Evidence for an oscillatory signature in atmospheric neutrino oscillation

Muon neutrino disappearance probability as a function of neutrino flight length L over neutrino energy E was studied. A dip in the L/E distribution was observed in the data, as predicted from the sinusoidal flavor transition probability of neutrino oscillation. The observed L/E distribution constrained nu_mu nu_tau neutrino oscillation parameters; 1.9x10^-3 < Delta m^2 < 3.0x10^-3 eV^2 and \sin^2(2theta) > 0.90 at 90% confidence level.Comment: 5 pages, 5 figures, submitted to PR

Search for nucleon decay via modes favored by supersymmetric grand unification models in Super-Kamiokande-I

We report the results for nucleon decay searches via modes favored by supersymmetric grand unified models in Super-Kamiokande. Using 1489 days of full Super-Kamiokande-I data, we searched for $p \to \bar{\nu} K^+$, $n \to \bar{\nu} K^0$, $p \to \mu^+ K^0$ and $p \to e^+ K^0$ modes. We found no evidence for nucleon decay in any of these modes. We set lower limits of partial nucleon lifetime 2.3$\times10^{33}$, 1.3$\times10^{32}$, 1.3$\times10^{33}$ and 1.0$\times10^{33}$ years at 90% confidence level for $p \to \bar{\nu} K^+$, $n \to \bar{\nu} K^0$, $p \to \mu^+ K^0$ and $p \to e^+ K^0$ modes, respectively. These results give a strong constraint on supersymmetric grand unification models.Comment: 14 pages, 13 figure

Solar neutrino measurements in Super-Kamiokande-I

The details of Super--Kamiokande--I's solar neutrino analysis are given. Solar neutrino measurement in Super--Kamiokande is a high statistics collection of $^8$B solar neutrinos via neutrino-electron scattering. The analysis method and results of the 1496 day data sample are presented. The final oscillation results for the data are also presented.Comment: 32pages, 57figures, submitted to Physical Review

Three flavor neutrino oscillation analysis of atmospheric neutrinos in Super-Kamiokande

We report on the results of a three-flavor oscillation analysis using Super-Kamiokande~I atmospheric neutrino data, with the assumption of one mass scale dominance ($\Delta m_{12}^2$$=$0). No significant flux change due to matter effect, which occurs when neutrinos propagate inside the Earth for $\theta_{13}$$\neq$0, has been seen either in a multi-GeV $\nu_e$-rich sample or in a $\nu_\mu$-rich sample. Both normal and inverted mass hierarchy hypotheses are tested and both are consistent with observation. Using Super-Kamiokande data only, 2-dimensional 90 % confidence allowed regions are obtained: mixing angles are constrained to $\sin^2\theta_{13} < 0.14$ and $0.37 < \sin^2\theta_{23} < 0.65$ for the normal mass hierarchy. Weaker constraints, $\sin^2\theta_{13} < 0.27$ and $0.37 < \sin^2\theta_{23} < 0.69$, are obtained for the inverted mass hierarchy case.Comment: 7 figures, 3 table

Search for Dark Matter WIMPs using Upward Through-going Muons in Super-Kamiokande

We present the results of indirect searches for Weakly Interacting Massive Particles (WIMPs) with 1679.6 live days of data from the Super-Kamiokande detector using neutrino-induced upward through-going muons. The search is performed by looking for an excess of high energy muon neutrinos from WIMP annihilations in the Sun, the core of the Earth, and the Galactic Center, as compared to the number expected from the atmospheric neutrino background. No statistically significant excess was seen. We calculate flux limits in various angular cones around each of the above celestial objects. We obtain conservative model-independent upper limits on WIMP-nucleon cross-section as a function of WIMP mass and compare these results with the corresponding results from direct dark matter detection experiments.Comment: 10 pages, 14 figures, Submitted to Phys. Rev.

Limit On the Neutrino Magnetic Moment Using 1496 Days of Super-Kamiokande-i Solar Neutrino Data

A search for a non-zero neutrino magnetic moment has been conducted using 1496 live days of solar neutrino data from {\SK}. Specifically, we searched for distortions to the energy spectrum of recoil electrons arising from magnetic scattering due to a non-zero neutrino magnetic moment. In the absence of clear signal, we found $\mu_{\nu} \leq 3.6 \times 10^{-10}$ $\mu_{B}$ at 90% C.L. by fitting to the Super-Kamiokande day/night spectra. The fitting took into account the effect of neutrino oscillation on the shapes of energy spectra. With additional information from other solar neutrino and KamLAND experiments constraining the oscillation region, a limit of $\mu_{\nu} \leq 1.1 \times 10^{-10}$ $\mu_{B}$ at 90% C.L. was obtained.Comment: 5 pages, 4 figure

