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Single cell transcriptomics for microbiomics approaches

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  • Full or part time
    Dr P Varga-Weisz
    Dr R Zabet
  • 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

Overview
The microbiome has emerged as an important factor in health and disease, affecting aspects such as obesity, metabolic disease, cancer and, potentially, brain health.
The microbiome composition is highly dynamic and affected by nutrition, co-housing, age and life style. The microbiome is an important factor in inflammatory bowel diseases (IBD), conditions that are quite prevalent (one in 250 of the population) can be severe and cannot be cured.
IBD is promoted by colitogenic bacteria, some of these, such as members of the TM7 phylum, are not well understood. Therefore, technologies that can provide new insights into microbiome diversity are much needed. Microbiomics is most commonly performed by 16S sequencing. However, this will not discover functional aspects of diversity that are likely important.
We propose to develop single cell transcriptomics for microbiomics approaches, building on recent progress on drop based sequencing technology.
Single cell transcriptomic approaches on bacteria provide many challenges, such as low abundance of transcripts and efficient amplification of material, but some of these have recently been addressed (“Single prokaryotic cell isolation and total transcript amplification protocol for transcriptomic analysis”, Kang et al., Nature Protocols volume 10, pages 974–984, 2015).
Combining such breakthroughs with drop technologies and next generation sequencing will provide further breakthroughs. We are at the right moment in time to further invest in the development of such technologies.


The University of Essex
The University of Essex is University of the Year - Times Higher Education (THE) Awards 2018. In the recent Research Excellence Framework 77% of research at the University of Essex research is ’world leading’ or ’internationally excellent’ (REF 2014).We offer world-class supervision and training opportunities and our research students work at the heart of an internationally-acknowledged and well-connected research community. In the 2013 Postgraduate Research Experience Survey, 84% of respondents said that they were satisfied with the quality of their research degree. At Essex we win awards for our pioneering student support schemes. We are the most recent winners of the prestigious Times Higher Education award for Outstanding Support for Students. Essex is a genuine global community. With more than 130 countries represented within our student body, and 40% of our students from overseas, we are one of the most internationally-diverse universities in the UK.

Funding Notes

Funding
The award consists of a full Home/EU fee waiver or equivalent fee discount for overseas students (further fee details), a doctoral stipend equivalent to the Research Councils UK National Minimum Doctoral Stipend (£15,009 in 2019-20), plus £2,500 training bursary via Proficio funding, which may be used to cover the cost of advanced skills training including conference attendance and travel.

You are encouraged to contact the supervisors before application: [Email Address Removed] or [Email Address Removed] If you have any queries with the online application process, please contact [Email Address Removed]

How good is research at University of Essex in Biological Sciences?

FTE Category A staff submitted: 23.00

Research output data provided by the Research Excellence Framework (REF)

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