Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers

Limits on the Peculiar Velocities of Two Distant Clusters Using the Kinematic Sunyaev-Zel'dovich Effect

We report millimeter-wavelength observations of the Sunyaev-Zel'dovich (S-Z) effect in two distant galaxy clusters. A relativistically correct analysis of the S-Z data is combined with the results of X-ray observations to determine the radial peculiar velocities v_r of the clusters. We observed Abell 2163 (z=.201) in three mm-wavelength bands centered at 2.1, 1.4, and 1.1 mm. We report a significant detection of the thermal component of the S-Z effect seen as both a decrement in the brightness of the CMB at 2.1 mm, and as an increment at 1.1 mm. Including uncertainties due to the calibration of the instrument, distribution and temperature of the IC gas, and astrophysical confusion, a simultaneous fit to the data in all three bands gives v_r=+490 +1370/-880 km/s at 68% confidence. We observed Abell 1689 (z=.181) in the 2.1 and 1.4 mm bands. Including the same detailed accounting of uncertainty, a simultaneous fit to the data in both bands gives v_r=+170 +815/-630 km/s. The limits on the peculiar velocities of A2163 and A1689 correspond to deviations from the uniform Hubble flow of <= 2-3%.Comment: 21 pages, 13 postscript figures, LaTeX(aaspptwo.sty), ApJ(in press

An iron-oxygen intermediate formed during the catalytic cycle of cysteine dioxygenase

Cysteine dioxygenase is a key enzyme in the breakdown of cysteine, but its mechanism remains controversial. A combination of spectroscopic and computational studies provides the first evidence of a short-lived intermediate in the catalytic cycle. The intermediate decays within 20 ms and has absorption maxima at 500 and 640 nm

Shape-based peak identification for ChIP-Seq

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.htmlComment: 12 pages, 6 figure

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria

Virtual patients design and its effect on clinical reasoning and student experience : a protocol for a randomised factorial multi-centre study

Background Virtual Patients (VPs) are web-based representations of realistic clinical cases. They are proposed as being an optimal method for teaching clinical reasoning skills. International standards exist which define precisely what constitutes a VP. There are multiple design possibilities for VPs, however there is little formal evidence to support individual design features. The purpose of this trial is to explore the effect of two different potentially important design features on clinical reasoning skills and the student experience. These are the branching case pathways (present or absent) and structured clinical reasoning feedback (present or absent). Methods/Design This is a multi-centre randomised 2x2 factorial design study evaluating two independent variables of VP design, branching (present or absent), and structured clinical reasoning feedback (present or absent).The study will be carried out in medical student volunteers in one year group from three university medical schools in the United Kingdom, Warwick, Keele and Birmingham. There are four core musculoskeletal topics. Each case can be designed in four different ways, equating to 16 VPs required for the research. Students will be randomised to four groups, completing the four VP topics in the same order, but with each group exposed to a different VP design sequentially. All students will be exposed to the four designs. Primary outcomes are performance for each case design in a standardized fifteen item clinical reasoning assessment, integrated into each VP, which is identical for each topic. Additionally a 15-item self-reported evaluation is completed for each VP, based on a widely used EViP tool. Student patterns of use of the VPs will be recorded. In one centre, formative clinical and examination performance will be recorded, along with a self reported pre and post-intervention reasoning score, the DTI. Our power calculations indicate a sample size of 112 is required for both primary outcomes

Geocentrism reexamined

The universe is nearly isotropic on very large scales. It is much more difficult to show that the universe is radially homogeneous (independent of distance), or equivalently, that it is isotropic about distant points. This taken as an axiom, since if it were not true, then we would occupy a preferred position. This paper considers several empirical arguments for radial homogeneity based on the cosmic microwave background (CMB). The tightest limits on inhomogeneity on the scale of the horizon are of order ten percent but will improve soon. These limits involve the Sunyaev-Zel'dovich effect in clusters of galaxies, excitation of low-energy atomic transitions, and the accurately thermal spectrum of the CMB. Weaker limits from primordial nucleosynthesis are discussed briefly.Comment: RevTeX source, 14 pages, no figs. To appear Phys Rev

A Weak Gravitational Lensing and X-ray Analysis of Abell 2163

We report on the detection of dark matter in the cluster of galaxies Abell~2163 using the weak gravitational distortion of background galaxies, and an analysis of the cluster X-ray emission. We find that while the qualitative distributions of the cluster light and the dark matter are similar -- shallow and extended, with significant substructure -- the X-ray morphology shows a more regular overall appearance. We interpret the joint lensing and X-ray observations as a signature of a merger event in the cluster. We present new ROSAT/HRI data and reanalyze ROSAT/PSPC data, accounting for the effect of a varying background to determine the best fit parameters in the $\beta$-model formalism. We combine the surface brightness fits with two determinations of the radial temperature profile to determine the total mass. Although there are slight variations in the total mass determinations introduced by the uncertainties in the $\beta$-fit, the main contributor to the error arises from the uncertainties in the temperature determinations. Even though the morphologies of the dark matter/light and X-ray gas are quite different, we find that the total mass determined from the X-ray and weak lensing estimates are consistent with each other within the $2\sigma$ error bars, with the X-ray inferred mass a factor of $\simeq 2$ larger. However, as the lensing mass estimates are differential (the surface density at any point is determined relative to the mean in a control annulus), the shallow, extended nature of the mass profile biases the lensing inferred mass downwards. We estimate the correction for this effect and find very good agreement between the corrected lensing and X-ray results. We determine the gas mass fraction and find $f_g \simeq 0.07h^{-3/2}$ at all radii and a constant mass-to-light ratio of $M/L_VComment: 30 pages, latex file. Postscript file also available at ftp://magicbean.berkeley.edu/pub/squires/a2163/a2163_paper.ps.g