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-depleted Murine Embryonic Stem Cells

Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintenance of pluripotency and lineage specification are poorly understood, but recent results point to a key role for epigenetic mechanisms. In this study, we focus on quantifying the impact of histone 3 acetylation (H3K9,14ac) on gene expression in murine embryonic stem cells. We analyze genome-wide histone acetylation patterns and gene expression profiles measured over the first five days of cell differentiation triggered by silencing Nanog, a key transcription factor in ESC regulation. We explore the temporal and spatial dynamics of histone acetylation data and its correlation with gene expression using supervised and unsupervised statistical models. On a genome-wide scale, changes in acetylation are significantly correlated to changes in mRNA expression and, surprisingly, this coherence increases over time. We quantify the predictive power of histone acetylation for gene expression changes in a balanced cross-validation procedure. In an in-depth study we focus on genes central to the regulatory network of Mouse ESC, including those identified in a recent genome-wide RNAi screen and in the PluriNet, a computationally derived stem cell signature. We find that compared to the rest of the genome, ESC-specific genes show significantly more acetylation signal and a much stronger decrease in acetylation over time, which is often not reflected in an concordant expression change. These results shed light on the complexity of the relationship between histone acetylation and gene expression and are a step forward to dissect the multilayer regulatory mechanisms that determine stem cell fate.Comment: accepted at PLoS Computational Biolog

The Fission Yeast Stress-Responsive MAPK Pathway Promotes Meiosis via the Phosphorylation of Pol II CTD in Response to Environmental and Feedback Cues

The RRM-type RNA-binding protein Mei2 is a master regulator of meiosis in fission yeast, in which it stabilizes meiosis-specific mRNAs by blocking their destruction. Artificial activation of Mei2 can provoke the entire meiotic process, and it is suspected that Mei2 may do more than the stabilization of meiosis-specific mRNAs. In our current study using a new screening system, we show that Mei2 genetically interacts with subunits of CTDK-I, which phosphorylates serine-2 residues on the C-terminal domain of RNA polymerase II (Pol II CTD). Phosphorylation of CTD Ser-2 is essential to enable the robust transcription of ste11, which encodes an HMG-type transcription factor that regulates the expression of mei2 and other genes necessary for sexual development. CTD Ser-2 phosphorylation increases under nitrogen starvation, and the stress-responsive MAP kinase pathway, mediated by Wis1 MAPKK and Sty1 MAPK, is critical for this stress response. Sty1 phosphorylates Lsk1, the catalytic subunit of CTDK-I. Furthermore, a feedback loop stemming from activated Mei2 to Win1 and Wis4 MAPKKKs operates in this pathway and eventually enhances CTD Ser-2 phosphorylation and ste11 transcription. Hence, in addition to starting meiosis, Mei2 functions to reinforce the commitment to it, once cells have entered this process. This study also demonstrates clearly that the stress-responsive MAP kinase pathway can modulates gene expression through phosphorylation of Pol II CTD

Interactions between growth-dependent changes in cell size, nutrient supply and cellular elemental stoichiometry of marine Synechococcus

The factors that control elemental ratios within phytoplankton, like carbon:nitrogen:phosphorus (C:N:P), are key to biogeochemical cycles. Previous studies have identified relationships between nutrient-limited growth and elemental ratios in large eukaryotes, but little is known about these interactions in small marine phytoplankton like the globally important Cyanobacteria. To improve our understanding of these interactions in picophytoplankton, we asked how cellular elemental stoichiometry varies as a function of steady-state, N- and P-limited growth in laboratory chemostat cultures of Synechococcus WH8102. By combining empirical data and theoretical modeling, we identified a previously unrecognized factor (growth-dependent variability in cell size) that controls the relationship between nutrient-limited growth and cellular elemental stoichiometry. To predict the cellular elemental stoichiometry of phytoplankton, previous theoretical models rely on the traditional Droop model, which purports that the acquisition of a single limiting nutrient suffices to explain the relationship between a cellular nutrient quota and growth rate. Our study, however, indicates that growth-dependent changes in cell size have an important role in regulating cell nutrient quotas. This key ingredient, along with nutrient-uptake protein regulation, enables our model to predict the cellular elemental stoichiometry of Synechococcus across a range of nutrient-limited conditions. Our analysis also adds to the growth rate hypothesis, suggesting that P-rich biomolecules other than nucleic acids are important drivers of stoichiometric variability in Synechococcus. Lastly, by comparing our data with field observations, our study has important ecological relevance as it provides a framework for understanding and predicting elemental ratios in ocean regions where small phytoplankton like Synechococcus dominates