Quantitative visualization of ChIP-chip data by using linked views

Most analyses of ChIP-chip in vivo DNA binding have focused on qualitative descriptions of whether genomic regions are bound or not. There is increasing evidence, however, that factors bind in a highly overlapping manner to the same genomic regions and that it is quantitative differences in occupancy on these commonly bound regions that are the critical determinants of the different biological specificity of factors. As a result, it is critical to have a tool to facilitate the quantitative visualization of differences between transcription factors and the genomic regions they bind to understand each factor's unique roles in the network. We have developed a framework which combines several visualizations via brushing-and-linking to allow the user to interactively analyze and explore in vivo DNA binding data of multiple transcription factors. We describe these visualization types and also provide a discussion of biological examples in this paper

Expression of Ca2+-dependent Synaptotagmin Isoforms in Mouse and Rat Parotid Acinar Cells

Synaptotagmin is a Ca2+ sensing protein, which triggers a fusion of synaptic vesicles in neuronal transmission. Little is known regarding the expression of Ca2+-dependent synaptotagmin isoforms and their contribution to the release of secretory vesicles in mouse and rat parotid acinar cells. We investigated a type of Ca2+-dependent synaptotagmin and Ca2+ signaling in both rat and mouse parotid acinar cells using RT-PCR, microfluorometry, and amylase assay. Mouse parotid acinar cells exhibited much more sensitive amylase release in response to muscarinic stimulation than did rat parotid acinar cells. However, transient [Ca2+]i increases and Ca2+ influx in response to muscarinic stimulation in both cells were identical, suggesting that the expression or activity of the Ca2+ sensing proteins is different. Seven Ca2+-dependent synaptotagmins, from 1 to 7, were expressed in the mouse parotid acinar cells. However, in the rat parotid acinar cells, only synaptotagmins 1, 3, 4 and 7 were expressed. These results indicate that the expression of Ca2+-dependent synaptotagmins may contribute to the release of secretory vesicles in parotid acinar cells

Utilization of IκB–EGFP Chimeric Gene as an Indicator to Identify Microbial Metabolites with NF-κB Inhibitor Activity

NF-κB regulates several important expressions, such as cytokine release, anti-apoptosis, adhesion molecule expression, and cell cycle processing. Several NF-κB inhibitors have been discovered as an anti-tumor or anti-inflammatory drug. The activity of NF-κB transcription factor is negatively regulated by IκB binding. In this study, IκB assay system was established and IκB–EGFP fusion protein was used as an indicator to monitor the effects of substances on the IκB degradation. The results indicated that the chosen hydroquinone could inhibit the IκB degradation and cause the cell de-attachment from the bottom of culture plate. In addition, this system could also monitor the IκB degradation of microbial metabolite of natural mixtures of propolis. Thus, the IκB assay system may be a good system for drug discovery related to microbial metabolite

Persistent sulfate formation from London Fog to Chinese haze

Sulfate aerosols exert profound impacts on human and ecosystem health, weather, and climate, but their formation mechanism remains uncertain. Atmospheric models consistently underpredict sulfate levels under diverse environmental conditions. From atmospheric measurements in two Chinese megacities and complementary laboratory experiments, we show that the aqueous oxidation of SO2 by NO2 is key to efficient sulfate formation but is only feasible under two atmospheric conditions: on fine aerosols with high relative humidity and NH3 neutralization or under cloud conditions. Under polluted environments, this SO2 oxidation process leads to large sulfate production rates and promotes formation of nitrate and organic matter on aqueous particles, exacerbating severe haze development. Effective haze mitigation is achievable by intervening in the sulfate formation process with enforced NH3 and NO2 control measures. In addition to explaining the polluted episodes currently occurring in China and during the 1952 London Fog, this sulfate production mechanism is widespread, and our results suggest a way to tackle this growing problem in China and much of the developing world

