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Cell-free DNA (cfDNA) in aquatic environments: exploring an untapped source of genetic information (MOCKUENV19ARIES)

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  • Full or part time
    Prof Thomas Mock
    Prof C Van Oosterhout
    Prof V Moulton
  • 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

DNA outside of cells may account for the largest fraction of total DNA in many environments such as the oceans and their sediments. This cell-free DNA (cfDNA) can either be dissolved, complexed or adsorbed onto particels and minerals and is the product of active or passive release from organisms. Depending on environmental conditions, cfDNA may persist undamaged for thousands of years and therefore provides an archive of genetic information that can be used to reconstruct past changes in biodiversity. Furthermore, cfDNA might be the source of genetic material that quickly spreads through biota via horizontal gene transfer, hence contributing to the speed of adaptation and therefore evolutionary plasticity. Despite the significance of cfDNA, there was no method available to isolate and purify it from environmental samples without contamination by DNA released from cells. To overcome this challenge, we developed a non-disruptive, non-invasive and targeted method for ‘fishing’ cfDNA from water samples based on a modified CRISPR/Cas system developed in our laboratory. The student will use cultures of various different aquatic microbes (e.g. bacteria, microalgae, fungi) which will grow under different condition to see if and when they actively or passively release DNA.

Furthermore, the student will sample natural aquatic environments including lakes, rivers and different oceans to isolate and sequence cell-free phylogenetic marker genes (16/18S) and selected cell-free functional genes (e.g. hydrolases). To compare these results to DNA from inside cells, the student will isolate cells from the same samples, extract their DNA and sequence the same genes targeted for cfDNA. Thus, this study will incept the field of environmental genomics of cfDNA and will provide first insights into the biodiversity of cfDNA vs cell-bound environmental DNA from diverse aquatic environments. Consequently, the student will benfit from working with a cutting-edge method that potentially produces transformative research in a highly collaborative environment as demonstrated by the multidisciplinary nature of the supervisory team.


Person Specification
We are looking for an enthusiastic student with expertise in either of the following areas of research: molecular biology/ecology, evolution, bioinformatics.

Start Date: October 2019
Mode of Study: Full-time or Part-time
Studentship length: 3.5 years
Minimum entry requirement: UK 2:1

Funding Notes

This project has been shortlisted for funding by the ARIES NERC Doctoral Training Partnership. Undertaking a PhD with ARIES will involve attendance at training events.
ARIES is committed to equality & diversity, and inclusion of students of any and all backgrounds.
Applicants from quantitative disciplines with limited environmental science experience may be considered for an additional 3-month stipend to take appropriate advanced-level courses. Usually only UK and EU nationals who have been resident in the UK for 3 years are eligible for a stipend. Shortlisted applicants will be interviewed on 26th/27th February 2019.

Further information: www.aries-dtp.ac.uk or contact us: [Email Address Removed]


References

1. Torti A., Lever M.A., Jørgensen B.B. (2015) Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Marine Genomics (DOI: https://doi.org/10.1016/j.margen.2015.08.007)
2. Aalipour A., Dudley J., Park S.M., Murty S., Chabon J.J., Boyle E.A., Diehn M., Gambhir S.S. (2018) Deactivated CRISPR Associated Protein 9 for Minor-Allele Enrichment in Cell-Free DNA. Clinical Chemistry (DOI: 10.1373/clinchem.2017.278911)
3. Jian P. & Lo D.Y.M. (2016) The long and short of circulating cell-free DNA and ins and outs of molecular diagnostics. Trends in Genetics (DOI:https://doi.org/10.1016/j.tig.2016.03.009)
4. 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)
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)



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