Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.

The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment.Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome.These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies

Magnetic Photon Splitting: Computations of Proper-time Rates and Spectra

The splitting of photons in the presence of an intense magnetic field has recently found astrophysical applications in polar cap models of gamma-ray pulsars and in magnetar scenarios for soft gamma repeaters. Numerical computation of the polarization-dependent rates of this third order QED process for arbitrary field strengths and energies below pair creation threshold is difficult: thus early analyses focused on analytic developments and simpler asymptotic forms. The recent astrophysical interest spurred the use of the S-matrix approach by Mentzel, Berg and Wunner to determine splitting rates. In this paper, we present numerical computations of a full proper-time expression for the rate of splitting that was obtained by Stoneham, and is exact up to the pair creation threshold. While the numerical results derived here are in accord with the earlier asymptotic forms due to Adler, our computed rates still differ by as much as factors of 3 from the S-matrix re-evaluation of Wilke and Wunner, reflecting the extreme difficulty of generating accurate S-matrix numerics for fields below about \teq{4.4\times 10^{13}}Gauss. We find that our proper-time rates appear very accurate, and exceed Adler's asymptotic specializations significantly only for photon energies just below pair threshold and for supercritical fields, but always by less than a factor of around 2.6. We also provide a useful analytic series expansion for the scattering amplitude valid at low energies.Comment: 13 pages, AASTeX format, including 3 eps figures, ApJ in pres

High Energy Neutrinos and Photons from Curvature Pions in Magnetars

We discuss the relevance of the curvature radiation of pions in strongly magnetized pulsars or magnetars, and their implications for the production of TeV energy neutrinos detectable by cubic kilometer scale detectors, as well as high energy photons.Comment: 19 pages, 4 figures, to appear in JCA

Key dating features for timber-framed dwellings in Surrey

This article is made available through the Brunel Open Access Publishing Fund. Copyright @ The Vernacular Architecture Group 2013. MORE OpenChoice articles are open access and distributed under the terms of the Creative Commons Attribution License 3.0.The main component of the Surrey Dendrochronology Project is the accurate dating of 177 ‘dwellings’, nearly all by tree-ring analysis. The dates are used to establish date ranges for 52 ‘key features’, which cover many aspects of timber-framing from building type to details of carpentry. It is shown that changes of method and fashion were in many cases surprisingly rapid, almost abrupt in historical terms. Previous dating criteria for timber-framed dwellings in the county have been refined and new criteria introduced. Clusters of change from the 1440s and the 1540s are shown and some possible historical links suggested.The Heritage Lottery Fund, the Domestic Buildings Research Group (Surrey), the Surrey Archaeological Society and the historical societies of Charlwood, Farnham and Nutfield

Modeling the non-recycled Fermi gamma-ray pulsar population

We use Fermi Gamma-ray Space Telescope detections and upper limits on non-recycled pulsars obtained from the Large Area Telescope (LAT) to constrain how the gamma-ray luminosity L depends on the period P and the period derivative \dot{P}. We use a Bayesian analysis to calculate a best-fit luminosity law, or dependence of L on P and \dot{P}, including different methods for modeling the beaming factor. An outer gap (OG) magnetosphere geometry provides the best-fit model, which is L \propto P^{-a} \dot{P}^{b} where a=1.36\pm0.03 and b=0.44\pm0.02, similar to but not identical to the commonly assumed L \propto \sqrt{\dot{E}} \propto P^{-1.5} \dot{P}^{0.5}. Given upper limits on gamma-ray fluxes of currently known radio pulsars and using the OG model, we find that about 92% of the radio-detected pulsars have gamma-ray beams that intersect our line of sight. By modeling the misalignment of radio and gamma-ray beams of these pulsars, we find an average gamma-ray beaming solid angle of about 3.7{\pi} for the OG model, assuming a uniform beam. Using LAT-measured diffuse fluxes, we place a 2{\sigma} upper limit on the average braking index and a 2{\sigma} lower limit on the average surface magnetic field strength of the pulsar population of 3.8 and 3.2 X 10^{10} G, respectively. We then predict the number of non-recycled pulsars detectable by the LAT based on our population model. Using the two-year sensitivity, we find that the LAT is capable of detecting emission from about 380 non-recycled pulsars, including 150 currently identified radio pulsars. Using the expected five-year sensitivity, about 620 non-recycled pulsars are detectable, including about 220 currently identified radio pulsars. We note that these predictions significantly depend on our model assumptions.Comment: 26 pages, 10 figures, Accepted by ApJ on 8 September 201

Bat Quickness and Bat Velocity for Left- and Right-Handed Softball Swings

Please view abstract in the attached PDF fil

Molar mass and solution conformation of branched alpha(1 - 4), alpha(1 - 6) Glucans. Part I: Glycogens in water

Solution molar masses and conformations of glycogens from different sources (rabbit, oyster, mussel and bovine) were analysed using sedimentation velocity in the analytical ultracentrifuge, size-exclusion chromatography coupled to multi-angle laser light scattering (SEC-MALLS), size-exclusion chromatography coupled to a differential pressure viscometer and dynamic light scattering. Rabbit, oyster and mussel glycogens consisted of one population of high molar mass (weight averages ranging from 4.6 x 106 to 1.1 x 107 g/mol) as demonstrated by sedimentation velocity and SEC-MALLS, whereas bovine glycogen had a bimodal distribution of significantly lower molar mass (1.0 x 105 and 4.5 x 105 g/mol). The spherical structure of all glycogen molecules was demonstrated in the slopes of the Mark-Houwink-Kuhn-Sakurada-type power-law relations for sedimentation coefficient (s20,wo), intrinsic viscosity ([η]), radius of gyration (rg,z) and radius of hydration (rH,z), respectively, and was further supported by the � (=rg,z/rH,z) function, the fractal dimension and the Perrin function. The degree of branching was estimated to be ∼10% from the shrinking factors, g′ (=[η]branched/[η]linear) and also h (=(f/fo)branched/(f/fo)linear), respectively, where (f/fo) is the translational frictional ratio, consistent with expectation. © 2007 Elsevier Ltd. All rights reserved