168 research outputs found
GRAPE: GRaphical Abstracted Protein Explorer
The region surrounding a protein, known as the surface of interaction or molecular surface, can provide valuable insight into its function. Unfortunately, due to the complexity of both their geometry and their surface fields, study of these surfaces can be slow and difficult and important features may be hard to identify. Here, we describe our GRaphical Abstracted Protein Explorer, or GRAPE, a web server that allows users to explore abstracted representations of proteins. These abstracted surfaces effectively reduce the level of detail of the surface of a macromolecule, using a specialized algorithm that removes small bumps and pockets, while preserving large-scale structural features. Scalar fields, such as electrostatic potential and hydropathy, are smoothed to further reduce visual complexity. This entirely new way of looking at proteins complements more traditional views of the molecular surface. GRAPE includes a thin 3D viewer that allows users to quickly flip back and forth between both views. Abstracted views provide a fast way to assess both a molecule's shape and its different surface field distributions. GRAPE is freely available at http://grape.uwbacter.org
Heating rate and electrode charging measurements in a scalable, microfabricated, surface-electrode ion trap
We characterise the performance of a surface-electrode ion "chip" trap
fabricated using established semiconductor integrated circuit and
micro-electro-mechanical-system (MEMS) microfabrication processes which are in
principle scalable to much larger ion trap arrays, as proposed for implementing
ion trap quantum information processing. We measure rf ion micromotion parallel
and perpendicular to the plane of the trap electrodes, and find that on-package
capacitors reduce this to <~ 10 nm in amplitude. We also measure ion trapping
lifetime, charging effects due to laser light incident on the trap electrodes,
and the heating rate for a single trapped ion. The performance of this trap is
found to be comparable with others of the same size scale.Comment: 6 pages, 10 figure
Quantum computing implementations with neutral particles
We review quantum information processing with cold neutral particles, that
is, atoms or polar molecules. First, we analyze the best suited degrees of
freedom of these particles for storing quantum information, and then we discuss
both single- and two-qubit gate implementations. We focus our discussion mainly
on collisional quantum gates, which are best suited for atom-chip-like devices,
as well as on gate proposals conceived for optical lattices. Additionally, we
analyze schemes both for cold atoms confined in optical cavities and hybrid
approaches to entanglement generation, and we show how optimal control theory
might be a powerful tool to enhance the speed up of the gate operations as well
as to achieve high fidelities required for fault tolerant quantum computation.Comment: 19 pages, 12 figures; From the issue entitled "Special Issue on
Neutral Particles
Fabrication and heating rate study of microscopic surface electrode ion traps
We report heating rate measurements in a microfabricated gold-on-sapphire
surface electrode ion trap with trapping height of approximately 240 micron.
Using the Doppler recooling method, we characterize the trap heating rates over
an extended region of the trap. The noise spectral density of the trap falls in
the range of noise spectra reported in ion traps at room temperature. We find
that during the first months of operation the heating rates increase by
approximately one order of magnitude. The increase in heating rates is largest
in the ion loading region of the trap, providing a strong hint that surface
contamination plays a major role for excessive heating rates. We discuss data
found in the literature and possible relation of anomalous heating to sources
of noise and dissipation in other systems, namely impurity atoms adsorbed on
metal surfaces and amorphous dielectrics.Comment: 17 pages, 5 figure
Phylogeny of Diving Beetles Reveals a Coevolutionary Arms Race between the Sexes
BACKGROUND: Darwin illustrated his sexual selection theory with male and female morphology of diving beetles, but maintained a cooperative view of their interaction. Present theory suggests that instead sexual conflict should be a widespread evolutionary force driving both intersexual coevolutionary arms races and speciation. METHODOLOGY/PRINCIPAL FINDINGS: We combined Bayesian phylogenetics, complete taxon sampling and a multi-gene approach to test the arms race scenario on a robust diving beetle phylogeny. As predicted, suction cups in males and modified dorsal surfaces in females showed a pronounced coevolutionary pattern. The female dorsal modifications impair the attachment ability of male suction cups, but each antagonistic novelty in females corresponds to counter-differentiation of suction cups in males. CONCLUSIONS: A recently diverged sibling species pair in Japan is possibly one consequence of this arms race and we suggest that future studies on hypoxia might reveal the key to the extraordinary selection for female counter-adaptations in diving beetles
Electron spin coherence exceeding seconds in high purity silicon
Silicon is undoubtedly one of the most promising semiconductor materials for
spin-based information processing devices. Its highly advanced fabrication
technology facilitates the transition from individual devices to large-scale
processors, and the availability of an isotopically-purified Si form
with no magnetic nuclei overcomes what is a main source of spin decoherence in
many other materials. Nevertheless, the coherence lifetimes of electron spins
in the solid state have typically remained several orders of magnitude lower
than what can be achieved in isolated high-vacuum systems such as trapped ions.
Here we examine electron spin coherence of donors in very pure Si
material, with a residual Si concentration of less than 50 ppm and donor
densities of per cm. We elucidate three separate mechanisms
for spin decoherence, active at different temperatures, and extract a coherence
lifetime up to 2 seconds. In this regime, we find the electron spin is
sensitive to interactions with other donor electron spins separated by ~200 nm.
