Molecular Stress in Changing Aquatic Environments (3 PhD Scholarships)

University of Hull

To celebrate the University's research successes, the University of Hull is offering a full-time UK/EU PhD Scholarship or International Fees Bursary for candidates applying for each of the following projects.

Closing date: - Thursday 8th February 2018

Studentships will start on 17th September 2018

For more information, Interested students are encouraged to contact Dr. Katharina Wollenberg Valero (cluster lead): k.wollenberg-valero@hull.ac.uk. Please include a brief description of the project you are interested in, your research interests and experience and a CV in your email.

Summary of Cluster

The University of Hull has strong research ties to the marine environment. To strengthen these ties, the “Molecular Stress in Changing Aquatic Environments” research cluster is seeking applications to begin fully funded 3-year PhD studies in Fall 2018. Our research cluster aims to deconstruct the cause-and effect network between aquatic environmental change (climate change, human-induced pollution) and organismal stress response at the molecular level, and to utilize this information to generate tools and strategies for mitigating the ecosystem effects of global change. We take a systems approach, collaboratively bridging a variety of disciplines (ecology & evolution, toxicology, genomics, proteomics, analytical and computational chemistry, and computational biology) to achieve these goals. Some of our research at Hull has been prominently featured in a recent research outlook in the Oct. 2017 issue of Nature (https://www.nature.com/nature/journal/v550/n7675_supp/full/550S54a.html). We are seeking three PhD students to work in a combination of field, research institute / industrial (aquaculture), and lab settings, and across a range of aquatic vertebrate and invertebrate species. They will develop expertise through in-house access to biotechnology infrastructure (Genome sequencing, HPLC Mass Spec), and the largest supercomputer in the North of England (VIPER). Students will be advised by a team of academics with vibrant research programs, and work closely with collaboration partners at CCmar in Faro, Portugal; Cromarty Mussel farms, in Cromarty Firth, Scotland; the East China Fisheries Research Institute, Shanghai, China; and the British Antarctic Survey. Our strong links with industry partners will ensure that the work will have immediately applicable outcomes and students gain industry-relevant skills and contacts. Students will also be provided with the skills and expertise necessary to succeed in policy making and academia.

Prospective students are expected to be good team players, as their independent projects will jointly contribute to cluster research goals. Ability to pursue independent research, excellent writing, and fluency in English is expected. We encourage applications from students whose backgrounds are traditionally underrepresented in STEM fields. To apply, see information below.

Summary of PhD Project 1 - Universal components of the molecular stress response to changing aquatic environments.

“Environmental change” describes a combination of a variety of stressors (changed temperatures, ocean acidification, human pollutants) affecting aquatic species. However, the molecular-level stress responses of organisms to these diverse stimuli are not yet well characterized. This PhD project will investigate common versus species-specific regulatory, epigenetic and proteomic responses to combined short-term environmental and biotic stressors in different aquatic vertebrates, obtained from laboratory experiments on zebrafish and studies at a sea bass aquaculture research institute (http://www.ccmar.ualg.pt/). Additional collaboration is established with the East China Fisheries Research Institute. Candidate genes and proteins are involved in the oxidative stress response and redox metabolism, as well as in the generation of molecules used in stress communication. Results will be generated using cutting-edge laboratory methods of genomics, epigenetics, and proteomics.

The position is supervised by Dr. Katharina Wollenberg Valero and co-supervised by Dr. Pedro Beltran-Alvarez and Prof. Jeanette Rotchell. Dr. Lesley Morrell will serve as project advisor. It is thematically aligned to the EU-funded “Sullied Sediments” project (http://northsearegion.eu/sullied-sediments/). Applicants should have or are expected to attain at least a 2.1 undergraduate degree in Biology or a related discipline, together with relevant research experience. It is anticipated that the successful applicant will have a 1st class undergraduate degree or Masters level qualification. As this is an interdisciplinary project, ideal candidates will have a background or demonstrated interest in at least one of the main subject areas - e.g. Genetics, Molecular Biology, and be willing to develop skills in the other areas (Toxicology).

