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Molecular underpinnings of adaptive evolution of diatoms in polar oceans (MOCKTU18LEV)

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  • Full or part time
    Prof Thomas Mock
    Prof C Van Oosterhout
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

The overarching aim of this PhD studentship is to apply CRISPR-Cas mediated genome editing in the polar diatom Fragilariopsis cylindrus to identify (epi)genes and their alleles, which underpin the evolution and adaptation of this model polar phytoplankton species. Recent and ongoing research has identified a number of genes and allelic variants in polar diatoms that are highly expressed under stressful environmental conditions (Mock et al. 2017 Nature, DOI: 10.1038/nature20803 https://www.nature.com/articles/nature20803). We hypothesise that these genetic variants enable phenotypic plasticity and an adaptive response to changing conditions due to global warming). Our group pioneered the application of CRISPR-Cas for genome editing in diatoms. The student will extend genome editing to polar eukaryotic organisms, which have not been subjected to genome editing yet. The student will be working together with an experienced postdoctoral research associate (PDRA), who developed the CRISPR-Cas protocol for diatoms and the protocol to transform F. cylindrus. The student will knockout genes identified by the PDRA through comparative genomics and experimental evolution. The knockout cell lines will be subjected to competition experiments with wild-type cells. Furthermore, the student will physiologically and biochemically characterize the mutant cell lines according to the predicted functions of the mutated genes. Thus, this studentship is at the cutting edge of polar research as it will a) enable to apply the latest genome editing tools to address fundamental questions about the evolution of key polar primary producers and their ability to respond to a rapidly changing polar environment, and b) it will go beyond mere statistical inference by providing an experimental validation of the cause-effect relationship between (epi)genes and adaptation to environmental change in one of the most threatened ecosystems on our planet.

For more information on the supervisor for this project, please go here: http://mocklab.com/people/

The type of programme: PhD

The start date of the project: April 2018

The mode of study: full-time

First degree subjects: Biological Sciences, including medicine. Minimum standard entry requirement is 2:1.

Funding Notes

This studentship is funded by the Leverhulme for three years. Funding is available to UK/EU applicants and comprises of payment of tuition fees and a maintenance stipend at RCUK rates. Overseas applicants may apply but they are required to pay the difference between home/EU and overseas tuition fees. (in 2017/18 the difference is £13,805 but fees are subject to an annual increase)

References

1) Belshaw N., Grouneva I., Aram L., Gal A., Hopes A., Mock T. (2017) Efficient CRISPR/Cas-mediated homologous recombination in the model diatom Thalassiosira pseudonana. bioRxiv
(https://www.biorxiv.org/content/early/2017/11/09/215582)
2) Hopes A., Nekrasov V., Belshaw N., Grouneva I., Kamoun S., Mock T. (2017) Genome editing in diatoms using CRISPR-Cas to induce precise bi-allelic deletions. Bio-Protocol
(DOI: 10.21769/BioProtoc.2625, http://www.bio-protocol.org/e2625)
3) Hopes A., Nekrasov V., Kamoun S., Mock T. (2016) Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana. Plant Methods
(DOI: 10.1186/s13007-016-0148-0, https://plantmethods.biomedcentral.com/articles/10.1186/s13007-016-0148-0)
4) Paajanen P., Strauss J., van Oosterhout C., McMullan M., Clark D.M., Mock T. (2017) Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus. Scientific Data
(DOI: 10.33810.1038/sdata.2017.149, https://www.nature.com/articles/sdata2017149)
5) Mock T., Otillar R.P., Strauss J., McMullan M., Paajanen P., Schmutz J., Salamov A., Sanges R., Toseland A., Ward B.J., Allen A.E., Dupont C.L., Frickenhaus S., Maumus F., Veluchamy A., Wu T., Barry K.W., Falciatore A., Ferrante M.I., Fortunato A.E., Glöckner G., Gruber A., Hipkin R., Janech M.G., Kroth P.G., Leese F., Lindquist E.A., Lyon B.R., Martin J., Mayer C., Parker M., Quesneville H., Raymond J.A., Uhlig C., Valas R.E., Valentin K.U. Worden A.Z., Armbrust E.V., Clark M.D., Bowler C., Green B.R. Moulton V., Van Oosterhout C., Grigoriev I.V. (2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature
(DOI: 10.1038/nature20803, https://www.nature.com/articles/nature20803)


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