Comparison Between Expression Microarrays and RNA-Sequencing Using UKBEC Dataset Identified a trans-eQTL Associated with MPZ Gene in Substantia Nigra

In recent years, the advantages of RNA-sequencing (RNA-Seq) have made it the platform of choice for measuring gene expression over traditional microarrays. However, RNA-Seq comes with bioinformatical challenges and higher computational costs. Therefore, this study set out to assess whether the increased depth of transcriptomic information facilitated by RNA-Seq is worth the increased computation over microarrays, specifically at three levels: absolute expression levels, differentially expressed genes identification, and expression QTL (eQTL) mapping in regions of the human brain. Using the United Kingdom Brain Expression Consortium (UKBEC) dataset, there is high agreement of gene expression levels measured by microarrays and RNA-seq when quantifying absolute expression levels and when identifying differentially expressed genes. These findings suggest that depending on the aims of a study, the relative ease of working with microarray data may outweigh the computational time and costs of RNA-Seq pipelines. On the other, there was low agreement when mapping eQTLs. However, a number of eQTLs associated with genes that play important roles in the brain were found in both platforms. For example, a trans-eQTL was mapped that is associated with the MPZ gene in the substantia nigra. These eQTLs that we have highlighted are extremely promising candidates that merit further investigation

Liverpool Telescope 2: a new robotic facility for time domain astronomy in 2020

The robotic 2m Liverpool Telescope, based on the Canary island of La Palma, has a diverse instrument suite and a strong track record in time domain science, with highlights including early time photometry and spectra of supernovae, measurements of the polarization of gamma-ray burst afterglows, and high cadence light curves of transiting extrasolar planets. In the next decade the time domain will become an increasingly prominent part of the astronomical agenda with new facilities such as LSST, SKA, CTA and Gaia, and promised detections of astrophysical gravitational wave and neutrino sources opening new windows on the transient universe. To capitalise on this exciting new era we intend to build Liverpool Telescope 2: a new robotic facility on La Palma dedicated to time domain science. The next generation of survey facilities will discover large numbers of new transient sources, but there will be a pressing need for follow-up observations for scientific exploitation, in particular spectroscopic follow-up. Liverpool Telescope 2 will have a 4-metre aperture, enabling optical/infrared spectroscopy of faint objects. Robotic telescopes are capable of rapid reaction to unpredictable phenomena, and for fast-fading transients like gamma-ray burst afterglows. This rapid reaction enables observations which would be impossible on less agile telescopes of much larger aperture. We intend Liverpool Telescope 2 to have a world-leading response time, with the aim that we will be taking data with a few tens of seconds of receipt of a trigger from a ground- or space-based transient detection facility. We outline here our scientific goals and present the results of our preliminary optical design studies. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

Fracture of complex metallic alloys: An atomistic study of model systems

Molecular dynamics simulations of crack propagation are performed for two extreme cases of complex metallic alloys (CMAs): In a model quasicrystal the structure is determined by clusters of atoms, whereas the model C15 Laves phase is a simple periodic stacking of a unit cell. The simulations reveal that the basic building units of the structures also govern their fracture behaviour. Atoms in the Laves phase play a comparable role to the clusters in the quasicrystal. Although the latter are not rigid units, they have to be regarded as significant physical entities.Comment: 6 pages, 4 figures, for associated avi file, see http://www.itap.physik.uni-stuttgart.de/~frohmut/MOVIES/C15.LJ.011.100.av

A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease

Peer reviewedPublisher PD

Effectiveness, cost-effectiveness and cost-benefit of a single annual professional intervention for the prevention of childhood dental caries in a remote rural Indigenous community

Background The aim of the study is to reduce the high prevalence of tooth decay in children in a remote, rural Indigenous community in Australia, by application of a single annual dental preventive intervention. The study seeks to (1) assess the effectiveness of an annual oral health preventive intervention in slowing the incidence of dental caries in children in this community, (2) identify the mediating role of known risk factors for dental caries and (3) assess the cost-effectiveness and cost-benefit of the intervention. Methods/design The intervention is novel in that most dental preventive interventions require regular re-application, which is not possible in resource constrained communities. While tooth decay is preventable, self-care and healthy habits are lacking in these communities, placing more emphasis on health services to deliver an effective dental preventive intervention. Importantly, the study will assess cost-benefit and cost-effectiveness for broader implementation across similar communities in Australia and internationally. Discussion There is an urgent need to reduce the burden of dental decay in these communities, by implementing effective, cost-effective, feasible and sustainable dental prevention programs. Expected outcomes of this study include improved oral and general health of children within the community; an understanding of the costs associated with the intervention provided, and its comparison with the costs of allowing new lesions to develop, with associated treatment costs. Findings should be generalisable to similar communities around the world. The research is registered with the Australian New Zealand Clinical Trials Registry (ANZCTR), registration number ACTRN12615000693527; date of registration: 3rd July 2015

