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The Honeybee: An Emerging Model Organism for Epigenetics

  • Supervisor: Dr Paul Hurd (primary supervisor), Dr Rob Lowe (secondary supervisor)
  • Deadline: 31st January 2018
  • Funding: QMUL (students worldwide)

About the Project

A molecular and computational PhD project in epigenetics. 

Applications are invited for a fully-funded PhD studentship under the supervision of Dr Hurd (http://www.sbcs.qmul.ac.uk/staff/paulhurd.html) and Dr Lowe (http://www.qmul.ac.uk/blizard/staff/centre-for-genomics-and-child-health/staff/robert-lowe.html), to study the role of epigenetics in honeybee development using state-of-the-art molecular, proteomic, genomic and computational techniques. The aim of this interdisciplinary PhD project is to exploit the unique opportunities of the honeybee system and understand how individual dietary components shape honeybee phenotype through epigenetic mechanisms. 

The Hurd group aims to understand how the environment shapes phenotype through epigenetic mechanisms and to do this we have established the honeybee as an important emerging model organism, since the control of developmental trajectory is a superb paradigm for how an environmental factor (nutrition) interacts with a single genotype to produce multiple phenotypes. This phenotypic polymorphism represents one of the most striking examples of developmental plasticity in any phylum. The Hurd lab was the first to characterise distinct histone post-translational modifications in the honeybee and show caste-specific differences in chromatin structure. Through previous Royal Society funding and current BBSRC and EU Project Grant funding, we have produced experimental models and data that describe aspects of honeybee development, health, genome plasticity, behaviour and nutrition-genome interactions. In order to do this, we use state-of-the-art genomic, computational and molecular tools in combination with hands-on apiculture from our onsite honeybee research hives. 

The proposed PhD project, will use well-established in vitro honeybee rearing techniques, to examine the role of key nutritional components during larval development and determine the mechanisms by which they affect the plasticity of the epigenome. In addition to in vitro honeybee larval feeding and dissection techniques, the student will learn chromatin biology and epigenomic techniques in order to determine the global levels, sites, and patterns of histone modifications in larval tissue from different dietary treatments. Current start-of-the-art molecular techniques will be used in the characterisation of modified nucleosomes. This includes; antibody-based techniques (western blotting and chromatin immunoprecipitation), quantitative real-time PCR for the identification of enriched genomic locations and RNA/DNA purification and manipulation. Furthermore, the student will learn to conduct genome-wide epigenomic mapping experiments, gaining experience in next-generation sequencing methods including RNA-seq and ChIP-seq library preparation. 
Importantly, the student will also learn and perform the analyses of genomic data under the supervision and guidance of Dr Lowe. A long-term collaborator, Dr Lowe has extensive experience in the computational analysis of epigenomic datasets and will train the student in the analysis of ChIP-seq data using standard algorithms and pipelines; consisting of data quality verification, read mapping differential peak calling, and RNA-seq data using read mapping and differential analyses. The proposed project will enable the candidate to develop, learn and integrate computational approaches with unique biology, in order to gain a fundamental understanding of biological data in an economically and ecologically important organism. Crucially, this will greatly enhance the student’s future career prospects, adding them to the limited pool of scientists competent in both ‘wet work’ and in silico analyses. 

This truly multidisciplinary project, in an area that is at the forefront of modern biology, enabling the student to integrate into more than one aspect of the School’s research community. In addition, the Hurd and Lowe labs are founding members and core groups of the QMUL Epigenetics Hub (http://www.qmul.ac.uk/blizard/qmul-epigenetics-hub/). This provides considerable added value and experience for the training of the student. Joint weekly lab meetings are held and attended by all groups, providing a very knowledgeable, stimulating, varied and dynamic environment. Member’s work with epigenomic datasets and mechanistic aspects of epigenetics are comparable to those detailed in this proposal. The student will be expected to give a seminar on their work every four months, which will not only develop their presentation skills but will provide an advisory group of six other group leaders. 

Funding

This position is funded by a QMUL Principal's Postgraduate Research Studentship and is available to EU, UK and International citizens. It will cover tuition fees as well as provide an annual tax-free maintenance allowance for 3 years at Research Councils UK rates (£16,553 in 2017-18). 

Elgibility and Applying

Applications are invited from outstanding candidates with or expecting to receive a first or upper-second class honours degree in an area relevant to the project. An masters degree is desirable, but not essential.

Informal enquiries about the project should be made by email to Dr. Paul Hurd (p.j.hurd@qmul.ac.uk) or Dr Rob Lowe (r.lowe@qmul.ac.uk). For formal applications, please submit an online application before the stated deadline.

Apply Online

References

  • Dickman, M. J., Kucharski, R., Maleszka, R. & Hurd, P. J. Extensive histone post-translational modification in honey bees. Insect Biochemistry and Molecular Biology 43, 125–137 (2013). 
  • Lowe R, Holland ML, Caton PW, Gemma C, Carbajosa G, Danson AF, Carpenter AA, Loche E, Ozanne SE, Rakyan VK. (2016) Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice. Science, 353, 495-498. 
  • Kucharski, R., Maleszka, J., Foret, S. & Maleszka, R. Nutritional Control of Reproductive Status in Honeybees via DNA Methylation. Science 319, 1827–1830 (2008). 
  • Yan, H., Simola, D. F., Bonasio, R., Liebig, J., Berger, S. L. and Reinbery, D. Euscoial insects as emerging models for behavioural epigenetics. Nat. Rev. Genet. 15, 677-688 (2014).
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