440 research outputs found
Robust and Scalable Scheme to Generate Large-Scale Entanglement Webs
We propose a robust and scalable scheme to generate an -qubit state
among separated quantum nodes (cavity-QED systems) by using linear optics and
postselections. The present scheme inherits the robustness of the Barrett-Kok
scheme [Phys. Rev. A {\bf 71}, 060310(R) (2005)]. The scalability is also
ensured in the sense that an arbitrarily large -qubit state can be
generated with a quasi-polynomial overhead . The
process to breed the states, which we introduce to achieve the scalability,
is quite simple and efficient, and can be applied for other physical systems.Comment: 5 pages, 3 figure
Spontaneous breaking of continuous translational invariance
Unbroken continuous translational invariance is often taken as a basic
assumption in discussions of spontaneous symmetry breaking (SSB), which singles
out SSB of translational invariance itself as an exceptional case. We present a
framework which allows us to treat translational invariance on the same footing
as other symmetries. It is shown that existing theorems on SSB can be
straightforwardly extended to this general case. As a concrete application, we
analyze the Nambu-Goldstone modes in a (ferromagnetic) supersolid. We prove on
the ground of the general theorems that the Bogoliubov mode stemming from a
spontaneously broken internal U(1) symmetry and the longitudinal phonon due to
a crystalline order are distinct physical modes.Comment: 14 pages, 4 pdf/jpg figures, REVTeX 4.1; v2: section IV expanded, new
appendix and references added, numerous other minor modifications throughout
the tex
Defect of Adaptation to Hypoxia in Patients With COPD Due to Reduction of Histone Deacetylase 7
BackgroundHypoxia inducible factor (HIF)-1 plays an important role in cellular adaptation to hypoxia by activating oxygen-regulated genes such as vascular endothelial growth factor (VEGF) and erythropoietin. Sputum VEGF levels are reported to be decreased in COPD, despite hypoxia. Here we show that patients with COPD fail to induce HIF-1Ξ± and VEGF under hypoxic condition because of a reduction in histone deacetylase (HDAC) 7.MethodsPeripheral blood mononuclear cells (PBMCs) were obtained from patients with moderate to severe COPD (n = 21), smokers without COPD (n = 12), and nonsmokers (n = 15). PBMCs were exposed to hypoxia (1% oxygen, 5% CO2, and 94% N2) for 24 h, and HIF-1Ξ± and HDAC7 protein expression in nuclear extracts were determined by sodium dodecyl sulfate poly acrylamide gel electrophoresis (SDS-PAGE)/Western blotting.ResultsHIF-1Ξ± was significantly induced by hypoxia in each group when compared with the normoxic condition (12-fold induction in nonsmokers, 24-fold induction in smokers without COPD, fourfold induction in COPD), but induction of HIF-1Ξ± under hypoxia was significantly lower in patients with COPD than in nonsmokers and smokers without COPD (P < .05 and P < .01, respectively). VEGF messenger RNA detected by quantitative real-time polymerase chain reaction was correlated with HIF-1Ξ± protein in nuclei (r = 0.79, P < .05), and HDAC7 protein expression was correlated with HIF-1Ξ± protein in nuclei (r = 0.46, P < .05). HDAC7 knockdown inhibited hypoxia-induced HIF-1Ξ± activity in U937 cells, and HIF-1Ξ± nuclear translocation and HIF-1Ξ± binding to the VEGF promoter in A549 cells.ConclusionsHDAC7 reduction in COPD causes a defect of HIF-1Ξ± induction response to hypoxia with impaired VEGF gene expression. This poor cellular adaptation might play a role in the pathogenesis of COPD
High genetic differentiation between an African and a non-African strain of Drosophila simulans revealed by segregation distortion and reduced crossover frequency
Abstract Drosophila simulans strains originating from Madagascar and nearby islands in the Indian Ocean often differ from those elsewhere in the number of sex comb teeth and the degree of morphological anomaly in hybrids with D. melanogaster. Here, we report a strong segregation distortion in the F1 intercross between two D. simulans strains originating from Madagascar and the US, possibly at both the gametic and zygotic levels. Strong bias against alleles of the Madagascar strain was observed for all ten marker loci distributed over the entire second chromosome in the F1 intercross, but only a few showed a weak distortion in the isogenic backgrounds of either strains. Significant deviations of genotype frequencies from Hardy-Weinberg proportions were consistently observed for the second chromosome. By contrast, the X and third chromosomes did not show any strong segregation distortion. Crossover frequency on the second chromosome was uniformly reduced in isogenic backgrounds whereas the map lengths in the F1 intercross were comparable to or larger than that of the standard D. melanogaster map. We discuss these findings in relation to previous studies on other traits and interspecific differences between D. mauritiana, which is endemic to Mauritius Island, and D. simulans
Effects of the Neutron Spin-Orbit Density on Nuclear Charge Density in Relativistic Models
The neutron spin-orbit density contributes to the nuclear charge density as a
relativistic effect. The contribution is enhanced by the effective mass
stemming from the Lorentz-scalar potential in relativistic models. This
enhancement explains well the difference between the cross sections of elastic
electron scattering off Ca and Ca which was not reproduced in
non-relativistic models. The spin-orbit density will be examined in more detail
in electron scattering off unstable nuclei which would be available in the
future.Comment: 4 pages with 3 eps figures, revte
Composite structural motifs of binding sites for delineating biological functions of proteins
Most biological processes are described as a series of interactions between
proteins and other molecules, and interactions are in turn described in terms
of atomic structures. To annotate protein functions as sets of interaction
states at atomic resolution, and thereby to better understand the relation
between protein interactions and biological functions, we conducted exhaustive
all-against-all atomic structure comparisons of all known binding sites for
ligands including small molecules, proteins and nucleic acids, and identified
recurring elementary motifs. By integrating the elementary motifs associated
with each subunit, we defined composite motifs which represent
context-dependent combinations of elementary motifs. It is demonstrated that
function similarity can be better inferred from composite motif similarity
compared to the similarity of protein sequences or of individual binding sites.
By integrating the composite motifs associated with each protein function, we
define meta-composite motifs each of which is regarded as a time-independent
diagrammatic representation of a biological process. It is shown that
meta-composite motifs provide richer annotations of biological processes than
sequence clusters. The present results serve as a basis for bridging atomic
structures to higher-order biological phenomena by classification and
integration of binding site structures.Comment: 34 pages, 7 figure
Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer
The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells
Spotlight on Geminin
In the previous issue of Breast Cancer Research, Gardner and co-workers describe a novel interaction between Geminin, a protein that prevents reinitiation of DNA replication, and Topoisomerase IIΞ± (TopoIIΞ±), an enzyme essential for removing catenated intertwines between sister chromatids. Geminin facilitates the action of TopoIIΞ±, thereby promoting termination of DNA replication at the same time it inhibits initiation. In this manner, Geminin ensures that cells duplicate their genome once, but only once, each time they divide. Remarkably, either depletion of Geminin or over-expression of Geminin inhibits the action of TopoIIΞ±, thereby making Geminin an excellent target for cancer chemotherapy
Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin
One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΞΞG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution
- β¦