SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems

Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected N6-methyl-adenine (m6A) at GATC and CATG recognition sites, motifs previously shown to be targeted by PBCV-1 DNA methyltransferases M.CviAI and M. CviAII, respectively. At the same time, PacBio analyses indicated that 10.9% of the PBCV-1 genome had large interpulse duration ratio (ipdRatio) values, the primary metric for DNA modification identification. These events represent 20.6x more sites than can be accounted for by all available adenines in GATC and CATG motifs, suggesting base or backbone modifications other than methylation might be present. To define methylation stability, we cross-compared methylation status of each GATC and CATG sequence in three biological replicates and found ∼81% of sites were stably methylated, while ∼2% consistently lack methylation. The remaining 17% of sites were stochastically methylated. When methylation status was analyzed for both strands of each target, we show that palindromes existed in completely non-methylated states, fully-methylated states, or hemi-methylated states, though GATC sites more often lack methylation than CATG sequences. Given that both sequences are targeted by not just methyltransferases, but by restriction endonucleases that are together encoded by PBCV-1 as virus-originating restriction modification (RM) systems, there is strong selective pressure to modify all target sites. The finding that most instances of non-methylation are associated with hemi-methylation is congruent with observations that hemi-methylated palindromes are resistant to cleavage by restriction endonucleases. However, sites where hemi-methylation is conserved might represent a unique regulatory function for PBCV-1. This study serves as a baseline for future investigation into the epigenomics of chloroviruses and their giant virus relatives

A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction

PurposeTo describe the clinical findings of a patient with an early onset retinal dystrophy and a novel mutation in OTX2, and to compare these findings with previously reported cases.MethodsUsing direct sequencing, we screened 142 patients, who had either Leber congenital amaurosis (LCA) or early onset retinal dystrophy (EORD), for mutations in OTX2. All patients received a detailed ophthalmic examination including electroretinography and retinal imaging.ResultsOnly one mutation in OTX2 was identified. A novel heterozygous p.S138X stop mutation was identified in a seven-year-old male who had an infantile onset retinal dystrophy. The mutation was not present in either parent or in 181 blood donor samples. There was a history of failure to thrive in infancy, poor feeding, and growth hormone deficiency. Poor vision and nyctalopia was present from the first year. Funduscopy revealed a hyperpigmented peripapillary ring with a fine granular pigmentation of the RPE throughout the fundus. The scotopic bright flash ERG a-wave was subnormal and the waveform electronegative, in keeping with dysfunction both at the level of the photoreceptor and post-phototransduction. Visual function has been stable to date.ConclusionsMutations in OTX2 have been reported in association with major developmental malformations of the eye, with retinal dystrophies such as LCA, and with pituitary dysfunction and seizure activity in some cases. This case adds further support for a role of OTX2 both in retinal development and pituitary function, and highlights a novel retinal dystrophy phenotype seen in association with mutations in OTX2

Galaxy Clusters Selected with the Sunyaev-Zel'dovich Effect from 2008 South Pole Telescope Observations

We present a detection-significance-limited catalog of 21 Sunyaev-Zel'dovich selected galaxy clusters. These clusters, along with 1 unconfirmed candidate, were identified in 178 deg^2 of sky surveyed in 2008 by the South Pole Telescope to a depth of 18 uK-arcmin at 150 GHz. Optical imaging from the Blanco Cosmology Survey (BCS) and Magellan telescopes provided photometric (and in some cases spectroscopic) redshift estimates, with catalog redshifts ranging from z=0.15 to z>1, with a median z = 0.74. Of the 21 confirmed galaxy clusters, three were previously identified as Abell clusters, three were presented as SPT discoveries in Staniszewski et al, 2009, and three were first identified in a recent analysis of BCS data by Menanteau et al, 2010; the remaining 12 clusters are presented for the first time in this work. Simulated observations of the SPT fields predict the sample to be nearly 100% complete above a mass threshold of M_200 ~ 5x10^14 M_sun/h at z = 0.6. This completeness threshold pushes to lower mass with increasing redshift, dropping to ~4x10^14 M_sun/h at z=1. The size and redshift distribution of this catalog are in good agreement with expectations based on our current understanding of galaxy clusters and cosmology. In combination with other cosmological probes, we use the cluster catalog to improve estimates of cosmological parameters. Assuming a standard spatially flat wCDM cosmological model, the addition of our catalog to the WMAP 7-year analysis yields sigma_8 = 0.81 +- 0.09 and w = -1.07 +- 0.29, a ~50% improvement in precision on both parameters over WMAP7 alone.Comment: 19 pages, 9 figures, 4 appendice

Comparison of techniques for handling missing covariate data within prognostic modelling studies: a simulation study

