27 Projects, page 1 of 6
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.
The Chicxulub impact crater, Mexico, is unique. It is the only known terrestrial impact structure that has been directly linked to a mass extinction event, and the only terrestrial impact with a global ejecta layer. Of the three largest impact structures on Earth, Chicxulub is the best preserved. Chicxulub is also the only known terrestrial impact structure with an intact, unequivocal topographic "peak ring". Chicxulub's role in the K-Pg mass extinction and its exceptional state of preservation make it an important natural laboratory for the study of both large impact crater formation on Earth and other planets, and the effects of large impacts on the Earth's environment and ecology. Our understanding of the impact process is far from complete and, despite over 30 years of intense debate, we are still striving to answer the question as to why this impact was so catastrophic. Expedition 364 is the first drill hole into an intact topographic peak ring, and the first to penetrate the offshore portion of the Chicxulub crater. Peak rings are a ring of hills that protrude through the crater floor within large impact basins on the terrestrial planets, and there is no consensual agreement on either their formational mechanism or the nature of the rocks that form them. Geophysical data indicate that the peak ring at Chicxulub is formed from rocks that have a low velocity and density, and one explanation for this is that they are highly fractured and porous. Immediately after impact the peak ring was submerged under water, and located adjacent to a thick pool of hot melt rocks. Hence, we would expect intense hydrothermal activity within the peak ring. This activity may have provided a niche for exotic life forms, in a similar way that hydrothermal vent systems do in the oceans. Drilling the peak ring will determine the origin, lithology, and physical state of the rocks that form it, allow us to distinguish between competing models of peak-ring formation, as well as document the hydrothermal systems and any associated microbiology. Immediately after impact the ocean is, locally, likely to have been sterile. We will use core through the post-impact sediments to examine the recolonization of the ocean, including: what biota came back first (benthic, dinoflagellates, specialists vs generalists), and how long did it take to return to normal conditions? The proposed drilling directly contributes to IODP goals in the: Deep Biosphere and the Subseafloor Ocean and Environmental Change, Processes and Effects, in particular the environmental and biological perturbations caused by Chicxulub.
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.