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Computational image analysis assisted optimisation of retinal organoid cryopreservation

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  • Full or part time
    Prof Majlinda Lako
    Dr JP de Magalhaes
    Dr R Bauer
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Interested in using computers to better understand biology? Then this project might be what you are looking for! The aim is to use novel software and high-performance computers, in order to analyse retinal tissue after freezing and thawing. By improving our knowledge of how cryogenic processing affects this neural tissue, new methodologies for cryogenic processing will be studied. To this end, the student will work together with experts in the field, conduct wet-lab experiments, cryogenically process artificial retinal tissue obtained from stem cells, learn to use modern Artificial Intelligence tools to extract valuable information from experiments, and produce novel hypotheses that will generate better methodologies.

This project will enable you to gain highly interdisciplinary skills. In particular, you will be based at Newcastle University, while also doing visits to Asymptote Ltd (GE Healthcare) in Cambridge. There, you will learn the usage of the latest cryogenic processing hardware and techniques. Moreover, you will visit CERN to obtain training in modern computational biology tools (https://biodynamo.web.cern.ch). Importantly, you will be supervised by a multidisciplinary team comprising experts from the experimental, computational and industrial disciplines of cryopreservation. Furthermore, you will participate at weekly lab meetings of the supervisory team, and present your findings at international conferences and scientific journals.

HOW TO APPLY

Applications should be made by emailing [Email Address Removed] with a CV (including contact details of at least two academic (or other relevant) referees), and a covering letter – including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project and at the selected University. Applications not meeting these criteria will be rejected.

In addition to the CV and covering letter, please email a completed copy of the Additional Details Form (Word document) to [Email Address Removed]. A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.

Informal enquiries may be made to [Email Address Removed]

Please note that the closing date for applications is Monday 18th May at 12noon.

Funding Notes

This is a 4 year BBSRC CASE studentship under the Newcastle-Liverpool-Durham DTP. The successful applicant will receive research costs, tuition fees and stipend (£15,009 for 2019-20). The PhD will start in October 2020. Applicants should have, or be expecting to receive, a 2.1 Hons degree (or equivalent) in a relevant subject. EU candidates must have been resident in the UK for 3 years in order to receive full support. Please note, there are 2 stages to the application process.

References

1) Human‐induced pluripotent stem cells generate light responsive retinal organoids with variable and nutrient‐dependent efficiency. Stem Cells 36, no. 10 (2018): 1535-1551.

2) Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids. Biomaterials 199 (2019): 63-75.

3) Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa. Nature communications 9, no. 1 (2018): 4234.

4) Cryoprotectant toxicity: Biochemical mechanisms and functional genomics. Cryobiology 71, no. 1 (2015): 173.

5) A new approach for interpreting random forest models and its application to the biology of ageing. Bioinformatics 34, no. 14 (2018): 2449-2456.

6) Structural connectivity centrality changes mark the path toward Alzheimer's disease. Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring 11 (2019): 98-107.

7) Developmental self-construction and-configuration of functional neocortical neuronal networks. PLoS Comput Biol 10, no. 12 (2014): e1003994

8) Spatial considerations during cryopreservation of a large volume sample. Cryobiology 73, no. 1(2016), 47-54.

9) Physical events occurring during the cryopreservation of immortalized human T cells. PloS ONE 14, no. 5 (2019) e0217304.

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