Interventions to Promote Cancer Awareness and Early Presentation: Systematic Review

Low cancer awareness contributes to delay in presentation for cancer symptoms and may lead to delay in cancer diagnosis. The aim of this study was to review the evidence for the effectiveness of interventions to raise cancer awareness and promote early presentation in cancer to inform policy and future research. We searched bibliographic databases and reference lists for randomised controlled trials of interventions delivered to individuals, and controlled or uncontrolled studies of interventions delivered to communities. We found some evidence that interventions delivered to individuals modestly increase cancer awareness in the short term and insufficient evidence that they promote early presentation. We found limited evidence that public education campaigns reduce stage at presentation of breast cancer, malignant melanoma and retinoblastoma

Inhibition of activin/nodal signalling is necessary for pancreatic differentiation of human pluripotent stem cells

Peer reviewedPublisher PD

Biochemical properties of Paracoccus denitrificans FnrP:Reactions with molecular oxygen and nitric oxide

In Paracoccus denitrificans, three CRP/FNR family regulatory proteins, NarR, NnrR and FnrP, control the switch between aerobic and anaerobic (denitrification) respiration. FnrP is a [4Fe-4S] cluster containing homologue of the archetypal O2 sensor FNR from E. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to O2, and also NO, availability. Here we show that FnrP undergoes O2-driven [4Fe-4S] to [2Fe-2S] cluster conversion that involves up to 2 O2 per cluster, with significant oxidation of released cluster sulfide to sulfane observed at higher O2 concentrations. The rate of the cluster reaction was found to be ~6-fold lower than that of E. coli FNR, suggesting that FnrP can remain transcriptionally active under microaerobic conditions. This is consistent with a role for FnrP in activating expression of the high O2 affinity cytochrome c oxidase under microaerobic conditions. Cluster conversion resulted in dissociation of the transcriptionally active FnrP dimer into monomers. Therefore, along with E. coli FNR, FnrP belongs to the subset of FNR proteins in which cluster type is correlated with association state. Interestingly, two key charged residues, Arg140 and Asp154, that have been shown to play key roles in the monomer-dimer equilibrium in E. coli FNR are not conserved in FnrP, indicating that different protomer interactions are important for this equilibrium. Finally, the FnrP [4Fe-4S] cluster is shown to undergo reaction with multiple NO molecules, resulting in iron nitrosyl species and dissociation into monomers

The diagnostic suitability of a xerostomia questionnaire and the association between xerostomia, hyposalivation and medication use in a group of nursing home residents

The study objective was to explore the diagnostic suitability of the Xerostomia Inventory and the association between xerostomia, hyposalivation and medication use in a group of nursing home residents. A cross-sectional study was carried out in 50 physically impaired nursing home residents (20 men) with a mean age of 78.1 years (range, 53–98) in The Netherlands. The Xerostomia Inventory-Dutch version was completed for all residents and the data were subjected to exploratory factor analysis to determine the diagnostic suitability. Residents’ data on xerostomia, whole saliva secretion rates and hyposalivation-related medications used were collected and statistically analyzed. The diagnostic suitability of the Xerostomia Inventory-Dutch version appeared restricted. The prevalence of xerostomia was 52%, without gender and age difference. The prevalence of hyposalivation was 24% for resting, 60% for chewing-stimulated and 18% for acid-stimulated whole saliva. All whole saliva secretion rates were significantly lower in women than in men and in older than in younger residents. Forty-four percent of all medications used were hyposalivation-related and women used significantly more medications than men. Xerostomia was significantly negatively correlated with the resting whole saliva secretion rate. The number of hyposalivation-related medications used was not significantly correlated with the various whole saliva secretion rates. In nursing home residents, xerostomia, hyposalivation and using hyposalivation-related medications seem common and partially associated features