A droplet digital PCR detection method for rare L1 insertions in tumors

Background: The active human mobile element, long interspersed element 1 (L1) currently populates human genomes in excess of 500,000 copies per haploid genome. Through its mobility via a process called target primed reverse transcription (TPRT), L1 mobilization has resulted in over 100 de novo cases of human disease and has recently been associated with various cancer types. Large advances in high-throughput sequencing (HTS) technology have allowed for an increased understanding of the role of L1 in human cancer; however, researchers are still limited by the ability to validate potentially rare L1 insertion events detected by HTS that may occur in only a small fraction of tumor cells. Additionally, HTS detection of rare events varies greatly as a function of read depth, and new tools for de novo element discovery are needed to fill in gaps created by HTS. Results: We have employed droplet digital PCR (ddPCR) to detect rare L1 loci in mosaic human genomes. Our assay allows for the detection of L1 insertions as rare as one cell in every 10,000. Conclusions: ddPCR represents a robust method to be used alongside HTS techniques for detecting, validating and quantitating rare L1 insertion events in tumors and other tissues. Electronic supplementary material The online version of this article (doi:10.1186/s13100-014-0030-4) contains supplementary material, which is available to authorized users

The Buckland Park air shower array

The new Buckland Park Air Shower Array has been producing analyzed shower data since July 1984. The array is described and some preliminary performance figures are presented

The Intrinsically X-ray Weak Quasar PHL 1811. I. X-ray Observations and Spectral Energy Distribution

This is the first of two papers reporting observations and analysis of the unusually bright (m_b=14.4), luminous (M_B=-25.5), nearby (z=0.192) narrow-line quasar PHL 1811, focusing on the X-ray properties and the spectral energy distribution. Two Chandra observations reveal a weak X-ray source with a steep spectrum. Variability by a factor of 4 between the two observations separated by 12 days suggest that the X-rays are not scattered emission. The XMM-Newton spectra are modelled in the 0.3--5 keV band by a steep power law with \Gamma = 2.3\pm 0.1, and the upper limit on intrinsic absorption is 8.7 x 10^{20} cm^{-2}. The spectral slopes are consistent with power law indices commonly observed in NLS1s, and it appears that we observe the central engine X-rays directly. Including two recent Swift ToO snapshots, a factor of ~5 variability was observed among the five X-ray observations reported here. In contrast, the UV photometry obtained by the XMM-Newton OM and Swift UVOT, and the HST spectrum reveal no significant UV variability. The \alpha_{ox} inferred from the Chandra and contemporaneous HST spectrum is -2.3 \pm 0.1, significantly steeper than observed from other quasars of the same optical luminosity. The steep, canonical X-ray spectra, lack of absorption, and significant X-ray variability lead us to conclude that PHL 1811 is intrinsically X-ray weak. We also discuss an accretion disk model, and the host galaxy of PHL 1811.Comment: 45 pages, 9 figures, accepted for publication in Ap

Wide Area Network Access to CMS Data Using the Lustre Filesystem

In this paper, we explore the use of the Lustre cluster filesystem over the wide area network to access Compact Muon Solenoid (CMS) data stored on physical devices located hundreds of kilometres away. We describe the experimental testbed and report on the I/O performance of applications writing and reading data on the distributed Lustre filesystem established across the WAN. We compare the I/O performance of a CMS application to the performance obtained with IOzone, a standard benchmark tool. We then examine the I/O performance of the CMS application running multiple processes on a single server. And compare the Lustre results to results obtained on data stored on local filesystems. Our measurements reveal that the IOzone benchmark tool, accessing data sequentially, can saturate the Gbps network link that connects our Lustre client in Miami Florida to the Lustre storage located in Gainesville, Florida. We also find that the I/O rates of the CMS application is significantly less than what can be obtained with IOzone for sequential access to data

A Flux-Limited Sample of z~1 Ly-alpha Emitting Galaxies in the CDFS

We describe a method for obtaining a flux-limited sample of Ly-alpha emitters from GALEX grism data. We show that the multiple GALEX grism images can be converted into a three-dimensional (two spatial axes and one wavelength axis) data cube. The wavelength slices may then be treated as narrowband images and searched for emission-line galaxies. For the GALEX NUV grism data, the method provides a Ly-alpha flux-limited sample over the redshift range z=0.67-1.16. We test the method on the Chandra Deep Field South field, where we find 28 Ly-alpha emitters with faint continuum magnitudes (NUV>22) that are not present in the GALEX pipeline sample. We measure the completeness by adding artificial emitters and measuring the fraction recovered. We find that we have an 80% completeness above a Ly-alpha flux of 10^-15 erg/cm^2/s. We use the UV spectra and the available X-ray data and optical spectra to estimate the fraction of active galactic nuclei in the selection. We report the first detection of a giant Ly-alpha blob at z<1, though we find that these objects are much less common at z=1 than at z=3. Finally, we compute limits on the z~1 Ly-alpha luminosity function and confirm that there is a dramatic evolution in the luminosity function over the redshift range z=0-1.Comment: 18 pages, in press at The Astrophysical Journa

