Vacancies

There are currently three vacancies for UKRI-funded PhD studentships that will commence September/October 2021:

NERC SUPER DTP – fully funded, click here to apply

Application Deadline = 20th January 2021

An evo-devo approach to invasive biology and resilience to climate change

>> The Evo-Devo Approach

Predicting how species will fare with climate change and understanding invasive biology to aid remediation and are themes intrinsically coupled to evolutionary and developmental processes. In order to predict adaptation potential or ‘evolvability’ the genetic control of a trait, which is developmentally programmed, and its natural variation within and between closely related species must be understood [1,2]. By studying evolutionary and developmental biology together, and comparing results between closely related species, the evo-devo field provides rich examples of generating such understanding. Access to new methods previously constrained to ‘model’ systems, that the evo-devo field is now pioneering in ‘non-model’ groups, holds great promise for environmental research.

>> The System

Crepidula fornicata is invasive to the UK, it is damaging fisheries, habitats and biodiversity and is predicted to have a poleward shift in distribution, into Scottish waters, with oceanic warming. It is also a marine calcifier inhabiting coastal regions vulnerable to climatic changes such as warming and ocean acidification (OA). Recent OA experiments have shown C. fornicata are surprisingly resilient to severely acidified conditions [3]. These findings, in combination with the history of embryological study in this species, makes it an ideal system to probe questions of resilience and adaptation to climate change.

>> The Questions

This studentship will take the powerful evo-devo approach and apply it to questions of major environmental significance. You will compare shell development in C. fornicata to three closely related species within the genus Crepidula to address the following questions:

1.) What developmental mechanisms make C. fornicata invasive compared to its most closely related non-invasive relatives?

2.) What developmental mechanisms regulate the shell traits (strength, microstructures and thickness) that give C. fornicata superior resilience to ocean acidification and climate change compared to its most closely related relatives?

>> The Places

You will be based in the Sleight Lab at the University of Aberdeen, a supportive and dynamic environment where curiosity is encouraged and nurtured. In the Sleight Lab you will be part of a passionate team working with world-leading experts whilst having the mountains and ocean on your doorstep. You will also spend time working with your supervisor at the Institute of Aquaculture at the University of Stirling.

>>The Student

You will be a motivated and genuinely curious student seeking to use evolutionary and developmental biology to tackle problems of global scale – invasive biology and responses to climate change.

Essential skills: you will have a strong degree in a relevant field with particular enthusiasm for evolutionary biology and/or developmental biology. You will have experience conducting independent research and evidence of skills in data analysis.

Desirable skills: experience with marine invertebrate culture, molecular biology (nucleic acid extractions, cloning, PCR, gels etc), immunohistochemistry, bioinformatics and R, field collections and embryology are all desirable, but full training will be provided.

>> The Training and Opportunities

You will receive rigorous training in bioinformatics, histology, molecular biology and advanced imaging. You will have the opportunity to conduct field work to collect specimens and you will be encouraged and supported to apply for international summer schools for advanced training (such as the world-famous Embryology Course at the Marine Biology Laboratory in Woods Hole), and attend international conferences to present your research. You will publish your findings in leading research journals and graduate with a track-record apt for a career in academia, industry or wider fields.

References
[1.] Campbell et al. (2017) Conservation evo-devo: preserving biodiversity by understanding its origins. Trends Ecol Evol.

[2.] Simpson. (2002) Evolution of development in closely related species of flies and worms. Nat Rev Genet.

[3.] Kriefall et al. (2018) Resilience of Crepidula fornicata larvae in the face of severe coastal acidification. Front Mar Sci.

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BBSRC EASTBIO DTP – competition funded, click to apply

Application Deadline = 6th January 2021

How do molluscs build their shells? Deciphering calcium transport mechanisms in shellfish biomineralisation using genome-editing

Marine invertebrates have answered the most fundamental questions in biology. Jellyfish provided the first fluorescent protein, the giant axons of squid taught us nerve signalling is electrical and sea urchins untangled gene regulatory networks controlling early animal development. Biological research benefits from diversity however, current major models include just three species: fly, mouse and zebrafish.

This project seeks to develop CRISPR-Cas9 mediated genome-editing protocols in a novel shellfish model to answer a fundamental question on calcium transport in biomineralisation.

Recent studies have successfully demonstrated CRISPR-Cas9 mediated genome-editing in three mollusc species [1-3]. Using these protocols as a starting-point, you will target candidate calcium transport genes for systematic knock-out in order to resolve a controversial debate in shellfish biomineral production: is calcium transported to the shell through cells (transcellular) or,  in-between cells (paracellular)?

This studentship is targeted at a method development skillset that is highly desirable in industry and academia alike. The tool you will develop – CRISPR-Cas9 mediated genome-editing in shellfish – is desirable to aquaculture and biotechnology as it will facilitate the production of genetically modified (GM) animals with enhanced desirable traits (faster more efficient growth, disease resistance, stronger shells). In the USA AquaBounty’s human consumption approved transgenic salmon can reach market size in 16 months (versus 3 years for wild-type). The production of GM salmon was facilitated by a wealth of research and technologies from non-aquaculture model species (zebrafish) and, to bring this technology to aquaculture shellfish species, a genetically-enabled model system must be developed for molluscs.

The research question you will tackle focusses on calcium transport. Using CRISPR-Cas9 you will systematically disrupt transcellular and paracellular calcium transport in addition to available calcium in the growth medium to test the origin and transport mechanism used in molluscan calcification. You will resolve weather calcium is transported to the shell through cells (transcellular), in-between cells (paracellular) or, if there is not active organismal transport of calcium, and instead calcium is available in high enough concentrations in seawater to precipitate passively.

