An Optimal Protocol to Analyze the Rat Spinal Cord Proteome

Since the function of the spinal cord depends on the proteins found there, better defing the normal Spinal Cord Proteome is an important and challenging task. Although brain and cerebrospinal fluid samples from patients with different central nervous system (CNS) disorders have been studied, a thorough examination of specific spinal cord proteins and the changes induced by injury or associated to conditions such as neurodegeneration, spasticity and neuropathies has yet to be performed. In the present study, we aimed to describe total protein content in the spinal cord of healthy rats, employing different proteomics tools. Accordingly, we have developed a fast, easy, and reproducible sequential protocol for protein extraction from rat spinal cords. We employed conventional two dimensional electrophoresis (2DE) in different pH ranges (eg. 4–7, 3–11 NL) combined with identification by mass spectrometry (MALDI-TOF/TOF), as well as first dimension protein separation combined with Liquid Chromatography Mass Spectrometry/Mass Spectrometry (LC-MS/MS) to maximise the benefits of this technology. The value of these techniques is demonstrated here by the identification of several proteins known to be associated with neuroglial structures, neurotransmission, cell survival and nerve growth in the central nervous system. Furthermore this study identified many spinal proteins that have not previously been described in the literature and which may play an important role as either sensitive biomarkers of dysfunction or of recovery after Spinal Cord Injury

Z' Bosons at Colliders: a Bayesian Viewpoint

We revisit the CDF data on di-muon production to impose constraints on a large class of Z' bosons occurring in a variety of E_6 GUT based models. We analyze the dependence of these limits on various factors contributing to the production cross-section, showing that currently systematic and theoretical uncertainties play a relatively minor role. Driven by this observation, we emphasize the use of the Bayesian statistical method, which allows us to straightforwardly (i) vary the gauge coupling strength, g', of the underlying U(1)'; (ii) include interference effects with the Z' amplitude (which are especially important for large g'); (iii) smoothly vary the U(1)' charges; (iv) combine these data with the electroweak precision constraints as well as with other observables obtained from colliders such as LEP 2 and the LHC; and (v) find preferred regions in parameter space once an excess is seen. We adopt this method as a complementary approach for a couple of sample models and find limits on the Z' mass, generally differing by only a few percent from the corresponding CDF ones when we follow their approach. Another general result is that the interference effects are quite relevant if one aims at discriminating between models. Finally, the Bayesian approach frees us of any ad hoc assumptions about the number of events needed to constitute a signal or exclusion limit for various actual and hypothetical reference energies and luminosities at the Tevatron and the LHC.Comment: PDFLaTeX, 24 pages, 7 figures. Version with improved tables and figure

SUMO chain-induced dimerization activates RNF4

Dimeric RING E3 ligases interact with protein substrates and conformationally restrain the ubiquitin-E2-conjugating enzyme thioester complex such that it is primed for catalysis. RNF4 is an E3 ligase containing an N-terminal domain that binds its polySUMO substrates and a C-terminal RING domain responsible for dimerization. To investigate how RNF4 activity is controlled, we increased polySUMO substrate concentration by ablating expression of SUMO protease SENP6. Accumulation of SUMO chains in vivo leads to ubiquitin-mediated proteolysis of RNF4. In vitro we demonstrate that at concentrations equivalent to those found in vivo RNF4 is predominantly monomeric and inactive as an ubiquitin E3 ligase. However, in the presence of SUMO chains, RNF4 is activated by dimerization, leading to both substrate ubiquitylation and autoubiquitylation, responsible for degradation of RNF4. Thus the ubiquitin E3 ligase activity of RNF4 is directly linked to the availability of its polySUMO substrates

PIP5KIβ Selectively Modulates Apical Endocytosis in Polarized Renal Epithelial Cells

