Analysis of pathogen determinants recognized by the hypervariable immune receptor Dscam

   School of Biosciences

   Applications accepted all year round  Competition Funded PhD Project (Students Worldwide)

About the Project

Background: To mount an immune response, host organisms must first recognize the pathogen with which they are infected. The first line of defense against pathogen infection in animals is provided through the innate immune response. Many aspects of this response are conserved in invertebrates making the fruitfly Drosophila with its sophisticated genetic tools a model of choice. The fundamental knowledge obtained about the innate immune response in fruitflies has even been recognized by a Nobel prize.

Recently, the Drosophila Down syndrome cell adhesion molecule (Dscam) gene has been shown to act as pattern recognition receptor in phagocytosis, in addition to its role in neuronal wiring [1, 2]. The Dscam gene generates through alternative splicing over 36’000 different isoforms by inclusion of a single exon in each of the variable regions (Fig 1). Intriguingly, the splicing pattern of Dscam changes upon infection to express isoforms with a higher affinity towards the pathogen in mosquitoes [3]. We anticipate that Dscam splicing is also altered in Drosophila upon pathogen exposure to dramatically increase inclusion of specific isoforms. We currently don’t know the identity of the pathogen molecules recognized by Dscam, or how pathogens impact on adapting Dscam alternative splicing for pathogen recognition and if the same mechanism is also used in the human innate immune response.


1) Identify pathogens and conditions that induce preferential inclusion of single variable exons in Drosophila Dscam

2) Determine pathogen components that are recognized by Dscam and impact on its alternative splicing

3) Determine the mechanism(s) through which pathogens impact on alternative splicing regulation

Project description: From a wide array of pathogens available from the Institute of Microbiology and Infection at the University of Birmingham we will first identify those that induce inclusion of a narrow range of exons in the three variable regions as they are indicative of high affinity interactions. For this analysis we developed highly efficient Molecular Biology tools, including high throughput sequencing for efficient analysis [4].

Once we have obtained a broader choice of pathogens we will identify the bacterial molecules impacting on Dscam alternative splicing and determine if they bind to Dscam using genetic, molecular and biochemical approaches.

Alternative splicing is thought to provide a major mechanism for adaptation of cell function to changing environments, e.g. during infection. The Dscam splicing pattern is initially established in a predefined ratios, but probabilistically at a cellular level [4, 5]. We will establish a GFP-based Dscam alternative splicing reporter to identify the pathways, how pathogens lead to adaptive changes in alternative splicing during an innate immune response.

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Please find additional funding text below. For further funding details, please see the ‘Funding’ section.

The School of Biosciences offers a number of UK Research Council (e.g. BBSRC, NERC) PhD studentships each year. Fully funded research council studentships are normally only available to UK nationals (or EU nationals resident in the UK) but part-funded studentships may be available to EU applicants resident outside of the UK. The deadline for applications for research council studentships is 31 January each year.

Each year we also have a number of fully funded Darwin Trust Scholarships. These are provided by the Darwin Trust of Edinburgh and are for non-UK students wishing to undertake a PhD in the general area of Molecular Microbiology. The deadline for this scheme is also 31 December 2020.

Biological Sciences (4) Computer Science (8) Mathematics (25)

Funding Notes

All applicants should indicate in their applications how they intend to fund their studies. We have a thriving community of international PhD students. For this project fellowships from the Darwin Trust are availabel, but we also encourage applications at any time from students able to find their own funding or who wish to apply for their own funding (e.g. Commonwealth Scholarship, Islamic Development Bank).

The postgraduate funding database provides further information on funding opportunities available View Website and further information is also available on the School of Biosciences website View Website

Too apply please go to and generate an account: View Website


[1] Watson FL et al (2005) Science 309: 1874.
[2] Hemani Y and Soller M (2012) Biochem Soc Trans 40: 804.
[3] Dong Y et al (2006) PLoS Biology 4: e229.
[4] Haussmann IU et al. (2019) NAR 47:1389.
[5] Miura SK et al (2013) Cell 155:1166.

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