Observation of ηc→ωω\eta_c\to\omega\omega in J/ψ→γωωJ/\psi\to\gamma\omega\omega

Using a sample of $(1310.6\pm7.0)\times10^6$ $J/\psi$ events recorded with the BESIII detector at the symmetric electron positron collider BEPCII, we report the observation of the decay of the $(1^1 S_0)$ charmonium state $\eta_c$ into a pair of $\omega$ mesons in the process $J/\psi\to\gamma\omega\omega$. The branching fraction is measured for the first time to be $\mathcal{B}(\eta_c\to\omega\omega)= (2.88\pm0.10\pm0.46\pm0.68)\times10^{-3}$, where the first uncertainty is statistical, the second systematic and the third is from the uncertainty of $\mathcal{B}(J/\psi\to\gamma\eta_c)$. The mass and width of the $\eta_c$ are determined as $M=(2985.9\pm0.7\pm2.1)\,$MeV/$c^2$ and $\Gamma=(33.8\pm1.6\pm4.1)\,$MeV.Comment: 13 pages, 6 figure

Study of J/ψJ/\psi and ψ(3686)→Σ(1385)0Σˉ(1385)0\psi(3686)\rightarrow\Sigma(1385)^{0}\bar\Sigma(1385)^{0} and Ξ0Ξˉ0\Xi^0\bar\Xi^{0}

We study the decays of $J/\psi$ and $\psi(3686)$ to the final states $\Sigma(1385)^{0}\bar\Sigma(1385)^{0}$ and $\Xi^0\bar\Xi^{0}$ based on a single baryon tag method using data samples of $(1310.6 \pm 7.0) \times 10^{6}$ $J/\psi$ and $(447.9 \pm 2.9) \times 10^{6}$ $\psi(3686)$ events collected with the BESIII detector at the BEPCII collider. The decays to $\Sigma(1385)^{0}\bar\Sigma(1385)^{0}$ are observed for the first time. The measured branching fractions of $J/\psi$ and $\psi(3686)\rightarrow\Xi^0\bar\Xi^{0}$ are in good agreement with, and much more precise, than the previously published results. The angular parameters for these decays are also measured for the first time. The measured angular decay parameter for $J/\psi\rightarrow\Sigma(1385)^{0}\bar\Sigma(1385)^{0}$, $\alpha =-0.64 \pm 0.03 \pm 0.10$, is found to be negative, different to the other decay processes in this measurement. In addition, the "12\% rule" and isospin symmetry in the $J/\psi$ and $\psi(3686)\rightarrow\Xi\bar\Xi$ and $\Sigma(1385)\bar{\Sigma}(1385)$ systems are tested.Comment: 11 pages, 7 figures. This version is consistent with paper published in Phys.Lett. B770 (2017) 217-22

Improved measurement of the absolute branching fraction of D+→Kˉ0μ+νμD^{+}\rightarrow \bar K^0 \mu^{+}\nu_{\mu}

By analyzing 2.93 fb$^{-1}$ of data collected at $\sqrt s=3.773$ GeV with the BESIII detector, we measure the absolute branching fraction ${\mathcal B}(D^{+}\rightarrow\bar K^0\mu^{+}\nu_{\mu})=(8.72 \pm 0.07_{\rm stat.} \pm 0.18_{\rm sys.})\%$, which is consistent with previous measurements within uncertainties but with significantly improved precision. Combining the Particle Data Group values of ${\mathcal B}(D^0\to K^-\mu^+\nu_\mu)$, ${\mathcal B}(D^{+}\rightarrow\bar K^0 e^{+}\nu_{e})$, and the lifetimes of the $D^0$ and $D^+$ mesons with the value of ${\mathcal B}(D^{+}\rightarrow\bar K^0 \mu^{+}\nu_{\mu})$ measured in this work, we determine the following ratios of partial widths: $\Gamma(D^0\to K^-\mu^+\nu_\mu)/\Gamma(D^{+}\rightarrow\bar K^0\mu^{+}\nu_{\mu})=0.963\pm0.044$ and $\Gamma(D^{+}\rightarrow\bar K^0 \mu^{+}\nu_{\mu})/\Gamma(D^{+}\rightarrow\bar K^0 e^{+}\nu_{e})=0.988\pm0.033$.Comment: 9 pages; 8 figure