Localized synthesis of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] at clathrin coated pits (CCPs) is crucial for the recruitment of adaptors and other components of the internalization machinery, as well as for regulating actin dynamics during endocytosis. PtdIns(4,5)P2 is synthesized from phosphatidylinositol 4-phosphate by any of three phosphatidylinositol 5-kinase type I (PIP5KI) isoforms (α, β or γ). PIP5KIβ localizes almost exclusively to the apical surface in polarized mouse cortical collecting duct cells, whereas the other isoforms have a less polarized membrane distribution. We therefore investigated the role of PIP5KI isoforms in endocytosis at the apical and basolateral domains. Endocytosis at the apical surface is known to occur more slowly than at the basolateral surface. Apical endocytosis was selectively stimulated by overexpression of PIP5KIβ whereas the other isoforms had no effect on either apical or basolateral internalization. We found no difference in the affinity for PtdIns(4,5)P2-containing liposomes of the PtdIns(4,5)P2 binding domains of epsin and Dab2, consistent with a generic effect of elevated PtdIns(4,5)P2 on apical endocytosis. Additionally, using apical total internal reflection fluorescence imaging and electron microscopy we found that cells overexpressing PIP5KIβ have fewer apical CCPs but more internalized coated structures than control cells, consistent with enhanced maturation of apical CCPs. Together, our results suggest that synthesis of PtdIns(4,5)P2 mediated by PIP5KIβ is rate limiting for apical but not basolateral endocytosis in polarized kidney cells. PtdIns(4,5)P2 may be required to overcome specific structural constraints that limit the efficiency of apical endocytosis. © 2013 Szalinski et al

Testing spatial noncommutativiy via the Aharonov-Bohm effect

The possibility of detecting noncommutative space relics is analyzed using the Aharonov-Bohm effect. We show that, if space is noncommutative, the holonomy receives non-trivial kinematical corrections that will produce a diffraction pattern even when the magnetic flux is quantized. The scattering problem is also formulated, and the differential cross section is calculated. Our results can be extrapolated to high energy physics and the bound $\theta \sim [ 10 {TeV}]^{-2}$ is found. If this bound holds, then noncommutative effects could be explored in scattering experiments measuring differential cross sections for small angles. The bound state Aharonov- Bohm effect is also discussed.Comment: 16 pp, Revtex 4, 2 fig, new references added. To appear in PR

Non-Commutative Quantum Mechanics

A general non-commutative quantum mechanical system in a central potential $V=V(r)$ in two dimensions is considered. The spectrum is bounded from below and for large values of the anticommutative parameter $\theta$, we find an explicit expression for the eigenvalues. In fact, any quantum mechanical system with these characteristics is equivalent to a commutative one in such a way that the interaction $V(r)$ is replaced by $V = V ({\hat H}_{HO}, {\hat L}_z)$, where ${\hat H}_{HO}$ is the hamiltonian of the two-dimensional harmonic oscillator and ${\hat L}_z$ is z- component of the angular momentum. For other finite values of $\theta$ the model can be solved by using perturbation theory.Comment: Minors corrections and some references removed. To appear in PR

Measurements of neutrino oscillation in appearance and disappearance channels by the T2K experiment with 6.6 x 10(20) protons on target

111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee comments111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee comments111 pages, 45 figures, submitted to Physical Review D. Minor revisions to text following referee commentsWe thank the J-PARC staff for superb accelerator performance and the CERN NA61/SHINE Collaboration for providing valuable particle production data. We acknowledge the support of MEXT, Japan; NSERC, NRC, and CFI, Canada; CEA and CNRS/IN2P3, France; DFG, Germany; INFN, Italy; National Science Centre (NCN), Poland; RSF, RFBR and MES, Russia; MINECO and ERDF funds, Spain; SNSF and SER, Switzerland; STFC, UK; and the U. S. Deparment of Energy, USA. We also thank CERN for the UA1/NOMAD magnet, DESY for the HERA-B magnet mover system, NII for SINET4, the WestGrid and SciNet consortia in Compute Canada, GridPP, UK, and the Emerald High Performance Computing facility in the Centre for Innovation, UK. In addition, participation of individual researchers and institutions has been further supported by funds from ERC (FP7), EU; JSPS, Japan; Royal Society, UK; and DOE Early Career program, USA

Measurement of the electron neutrino charged-current interaction rate on water with the T2K ND280 pi(0) detector

10 pages, 6 figures, Submitted to PRDhttp://journals.aps.org/prd/abstract/10.1103/PhysRevD.91.112010© 2015 American Physical Society11 pages, 6 figures, as accepted to PRD11 pages, 6 figures, as accepted to PRD11 pages, 6 figures, as accepted to PR