Background: There is no consensus on the most appropriate approach to handle missing covariate data within prognostic modelling studies. Therefore a simulation study was performed to assess the effects of different missing data techniques on the performance of a prognostic model. Methods: Datasets were generated to resemble the skewed distributions seen in a motivating breast cancer example. Multivariate missing data were imposed on four covariates using four different mechanisms; missing completely at random (MCAR), missing at random (MAR), missing not at random (MNAR) and a combination of all three mechanisms. Five amounts of incomplete cases from 5% to 75% were considered. Complete case analysis (CC), single imputation (SI) and five multiple imputation (MI) techniques available within the R statistical software were investigated: a) data augmentation (DA) approach assuming a multivariate normal distribution, b) DA assuming a general location model, c) regression switching imputation, d) regression switching with predictive mean matching (MICE-PMM) and e) flexible additive imputation models. A Cox proportional hazards model was fitted and appropriate estimates for the regression coefficients and model performance measures were obtained. Results: Performing a CC analysis produced unbiased regression estimates, but inflated standard errors, which affected the significance of the covariates in the model with 25% or more missingness. Using SI, underestimated the variability; resulting in poor coverage even with 10% missingness. Of the MI approaches, applying MICE-PMM produced, in general, the least biased estimates and better coverage for the incomplete covariates and better model performance for all mechanisms. However, this MI approach still produced biased regression coefficient estimates for the incomplete skewed continuous covariates when 50% or more cases had missing data imposed with a MCAR, MAR or combined mechanism. When the missingness depended on the incomplete covariates, i.e. MNAR, estimates were biased with more than 10% incomplete cases for all MI approaches. Conclusion: The results from this simulation study suggest that performing MICE-PMM may be the preferred MI approach provided that less than 50% of the cases have missing data and the missing data are not MNAR

Quantitative localized proton-promoted dissolution kinetics of calcite using scanning electrochemical microscopy (SECM)

Scanning electrochemical microscopy (SECM) has been used to determine quantitatively the kinetics of proton-promoted dissolution of the calcite (101̅4) cleavage surface (from natural “Iceland Spar”) at the microscopic scale. By working under conditions where the probe size is much less than the characteristic dislocation spacing (as revealed from etching), it has been possible to measure kinetics mainly in regions of the surface which are free from dislocations, for the first time. To clearly reveal the locations of measurements, studies focused on cleaved “mirror” surfaces, where one of the two faces produced by cleavage was etched freely to reveal defects intersecting the surface, while the other (mirror) face was etched locally (and quantitatively) using SECM to generate high proton fluxes with a 25 μm diameter Pt disk ultramicroelectrode (UME) positioned at a defined (known) distance from a crystal surface. The etch pits formed at various etch times were measured using white light interferometry to ascertain pit dimensions. To determine quantitative dissolution kinetics, a moving boundary finite element model was formulated in which experimental time-dependent pit expansion data formed the input for simulations, from which solution and interfacial concentrations of key chemical species, and interfacial fluxes, could then be determined and visualized. This novel analysis allowed the rate constant for proton attack on calcite, and the order of the reaction with respect to the interfacial proton concentration, to be determined unambiguously. The process was found to be first order in terms of interfacial proton concentration with a rate constant k = 6.3 (± 1.3) × 10–4 m s–1. Significantly, this value is similar to previous macroscopic rate measurements of calcite dissolution which averaged over large areas and many dislocation sites, and where such sites provided a continuous source of steps for dissolution. Since the local measurements reported herein are mainly made in regions without dislocations, this study demonstrates that dislocations and steps that arise from such sites are not needed for fast proton-promoted calcite dissolution. Other sites, such as point defects, which are naturally abundant in calcite, are likely to be key reaction sites

The Halo Mass of Optically Luminous Quasars at z ,F≈ ,F1-2 Measured via Gravitational Deflection of the Cosmic Microwave Background

© 2019. The American Astronomical Society. All rights reserved.We measure the average deflection of cosmic microwave background photons by quasars at 〈Z〉= 1.7. Our sample is selected from the Sloan Digital Sky Survey to cover the redshift range 0.9 ≤z≤2.2 with absolute i-band magnitudes of M i ≤-24 (K-corrected to z = 2). A stack of nearly 200,000 targets reveals an 8δ detection of Planck's estimate of the lensing convergence toward the quasars. We fit the signal with a model comprising a Navarro-Frenk-White density profile and a two-halo term accounting for correlated large-scale structure, which dominates the observed signal. The best-fitting model is described by an average halo mass log 10 (M h h -1 M)12.6 ±0.2 = and linear bias b=2.7±0.3 at 〈Z 〉= 1.7, in excellent agreement with clustering studies. We also report a hint, at a 90% confidence level, of a correlation between the convergence amplitude and luminosity, indicating that quasars brighter than Mi≲ -26 reside in halos of typical mass M h ≈ 10 13 h -1 M, scaling roughly as M h ∞ L opt 3/4 at M i ≲-24 mag, in good agreement with physically motivated quasar demography models. Although we acknowledge that this luminosity dependence is a marginal result, the observed Mh-L opt relationship could be interpreted as a reflection of the cutoff in the distribution of black hole accretion rates toward high Eddington ratios: the weak trend of Mh with Lopt observed at low luminosity becomes stronger for the most powerful quasars, which tend to be accreting close to the Eddington limit.Peer reviewedFinal Accepted Versio

