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Developing a marine microalgal system for environmental epigenetics. PhD in Biosciences (NERC GW4 + DTP)

  • Full or part time
  • Application Deadline
    Monday, January 06, 2020
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead Supervisor
Dr Vinod Kumar, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors
Dr Katherine Helliwell, Marine Biology Association; Department of Biosciences, College of Life and Environmental Sciences, University of Exeter
Dr Adam Monier, Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter

Location: University of Exeter, Streatham Campus, Exeter EX4 4QJ

This project is one of a number that are in competition for funding from the NERC GW4+ Doctoral Training Partnership (GW4+ DTP). The GW4+ DTP consists of the GW4 Alliance of research-intensive universities: the University of Bath, University of Bristol, Cardiff University and the University of Exeter plus five unique and prestigious Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology & Hydrology, the Natural History Museum and Plymouth Marine Laboratory. The partnership aims to provide a broad training in the Earth, Environmental and Life sciences, designed to train tomorrow’s leaders in scientific research, business, technology and policy-making. For further details about the programme please see http://nercgw4plus.ac.uk/

For eligible successful applicants, the studentships comprises:

- An stipend for 3.5 years (currently £15,009 p.a. for 2019/20) in line with UK Research and Innovation rates
- Payment of university tuition fees;
- A research budget of £11,000 for an international conference, lab, field and research expenses;
- A training budget of £3,250 for specialist training courses and expenses.
- Travel and accommodation is covered for all compulsory DTP cohort events.
- No course fees for courses run by the DTP

We are currently advertising projects for a total of 10 studentships at the University of Exeter


Project Background: Phenotypic plasticity, the ability to optimise genetically encoded processes to the dynamic environment, defines fitness and adaptation of biological systems in both terrestrial and aquatic environments. This is mainly achieved through reprogramming of genome organization, structure and dynamics. These mechanisms are cornerstones for acclimatization of short-term fluctuations, adaptations to seasonal changes; and is also the major driving force of evolution. This is extremely important in the context of the current challenges faced by the marine ecosystem as a consequence of global climate change and increasing temperatures, which pose a severe threat to the marine ecosystems. Marine phytoplankton, the major contributors of global photosynthesis, play a significant role in biogeochemical processes and primary productivity forming the basis for marine food chain. In addition to the detrimental impact of elevated temperature on their growth and productivity, poleward migration of phytoplankton as a consequence of warming oceans threaten marine biodiversity and economy through reducing food supply for fish and other marine life. Understanding the genetic and epigenetic mechanisms that drive the response and adaptation of marine phytoplankton to dynamic and fluctuating environment is key to understanding the impact of climate change on biosphere and for devising strategies for mitigation.

Project Aims and Methods

The project aims to develop the unicellular eukaryotic phytoplanton Ostreococcus tauri as a system to study environmental epigenetics. O. tauri is widely-distributed marine alga, known to form dramatic blooms in coastal ecosystems. As a genome-sequenced, genetically-tractable model algal species, with a highly compact genome, O. tauri represents an excellent model system to study eukaryote epigenetics. The student will investigate the role of epigenetic mechanisms in governing the cellular responses to dynamic environmental conditions. The first objective will be to determine the global nucleosome occupancy and chromatin architecture as well as to investigate DNA methylation under standard growth conditions. This will be further advanced to study the role of epigenetic processes in environmental responses. As a case study the project will concentrate on temperature and light by studying chromatin dynamics and DNA methylation in the context of environmental reprogramming of gene expression. The primary aim will be to determine the possible role of these mechanisms in transcriptional reprogramming that underpin acclimation and adaptation to changes in temperature and light. The student will use molecular biology approaches including RNA-seq and ChIP-seq in the study. The student will be involved in shaping up the final research trajectory and research focus.

Funding Notes

NERC GW4+ funded studentship available for September 2020 entry. For eligible students, the studentship will provide funding of fees and a stipend which is currently £15,009 per annum for 2019-20.

References

References / Background reading list

1.Epigenetics and the environment: emerging patterns and implications. Nat. Rev. Genet. (2012). 13:97-109.
2.Epigenetics, plasticity and evolution: How do we link epigenetic change to phenotype? J. Exp. Zool. (Mol. Dev. Evol.). (2014). 322B:208–220.
3. Marine Environmental Epigenetics. Annu. Rev. Mar. Sci. (2019). 11:335–68
4. Climate-driven basin-scale decadal oscillations of oceanic phytoplankton. Science (2009). 326: 1253-1256.
5. Climate drives sea change. Science (2007). 315:1084-1085.
6. Ostreococcus tauri: seeing through the genes to the genome. Trends in Genetics (2007). 23:151-154.
7. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Nat. Acad. Sci. (2006) 103: 11647–11652.

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