Owing to the relevance to aquaculture and biotechnology (via the tool development), as well as wider fields such as invasive species remediation (Crepidula fornicata is invasive and damaging in the UK, CRISPR-Cas9 could be used to develop gene-drive remediation technology) there is scope to direct your research to more applied avenues. In order to aid exploration into the wider applications of your tools and knowledge, you will work with an industrial CASE partner – Mikota Ltd.

You will join the Sleight Lab at the University of Aberdeen, a supportive environment where curiosity is encouraged and nurtured. You will receive rigorous training in bioinformatics, molecular biology, animal culture and embryology (including microinjection). In addition, you will be supported to apply for international summer schools for advanced training (such as the world-famous Embryology Course at the Marine Biology Laboratory USA), and attend international conferences to present your research. You will publish your findings in leading research journals and graduate with a track-record apt for a career in academia, industry or wider fields.

References
[1.] Perry KJ & Henry JQ, (2015). CRISPR/Cas9‐mediated genome modification in the mollusc, Crepidula fornicata. Genesis. 53(2), 237-244.
[2.] Crawford K, et al. (2020). Highly efficient knockout of a squid pigmentation gene. Current Biology. 30(17), 3484-3490.
[3.] Abe M & Kuroda R, (2019). The development of CRISPR for a mollusc establishes the formin Lsdia1 as the long-sought gene for snail dextral/sinistral coiling. Development. 146(9).

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NERC SUPER DTP – fully funded, click to apply

Vicky Sleight = Second supervisor. This project is based with Helena Reinardy at the Scottish Association for Marine Science. For enquiries on this one please contact Helena on: Helena.reinardy [at] sams.ac.uk
Application Deadline = January 25th 2021

Multistressor impacts of ocean acidification and warming on regeneration and biomineralisation in coastal sea urchins

Ocean acidification and rising sea surface temperatures at high latitudes
Colder water has a higher capacity for absorbing atmospheric carbon dioxide, and in combination with increased microbial communities in coastal water, there is a greater possibility for northern coastal waters having a reduced pH buffering capacity in future climate change scenarios. This can lead to seasonal undersaturation of aragonite, magnesium calcite (MgCa), and other forms of calcite that organisms utilise to build their calcite skeletons. MgCa calcifiers are therefore vulnerable to changing carbonate chemistry in Scottish temperate latitudes due to the trade off in dissolution at lower pH with skeletal strength. Biomineralising organisms such as MgCa sea urchins inhabiting shallow coastal waters are adapted to this dynamic system with extreme environmental fluctuations, but the mechanisms for coping with extended periods of low pH in combination with elevated temperatures predicted in a warming climate are unknown. In particular, it is unclear if multiple stressors will be linear/additive in affect, or act synergistically to exacerbate challenging conditions predicted in future climate change scenarios.

Echinoderm regeneration and biomineralisation
Echinoderms are renowned for their regenerative abilities, mostly studied in starfish arm regeneration and sea cucumber internal organ evisceration. Sea urchins are a new and promising model for echinoderm regeneration and biomineralisation due to the extensive molecular, developmental, genetic, and genomic tools available, and their environmental importance in ubiquitous coastal ecosystems. Sea urchins have a demonstrated capacity for wound healing and extensive regrowth of MgCa spine structures, outer epidermis, and tube feet muscle and neural tissues, and their open circulatory system allows the immune cells to access all tissues and drive the regeneration processes. The model has also provided the first evidence of involvement of stem cells in the regeneration process in echinoderms. The gene regulatory networks and molecular pathways that guide regeneration and skeletogenesis in echinoderms are well-resolved, we have a good understanding of how urchins build and repair their skeletons, but less is known about how they will cope with the multiple stressors of climate change. The wealth of mechanistic understanding in urchins, from genotype to phenotype, in addition to their ecological importance, makes them the perfect model to probe and predict the biological impacts of multiple climate-stressors.

The project

The studentship will centre on two inter-connected questions: How will sea urchins remineralise and regenerate their tissues in a future multi-stressor environment? And Are the effects of multiple climate-change associated stressors additive, antagonistic, or synergistic? It will utilise the sea urchin regeneration assay to investigate multiple-climatic stressors using experimental conditions of ocean acidification (OA) and warming.

The phenotypic assay has been developed to visualise and quantify spine and tube feet regeneration from a single ambulacral section, by photographing regrowth underwater and analysing the images. In addition to the phenotypic assay, molecular and cellular analyses will be included: targeted gene expression, in-situ hybridisation, and histology on regenerating tube feet and spines, with the potential for complementary transcriptomics and proteomics, representing analyses across levels of biological organisation from genes, cells, and organismal physiology.  Comparison experiments with different species will investigate interspecific variation in stressor susceptibility, and species from different latitudinal distributions will provide insight into cold-adapted or warmer-adapted mechanisms. Elemental ratio analysis of calcium carbonate structures will allow characterisation of magnesium content and provide further insights into possible skeletal trade-offs under OA and elevated temperature conditions.

Environmental multi-stressor studies rely heavily on ecological impacts on community responses, and there is the need to drive the research to encompass molecular analyses, which can elucidate the underpinning mechanisms driving the larger ecological changes. The proposed research will enable a truly interdisciplinary approach, spanning ecology, environmental biology, ecotoxicology, and molecular, biochemical, and biomechanical analyses for a holistic understanding of impacts and effects.

The project is co-supervised by Prof. Michael Burrows (SAMS UHI), Dr Helena Reinardy (SAMS UHI), and Dr Victoria Sleight (University of Aberdeen). The studentship will be based at SAMS UHI which has suitable aquarium facilities with sea urchin stocks and molecular biology, biochemistry, and analytical chemistry laboratories. It is anticipated that 1 year of the studentship will be a placement in the Sleight Laboratory.