Summary of PhD Project 2 - Universal biotic stress compounds and their function under ocean acidification.

“Environmental change” describes a combination of a variety of stressors (changed temperatures, ocean acidification, human pollutants) affecting aquatic species. Recently, it has become evident that such environmental changes negatively affect chemical communication. This project will expose aquatic invertebrates inhabiting cold waters to combined environmental and biotic stressors, including laboratory experiments with polychaete marine ragworm and shore crab, as well as studies on blue mussel in field aquaculture at Cromarty Mussel farms (located within European Marine Science Park, http://www.europeanmarinesciencepark.co.uk/). Additional collaboration is established with the British Antarctic Survey and East China Fisheries Research Institute. Stress compounds obtained from these experiments, will be identified using HPLC and Mass spectrometry at UoH. In order to gain molecular-level insights on the change in function of biotic stress compounds under ocean acidification scenarios, we will use VIPER to compute conformational changes in signalling components, their analytical signatures, and biological consequences.

The position is supervised by Dr. Joerg Hardege and co-supervised by Dr. David Benoit. Further project advisors are Dr. Kevin Welham, Dr. Catherine L. Waller and Dr. Lesley Morrell. Applicants should have at least a 2.1 undergraduate degree in Chemistry, Computational Chemistry, Biochemistry, Molecular Biology or related discipline, together with relevant research experience. It is anticipated that the successful applicant will have a 1st class undergraduate degree or Masters level qualification. As this is an interdisciplinary project, ideal candidates will have a background or demonstrated interest in at least one of the main subject areas and be willing to develop skills in the other areas.

Summary of PhD Project 3 - Modelling organismal responses in aquatic ecosystems.

This project has two key goals. Firstly, to identify universal and species-specific biochemical and genomic networks of the organismal stress response. Secondly to generate computational models to categorise individual stress responses and to assess stress in an aquacultural or environmental setting using biosensors. In order to gain insights into how ecosystem responses to stress can be predicted and its eventual outcomes, a wide collection of data sources will be used for to capture and model the data. These range from environmental stressors, biotic stressors to genetic, phenotypic and ecological data over a range of timescales. This can be achieved by exploiting new advances in artificial intelligence, which can observe huge quantities of data and map them onto a specific output. In addition, this project will utilise the University’s VIPER High Performance Computer (http://hpc.wordpress.hull.ac.uk/). This project will start using simulated parameters for this purpose, and then proceed to refine models using experimental data. By doing this, we will be able to predict future trends, tipping points, and the effects on the ecosystem as a whole. The models will be tested and further calibrated against the experimentally generated data, and to test levels of stress in our industry partner aquaculture facilities.

This position will be supervised by Dr. Alexander Turner and co-supervised by Dr. Katharina Wollenberg Valero. Additionally, Dr. Bryce Beukers-Stewart (University of York) will serve as external advisor. Applicants should have or are expected to attain at least a 2.1 undergraduate degree in Computational Biology, Computer Science, or related discipline, together with relevant research experience and background in Linux programming. It is anticipated that the successful applicant will have a 1st class undergraduate degree or Masters level qualification. As this is an interdisciplinary project, ideal candidates will have a background or demonstrated interest in Computational Science, and be willing to develop skills in Computational Genomics and quantitative Ecology.

To apply for these Scholarships please click on the Apply button below.

http://www2.hull.ac.uk/student/admissions/postgraduate/phd-scholarships.aspx

Full-time UK/EU PhD Scholarships will include fees at the ‘home/EU' student rate and maintenance (£14,553 in 2017/18) for three years, depending on satisfactory progress.

Full-time International Fee PhD Studentships will include full fees at the International student rate for three years, dependent on satisfactory progress.

PhD students at the University of Hull follow modules for research and transferable skills development and gain a Masters level Certificate, or Diploma, in Research Training, in addition to their research degree.

Successful applicants will be informed of the award as soon as possible and by 2nd April 2018 at the latest.

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Type / Role:

PhD

Location(s):

Northern England