Molecular and Genetic Evidence for a Virus-Encoded Glycosyltransferase Involved in Protein Glycosylation

AbstractThe major capsid protein, Vp54, of chlorella virus PBCV-1 is a glycoprotein that contains either one glycan of ∼30 sugar residues or two similar glycans of ∼15 residues. Previous analysis of PBCV-1 antigenic mutants that contained altered Vp54 glycans led to the conclusion that unlike other glycoprotein-containing viruses, most, if not all, of the enzymes involved in the synthesis of the Vp54 glycan are probably encoded by PBCV-1 (I.-N. Wang et al., 1993, Proc. Natl. Acad. Sci. USA 90, 3840–3844). In this report we used molecular and genetic approaches to begin to identify these virus genes. Comparing the deduced amino acid sequences of the putative 375 PBCV-1 protein-encoding genes to databases identified seven potential glycosyltransferases. One gene, designated a64r, encodes a 638-amino-acid protein that has four motifs conserved in “Fringe type” glycosyltransferases. Analysis of 13 PBCV-1 antigenic mutants revealed mutations in a64r that correlated with a specific antigenic variation. Dual-infection experiments with different antigenic mutants indicated that viruses that contained wild-type a64r could complement and recombine with viruses that contained mutant a64r to form wild-type virus. Therefore, we conclude that a64r encodes a glycosyltransferase involved in synthesizing the Vp54 glycan. This is the first report of a virus-encoded glycosyltransferase involved in protein glycosylation

Convergence of simulated annealing by the generalized transition probability

We prove weak ergodicity of the inhomogeneous Markov process generated by the generalized transition probability of Tsallis and Stariolo under power-law decay of the temperature. We thus have a mathematical foundation to conjecture convergence of simulated annealing processes with the generalized transition probability to the minimum of the cost function. An explicitly solvable example in one dimension is analyzed in which the generalized transition probability leads to a fast convergence of the cost function to the optimal value. We also investigate how far our arguments depend upon the specific form of the generalized transition probability proposed by Tsallis and Stariolo. It is shown that a few requirements on analyticity of the transition probability are sufficient to assure fast convergence in the case of the solvable model in one dimension.Comment: 11 page

Van der Waals density functional: Self-consistent potential and the nature of the van der Waals bond

We derive the exchange-correlation potential corresponding to the nonlocal van der Waals density functional [M. Dion, H. Rydberg, E. Schroder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)]. We use this potential for a self-consistent calculation of the ground state properties of a number of van der Waals complexes as well as crystalline silicon. For the latter, where little or no van der Waals interaction is expected, we find that the results are mostly determined by semilocal exchange and correlation as in standard generalized gradient approximations (GGA), with the fully nonlocal term giving little effect. On the other hand, our results for the van der Waals complexes show that the self-consistency has little effect at equilibrium separations. This finding validates previous calculations with the same functional that treated the fully nonlocal term as a post GGA perturbation. A comparison of our results with wave-function calculations demonstrates the usefulness of our approach. The exchange-correlation potential also allows us to calculate Hellmann-Feynman forces, hence providing the means for efficient geometry relaxations as well as unleashing the potential use of other standard techniques that depend on the self-consistent charge distribution. The nature of the van der Waals bond is discussed in terms of the self-consistent bonding charge.Comment: submitted to Phys. Rev.

Dual Superconductor Scenario of Confinement: A Systematic Study of Gribov Copy Effects

We perform a study of the effects from maximal abelian gauge Gribov copies in the context of the dual superconductor scenario of confinement, on the basis of a novel approach for estimation of systematic uncertainties from incomplete gauge fixing. We present numerical results, in SU(2) lattice gauge theory, using the overrelaxed simulated annealing gauge fixing algorithm. We find abelian and non-abelian string tensions to differ significantly, their ratio being 0.92(4) at BETA = 2.5115. An approximate factorization of the abelian potential into monopole and photon contributions has been confirmed, the former giving rise to the abelian string tension.Comment: 35 pages uucompressed LaTeX with 10 encapsuled postscript figure

Quantum heuristic algorithm for traveling salesman problem

We propose a quantum heuristic algorithm to solve a traveling salesman problem by generalizing Grover search. Sufficient conditions are derived to greatly enhance the probability of finding the tours with extremal costs, reaching almost to unity and they are shown characterized by statistical properties of tour costs. In particular for a Gaussian distribution of the tours along the cost we show that the quantum algorithm exhibits the quadratic speedup of its classical counterpart, similarly to Grover search.Comment: Published versio

Statistical mechanics of a single particle in a multiscale random potential: Parisi landscapes in finite dimensional Euclidean spaces

We construct a N-dimensional Gaussian landscape with multiscale, translation invariant, logarithmic correlations and investigate the statistical mechanics of a single particle in this environment. In the limit of high dimension N>>1 the free energy of the system and overlap function are calculated exactly using the replica trick and Parisi's hierarchical ansatz. In the thermodynamic limit, we recover the most general version of the Derrida's Generalized Random Energy Model (GREM). The low-temperature behaviour depends essentially on the spectrum of length scales involved in the construction of the landscape. If the latter consists of K discrete values, the system is characterized by a K-step Replica Symmetry Breaking solution. We argue that our construction is in fact valid in any finite spatial dimensions $N\ge 1$. We discuss implications of our results for the singularity spectrum describing multifractality of the associated Boltzmann-Gibbs measure. Finally we discuss several generalisations and open problems, the dynamics in such a landscape and the construction of a Generalized Multifractal Random Walk.Comment: 25 pages, published version with a few misprints correcte