A Measurement of the Correlation of Galaxy Surveys with CMB Lensing Convergence Maps from the South Pole Telescope

We compare cosmic microwave background lensing convergence maps derived from South Pole Telescope (SPT) data with galaxy survey data from the Blanco Cosmology Survey, WISE, and a new large Spitzer/IRAC field designed to overlap with the SPT survey. Using optical and infrared catalogs covering between 17 and 68 deg^2 of sky, we detect a correlation between the SPT convergence maps and each of the galaxy density maps at >4σ, with zero correlation robustly ruled out in all cases. The amplitude and shape of the cross-power spectra are in good agreement with theoretical expectations and the measured galaxy bias is consistent with previous work. The detections reported here utilize a small fraction of the full 2500 deg^2 SPT survey data and serve as both a proof of principle of the technique and an illustration of the potential of this emerging cosmological probe

A Measurement of the Cosmic Microwave Background Damping Tail from the 2500-square-degree SPT-SZ survey

We present a measurement of the cosmic microwave background (CMB) temperature power spectrum using data from the recently completed South Pole Telescope Sunyaev-Zel'dovich (SPT-SZ) survey. This measurement is made from observations of 2540 deg$^2$ of sky with arcminute resolution at $150\,$GHz, and improves upon previous measurements using the SPT by tripling the sky area. We report CMB temperature anisotropy power over the multipole range $650<\ell<3000$. We fit the SPT bandpowers, combined with the seven-year Wilkinson Microwave Anisotropy Probe (WMAP7) data, with a six-parameter LCDM cosmological model and find that the two datasets are consistent and well fit by the model. Adding SPT measurements significantly improves LCDM parameter constraints; in particular, the constraint on $\theta_s$ tightens by a factor of 2.7. The impact of gravitational lensing is detected at $8.1\, \sigma$, the most significant detection to date. This sensitivity of the SPT+WMAP7 data to lensing by large-scale structure at low redshifts allows us to constrain the mean curvature of the observable universe with CMB data alone to be $\Omega_k=-0.003^{+0.014}_{-0.018}$. Using the SPT+WMAP7 data, we measure the spectral index of scalar fluctuations to be $n_s=0.9623 \pm 0.0097$ in the LCDM model, a $3.9\,\sigma$ preference for a scale-dependent spectrum with $n_s<1$. The SPT measurement of the CMB damping tail helps break the degeneracy that exists between the tensor-to-scalar ratio $r$ and $n_s$ in large-scale CMB measurements, leading to an upper limit of $r<0.18$ (95%,C.L.) in the LCDM+$r$ model. Adding low-redshift measurements of the Hubble constant ($H_0$) and the baryon acoustic oscillation (BAO) feature to the SPT+WMAP7 data leads to further improvements. The combination of SPT+WMAP7+$H_0$+BAO constrains $n_s=0.9538 \pm 0.0081$ in the LCDM model, a $5.7\,\sigma$ detection of $n_s < 1$, ... [abridged]Comment: 21 pages, 10 figures. Replaced with version accepted by ApJ. Data products are available at http://pole.uchicago.edu/public/data/story12

A Direct Measurement of the Linear Bias of Mid-infrared-selected Quasars at z ap 1 Using Cosmic Microwave Background Lensing

We measure the cross-power spectrum of the projected mass density as traced by the convergence of the cosmic microwave background lensing field from the South Pole Telescope (SPT) and a sample of Type 1 and 2 (unobscured and obscured) quasars at langzrang ~ 1 selected with the Wide-field Infrared Survey Explorer, over 2500 deg2. The cross-power spectrum is detected at ≈7σ, and we measure a linear bias b = 1.61 ± 0.22, consistent with clustering analyses. Using an independent lensing map, derived from Planck observations, to measure the cross-spectrum, we find excellent agreement with the SPT analysis. The bias of the combined sample of Type 1 and 2 quasars determined in this work is similar to that previously determined for Type 1 quasars alone; we conclude that obscured and unobscured quasars trace the matter field in a similar way. This result has implications for our understanding of quasar unification and evolution schemes.Peer reviewe