We apply a magnetic field gradient in order to suppress such interactions and
obtain an extrapolated electron spin of 10 seconds at 1.8 K. These
coherence lifetimes are without peer in the solid state by several orders of
magnitude and comparable with high-vacuum qubits, making electron spins of
donors in silicon ideal components of a quantum computer, or quantum memories
for systems such as superconducting qubits.Comment: 18 pages, 4 figures, supplementary informatio
Detection of Babesia divergens in southern Norway by using an immunofluorescence antibody test in cow sera
<p>Abstract</p> <p>Background</p> <p>The incidence of bovine babesiosis, caused by <it>Babesia divergens </it>(Apicomplexa: Piroplasmida) has decreased markedly since the 1930 s, but may re-emerge as a consequence of climate change and changes in legislation and pasturing practices. This is a potentially serious disease, with both economical and animal welfare consequences. Therefore, there is a need to survey the distribution of <it>B. divergens</it>.</p> <p>Methods</p> <p>We tested sera from 306 healthy pastured cows from 24 farms along the southern Norwegian coast by using an indirect immunofluorescence IgG antibody test (IFAT). Fractions of seropositive cows were compared by calculating 95% CI.</p> <p>Results</p> <p>The results of this test showed that 27% of the sera were positive for <it>B. divergens </it>antibodies. The fraction of antibody-positive sera that we detected showed a two-humped distribution, with a high fraction of positives being found in municipalities in the western and eastern parts of the study area, while the municipalities between these areas had few or no positive serum samples.</p> <p>Conclusions</p> <p>Neither the farmers' observations nor the Norwegian Dairy Herd Recording System give an adequate picture of the distribution of bovine babesiosis. Serological testing of cows by using IFAT is a convenient way of screening for the presence of <it>B. divergens </it>in an area.</p
Wood Utilization Is Dependent on Catalase Activities in the Filamentous Fungus Podospora anserina
Catalases are enzymes that play critical roles in protecting cells against the toxic effects of hydrogen peroxide. They are implicated in various physiological and pathological conditions but some of their functions remain unclear. In order to decipher the role(s) of catalases during the life cycle of Podospora anserina, we analyzed the role of the four monofunctional catalases and one bifunctional catalase-peroxidase genes present in its genome. The five genes were deleted and the phenotypes of each single and all multiple mutants were investigated. Intriguingly, although the genes are differently expressed during the life cycle, catalase activity is dispensable during both vegetative growth and sexual reproduction in laboratory conditions. Catalases are also not essential for cellulose or fatty acid assimilation. In contrast, they are strictly required for efficient utilization of more complex biomass like wood shavings by allowing growth in the presence of lignin. The secreted CATB and cytosolic CAT2 are the major catalases implicated in peroxide resistance, while CAT2 is the major player during complex biomass assimilation. Our results suggest that P. anserina produces external H2O2 to assimilate complex biomass and that catalases are necessary to protect the cells during this process. In addition, the phenotypes of strains lacking only one catalase gene suggest that a decrease of catalase activity improves the capacity of the fungus to degrade complex biomass
Risk of Soft-Tissue Sarcoma Among 69 460 Five-Year Survivors of Childhood Cancer in Europe
Background: Childhood cancer survivors are at risk of subsequent primary soft-tissue sarcomas (STS), but the risks of specific STS histological subtypes are unknown. We quantified the risk of STS histological subtypes after specific types of childhood cancer. Methods: We pooled data from 13 European cohorts, yielding a cohort of 69 460 five-year survivors of childhood cancer. Standardized incidence ratios (SIRs) and absolute excess risks (AERs) were calculated. Results: Overall, 301 STS developed compared with 19 expected (SIR = 15.7, 95% confidence interval [CI] = 14.0 to 17.6). The highest standardized incidence ratios were for malignant peripheral nerve sheath tumors (MPNST; SIR = 40.6, 95% CI = 29.6 to 54.3), leiomyosarcomas (SIR = 29.9, 95% CI = 23.7 to 37.2), and fibromatous neoplasms (SIR = 12.3, 95% CI = 9.3 to 16.0). SIRs for MPNST were highest following central nervous system tumors (SIR = 80.5, 95% CI = 48.4 to 125.7), Hodgkin lymphoma (SIR = 81.3, 95% CI = 35.1 to 160.1), and Wilms tumor (SIR = 76.0, 95% CI = 27.9 to 165.4). Standardized incidence ratios for leiomyosarcoma were highest following retinoblastoma (SIR = 342.9, 95% CI = 245.0 to 466.9) and Wilms tumor (SIR = 74.2, 95% CI = 37.1 to 132.8). AERs for all STS subtypes were generally low at all years from diagnosis (AER < 1 per 10 000 person-years), except for leiomyosarcoma following retinoblastoma, for which the AER reached 52.7 (95% CI = 20.0 to 85.5) per 10 000 person-years among patients who had survived at least 45 years from diagnosis of retinoblastoma. Conclusions: For the first time, we provide risk estimates of specific STS subtypes following childhood cancers and give evidence that risks of MPNSTs, leiomyosarcomas, and fibromatous neoplasms are particularly increased. While the multiplicative excess risks relative to the general population are substantial, the absolute excess risk of developing any STS subtype is low, except for leiomyosarcoma after retinoblastoma. These results are likely to be informative for both survivors and health care providers
- …