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Western University
Country: Canada
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27 Projects, page 1 of 6
  • Funder: NSF Project Code: 6113082
    Partners: UWO
  • Funder: UKRI Project Code: NE/T014482/1
    Funder Contribution: 7,609 GBP
    Partners: UWO, University of Edinburgh

    MRC : Heather Grant : MR/N013166/1 HIV is still a huge burden world-wide, with 1.7 million new infections each year (UNAIDS, 2019). The roll out of anti-retroviral therapies (ART) has worked to reduce the numbers of AIDS related deaths and onward transmissions, but to curb further infections still, UNAIDS goals are that 95% of the population should know their status, 95% of those should be on treatment, and 95% of those should be virally supressed. Characterising drivers of new infections will help to identify gaps to be closed. Comparing viral sequences from different patients can be used for epidemiological studies. HIV sequence data for the polymerase gene (pol) is routinely collected for drug-resistance testing, but can then be used secondarily for these purposes, once anonymized, keeping only basic demographic information. Genetic distance (that is, the number of mutational differences between any two viruses) can be used to link closely related viruses together. (A lower genetic distance suggests they shared a common ancestor more recently). HIV mutations are introduced into the genome with each replication cycle. Mutation is said to have its own 'clock' so that changes builds up, on average, in a predictable way over time. Therefore, the genetic distance and time of sampling, can be used to draw linkage, infer networks, patterns of transmission, and other characterisations of the network such as degree distribution. These insights tied with demographic information can inform public health policy. For instance, individuals from groups deemed at high-risk might be advised to take pre-exposure prophylaxis (PrEP). HIV diversity is extremely high, since the virus has been evolving in humans for maybe a hundred years, long before it was first described. It is classified into major lineages (subtypes) that formed early on during its expansion. Where an individual is infected with more than one HIV variant, recombination between the two can occur, creating a hybrid virus, and thus more diversity. This almost certainly happen between two identical viruses from the same infection, but will be undetectable since the new virus is the same as both parents. Where highly divergent viruses recombine, (such as those from different subtypes), this becomes more obvious as there is enough signal to distinguish the two parental viruses. This process of recombination between divergent viruses breaks apart linkages, where one half of the genome might link to the first parental virus, and the other half to the second. Now, if the whole sequence was to be considered in a linkage analysis, no connections would be made as the new sequence is now sufficiently different to both parents. As HIV moves along the transmission network, it will occasionally find itself part of a dual infection, and may take part in a recombination event. This could happen at any time point in time, making it more difficult to spot, as other mutations build up, and the molecular clock moves the virus forward. Dynamic Stochastic Block Modelling is a way of modelling network data, and in our case will be used to find groups or communities of similar viruses over time. This approach will better classify HIV diversity and model networks over time; highly appropriate for a fast-evolving recombinogenic virus. Simulation experiments will be carried out to test the principle and validate the approach. Finally, we will apply this to near-full genome HIV data from Uganda. This research will be undertaken under the supervision of Associate Professor Art Poon in the Department of Pathology and Laboratory Medicine at Western University, Ontario, Canada.

  • Funder: UKRI Project Code: NE/X00726X/1
    Funder Contribution: 11,021 GBP
    Partners: UWO, University of Cambridge

    AHRC : Tadeusz Wojtych : AH/L503824/1 How do textbooks promote reconciliation? Over the past decade, new history textbooks have been published in Canada and in Central Europe. In Ontario and Quebec, the 2015 Truth and Reconciliation Commission report provided a stimulus for reform. In Europe, historians from Germany and Poland wrote a textbook - approved in both countries - which seeks to overcome the historical animosity between the two nations. In what ways are these new textbooks different from the old ones? How is reconciliation understood in different cultural contexts? The student and the supervisor will co-author a blog entry about textbook reforms in Europe and Canada and, in the long run, publish a journal article. The student will also create a British-Canadian Network of Textbook Experts - a community of education researchers and practitioners - with the intention of fostering new transatlantic research and consultancy partnerships. The members will meet at a virtual networking event in November 2022. Collectively, the placement explores how Europeans and Canadians can benefit from each other's experience with curricula and textbook development.

  • Funder: UKRI Project Code: NE/W006707/1
    Funder Contribution: 649,335 GBP
    Partners: University of Liverpool, UWO

    The geodynamo is the engine at the heart of our planet generating our protective magnetic field. Today, the geodynamo is powered by the freezing of iron onto the ever-growing solid inner core, but in the past the geodynamo is thought to have been driven by purely thermal energy, just like a pot of boiling water. The switching between these two power sources represents Earth's largest energy transition. When it happened, and what power source kept "the engine running" during the switch is not well constrained. Earth's magnetic field is generated by the geodynamo, so changes in Earth's ancient magnetic field may be the only way to detect this energy transition. The geodynamo energy transition represents the dying thermal power source and should be marked by a period of extremely weak magnetic field. This weak field can be preserved in rocks because nanoscale magnetic particles found within them lock in memories of the ancient magnetic fields in which they formed. However, over time these magnetic memories fade, but for some particles, their memories fade much faster than we expect, giving rise to false records of the ancient Earth, which appear to be weaker than they really are. Our best estimate for the geodynamo energy transition is during the Ediacaran, around 550-600 million years ago. Recent studies of this time period have revealed an extremely weak magnetic field, more than ten times weaker the field today, which may indicate a dying thermally driven dynamo just prior to the transition. The results from some of these studies, however, have characteristics that are typical of forgetful magnetic particles. This raises a critical question: Are weak signals from "forgetful" rocks being confused with a weak dynamo undergoing a major energy transition? To address this, we are using a pioneering new approach to seamlessly integrate the laboratory experiments used to determine ancient field strengths with recent theoretical advances in simulating the behavior of magnetic particles. Taking samples that preserve a weak Ediacaran field, we will decompose them into their constituent magnetic particles. Then, using new micromagnetic models (models that predict magnetic behavior at the molecular level) we will reassemble the samples numerically and simulate their magneto- geological history. With this approach we will determine if the weak field these samples remember is a faithful memory of the field half a billion years ago and the implications this has for Earth as it experienced a major transition of its internal power. Furthermore, with this new workflow for integrating experimental observations and emergent theory, it will be possible to apply our pioneering techniques to tackle key paleo-, rock and environmental questions spanning a diverse range of disciplines, from tectonics to archeology, or volcanology to the evolution of the Moon, Mars and other planetary bodies.

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