PhD Projects

This project will focus on the natural variability of shell thickness and structure from different geographic areas, testing the hypothesis that the calcareous shell is more difficult to secrete and also to maintain in colder waters. We will also study museum collections. This historic data will provide comparisons allowing us to address any evolutionary scale changes in shell structure and composition in the last 4 million years, during which there were considerable changes in the Earth’s climate. 

PhD student: Luca Telesca

PhD registered at: University of Cambridge

PhD supervisors: Elizabeth Harper and Lloyd Peck

Mobility Placement: Museum National d’Histoire Naturelle de Paris and University of Bielefeld.

Remarkably little is currently known about the pan-European population genetic structure of our chosen species. Many studies to date have focused on highly restricted geographic areas, using a small number of markers. We will exploit state-of-the-art methods to develop a highly detailed European map of the population structure of these 4 species and identify genes associated with particular environmental conditions. In addition, there will be a further related project to identify the population structure in the UK Biodiversity target species Ostrea edulis for conservation purposes and also identification of potential broodstock populations for the emerging Ostrea fishery.

PhD student: David Vendrami

PhD registered at: University of Bielefeld

PhD supervisors: Joseph Hoffman and Elizabeth Harper

Mobility Placement: University of Edinburgh, British Antarctic Survey, University of Cambridge

The blue mussel M. edulis is a highly important commercial species that has been experimentally shown to be highly sensitive to decreased pH. The Scottish sea lochs provide a natural experimental system with access to a range of contrasting habitats with varying degrees of naturally acidified and diluted seawater. We will study the effect of these environmental conditions on shell production both in wild and farmed animals alongside laboratory manipulation. We will also carry out high resolution population genetic analyses to identify genes associated with adaptation to the different environments.

PhD student: Kati Michalek

PhD registered at: The University of the Highlands and Islands with the student based at The Scottish Association of Marine Sciences

PhD supervisors: Kim Last and Tom Wilding

Mobility Placement: University of Bielefeld and the British Antarctic Survey

The aim of this project is to gain a better understanding of the energy allocation decisions at the organismal level and the relative importance of various environmental stressors. The costs of calcification will be determined for the mussels M. edulis / trossulus and their hybrids, the clam M. arenaria and the oyster Crassostrea gigas utilizing laboratory and field experiments. Identical experiments will be carried out in Sweden (low salinity, high pCO2 variability) and the Baltic (high salinity, low pCO2 variability) under both winter and summer conditions to identify seasonal differences.

PhD student: Trystan Sanders

PhD registered at: University of Kiel

PhD supervisors: Frank Melzner and Sam Dupont

Mobility Placement: University of Gothenburg

This project will use shell damage-repair experiments and Next Generation transcriptional profiling to identify genes associated with calcification in molluscs, specifically concentrating on mantle tissue. Analyses will include biological annotation, in silico generation of biomineralisation pathways and  gene network analyses. Rigorous statistical analyses will be used in a comparative approach to identify mollusc-specific repair processes and those associated with aragonite and calcite pathways.

PhD student: Teja Yarra

PhD registered at: The University of Edinburgh with student based at the British Antarctic Survey

PhD supervisors: Melody Clark and Karim Gharbi

Mobility Placement: Scottish Association of Marine sciences, University of Edinburgh  and The Centre for Marine Sciences.

This project will use proteomics techniques to identify shell matrix proteins. The aim is to identify a wide range of gene families that are integral to calcification across the 4 mollusc species of interest, specifically those key proteins that control shell formation. Quantitative proteomics experiments will also be carried out on shell samples obtained from organisms maintained under different environmental conditions and shell repair experiments to highlight the effect of environmental stress on the biomineralisation processes via protein regulation.

PhD student: Jaison Arivalagan

PhD registered at: Université Pierre et Marie Curie (UPMC), student based at Museum National d’Histoire Naturelle de Paris

PhD supervisors: Sophie Berland and Arul Marie

Mobility Placement: The British Antarctic Survey, The University of Edinburgh, The University of Gothenburg and The Centre for Marine Sciences.

Little attention has been given to factors regulating shell formation. Hence, the aim of this project is to explore sensing and regulatory mechanisms associated with shell formation and repair and establish how changes in the external environment modify mantle physiology causing functional changes and modifications in shell composition and thickness. This will be achieved by: In silico analysis of publicly available and network sequence data to identify candidate genes, mapping the expression of these genes in mantle tissue using immunohistocytochemistry, conducting reverse pharmacology assays and ligand binding assays under different environmental conditions.

