compared using the software programs geNorm and NormFinder. To show the impact of reference genes on data analysis, we took PGK1 as a target gene normalized by each reference gene, and performed one-way ANOVA and the equivalence test.</p> <p>Results</p> <p>With the geNorm and NormFinder software programs, analysis of TBP and HPRT1 showed the best stability in all tissue samples, while 18s and ACTB were less stable. When 18s or ACTB was used for normalization, no significant difference of PGK1 expression (p > 0.05) was found among HCC tissues with and without metastasis, and normal liver specimens; however, dramatically differences (p < 0.001) were observed when either TBP or the combination of TBP and HPRT1 were selected as reference genes.</p> <p>Conclusion</p> <p>TBP and HPRT1 are the most reliable reference genes for q-PCR normalization in HBV-related HCC specimens. However, the well-used ACTB and 18S are not suitable, which actually lead to the misinterpretation of the results in gene expression analysis.</p

Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses

<p>Abstract</p> <p>Background</p> <p>Housekeeping genes are routinely used as endogenous references to account for experimental differences in gene expression assays. However, recent reports show that they could be de-regulated in different diseases, model animals, or even under varied experimental conditions, which may lead to unreliable results and consequently misinterpretations. This study focused on the selection of suitable reference genes for quantitative PCR in human hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) with different clinical outcomes.</p> <p>Methods</p> <p>We evaluated 6 commonly used housekeeping genes' expression levels in 108 HBV-related HCCs' matched tumor and non-tomor tissue samples with different clinical outcomes and 26 normal liver specimens by real-time PCR. The expression stability of the 6 genes was compared using the software programs geNorm and NormFinder. To show the impact of reference genes on data analysis, we took PGK1 as a target gene normalized by each reference gene, and performed one-way ANOVA and the equivalence test.</p> <p>Results</p> <p>With the geNorm and NormFinder software programs, analysis of TBP and HPRT1 showed the best stability in all tissue samples, while 18s and ACTB were less stable. When 18s or ACTB was used for normalization, no significant difference of PGK1 expression (p > 0.05) was found among HCC tissues with and without metastasis, and normal liver specimens; however, dramatically differences (p < 0.001) were observed when either TBP or the combination of TBP and HPRT1 were selected as reference genes.</p> <p>Conclusion</p> <p>TBP and HPRT1 are the most reliable reference genes for q-PCR normalization in HBV-related HCC specimens. However, the well-used ACTB and 18S are not suitable, which actually lead to the misinterpretation of the results in gene expression analysis.</p

Measurement of the proton form factor by studying e+e−→ppˉe^{+} e^{-}\rightarrow p\bar{p}

Using data samples collected with the BESIII detector at the BEPCII collider, we measure the Born cross section of $e^{+}e^{-}\rightarrow p\bar{p}$ at 12 center-of-mass energies from 2232.4 to 3671.0 MeV. The corresponding effective electromagnetic form factor of the proton is deduced under the assumption that the electric and magnetic form factors are equal $(|G_{E}|= |G_{M}|)$. In addition, the ratio of electric to magnetic form factors, $|G_{E}/G_{M}|$, and $|G_{M}|$ are extracted by fitting the polar angle distribution of the proton for the data samples with larger statistics, namely at $\sqrt{s}=$ 2232.4 and 2400.0 MeV and a combined sample at $\sqrt{s}$ = 3050.0, 3060.0 and 3080.0 MeV, respectively. The measured cross sections are in agreement with recent results from BaBar, improving the overall uncertainty by about 30\%. The $|G_{E}/G_{M}|$ ratios are close to unity and consistent with BaBar results in the same $q^{2}$ region, which indicates the data are consistent with the assumption that $|G_{E}|=|G_{M}|$ within uncertainties.Comment: 13 pages, 24 figure

Observation of the ψ(13D2)\psi(1^3D_2) state in e+e−→π+π−γχc1e^+e^-\to\pi^+\pi^-\gamma\chi_{c1} at BESIII

We report the observation of the $X(3823)$ in the process $e^+e^-\to \pi^+\pi^-X(3823) \to \pi^+\pi^-\gamma\chi_{c1}$ with a statistical significance of $6.2\sigma$, in data samples at center-of-mass energies $\sqrt{s}=$4.230, 4.260, 4.360, 4.420 and 4.600~GeV collected with the BESIII detector at the BEPCII electron positron collider. The measured mass of the $X(3823)$ is $(3821.7\pm 1.3\pm 0.7)$~MeV/$c^2$, where the first error is statistical and the second systematic, and the width is less than $16$~MeV at the 90\% confidence level. The products of the Born cross sections for $e^+e^-\to \pi^+\pi^-X(3823)$ and the branching ratio $\mathcal{B}[X(3823)\to \gamma\chi_{c1,c2}]$ are also measured. These measurements are in good agreement with the assignment of the $X(3823)$ as the $\psi(1^3D_2)$ charmonium state.Comment: 7 pages, 3 figures, version to appear in Phys. Rev. Let