P-624: Changes in plasma renin match the antihypertensive effects of aliskiren in patients with hypertension: Placebo/irbesartan-controlled trial with the orally active renin inhibitor aliskiren

For several decades, the lack of oral availability and poor antihypertensive effects of renin inhibitors (RI), despite seemingly powerful inhibition of conventionally measured plasma renin activity (PRA), have discredited RI as cardiovascular drugs. Aliskiren is a novel orally effective RI with antihypertensive potency comparable to losartan or irbesartan. The present study investigated the effects of aliskiren and irbesartan on PRA, measured by the reliable antibody trapping technique, as well as on plasma active renin concentration (ARC) and sitting systolic blood pressure (SBP). In 569 patients with mild to moderate hypertension (baseline sphygmomanometric sitting blood pressure 152±12/99±4 mmHg, mean±SD), PRA and ARC, as well as SBP were measured before and after 8 weeks of treatment with once daily oral doses of aliskiren (150, 300 or 600mg), irbesartan 150mg or placebo. The effects of study treatments on PRA, ARC and SBP are summarized in the Table. Treatment N PRA (ng/mL/h) ARC (pg/mL) SBP (mmHg) Baseline Week 8 Baseline Week 8 Baseline Week 8 Placebo 111 0.72 0.64 6.2 5.6 152 ± 12 147 ± 18 Aliskiren 150mg 112 0.66 0.20 6.0 15.3 151 ± 11 140 ± 14 Aliskiren 300mg 115 0.59 0.17 6.1 21.0 152 ± 10 137 ± 14 Aliskiren 600mg 113 0.64 0.16 5.8 34.9 153 ± 12 137 ± 16 Irbesartan 150mg 118 0.64 1.33 5.5 11.3 153 ± 11 140 ± 16 PRA and ARC values are geometric means; SBP values are mean ± SD Aliskiren reduced PRA by 69%, 71% and 75% at 150, 300 and 600mg respectively, while irbesartan doubled PRA. Most of the antihypertensive effect of aliskiren was obtained with the lowest dose, but higher doses slightly further decreased SBP. Aliskiren 150mg and irbesartan 150mg provided similar increases in ARC and hence comparably blocked the renin-angiotensin system (RAS), and the achieved SBP was also the same. Aliskiren 300mg and 600mg caused greater increases in ARC compared with irbesartan 150mg (p<0.05), and further decreases in SBP. The dose-dependent increases in ARC observed with aliskiren document increasing blockade of the RAS. In conclusion, aliskiren provides a parallel reduction in PRA and SBP, a dose-dependent blockade of the RAS and is at least as effective as irbesartan at comparable dosages (150mg

Cell-associated bacteria in the human lung microbiome

Abstract Background Recent studies have revealed that bronchoalveolar lavage (BAL) fluid contains previously unappreciated communities of bacteria. In vitro and in vivo studies have shown that host inflammatory signals prompt bacteria to disperse from cell-associated biofilms and adopt a virulent free-living phenotype. The proportion of the lung microbiota that is cell-associated is unknown. Results Forty-six BAL specimens were obtained from lung transplant recipients and divided into two aliquots: ‘whole BAL’ and ‘acellular BAL,’ the latter processed with a low-speed, short-duration centrifugation step. Both aliquots were analyzed via bacterial 16S rRNA gene pyrosequencing. The BAL specimens represented a wide spectrum of lung health, ranging from healthy and asymptomatic to acutely infected. Bacterial signal was detected in 52% of acellular BAL aliquots, fewer than were detected in whole BAL (96%, p ≤ 0.0001). Detection of bacteria in acellular BAL was associated with indices of acute infection [BAL neutrophilia, high total bacterial (16S) DNA, low community diversity, p < 0.01 for all] and, independently, with low relative abundance of specific taxonomic groups (p < 0.05). When whole and acellular aliquots from the same bronchoscopy were directly compared, acellular BAL contained fewer bacterial species (p < 0.05); whole and acellular BAL similarity was positively associated with evidence of infection and negatively associated with relative abundance of several prominent taxa (p < 0.001). Acellular BAL contained decreased relative abundance of Prevotella spp. (p < 0.05) and Pseudomonas fluorescens (p < 0.05). Conclusions We present a novel methodological and analytical approach to the localization of lung microbiota and show that prominent members of the lung microbiome are cell-associated, potentially via biofilms, cell adhesion, or intracellularity.http://deepblue.lib.umich.edu/bitstream/2027.42/111056/1/40168_2014_Article_75.pd

