Global, site-specific analysis of neuronal protein S-acylation

Protein S-acylation (palmitoylation) is a reversible lipid modification that is an important regulator of dynamic membrane-protein interactions. Proteomic approaches have uncovered many putative palmitoylated proteins however, methods for comprehensive palmitoylation site characterization are lacking. We demonstrate a quantitative site-specific-Acyl-Biotin-Exchange (ssABE) method that allowed the identification of 906 putative palmitoylation sites on 641 proteins from mouse forebrain. 62% of sites map to known palmitoylated proteins and 102 individual palmitoylation sites are known from the literature. 54% of palmitoylation sites map to synaptic proteins including many GPCRs, receptors/ion channels and peripheral membrane proteins. Phosphorylation sites were also identified on a subset of peptides that were palmitoylated, demonstrating for the first time co-identification of these modifications by mass spectrometry. Palmitoylation sites were identified on over half of the family of palmitoyl-acyltransferases (PATs) that mediate protein palmitoylation, including active site thioester-linked palmitoyl intermediates. Distinct palmitoylation motifs and site topology were identified for integral membrane and soluble proteins, indicating potential differences in associated PAT specificity and palmitoylation function. ssABE allows the global identification of palmitoylation sites as well as measurement of the active site modification state of PATs, enabling palmitoylation to be studied at a systems level

Qubits from Number States and Bell Inequalities for Number Measurements

Bell inequalities for number measurements are derived via the observation that the bits of the number indexing a number state are proper qubits. Violations of these inequalities are obtained from the output state of the nondegenerate optical parametric amplifier.Comment: revtex4, 7 pages, v2: results identical but extended presentation, v3: published versio

Cell‐type specific visualization and biochemical isolation of endogenous synaptic proteins in mice

In recent years, the remarkable molecular complexity of synapses has been revealed, with over 1000 proteins identified in the synapse proteome. Although it is known that different receptors and other synaptic proteins are present in different types of neurons, the extent of synapse diversity across the brain is largely unknown. This is mainly due to the limitations of current techniques. Here we report an efficient method for the purification of synaptic protein‐complexes, fusing a high‐affinity tag to endogenous PSD95 in specific cell types. We also developed a strategy which enables the visualization of endogenous PSD95 with fluorescent‐proteins tag in Cre‐recombinase expressing cells. We demonstrate the feasibility of proteomic analysis of synaptic protein‐complexes and visualization of these in specific cell types. We find that the composition of PSD95‐complexes purified from specific cell types differs from those extracted from tissues with diverse cellular composition. The results suggest that there might be differential interactions in the PSD95‐complexes in different brain regions. We have detected differentially interacting proteins by comparing datasets from the whole hippocampus and the CA3 subfield of the hippocampus. Therefore, these novel conditional PSD95 tagging lines will not only serve as powerful tools for precisely dissecting synapse diversity in specific brain regions and subsets of neuronal cells, but also provide an opportunity to better understand brain region‐ and cell type‐specific alterations associated with various psychiatric/neurological diseases. These newly developed conditional gene‐tagging methods can be applied to many different synaptic proteins and will facilitate research on the molecular complexity of synapses

Growth Kinetics in a Phase Field Model with Continuous Symmetry

We discuss the static and kinetic properties of a Ginzburg-Landau spherically symmetric $O(N)$ model recently introduced (Phys. Rev. Lett. {\bf 75}, 2176, (1995)) in order to generalize the so called Phase field model of Langer. The Hamiltonian contains two $O(N)$ invariant fields $\phi$ and $U$ bilinearly coupled. The order parameter field $\phi$ evolves according to a non conserved dynamics, whereas the diffusive field $U$ follows a conserved dynamics. In the limit $N \to \infty$ we obtain an exact solution, which displays an interesting kinetic behavior characterized by three different growth regimes. In the early regime the system displays normal scaling and the average domain size grows as $t^{1/2}$, in the intermediate regime one observes a finite wavevector instability, which is related to the Mullins-Sekerka instability; finally, in the late stage the structure function has a multiscaling behavior, while the domain size grows as $t^{1/4}$.Comment: 9 pages RevTeX, 9 figures included, files packed with uufiles to appear on Phy. Rev.

Can one written word mean many things? Prereaders’ assumptions about the stability of written words’ meanings

Results of three experiments confirmed previous findings that in a moving word task, prereaders 3 to 5 years of age judge as if the meaning of a written word changes when it moves from a matching to a nonmatching toy (e.g., when the word “dog” moves from a dog to a boat). We explore under what circumstances children make such errors, we identify new conditions under which children were more likely correctly to treat written words’ meanings as stable: when the word was placed alongside a nonmatching toy without having been alongside a matching toy previously, when two words were moved from a matching toy to a nonmatching toy, and when children were asked to change what the print said. Under these conditions, children more frequently assumed that physical forms had stable meanings as they do with other forms of external representation

A Zoology of Bell inequalities resistant to detector inefficiency

We derive both numerically and analytically Bell inequalities and quantum measurements that present enhanced resistance to detector inefficiency. In particular we describe several Bell inequalities which appear to be optimal with respect to inefficient detectors for small dimensionality d=2,3,4 and 2 or more measurement settings at each side. We also generalize the family of Bell inequalities described in Collins et all (Phys. Rev. Lett. 88, 040404) to take into account the inefficiency of detectors. In addition we consider the possibility for pairs of entangled particles to be produced with probability less than one. We show that when the pair production probability is small, one must in general use different Bell inequalities than when the pair production probability is high.Comment: 12 pages, revtex. Appendix completed, minor revision

Charm Quark Contribution to K+ -> pi+ nu anti-nu at Next-to-Next-to-Leading Order