Search for C-parity violation in J/ψ→γγJ/ \psi \to \gamma\gamma and γϕ \gamma \phi

Using $1.06\times10^8$ $\psi(3686)$ events recorded in $e^{+}e^{-}$ collisions at $\sqrt{s}=$ 3.686 GeV with the BESIII at the BEPCII collider, we present searches for C-parity violation in $J/\psi \to \gamma\gamma$ and $\gamma \phi$ decays via $\psi(3686) \to J/\psi \pi^+\pi^-$. No significant signals are observed in either channel. Upper limits on the branching fractions are set to be $\mathcal{B}(J/\psi \to \gamma\gamma) < 2.7 \times 10^{-7}$ and $\mathcal{B}(J/\psi \to \gamma\phi) < 1.4 \times 10^{-6}$ at the 90\% confidence level. The former is one order of magnitude more stringent than the previous upper limit, and the latter represents the first limit on this decay channel.Comment: 7 pages, 2 figure

Search for the radiative transitions ψ(3770)→γηc\psi(3770)\to\gamma\eta_c and γηc(2S)\gamma\eta_c(2S)

By using a 2.92 fb$^{-1}$ data sample taken at $\sqrt{s} = 3.773$ GeV with the BESIII detector operating at the BEPCII collider, we search for the radiative transitions $\psi(3770)\to\gamma\eta_c$ and $\gamma\eta_c(2S)$ through the hadronic decays $\eta_c(\eta_c(2S))\to K^0_SK^\pm\pi^\mp$. No significant excess of signal events above background is observed. We set upper limits at a 90% confidence level for the product branching fractions to be $\mathcal{B}(\psi(3770)\to\gamma\eta_c)\times \mathcal{B}(\eta_c\to K^0_SK^\pm\pi^\mp) < 1.6\times10^{-5}$ and $\mathcal{B}(\psi(3770)\to\gamma\eta_c(2S))\times \mathcal{B}(\eta_c(2S)\to K^0_SK^\pm\pi^\mp) < 5.6\times10^{-6}$. Combining our result with world-average values of $\mathcal{B}(\eta_c(\eta_c(2S))\to K^0_SK^\pm\pi^\mp)$, we find the branching fractions $\mathcal{B}(\psi(3770)\to\gamma\eta_c) < 6.8\times10^{-4}$ and $\mathcal{B}(\psi(3770)\to\gamma\eta_c(2S)) < 2.0\times10^{-3}$ at a 90% confidence level.Comment: 10 pages, 4 figure

Observation of the isospin-violating decay J/ψ→ϕπ0f0(980)J/\psi \to \phi\pi^{0}f_{0}(980)

Using a sample of 1.31 billion $J/\psi$ events collected with the BESIII detector at the BEPCII collider, the decays $J/\psi \to \phi \pi^{+}\pi^{-}\pi^{0}$ and $J/\psi \to \phi \pi^{0}\pi^{0}\pi^{0}$ are investigated. The isospin violating decay $J/\psi \to \phi \pi^{0} f_{0}(980)$ with $f_{0}(980) \to \pi\pi$, is observed for the first time. The width of the $f_{0}(980)$ obtained from the dipion mass spectrum is found to be much smaller than the world average value. In the $\pi^{0} f_{0}(980)$ mass spectrum, there is evidence of $f_1(1285)$ production. By studying the decay $J/\psi \to \phi\eta'$, the branching fractions of $\eta' \to \pi^{+}\pi^{-}\pi^{0}$ and $\eta' \to \pi^{0}\pi^{0}\pi^{0}$, as well as their ratio, are also measured.Comment: 10 pages, 10 figures, published in Phys. Rev.

An amplitude analysis of the π0π0\pi^{0}\pi^{0} system produced in radiative J/ψJ/\psi decays

An amplitude analysis of the $\pi^{0}\pi^{0}$ system produced in radiative $J/\psi$ decays is presented. In particular, a piecewise function that describes the dynamics of the $\pi^{0}\pi^{0}$ system is determined as a function of $M_{\pi^{0}\pi^{0}}$ from an analysis of the $(1.311\pm0.011)\times10^{9}$ $J/\psi$ decays collected by the BESIII detector. The goal of this analysis is to provide a description of the scalar and tensor components of the $\pi^0\pi^0$ system while making minimal assumptions about the properties or number of poles in the amplitude. Such a model-independent description allows one to integrate these results with other related results from complementary reactions in the development of phenomenological models, which can then be used to directly fit experimental data to obtain parameters of interest. The branching fraction of $J/\psi \to \gamma \pi^{0}\pi^{0}$ is determined to be $(1.15\pm0.05)\times10^{-3}$, where the uncertainty is systematic only and the statistical uncertainty is negligible.Comment: Submitted to Phys. Rev. D 19 pages, 4 figure