The Calibration of Mid-Infrared Star Formation Rate Indicators

With the goal of investigating the degree to which the mid-infrared emission traces the star formation rate (SFR), we analyze Spitzer 8 um and 24 um data of star-forming regions in a sample of 33 nearby galaxies with available HST/NICMOS images in the Paschen-alpha (1.8756 um) emission line. The galaxies are drawn from the Spitzer Infrared Nearby Galaxies Survey (SINGS) sample, and cover a range of morphologies and a factor ~10 in oxygen abundance. Published data on local low-metallicity starburst galaxies and Luminous Infrared Galaxies are also included in the analysis. Both the stellar-continuum-subtracted 8 um emission and the 24 um emission correlate with the extinction-corrected Pa-alpha line emission, although neither relationship is linear. Simple models of stellar populations and dust extinction and emission are able to reproduce the observed non-linear trend of the 24 um emission versus number of ionizing photons, including the modest deficiency of 24 um emission in the low metallicity regions, which results from a combination of decreasing dust opacity and dust temperature at low luminosities. Conversely, the trend of the 8 um emission as a function of the number of ionizing photons is not well reproduced by the same models. The 8 um emission is contributed, in larger measure than the 24 um emission, by dust heated by non-ionizing stellar populations, in agreement with previous findings. Two SFR calibrations, one using the 24 um emission and the other using a combination of the 24 um and H-alpha luminosities (Kennicutt et al. 2007), are presented. No calibration is presented for the 8 um emission, because of its significant dependence on both metallicity and environment. The calibrations presented here should be directly applicable to systems dominated by on-going star formation.Comment: 67 pages, 15 figures, accepted for publication on the Astrophysical Journal; replacement contains: correction to equation 8; important tweaks to equation 9; various typos correcte

The promoter from SlREO, a highly-expressed, root-specific Solanum lycopersicum gene, directs expression to cortex of mature roots

Root-specific promoters are valuable tools for targeting transgene expression, but many of those already described have limitations to their general applicability. We present the expression characteristics of SlREO, a novel gene isolated from tomato (Solanum lycopersicum L.). This gene was highly expressed in roots but had a very low level of expression in aerial plant organs. A 2.4-kb region representing the SlREO promoter sequence was cloned upstream of the uidA GUS reporter gene and shown to direct expression in the root cortex. In mature, glasshouse-grown plants this strict root specificity was maintained. Furthermore, promoter activity was unaffected by dehydration or wounding stress but was somewhat suppressed by exposure to NaCl, salicylic acid and jasmonic acid. The predicted protein sequence of SlREO contains a domain found in enzymes of the 2-oxoglutarate and Fe(II)-dependent dioxygenase superfamily. The novel SlREO promoter has properties ideal for applications requiring strong and specific gene expression in the bulk of tomato root tissue growing in soil, and is also likely to be useful in other Solanaceous crop

Switching the Interpenetration of Confined Asymmetric Polymer Brushes

The interpenetration of two polymer brushes on approaching flat surfaces has been investigated. When compacting polymer brushes with an asymmetric charge on each surface, one neutral and the other weakly charged, we find that the brush interpenetration becomes a parameter that can be controlled by the pH of the hydrating solution. The switching between high and low degrees of brush interpenetration was investigated with numerical self-consistent field theory (nSCF) and experimentally using a sample environment which combines neutron reflectometry with a surface force type apparatus. Initially, a pair of uncharged poly(ethylene oxide), PEO, brushes are examined, where one of the brushes is deuterated to distinguish it from a hydrogenous counterpart. We find in both nSCF and these experiments that there is no significant overlap between the brushes as both compact into polymer blocks with little hydration. However, when a weak polyelectrolyte poly(2-(dimethylamino)ethyl methacrylate), PDMAEMA, brush is confined against a deuterated neutral PEO brush and the pH of the hydrating solution is below the polycation’s pKa of 7.5, then the presence of charged groups on the PDMAEMA allows significant interpenetration to occur between the two polymer brushes on contact. This interpenetration remains once the polymer brushes dehydrate due to the confining pressure that is applied. Raising the pH to a value above the pKa, removes the charges from the polyelectrolyte brush resulting in little to no interpenetration between the two brushes. Therefore, by simply adjusting the pH of the hydrating solution the interpenetration state between polymer brush pairs can be switched when one brush is a weak polyelectrolyte. Since polymer brushes are widely investigated and used to reduce friction between solid surfaces, this effect may have significant implications in the design and operation of polymer brushes with controllable friction properties