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Identifying the pathways that control extra-embryonic cells


   School of Life Sciences

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  Prof K Sampath  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

In many animals, interactions between cells that make the animal – “embryonic progenitors”, and supporting cells that are not a part of the animal – “extra-embryonic cells”, are essential for normal embryonic development. In many mammals, the extra-embryonic tissue i.e. the “placenta” which is derived from interactions between maternal and embryonic cells. Embryos of many fish species form an extra-embryonic structure called the ‘yolk syncytial layer’ (YSL), which is a transient tissue of multiple nuclei in a shared yolk cytoplasm (i.e. ‘syncytium’). Signalling from the YSL to embryonic progenitor cells is crucial for normal fish development and morphogenesis. Although progress has been made in identifying embryonic progenitor differentiation programmes across many organisms, how extra-embryonic tissues develop is not well understood. The key molecular drivers are not known and whether the mechanisms of extra-embryonic tissue formation are related or distinct between humans and other animals (e.g. fish) is not known.

Aim(s) of the project:

1) To identify key molecular pathways altered in zebrafish YSL mutants from recently generated zebrafish datasets in the Sampath laboratory.

2) To perform analysis of available human syncytiotrophoblast transcriptomic datasets and identify pathways shared between zebrafish YSL and human syncytiotrophoblasts.

3) To analyse one pathway in-depth through in vivo perturbations in zebrafish embryos.

For the mini-project, transcriptomic analysis of human versus zebrafish datasets will be performed. In parallel, the student will learn some routine molecular embryology methods (RNA synthesis, whole mount in situ hybridization), and imaging in zebrafish embryos.

Doctoral project: Upon successful identification of shared pathways from transcriptomic analyses, for the doctoral project, one key pathway will be selected for in-depth analysis in vivo in zebrafish embryos through overexpression and knock-down assays, genetics/genome editing, and imaging.

Supervisory arrangement:The experimental work and in particular, zebrafish work will be supervised by Sampath; Imaging and computational analysis will be overseen by Mishima and Hebenstreit. The student will meet with the main supervisor at least 1 x per week, and all supervisors 1x per month (or more frequently, when required) to discuss the project.

BBSRC Strategic Research Priority: Understanding the rules of life  Systems Biology, and Stem Cells, Sustainable Agriculture and Food - Animal Health and Welfare, and Integrated Understanding of Health - Regenerative Biology.

Techniques that will be undertaken during the project:

Molecular biology: Standard molecular biology including DNA and RNA extraction, RNA synthesis, PCR and qRT-PCR

Zebrafish embryonic development and genetics, cell biology techniques including microinjections, genetic crosses, WISH and FISH (in situ hybridization)

Imaging: standard light and fluorescence microscopy, spinning disc confocal microscopy and multiphoton FLIM

Data analysis:

Transcriptomic data analysis - basic command-line scripting, NGS data analysis of zebrafish YSL and human syncytiotrophoblasts, statistical analysis using R, pathway analysis, GO analysis, visualization methods (clustering, heatmaps), multivariate statistics (PCA), comparative genomics

Image analysis: 3D segmentation and image analysis, Scripting with Fiji/ImageJ


Funding Notes

Studentships provide:
Full Tuition fees
A tax free annual stipend for living expenses (in academic year 2022-23 this was £17,668)
A travel / conference budget
A generous consumables budget
Use of a laptop for the duration of the programme.
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