Single agent rituximab in patients with follicular or mantle cell lymphoma: clinical and biological factors that are predictive of response and event-free survival as well as the effect of rituximab on the immune system: a study of the Swiss Group for Clinical Cancer Research (SAKK)

Background: Predictive factors of rituximab efficacy and its effect on the immune system are still not defined. Patients and methods: Three hundred and six patients with follicular or mantle cell lymphoma received four weekly doses of rituximab (induction) and no further treatment (arm A) or four more doses at 2-month intervals (arm B). Results: Response rate to induction was 44%. Independent predictive factors for response were disease bulk <5 cm, follicular histology, normal hemoglobin and low lymphocyte count. Factors associated with event-free survival (EFS) were having responded to induction, having received not more than one line of therapy, Ann Arbor stage I-III, high lymphocyte count, disease bulk <5 cm, Fc-gamma receptor genotype VV and receiving prolonged treatment. B cells were suppressed by treatment but recovered after a median of 12 months in arm A and 18 months in arm B. The median IgM level after 1 year was normal in arm A but was decreased to 73% of baseline in arm B. We observed 24 serious adverse events, equally distributed between arms. Ten patients receiving induction only and six patients receiving prolonged treatment developed a second tumor. Conclusions: We defined the characteristics predicting response and EFS to rituximab. Prolonged treatment results in longer EFS at the cost of a longer reduction in B cell and IgM levels, but without additional clinical toxicit

RELICS: Strong Lens Models for Five Galaxy Clusters From the Reionization Lensing Cluster Survey

Strong gravitational lensing by galaxy clusters magnifies background galaxies, enhancing our ability to discover statistically significant samples of galaxies at z>6, in order to constrain the high-redshift galaxy luminosity functions. Here, we present the first five lens models out of the Reionization Lensing Cluster Survey (RELICS) Hubble Treasury Program, based on new HST WFC3/IR and ACS imaging of the clusters RXC J0142.9+4438, Abell 2537, Abell 2163, RXC J2211.7-0349, and ACT-CLJ0102-49151. The derived lensing magnification is essential for estimating the intrinsic properties of high-redshift galaxy candidates, and properly accounting for the survey volume. We report on new spectroscopic redshifts of multiply imaged lensed galaxies behind these clusters, which are used as constraints, and detail our strategy to reduce systematic uncertainties due to lack of spectroscopic information. In addition, we quantify the uncertainty on the lensing magnification due to statistical and systematic errors related to the lens modeling process, and find that in all but one cluster, the magnification is constrained to better than 20% in at least 80% of the field of view, including statistical and systematic uncertainties. The five clusters presented in this paper span the range of masses and redshifts of the clusters in the RELICS program. We find that they exhibit similar strong lensing efficiencies to the clusters targeted by the Hubble Frontier Fields within the WFC3/IR field of view. Outputs of the lens models are made available to the community through the Mikulski Archive for Space TelescopesComment: Accepted to Ap

Transport and superconducting properties of Fe-based superconductors: SmFeAs(O1-x Fx) versus Fe1+y (Te1-x, Sex)

We present transport and superconducting properties - namely resistivity, magnetoresistivity, Hall effect, Seebeck effect, thermal conductivity, upper critical field - of two different families of Fe-based superconductors, which can be viewed in many respects as end members: SmFeAs(O1-xFx) with the largest Tc and the largest anisotropy and Fe1+y(Te1-x,Sex), with the largest Hc2, the lowest Tc and the lowest anisotropy. In the case of the SmFeAs(O1-xFx) series, we find that a single band description allows to extract an approximated estimation of band parameters such as carrier density and mobility from experimental data, although the behaviour of Seebeck effect as a function of doping demonstrates that a multiband description would be more appropriate. On the contrary, experimental data of the Fe1+y(Te1-x,Sex) series exhibit a strongly compensated behaviour, which can be described only within a multiband model. In the Fe1+y(Te1-x,Sex) series, the role of the excess Fe, tuned by Se stoichiometry, is found to be twofold: it dopes electrons in the system and it introduces localized magnetic moments, responsible for Kondo like scattering and likely pair-breaking of Cooper pairs. Hence, excess Fe plays a crucial role also in determining superconducting properties such as the Tc and the upper critical field Bc2. The huge Bc2 values of the Fe1+y(Te1-x,Sex) samples are described by a dirty limit law, opposed to the clean limit behaviour of the SmFeAs(O1-xFx) samples. Hence, magnetic scattering by excess Fe seems to drive the system in the dirty regime, but its detrimental pairbreaking role seems not to be as severe as predicted by theory. This issue has yet to be clarified, addressing the more fundamental issue of the interplay between magnetism and superconductivity