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University of Edinburgh

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7,653 Projects, page 1 of 1,531
  • Funder: UK Research and Innovation Project Code: 2890784

    Human cells are constantly exposed to external and internal stressors causing damage to the cell and its genome. To cope with diverse environmental changes and ensure the survival of the organism, cells developed diverse stress adaptation strategies. Whereas cellular stress usually leads to programmed cell death in normal cells, cancer cells can by-pass growth-limiting checkpoints resulting in tumor cell survival. Long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse physiological and pathological processes including stress response. However, the molecular basis of the lncRNA-directed regulation of stress responses remains enigmatic in the majority of studied cases. The Shkumatava laboratory has recently identified a cancer-associated lncRNA that buffers cellular stress. Genetic inactivation of the lncRNA leads to constant upregulation of the p53 pathway, which acts as a cellular sensor of DNA damage and a guardian of the genome. We found that this lncRNA engages with key DNA damage proteins via its conserved RNA sequence motifs. Our goal is now to define the function of these deeply conserved RNA elements and reveal how their association with the DNA damage machinery contributes to regulation of the cellular stress response and maintenance of the cell integrity. To achieve our goals, we employ state-of-the-art of technologies including genome editing in relevant mammalian cell lines, high resolution imaging, genome-wide sequencing approaches (RNA-seq, ChIP-seq, ATAC-seq), diverse cellular and molecular approaches including our novel high throughput incPRINT RNA-protein interaction technology. The student will develop specific skills in all mentioned above disciplines. The project will be jointly supervised by Dr Shkumatava who is an expert in RNA biology and Dr Buonomo who is an expert in genome stability and DNA damage response. In addition, we collaborate with bioinformaticians for data analyses.

  • Funder: UK Research and Innovation Project Code: 2110777

    Biology is being transformed by the use of quantitative methods to analyse molecular processes as the system level and understand the underlying dynamics of the responses of living organisms to changes in their environment. For example, exposure of bacteria to antibiotics leads to modification of their gene expression profile at multiple time scales. To understand these complex phenomena, mathematical models are essential but estimating parameters of these models from real experimental data is still very challenging because if the inherent noisiness of biological data. Indeed, parameter estimation from noisy gene expression data is crucial to building predictive computational models of intracellular kinetics. The most commonly used approaches in the literature use the linear-noise approximation or moment-closure within a Bayesian framework [1,2]. These methods have been shown to give accurate estimates for simple gene regulatory models with large amounts of data however they are computationally inefficient because of the Markov Chain Monte Carlo (MCMC) optimisation step. It is also the case that large amounts of time-series data are not typically available from many experimental setups. In this project the aim is to design a new inference method based on recent advances in the estimation of parameters using data-efficient machine-learning techniques [3] which hold promise for accurate estimation from sparse data. The project will involve the extension of these techniques from partial differential equation models to master equation models and its application to infer the parameters of molecular processes at the heart of DNA and RNA dynamics. The methods will be applied to data produced in the ElKaroui lab to analyse the bacterial response to exposure of DNA damaging antibiotics at the single cell level using microfluidics and fluorescence microscopy.

  • Funder: UK Research and Innovation Project Code: 2289133

    At the time when media historians and critics debate the demise of printed page and physical book and studies of book history proliferate, key voices in digital humanities (Hayles, Schnapp, Drucker) speak for necessity of media-specific enquiry and the impact of changing paradigms of reading and handling of book objects on publishing, education and cognition. Hayles explicitly points to the material and conceptual terrain of artists' books as a critical source of theoretical orientation in navigating new knowledges. Learning from artists' books, and deploying innovative methodologies of design research, this study will investigate relationships between the book form and gestures, spaces and architectures of reading. It will be framed theoretically by Mallarme's vision of 'book as an intellectual instrument, predetermined and architectural' and Genette's elaboration of paratextuality mobilized in examination of material, spatial and sensorial aspects of book space and reading in relation to specific sites of experience. While references to Mallarmé's experimental poem are ubiquitous in scholarship, and there is a growing interest in Genette's work on paratext, the architectural potentials of both have not been considered in research that links the book's form to physical spaces of its reading. Extending the research on the anatomy of the Architectural Book (Tavares) to exploration of the Artists' Books, this study will operate from the premise that the space of reading a complex sensorial book object (with its textures, surfaces, structure, rhythm and scale) is informed by the book itself, engaging the book's sensorial attributes through reading gestures and material practices. Recognising research potentials of the book as a critical object of knowledge, this research will develop from close examination of the multiplicity of forms of Artists' Books in the Modern & Contemporary Art Archive of NGS. Beginning with a selection of most challenging sensorial works from the collection, it will proceed through a series of research-driven curatorial events and material outputs that will examine spaces and surfaces of reading, modes of storing and handling, practices of archiving and cataloguing, reading gestures and display conventions. It will consider specific needs of the collection together with practices and experiences across various spaces, media and technologies of interaction, storage and display. This research will take place whilst NGS acts as client for a new National Collections Facility sited at Granton to be designed by professionally situated architects. The Research By Design mode of this study will run in parallel with the design work and will productively contribute to the development of public consultation and research spaces of the new facility. The research will result in three interconnected tangible outputs: the written and illustrated thesis in the form of an experimental book object, an exhibition that includes the collection-based display of selected book forms, and designs for reading/display and research spaces for the collection. From examining theories, material practices, typologies and technologies of book art, it will develop bespoke research methodologies and architectural designs/scenarios for engaging with book form that will investigate the historical and contemporary paradigms of reading and modes of experiencing image-text and book space. Complementing existing practices observed and examined in the collection, the project will extend and challenge existing scholarship on book form and conventions of sensorial engagement with books in conceptual, physical and digital spaces of collections, archives, reading, teaching and research.

  • Funder: Wellcome Trust Project Code: 102336
    Funder Contribution: 151,823 GBP
  • Funder: UK Research and Innovation Project Code: 1963375

    Functional spinal cord repair from new neurons and circuitry


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