Semi-quantitative, duplexed qPCR assay for the detection of leishmania spp. using bisulphite conversion technology

© 2019 by the authors. Leishmaniasis is caused by the flagellated protozoan Leishmania, and is a neglected tropical disease (NTD), as defined by theWorld Health Organisation (WHO). Bisulphite conversion technology converts all genomic material to a simplified form during the lysis step of the nucleic acid extraction process, and increases the efficiency of multiplex quantitative polymerase chain reaction (qPCR) reactions. Through utilization of qPCR real-time probes, in conjunction with bisulphite conversion, a new duplex assay targeting the 18S rDNA gene region was designed to detect all Leishmania species. The assay was validated against previously extracted DNA, from seven quantitated DNA and cell standards for pan-Leishmania analytical sensitivity data, and 67 cutaneous clinical samples for cutaneous clinical sensitivity data. Specificity was evaluated by testing 76 negative clinical samples and 43 bacterial, viral, protozoan and fungal species. The assay was also trialed in a side-by-side experiment against a conventional PCR (cPCR), based on the Internal transcribed spacer region 1 (ITS1 region). Ninety-seven percent of specimens from patients that previously tested positive for Leishmania were positive for Leishmania spp. with the bisulphite conversion assay, and a limit of detection (LOD) of 10 copies per PCR was achieved, while the LOD of the ITS1 methodology was 10 cells/1000 genomic copies per PCR. This method of rapid, accurate and simple detection of Leishmania can lead to improved diagnosis, treatment and public health outcomes

Modeling potential responses to smallpox as a bioterrorist weapon.

We constructed a mathematical model to describe the spread of smallpox after a deliberate release of the virus. Assuming 100 persons initially infected and 3 persons infected per infectious person, quarantine alone could stop disease transmission but would require a minimum daily removal rate of 50% of those with overt symptoms. Vaccination would stop the outbreak within 365 days after release only if disease transmission were reduced to <0.85 persons infected per infectious person. A combined vaccination and quarantine campaign could stop an outbreak if a daily quarantine rate of 25% were achieved and vaccination reduced smallpox transmission by > or = 33%. In such a scenario, approximately 4,200 cases would occur and 365 days would be needed to stop the outbreak. Historical data indicate that a median of 2,155 smallpox vaccine doses per case were given to stop outbreaks, implying that a stockpile of 40 million doses should be adequate

Fine structure in the gamma-ray sky

The EGRET results for gamma-ray intensities in and near the Galactic Plane have been analysed in some detail. Attention has been concentrated on energies above 1 GeV and the individual intensities in a $4^\circ$ longitude bin have been determined and compared with the large scale mean found from a nine-degree polynomial fit. Comparison has been made of the observed standard deviation for the ratio of these intensities with that expected from variants of our model. The basic model adopts cosmic ray origin from supernova remnants, the particles then diffusing through the Galaxy with our usual 'anomalous diffusion'. The variants involve the clustering of SN, a frequency distribution for supernova explosion energies, and 'normal', rather than 'anomalous' diffusion. It is found that for supernovae of unique energy, and our usual anomalous diffusion, clustering is necessary, particularly in the Inner Galaxy. An alternative, and preferred, situation is to adopt the model with a frequency distribution of supernova energies. The results for the Outer Galaxy are such that no clustering is required.Comment: 10 pages, 4 figures, 1 table, accepted for publication in J.Phys.G: Nucl.Part.Phy

The use of national datasets to baseline science education reform: exploring value-added approaches

This paper uses data from the National Pupil Database to investigate the differences in ‘performance’ across the range of science courses available following the 2006 Key Stage 4 (KS4) science reforms in England. This is a value-added exploration (from Key Stage 3 [KS3] to KS4) aimed not at the student or the school level, but rather at that of the course. Different methodological approaches to carrying out such an analysis, ranging from simple non-contextualized techniques, to more complex fully contextualized multilevel models, are investigated and their limitations and benefits are evaluated. Important differences between courses are found in terms of the typical ‘value’ they add to the students studying them with particular applied science courses producing higher mean KS4 outcomes for the same KS3 level compared with other courses. The implications of the emergence of such differences, in a context where schools are judged to a great extent on their value-added performance, are discussed. The relative importance of a variety of student characteristics in determining KS4 outcomes are also investigated. Substantive findings are that across all types of course, science prior attainment at KS3, rather than that of mathematics or English, is the most important predictor of KS4 performance in science, and that students of lower socio-economic status consistently make less progress over KS4 than might be expected, despite prior attainment being accounted for in the modelling

Silver antimony Ohmic contacts to moderately doped n-type germanium

A self doping contact consisting of a silver/antimony alloy that produces an Ohmic contact to moderately doped n-type germanium (doped to a factor of four above the metal-insulator transition) has been investigated. An evaporation of a mixed alloy of Ag/Sb (99%/1%) onto n-Ge ( ND=1×1018 cm−3) annealed at 400 °C produces an Ohmic contact with a measured specific contact resistivity of (1.1±0.2)×10−5 Ω-cm2. It is proposed that the Ohmic behaviour arises from an increased doping concentration at the Ge surface due to the preferential evaporation of Sb confirmed by transmission electron microscope analysis. It is suggested that the doping concentration has increased to a level where field emission will be the dominate conduction mechanism. This was deduced from the low temperature electrical characterisation of the contact, which exhibits Ohmic behaviour down to a temperature of 6.5 K

Eclogites and basement terrane tectonics in the northern arm of the Grenville orogen, NW Scotland

The presence of eclogites within continental crust is a key indicator of collisional orogenesis. Eclogites within the Eastern Glenelg basement inlier of the Northern Highland Terrane (NHT) have been re-dated in order to provide more accurate constraints on the timing of collision within the northern arm of the Grenville Orogen. The eclog-ites yield dates of ca.1200 Ma which are interpreted to record the onset of continent-continent interaction, and the NHT as a whole is thought to represent the lower plate in successive 1200-1000 Ma collision events. The Eastern Glenelg basement inlier is viewed as a fragment of the leading edge of the NHT continental basement that was partially subducted along a suture and then exhumed back up the subduction channel. Differences in ages of igneous protoliths and intrusive histories, and metamorphic events (this paper) between the NHT basement and the Laurentian foreland, suggests that they were separate crustal blocks until after ca. 1600 Ma. We therefore suggest that: (1) the NHT represents a fragment of Archean-Paleoproterozoic crust that was reworked within the ca. 1.7-1.6 Ga Labradorian-Gothian belt, although whether it was derived from Laurentia or Baltica is uncertain, and (2) amalgamation of the NHT with the Laurentian foreland did not occur until the terminal stages of the Grenville collision at ca. 1000 Ma

Timing and mechanism of the rise of the Shillong Plateau in the Himalayan foreland

The Shillong Plateau (northeastern India) constitutes the only significant topography in the Himalayan foreland. Knowledge of its surface uplift history is key to understanding topographic development and unraveling tectonic–climate–topographic coupling in the eastern Himalaya. We use the sedimentary record of the Himalayan foreland basin north of the Shillong Plateau to show that the paleo-Brahmaputra river was redirected north and west by the rising plateau at 5.2–4.9 Ma. We suggest that onset of plateau uplift is a result of increased fault-slip rates in response to stresses caused by the Indian lithosphere bending beneath the Himalaya