PhD student: Nadege Bjärnmark

PhD registered at: The University of the Algarve with the student based at The Centre for Marine Sciences

PhD supervisors: Kristina Snuttan Sundell and Deborah Power

Mobility Placement: The University of Gothenburg, The British Antarctic Survey and The University of Edinburgh

In order to gain in-depth knowledge on the transport mechanisms of the building components necessary for shell formation as well as on the regulation of ion transport processes direct studies on transporting epithelia is crucial. This project will use an advanced Ussing chamber system, which has been specifically been designed to study transport mechanisms and barrier functions in an intact, healthy and metabolically active epithelia and will characterise the transepithelial transport routes for inorganic ions essential for shell formation and their regulation of these routes.

PhD student: Kirsikka Sillanpaa

PhD registered at: The University of Gothenburg

PhD supervisors: Kristina Snuttan Sundell and Deborah Power

Mobility Placement: GEOMAR Helmholtz Centre for Ocean Research, The Centre for Marine sciences and The University of Edinburgh

Recent evidence suggests that the amorphous precursor phase of CaCO3 (ACC) is of importance in mollusc calcification. However, nothing is known about the cellular transport processes that enable intravesicular concentration of calcium and inorganic carbon in marine molluscs, or about the interactions of calcification with cellular pH and ion homeostasis.  Within this project we will investigate single cell approaches, focussing on the interaction between pH homeostatis and intravesicular ACC formation and  cellular trafficking of ACC vesicles.

PhD student: Kirti Ramesh

PhD registered at: The University of Kiel

PhD supervisors: Frank Melzner and Kristina Snuttan Sundell

Mobility Placement: University of Gothenburg and The University of Edinburgh.

Genetic breeding experiments will be performed on populations with different environmental histories to allow us to understand the origin of any observed variances. Animals will be assessed both from the natural environment and also those maintained under experimentally manipulated future climate change scenarios of temperature and pH. Daily survival of larvae, growth rate and settlement success will be measured to settlement and juvenile survival and growth followed over a 3 month period. It is expected that certain cultures will be more resilient than others and selected lines will be isolated and their potential as future aquaculture broodstock will be evaluated.

PhD student: Alexander Ventura

PhD registered at: The University of Gothenburg

PhD supervisors: Frank Melzner and Sam Dupont

Mobility Placement: GEOMAR Helmholtz Centre for Ocean Research and the Scottish Association of Marine Sciences

Support, Policy and Business

In addition to the PhD positions, 4 junior post-doctoral positions (Network Fellows) will be appointed to short-term posts within the network. They will be required to provide either a centralised resource or an overview of the applications of CACHE research. Therefore, although they will be based in a host institute, because of the requirement to interact with all partners, they will not have a fixed mobility period with any one institute.

The network will generate considerable amounts of sequence data and this Fellow will provide a centralised resource to collate such data, work with the PhD students to ensure they can access the data they need, help them with the analyses and engage in bioinformatics training activities. In addition they will prepare global analyses of the network data to maximise visibility of these data to the wider community.

Network Fellow: Carlos Caurcel

22 month post

Host Partner: University of Edinburgh.

This Fellow will review the data generated by the ITN partners, in the context of our existing understanding of the shellfish culture industry, to make qualitative predictions on the likely direction of the industry and the broader ecological consequences and prepare a report for stakeholders and industry.

Network Fellow: TBA

12 month post starting in month 36

Host Partner: The Scottish Association of Marine Sciences.

In the context of climate change and Peak oil, materials scientists are increasingly expected to propose energetically cheap and strong materials. Biomineralization is proposed as a potential answer to that challenge in various sectors, including industries producing globally large volumes, like the building and cement industries. The task of this fellow will be to evaluate the gap between the fundamental research and its potential development into technological applications.

Network Fellow: Dr Yan Wang-Duffort

24 month post

Host Partner: Royal Belgian Institute of Natural Sciences.

This Fellow will explore the existing and potential uses of the shells as by-products of aquaculture. The Fellow will first review and evaluate the use and the quantities of available discarded shells volumes left by the European aquaculture industry. Various uses as a source of biomaterials will be explored, such as raw material for building materials, insulation or even bone implants. They will also study the potential of seashell use to generate carbon credits, as they potentially represent fixed CO2 if used in a perennial structure.

Network Fellow: Dr James Morris

24 month post

Host Partner: Royal Belgian Institute of Natural Sciences.