St Andrews Research Repository

    Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism

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    MMP and Bioinformatics support was provided by the Bioinformatics Unit at St Andrews University funded by a Wellcome Trust ISSF grant 097831/Z/11/Z. This research was funded by Medial Research Council (, grant G0801971) (to JCS and SK) and the University of St Andrews. TS, TDO and JCR were supported by the Wellcome Trust (, grant number 098051). TDO was supported by the European Union 7th framework (EVIMalaR) ( TS was supported by the Medical Research Council (, grant number MR/J500355/1).Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology.Publisher PDFPeer reviewe

    Managing open access (OA) workflows at the University of St Andrews: challenges and Pathfinder solutions

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    © 2014. Janet Aucock. This is an open access article distributed under the Creative Commons Attribution Licence, which permits unrestricted use and distribution provided the original author and source are credited.This article arose out of a presentation given to the UKSG seminar on ‘Managing Open Access: pain points and workflows’. It presents a case study on the workflows in place at the University of St Andrews and how these are developing to meet funder compliance policies and the challenge of the new HEFCE Research Excellence Framework (REF) open access (OA) policy. The case study describes the research environment at St Andrews and in particular the challenges faced and how these may be answered. Since the seminar in May 2014, the Open Access Research Publications Support Team has engaged in a ‘Lean’ exercise to evaluate and streamline workflows within the institution. St Andrews is also now a partner in the LOCH project, one of the Jisc Pathfinder projects. The paper gives an update on recent activities and looks at strategies and practical ideas for improving workflows and removing pain points.Publisher PD

    Case studies in exploiting terrorist group divisions with disinformation and divisive/black propaganda

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    Counterterrorism operations should be exploiting the divisions and infighting of terrorist groups. The overall goal should be to make fewer mistakes than the jihadis, help increase inter-group and intra-group tension, and further their disconnection from the wider public. This paper argues that strategic psychological operations (PSYOP) that focus on exploiting rifts in leadership, differences in strategic planning, and ethnic, national and tribal differences within and among terrorist groups could be an integral part of overall counterterrorism efforts. Using three case studies, chosen because of the attention given to them in the international community and the illuminating group and leadership characteristics that can be found in many other jihadist organisations, the paper illustrates that PSYOP that expand on the existing framework could be very effective in countering the jihadist threat.Publisher PD

    MultiFi : multi-fidelity interaction with displays on and around the body

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    This work was supported by the EU FP7 project MAGELLAN under the grant number ICT-FP7-611526.Display devices on and around the body such as smartwatches, head-mounted displays or tablets enable users to interact on the go. However, diverging input and output fidelities of these devices can lead to interaction seams that can inhibit efficient mobile interaction, when users employ multiple devices at once. We present MultiFi, an interactive system that combines the strengths of multiple displays and overcomes the seams of mobile interaction with widgets distributed over multiple devices. A comparative user study indicates that combined head-mounted display and smartwatch interfaces can outperform interaction with single wearable devices.Postprin

    The tangent of the Syrian Uprising

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    Examines the stages and watersheds in the evolution of the Syrian UprisingPostprintPeer reviewe

    Bridging the gap in marine and terrestrial studies

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    Ecologists are interested in understanding natural phenomena and strive to make comparisons across systems to better understand broad ecological processes and patterns. Recent reviews showcased how marine and terrestrial ecologists (as an example of two isolated disciplines) can benefit from sharing information. Here, a literature review shows that marine studies often lack the generality needed to bridge the often observed gap between theory developed in marine and terrestrial systems. In order to stimulate constructive comparisons across systems, we discuss potential reasons for this lower generality, with the goal of more broadly understanding ecological processes and patterns.Publisher PDFPeer reviewe

    The effect of water temperature on routine swimming behaviour of new born guppies (Poecilia reticulata)

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    Funding for this research came from The Buckland Foundation, The Scottish Fisheries Museum Trust Ltd. Additional costs and supplies were provided by the School of Biology of The University of St Andrews.Guppies have successfully established populations in places with thermal regimes very different from the Tropical conditions in their native range. This indicates a remarkable capacity for thermal adaptation. Given their vulnerability to predation as juveniles, acute changes in temperature, which can alter predator-prey relationships, can impact juvenile survival and have amplified consequences at the population level. To understand how temperature may impact juvenile survival and gain insight into their success as an invasive species, we researched the effect of acute temperature changes on the routine swimming behaviour of juvenile guppies. Using a novel 3-dimensional tracking technique, we calculated 4 routine swimming parameters, speed, depth, and variation in speed or depth, at 6 different test temperatures (17, 20, 23, 26, 29, or 32°C). These temperatures cover their natural thermal range and also extended past it in order to include upper and lower thermal limits. Using model selection, we found that body length and temperature had a significant positive relationship with speed. Variation in speed decreased with rising temperatures and fish swam slightly closer to the bottom at higher temperatures. All juveniles increased variation in depth at higher temperatures, though larger individuals maintained slightly more consistent depths. Our results indicate that guppies have a large thermal range and show substantial plasticity in routine swimming behaviours, which may account for their success as an invasive species.Publisher PDFPeer reviewe

    Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

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    This work was supported by a Longer and Larger (LoLa) grant from the Biotechnology and Biological Sciences Research Council (grant numbers BB/G020744/1, BB/G019177/1, BB/G019274/1 and BB/G003203/1), the UK Department for Environment, Food and Rural Affairs and Zoetis, awarded to the Bacterial Respiratory Diseases of Pigs: 1 Technology (BRaDP1T) consortium. Part of this work was supported by The Wellcome Trust Overseas Programme in Vietnam (2010–2015) (089276/Z/09/Z) and the Vietnam Initiative on Zoonotic Infections (VIZIONS) award (WT/093724/Z/10/Z). S.D.B. is partly funded by the NIHR Cambridge BRC.Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.Publisher PDFPeer reviewe

    Dynamically controlled resonance fluorescence spectra from a doubly dressed single InGaAs quantum dot

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    We report the first experimental demonstration of the interference-induced spectral line elimination predicted by Zhu and Scully [Phys. Rev. Lett. 76, 388 (1996)] and Ficek and Rudolph [Phys. Rev. A 60, R4245 (1999)]. We drive an exciton transition of a self-assembled quantum dot in order to realize a two-level system exposed to a bichromatic laser field and observe the nearly complete elimination of the resonance fluorescence spectral line at the driving laser frequency. This is caused by quantum interference between coupled transitions among the doubly dressed excitonic states, without population trapping. We also demonstrate a multiphoton ac Stark effect with shifted subharmonic resonances and dynamical modifications of resonance fluorescence spectra by using double dressing.Publisher PDFPeer reviewe

    The effect of animal movement on line transect estimates of abundance

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    This work was supported by the University of St Andrews (; RG, STB, LT) and by a summer scholarship and PhD grant from The Carnegie Trust for the Universities of Scotland ( to RG.Line transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection within the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detectability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling provided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal movement is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from behind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.Publisher PDFPeer reviewe
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