We calculate the complete NNLO QCD corrections to the charm contribution of the rare decay K+ -> pi+ nu nu-bar. We encounter several new features, which were absent in lower orders. We discuss them in detail and present the results for the 2-loop matching conditions of the Wilson coefficients, the 3-loop anomalous dimensions, and the 2-loop matrix elements of the relevant operators that enter the NNLO renormalization group analysis of the Z-penguin and the electroweak box contribution. The inclusion of the NNLO QCD corrections leads to a significant reduction of the theoretical uncertainty from 9.8% down to 2.4% in the relevant parameter Pc, implying the leftover scale uncertainties in BR(K+ -> pi+ nu nu-bar) and in the determination of |V_td|, sin(2 beta), and gamma from the K -> pi nu nu system to be 1.3%, 1.0%, 0.006, and 1.2 degrees, respectively. For the charm quark MSbar mass mc=(1.30+-0.05) GeV and |V_us|= 0.2248 the NLO value Pc=0.37+-0.06 is modified to Pc=0.38+-0.04 at the NNLO level with the latter error fully dominated by the uncertainty in mc. We present tables for Pc as a function of mc and alphas(MZ) and a very accurate analytic formula that summarizes these two dependences as well as the dominant theoretical uncertainties. Adding the recently calculated long-distance contributions we find BR(K+ -> pi+ nu nu-bar)=(8.0+-1.1)*10^-11 with the present uncertainties in mc and the Cabibbo-Kobayashi-Maskawa elements being the dominant individual sources in the quoted error. We also emphasize that improved calculations of the long-distance contributions to K+ -> pi+ nu nu-bar and of the isospin breaking corrections in the evaluation of the weak current matrix elements from K+ -> pi0 e+ nu would be valuable in order to increase the potential of the two golden K -> pi nu nu decays in the search for new physics.Comment: 74 pages, 28 figures. Erratum added: We correct the treatment of anomalous triangle diagrams. The associated numerical correction is below a permille; v3: Typographical mistakes in (108), (111) and (112) corrected. Thanks to Xu Feng for pointing them out. Numerical results unchange

Initial-State Interactions in the Unpolarized Drell-Yan Process

We show that initial-state interactions contribute to the $\cos 2 \phi$ distribution in unpolarized Drell-Yan lepton pair production $p p$ and $p \bar p \to \ell^+ \ell^- X$, without suppression. The asymmetry is expressed as a product of chiral-odd distributions $h_1^\perp(x_1,\bm{p}_\perp^2)\times \bar h_1^\perp(x_2,\bm{k}_\perp^2)$, where the quark-transversity function $h_1^\perp(x,\bm{p}_\perp^2)$ is the transverse momentum dependent, light-cone momentum distribution of transversely polarized quarks in an {\it unpolarized} proton. We compute this (naive) $T$-odd and chiral-odd distribution function and the resulting $\cos 2 \phi$ asymmetry explicitly in a quark-scalar diquark model for the proton with initial-state gluon interaction. In this model the function $h_1^\perp(x,\bm{p}_\perp^2)$ equals the $T$-odd (chiral-even) Sivers effect function $f^\perp_{1T}(x,\bm{p}_\perp^2)$. This suggests that the single-spin asymmetries in the SIDIS and the Drell-Yan process are closely related to the $\cos 2 \phi$ asymmetry of the unpolarized Drell-Yan process, since all can arise from the same underlying mechanism. This provides new insight regarding the role of quark and gluon orbital angular momentum as well as that of initial- and final-state gluon exchange interactions in hard QCD processes.Comment: 22 pages, 6 figure

Development of InGaAs/AlGaAsSb Geiger mode avalanche photodiodes

Near-infrared linear mode Al 0.85 Ga 0.15 As 0.56 Sb 0.44 avalanche photodiodes (APDs) exhibit excellent temperature stability, potentially simplifying Geiger mode operation. We have carried out the first experimental evaluation of In 0.53 Ga 0.47 As/Al 0.85 Ga 0.15 As 0.56 Sb 0.44 APDs in Geiger mode. Characterization on multiple devices included temperature-dependent dark current, avalanche multiplication, dark count rate (DCR), afterpulsing, and single photon detection efficiency (SPDE). The temperature coefficient of breakdown voltage extracted from avalanche multiplication data was 13.5 mV⋅K−1 , much lower than InGaAs/InP Geiger mode APDs, reducing changes in operation voltage and offering possible protection from high optical power thermal attack in communication systems. At 200 K, SPDE were 5%–16% with DCR of 1–20 Mc⋅s−1 , comparable to InAlAs and early InP-based Single Photon APDs. The afterpulsing at 200 K was negligible for hold-off time > 50 μ s (reducing to 5 μ s at 250 K). These are similar to the performance of InGaAs/InAlAs and some InGaAs/InP Geiger mode APDs. The data reported in this article is available from the ORDA digital repository (https://doi.org/10.15131/shef.data.24125721)

A Soluble Phase Field Model

The kinetics of an initially undercooled solid-liquid melt is studied by means of a generalized Phase Field model, which describes the dynamics of an ordering non-conserved field phi (e.g. solid-liquid order parameter) coupled to a conserved field (e.g. thermal field). After obtaining the rules governing the evolution process, by means of analytical arguments, we present a discussion of the asymptotic time-dependent solutions. The full solutions of the exact self-consistent equations for the model are also obtained and compared with computer simulation results. In addition, in order to check the validity of the present model we confronted its predictions against those of the standard Phase field model and found reasonable agreement. Interestingly, we find that the system relaxes towards a mixed phase, depending on the average value of the conserved field, i.e. on the initial condition. Such a phase is characterized by large fluctuations of the phi field.Comment: 13 pages, 8 figures, RevTeX 3.1, submitted to Physical Review