The mRNA-bound proteome of the early fly embryo

Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins (RBPs) is the dominant force in embryo patterning. We used two mRNA interactome capture methods to identify RBPs bound to polyadenylated transcripts within the first two hours of D. melanogaster embryogenesis. We identified a high-confidence set of 476 putative RBPs and confirmed RNA-binding activities for most of 24 tested candidates. Most proteins in the interactome are known RBPs or harbor canonical RBP features, but 99 exhibited previously uncharacterized RNA-binding activity. mRNA-bound RBPs and TFs exhibit distinct expression dynamics, in which the newly identified RBPs dominate the first two hours of embryonic development. Integrating our resource with in situ hybridization data from existing databases showed that mRNAs encoding RBPs are enriched in posterior regions of the early embryo, suggesting their general importance in posterior patterning and germ cell maturation

Neutralino Dark Matter from MSSM Flat Directions in light of WMAP Result

The minimal supersymmetric standard model (MSSM) has a truly supersymmetric way to explain both the baryon asymmetry and cold dark matter in the present Universe, that is, ``Affleck-Dine baryo/DM-genesis.'' The associated late-time decay of Q-balls directly connects the origins of the baryon asymmetry and dark matter, and also predicts a specific nature of the LSP. In this paper, we investigate the prospects for indirect detection of these dark matter candidates observing high energy neutrino flux from the Sun, and hard positron flux from the halo. We also update the previous analysis of the direct detection in hep-ph/0205044 by implementing the recent result from WMAP satellite.Comment: 32 pages, including 40 figure

Likelihood Functions for Supersymmetric Observables in Frequentist Analyses of the CMSSM and NUHM1

On the basis of frequentist analyses of experimental constraints from electroweak precision data, g-2, B physics and cosmological data, we investigate the parameters of the constrained MSSM (CMSSM) with universal soft supersymmetry-breaking mass parameters, and a model with common non-universal Higgs masses (NUHM1). We present chi^2 likelihood functions for the masses of supersymmetric particles and Higgs bosons, as well as b to s gamma, b to mu mu and the spin-independent dark matter scattering cross section. In the CMSSM we find preferences for sparticle masses that are relatively light. In the NUHM1 the best-fit values for many sparticle masses are even slightly smaller, but with greater uncertainties. The likelihood functions for most sparticle masses are cut off sharply at small masses, in particular by the LEP Higgs mass constraint. Both in the CMSSM and the NUHM1, the coannihilation region is favoured over the focus-point region at about the 3-sigma level, largely but not exclusively because of g-2. Many sparticle masses are highly correlated in both the CMSSM and NUHM1, and most of the regions preferred at the 95% C.L. are accessible to early LHC running. Some slepton and chargino/neutralino masses should be in reach at the ILC. The masses of the heavier Higgs bosons should be accessible at the LHC and the ILC in portions of the preferred regions in the (M_A, tan beta) plane. In the CMSSM, the likelihood function for b to mu mu is peaked close to the Standard Model value, but much larger values are possible in the NUHM1. We find that values of the DM cross section > 10^{-10} pb are preferred in both the CMSSM and the NUHM1. We study the effects of dropping the g-2, b to s gamma, relic density and M_h constraints.Comment: 34 pages, 24 figure

Revisiting the Higgs Mass and Dark Matter in the CMSSM

Taking into account the available accelerator and astrophysical constraints, the mass of the lightest neutral Higgs boson h in the minimal supersymmetric extension of the Standard Model with universal soft supersymmetry-breaking masses (CMSSM) has been estimated to lie between 114 and ~ 130 GeV. Recent data from ATLAS and CMS hint that m_h ~ 125 GeV, though m_h ~ 119 GeV may still be a possibility. Here we study the consequences for the parameters of the CMSSM and direct dark matter detection if the Higgs hint is confirmed, focusing on the strips in the (m_1/2, m_0) planes for different tan beta and A_0 where the relic density of the lightest neutralino chi falls within the range of the cosmological cold dark matter density allowed by WMAP and other experiments. We find that if m_h ~ 125 GeV focus-point strips would be disfavoured, as would the low-tan beta stau-chi and stop -chi coannihilation strips, whereas the stau-chi coannihilation strip at large tan beta and A_0 > 0 would be favoured, together with its extension to a funnel where rapid annihilation via direct-channel H/A poles dominates. On the other hand, if m_h ~ 119 GeV more options would be open. We give parametrizations of WMAP strips with large tan beta and fixed A_0/m_0 > 0 that include portions compatible with m_h = 125 GeV, and present predictions for spin-independent elastic dark matter scattering along these strips. These are generally low for models compatible with m_h = 125 GeV, whereas the XENON100 experiment already excludes some portions of strips where m_h is smaller.Comment: 24 pages, 9 figure

Energy and system size dependence of \phi meson production in Cu+Cu and Au+Au collisions

We study the beam-energy and system-size dependence of \phi meson production (using the hadronic decay mode \phi -- K+K-) by comparing the new results from Cu+Cu collisions and previously reported Au+Au collisions at \sqrt{s_NN} = 62.4 and 200 GeV measured in the STAR experiment at RHIC. Data presented are from mid-rapidity (|y|<0.5) for 0.4 < pT < 5 GeV/c. At a given beam energy, the transverse momentum distributions for \phi mesons are observed to be similar in yield and shape for Cu+Cu and Au+Au colliding systems with similar average numbers of participating nucleons. The \phi meson yields in nucleus-nucleus collisions, normalised by the average number of participating nucleons, are found to be enhanced relative to those from p+p collisions with a different trend compared to strange baryons. The enhancement for \phi mesons is observed to be higher at \sqrt{s_NN} = 200 GeV compared to 62.4 GeV. These observations for the produced \phi(s\bar{s}) mesons clearly suggest that, at these collision energies, the source of enhancement of strange hadrons is related to the formation of a dense partonic medium in high energy nucleus-nucleus collisions and cannot be alone due to canonical suppression of their production in smaller systems.Comment: 20 pages and 5 figure

Collider aspects of flavour physics at high Q

This review presents flavour related issues in the production and decays of heavy states at LHC, both from the experimental side and from the theoretical side. We review top quark physics and discuss flavour aspects of several extensions of the Standard Model, such as supersymmetry, little Higgs model or models with extra dimensions. This includes discovery aspects as well as measurement of several properties of these heavy states. We also present public available computational tools related to this topic.Comment: Report of Working Group 1 of the CERN Workshop ``Flavour in the era of the LHC'', Geneva, Switzerland, November 2005 -- March 200

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts

Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation, and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. To our knowledge, nearly one-third were not previously annotated as RNA binding, and about 15% were not predictable by computational methods to interact with RNA. Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms. Our observations indicate the presence of a large number of mRNA binders with diverse molecular functions participating in combinatorial posttranscriptional gene-expression networks