1,632 research outputs found
Detection of Coxiella burnetii in complex matrices by using multiplex quantitative PCR during a major Q fever outbreak in the Netherlands
Q fever, caused by Coxiella burnetii, is a zoonosis with a worldwide distribution. A large rural area in the southeast of the Netherlands was heavily affected by Q fever between 2007 and 2009. This initiated the development of a robust and internally controlled multiplex quantitative PCR (qPCR) assay for the detection of C. burnetii DNA in veterinary and environmental matrices on suspected Q fever-affected farms. The qPCR detects three C. burnetii targets (icd, com1, and IS1111) and one Bacillus thuringiensis internal control target (cry1b). Bacillus thuringiensis spores were added to samples to control both DNA extraction and PCR amplification. The performance of the qPCR assay was investigated and showed a high efficiency; a limit of detection of 13.0, 10.6, and 10.4 copies per reaction for the targets icd, com1, and IS1111, respectively; and no crossreactivity with the nontarget organisms tested. Screening for C. burnetii DNA on 29 suspected Q fever-affected farms during the Q fever epidemic in 2008 showed that swabs from dust-accumulating surfaces contained higher levels of C. burnetii DNA than vaginal swabs from goats or sheep. PCR inhibition by coextracted substances was observed in some environmental samples, and 10- or 100-fold dilutions of samples were sufficient to obtain interpretable signals for both the C. burnetii targets and the internal control. The inclusion of an internal control target and three C. burnetii targets in one multiplex qPCR assay showed that complex veterinary and environmental matrices can be screened reliably for the presence of C. burnetii DNA during an outbreak. © 2011, American Society for Microbiology
Granularity-induced gapless superconductivity in NbN films: evidence of thermal phase fluctuations
Using a single coil mutual inductance technique, we measure the low
temperature dependence of the magnetic penetration depth in superconducting NbN
films prepared with similar critical temperatures around 16 K but with
different microstructures. Only (100) epitaxial and weakly granular (100)
textured films display the characteristic exponential dependence of
conventional BCS s-wave superconductors. More granular (111) textured films
exhibit a linear dependence, indicating a gapless state in spite of the s-wave
gap. This result is quantitatively explained by a model of thermal phase
fluctuations favored by the granular structure.Comment: 10 pages, 4 figures, to appear in Phys. Rev.
iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function
BACKGROUND: SAFB1 is a RNA binding protein implicated in the regulation of multiple cellular processes such as the regulation of transcription, stress response, DNA repair and RNA processing. To gain further insight into SAFB1 function we used iCLIP and mapped its interaction with RNA on a genome wide level. RESULTS: iCLIP analysis found SAFB1 binding was enriched, specifically in exons, ncRNAs, 3’ and 5’ untranslated regions. SAFB1 was found to recognise a purine-rich GAAGA motif with the highest frequency and it is therefore likely to bind core AGA, GAA, or AAG motifs. Confirmatory RT-PCR experiments showed that the expression of coding and non-coding genes with SAFB1 cross-link sites was altered by SAFB1 knockdown. For example, we found that the isoform-specific expression of neural cell adhesion molecule (NCAM1) and ASTN2 was influenced by SAFB1 and that the processing of miR-19a from the miR-17-92 cluster was regulated by SAFB1. These data suggest SAFB1 may influence alternative splicing and, using an NCAM1 minigene, we showed that SAFB1 knockdown altered the expression of two of the three NCAM1 alternative spliced isoforms. However, when the AGA, GAA, and AAG motifs were mutated, SAFB1 knockdown no longer mediated a decrease in the NCAM1 9–10 alternative spliced form. To further investigate the association of SAFB1 with splicing we used exon array analysis and found SAFB1 knockdown mediated the statistically significant up- and downregulation of alternative exons. Further analysis using RNAmotifs to investigate the frequency of association between the motif pairs (AGA followed by AGA, GAA or AAG) and alternative spliced exons found there was a highly significant correlation with downregulated exons. Together, our data suggest SAFB1 will play an important physiological role in the central nervous system regulating synaptic function. We found that SAFB1 regulates dendritic spine density in hippocampal neurons and hence provide empirical evidence supporting this conclusion. CONCLUSIONS: iCLIP showed that SAFB1 has previously uncharacterised specific RNA binding properties that help coordinate the isoform-specific expression of coding and non-coding genes. These genes regulate splicing, axonal and synaptic function, and are associated with neuropsychiatric disease, suggesting that SAFB1 is an important regulator of key neuronal processes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0220-7) contains supplementary material, which is available to authorized users
