(3 Phd studentships are currently available. For more details, please see below or contact me via firstname.lastname@example.org)
1) Ribosome profiling to reveal how temperature affects protein synthesis in diatoms (MOCK_U18DTP)
Diatoms are important microalgae with high biotechnological potential. Several aspects of diatom physiology including the silica frustule, lipid storage and photosynthesis are being applied to biotechnology. Areas of interest include nanotechnology, drug delivery, biofuels, solar capture and bioactive compounds. Given the ecological importance of diatoms and their applications for biotechnology, several different genetic tools have recently been developed in the Mock lab for the model diatom Thalassiosira pseudonana such as genome editing by CRISPR/Cas9 and ribosome profiling. The application of both tools in this project will enable the PhD student to obtain fundamental insights into how temperature affects translation in the model diatom Thalassiosira pseudonana. Since there are no data available yet on how temperature regulates protein synthesis in any algae on a mechanistic level, we suggest to apply ribosome profiling to provide fundamental insights into if and how temperature affects a) the location of translation start sites, b) the density of ribosomes on messenger RNAs and c) the speed of translating ribosomes. Furthermore, the role of codon usage and its impact on tRNA evolution in relation to the recently discovered tRNA-derived small non-coding RNAs for protein synthesis in diatoms will be investigated using the genome editing tool CRISPR/Cas in combination with ribosome profiling. We aim to modify the genetic code in T. pseudonana in order to obtain first insights into codon usage, tRNA expression and the role of tRNA-derived non-coding RNAs. Data from this project will lay the foundation for synthetic biology with diatoms as translation underpins the synthesis of various different enzymes and materials (e.g. silica) used in algal biotechnology.
2) Genome Editing for the Exploration of Biotechnological Applications and Evolutionary Potential of Microalgae (MOCK_UENV18EE)
Microalgae contribute more than 25% of global annual carbon fixation, which is equal to the carbon fixation of all tropical rainforests combined. Furthermore, microalgae are at the intersection of many different disciplines because of their interesting biology rooted in complex evolution and their key position in aquatic environments where they underpin global biogeochemical cycles and food webs.
Although many decades of research have elucidated the evolutionary forces underpinning their biology and ecology, only recently our group provided the first evidence of a previously unknown mechanism of Environmental Dependent Differential Allelic Expression discovered in a marine diatom. This evolutionary innovation seems to play a key role for how algae adapt to extreme fluctuating environments. In simple terms, allelic variants of the same genetic locus have diverged under Darwinian selection, facilitating adaptations to sometimes diametrically different environments. Evidence of this phenomenon is found throughout many microalgal communities, as well as other species with vast population sizes in the marine environment.
- Single cell DNA and allele-specific RNA-seq with model microalgae to identify gain or loss of heterozygosity and copy number variation, and assess the evolutionary forces underpinning allelic divergence and differential expression.
- Selected allelic variants of single genes and entire metabolic pathways will be subjected to editing using CRISPR/Cas.
- Testing the ecological significance and biotechnological potential of selected alleles using phenomics.
The student will receive training at the crossroads of functional molecular biology, population genomics and bioinformatics. The work extends to environmental biotechnology. Training will take place in UEA’s School of Environmental Sciences and the Computational Biology Laboratories at UEA and the Earlham Institute. Thus, training will be highly integrative and based on cutting edge tools. Specific training will be provided in how to work collaboratively, how to prioritize and how to organize and structure a complex work flow.
This project has been shortlisted for funding by the EnvEast NERC Doctoral Training Partnership, comprising the Universities of East Anglia, Essex and Kent, with over twenty other research partners. Undertaking a PhD with the EnvEast DTP will involve attendance at mandatory training events throughout the course of the PhD.
Shortlisted applicants will be interviewed on 12/13 February 2018.
For further information, please visit www.enveast.ac.uk/apply
3) Population Genomics and the Adaptive Evolution of Phytoplankton in Changing Oceans (VAN-OOSTERHOUT_UENV18EE)
Recent research by our group (Mock et al. (2017) Nature 541, 536-540) discovered a previously unknown evolutionary mechanism in the diatom (Fragilariopsis cylindrus) that enables it to thrive in the extreme polar environment. This species can survive polar winters while frozen in the sea ice, and it can form blooms when the conditions turn favourable again in the spring. We discovered F. cylindrus can rapidly adapt to these dramatically changing environmental conditions by the up- and down-regulation of alleles at many genes (~3,500). The alleles appear to have diverged from each other under Darwinian selection, so that each allelic copy is adapted to a particular environmental condition. Importantly, a current large algal genome project on Skeletonema marinoi also shows high levels of divergence of alleles, suggesting that this previously unknown evolutionary process is much more widespread.
The principal objective of this PhD project is to understand how diatoms can respond to global environmental change.
This PhD studentship will investigate the signature of natural selection in multiple genomes of S. marinoi that have been (and are currently being) sequenced. These samples are from a sediment core from the Loviisa nuclear power-plant in Finland (and a nearby control site). The sediment core samples (1980–2000) enable us to “look back into time” over a time period during which the local seawater temperature rapidly increased (from the cooling water of the power-plant). The student will conduct population genomic analyses using bioinformatics to understand how diatoms adapt to environmental change.
The student will part of a large research group and will employ and develop population genomic software to enable the processing and interpretation of these “big data”. The samples are provided by our Swedish collaborators (Prof Anna Godhe) and enable us to analyse adaptive evolution caused by environmental warming. The student will visit the lab in Sweden three times during this project.
We are looking for a highly-motivated student with good understanding of evolution and population genetics, who has some experience with bioinformatics.
This project has been shortlisted for funding by the EnvEast NERC Doctoral Training Partnership, comprising the Universities of East Anglia, Essex and Kent, with over twenty other research partners. Undertaking a PhD with the EnvEast DTP will involve attendance at mandatory training events throughout the course of the PhD.Shortlisted applicants will be interviewed on 12/13 February 2018.
For further information, please visit www.enveast.ac.uk/apply