The economic and innovation contribution of universities: a regional perspective
Universities and other higher education institutions (HEIs) have come to be regarded as key sources of knowledge utilisable in the pursuit of economic growth. Although there have been numerous studies assessing the economic and innovation impact of HEIs, there has been little systematic analysis of differences in the relative contribution of HEIs across regions. This paper provides an exploration of some of these differences in the context of the UK’s regions. Significant differences are found in the wealth generated by universities according to regional location and type of institution. Universities in more competitive regions are generally more productive than those located in less competitive regions. Also, traditional universities are generally more productive than their newer counterparts, with university productivity positively related to knowledge commercialisation capabilities. Weaker regions tend to be more dependent on their universities for income and innovation, but often these universities under-perform in comparison to counterpart institutions in more competitive regions. It is argued that uncompetitive regions lack the additional knowledge infrastructure, besides universities, that are more commonly a feature of more competitive regions
Gas nitriding and subsequent oxidation of Ti-6Al-4V alloys
Ti-6Al-4V alloys consisting of α-Ti grains and intergranular β-Ti islands were nitrided at 850°C for 1 to 12 h under a nitrogen pressure of 1 Pa. With increasing nitriding time, the Ti-N compound layer became thicker, and the α-Ti diffusion zone containing dissolved nitrogen became wider. In the Ti-N compound layer, the initially formed Ti2N became TiN as the nitriding progressed. The nitride layers were oxidized to rutile-TiO2 after oxidation at 700°C for 10 h in air
Measurements of double-helicity asymmetries in inclusive production in longitudinally polarized collisions at GeV
We report the double helicity asymmetry, , in inclusive
production at forward rapidity as a function of transverse momentum
and rapidity . The data analyzed were taken during
GeV longitudinally polarized collisions at the Relativistic Heavy Ion
Collider (RHIC) in the 2013 run using the PHENIX detector. At this collision
energy, particles are predominantly produced through gluon-gluon
scatterings, thus is sensitive to the gluon polarization
inside the proton. We measured by detecting the decay
daughter muon pairs within the PHENIX muon spectrometers in the
rapidity range . In this kinematic range, we measured the
to be ~(stat)~~(syst). The
can be expressed to be proportional to the product of the
gluon polarization distributions at two distinct ranges of Bjorken : one at
moderate range where recent RHIC data of jet and
double helicity spin asymmetries have shown evidence for significant gluon
polarization, and the other one covering the poorly known small- region . Thus our new results could be used to further
constrain the gluon polarization for .Comment: 335 authors, 10 pages, 4 figures, 3 tables, 2013 data. Version
accepted for publication by Phys. Rev. D. Plain text data tables for the
points plotted in figures for this and previous PHENIX publications are (or
will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Single electron yields from semileptonic charm and bottom hadron decays in AuAu collisions at GeV
The PHENIX Collaboration at the Relativistic Heavy Ion Collider has measured
open heavy-flavor production in minimum bias AuAu collisions at
GeV via the yields of electrons from semileptonic decays
of charm and bottom hadrons. Previous heavy-flavor electron measurements
indicated substantial modification in the momentum distribution of the parent
heavy quarks due to the quark-gluon plasma created in these collisions. For the
first time, using the PHENIX silicon vertex detector to measure precision
displaced tracking, the relative contributions from charm and bottom hadrons to
these electrons as a function of transverse momentum are measured in AuAu
collisions. We compare the fraction of electrons from bottom hadrons to
previously published results extracted from electron-hadron correlations in
collisions at GeV and find the fractions to be
similar within the large uncertainties on both measurements for
GeV/. We use the bottom electron fractions in AuAu and along
with the previously measured heavy flavor electron to calculate the
for electrons from charm and bottom hadron decays separately. We find
that electrons from bottom hadron decays are less suppressed than those from
charm for the region GeV/.Comment: 432 authors, 33 pages, 23 figures, 2 tables, 2011 data. v2 is version
accepted for publication by Phys. Rev. C. Plain text data tables for the
points plotted in figures for this and previous PHENIX publications are (or
will be) publicly available at http://www.phenix.bnl.gov/papers.htm
- …