Research Opportunities

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

3 Year, full-time PhD studentship

Project title: Museum genomics for understanding species decline and extinction
Eligibility: Home UK/EU applicants who must be permanently resident in UK/EU

Closing date: 22 April 2020

Start date: September 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2020/2021 £15,285)

University fees and bench fees at the Home/EU rate will be met by the University for the 3 years of the Studentship.

Supervisors: Dr. Saad Arif, Prof. Tim Shreeve, Dr. Michael Gerth, Dr. Maria DS Nunes

Project:

Background and aims:

Genetic diversity is part of biodiversity. The current biodiversity crisis is not only resulting in loss of species but rapid erosion of genetic diversity within species, increasing the likelihood of extinction. Advances in sequencing technologies, including those that can be applied to historic specimens, allows for charting genome-wide changes in genetic diversity through time.  Additionally, high-resolution genomic data can identify specific genetic changes associated with species declines. Butterfly species are particularly responsive to changes in the environment and offer an excellent opportunity to understand the genomic basis of the decline and local extinction in general. This project contributes to the integration of genomic studies into conservation programmes, using two butterfly case studies (Black-veined white and Wood white) with contrasting extinction process pathways.

Methodology and training:

In this project the PhD student will collaborate with the Oxford University Museum of Natural History (OUMNH), Natural History Museum (NHM London) and other museums across the UK and Europe to obtain a temporally-spaced sampling of Black-veined white and Wood white specimens. Some field work, in the UK and Europe, for collecting specimens and some ecological data from extant populations will also be required. Molecular work will involve DNA extraction from fresh and 100-200 year old dried museum samples. The student will use whole genomic data and/or reduced representation genomic data (e.g. HyRAD) to understand the genomic consequences of species’ decline and local extinction and the implications for conservation and reintroduction. Training in molecular work, bioinformatics and population genomics will be provided by the Centre of Functional Genomics at Oxford Brookes University.  
For further information contact Dr Saad Arif: sarif@brookes.ac.ukor Prof. Tim Shreeve: tgshreeve@brookes.ac.uk

Requirements:
Applicants should have  a first or upper second class honours degree from a Higher Education Institution in the UK or acceptable equivalent qualification in Biology, Ecology, Evolution, Conservation or related  discipline (excellent communication and quantitative skills are essential). A strong interest in one or more of the following: bioinformatics, genomics and conservation is essential. EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.  

How to apply:
Applications should be sent to hlsapplications@brookes.ac.uk and should include the following form

Application form »

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

4 Year, full-time iCASE studentship

Project title: Studying full length mRNAs at single-cell resolution

Eligibility: Home UK/EU applicants who must meet BBSRC's eligibility requirements

Closing date: 30 April 2020

Start date: September 2020

Bursary p.a.: Bursary of £15,285 for academic year 2020/21

University fees and bench fees at the Home/EU rate will be met by the University for the 4 years of the Studentship.

Supervisors: Dr Jordi Solana

Project:

Biology is undergoing a revolution with the introduction of single-cell methods. The cell is the fundamental unit of biological systems. The most common of these techniques, single-cell transcriptomics allows obtaining sequences from thousands of mRNAs in tens (or hundreds) of thousands of individual cells. The mRNAs of each cell are indicative of their cell type as they express cell type markers. Being able to study thousands of them individually unlocks the reconstruction of the dynamics that were formerly blended into tissue samples. Using this method in the planarian Schmidtea mediterranea, we were able to reconstruct the differentiation trajectories from pluripotent stem cells into dozens of mature cell types in a single differentiation tree.

However, most single-cell transcriptomic methods just allow sequencing of the 3’UTR ends of mRNAs. This prevents the analysis of many important cellular processes such as alternative splicing, RNA editing and alternative polyadenylation. Developing a method that can profile full-length mRNAs with single-cell resolution is an urgent need to establish the roles of those processes in cell differentiation, development and disease.

To establish this method, the Solana laboratory is teaming up with Oxford Nanopore Technologies (ONT). The Solana laboratory has expertise in single-cell transcriptomics. ONT is a world leader in long read RNA and DNA sequencing. The student will exploit and combine both of these technologies to develop a method that can profile mRNAs at full-length resolution in thousands of single cells. Once established, the student will use this method to study the role of alternative splicing, RNA editing and alternative polyadenylation in planarian stem cell differentiation. This will reveal new insights in stem cell biology and animal regeneration.
For further information contact Dr Jordi Solana jsolana@brookes.ac.uk

Requirements:
Attributes of suitable applicants:
The candidate should have a degree from a Higher Education Institution in the UK or acceptable equivalent qualification in biology or related subject. This project is supported through the Oxford Interdisciplinary Bioscience Doctoral Training Partnership (DTP) studentship programme. The student recruited to this project will join a cohort of students enrolled in the DTP’s interdisciplinary training programme, and will be able to take full advantage of the training and networking opportunities available through the DTP. For further details please  visit  http://www.biodtp.ox.ac.uk. NOTE: This student will be enrolled at Oxford Brookes University.

EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.

UK/EU candidates for awards must have a relevant connection with the United Kingdom. 

A relevant connection may be established if:

• The candidate has been ordinarily resident in the UK, meaning there are no restrictions on how long they can stay, and;
• has been 'ordinarily resident' in the UK for at least three years prior to the start of the Studentship grant, and;
• has not been residing in the UK wholly or mainly for the purpose of full-time education.

(This does not apply to UK nationals and EU nationals who were ordinarily resident in the
EU immediately before the period of full-time education).

Funding Notes

This project is funded for four years by the Biotechnology and Biological Sciences Research Council BBSRC. BBSRC eligibility criteria apply (Annex B,  View Website). EU nationals who do not meet BBSRC residence criteria are encouraged to contact the programme administrator to check their eligibility for BBSRC funding before submitting a formal application. Successful students will receive a stipend of no less than the standard RCUK stipend rate, bursary is £15,285 for academic year 2020/21

How to apply:
Applications should be sent to hlsapplications@brookes.ac.uk and should include the following form

Application form »

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences 

1 Year, full-time, self-funded Master by Research Project

Project title: Defining mechanisms underlying nephrotic syndrome.

Eligibility: Home UK/EU applicants who must be permanently resident in UK/EU

Closing date: 31 July 2020

Start date: September 2020 

There is no bursary or stipend attached to this project. The applicant is required to self-fund fees and living costs.

Supervisors: Dr Paul K Potter and Dr Alison Forhead
Project:

We have identified a novel model of Nephrotic Syndrome, a chronic renal disease, resulting from a point mutation in laminin alpha 5. This protein has recently been associated with chronic renal disease in patients and hence our mutant may provide insight into the pathogenesis of this important disease.

My interests lie in the mechanisms underlying chronic and age-relates disease and I have identified a number of mutant mouse lines with novel links between alleles and late onset phenotypes. Among these is the first model of a chronic renal disease, nephrotic syndrome, resulting from a mutation in the gene encoding the extracellular matrix protein, laminin alpha 5 (LAMA5). We have characterised the disease progression and identified proteomic changes in the kidney resulting from disease, but have yet to clearly identify a mechanism. We have eliminated some possibilities and have preliminary evidence that disease is not a result of ER stress caused by misfolded mutant protein. I wish to confirm these preliminary data and also investigate the effect of the mutation on glomerular basement membrane (GBM) structure as a possible mechanism. I also wish to confirm some of the proteomic findings. The fact that the phenotype can be ameliorated by genetic background suggest these are pathways that may lead to novel drug-based interventions.

The project will provide training in a number of laboratory techniques. To confirm the lack of ER stress we will employ mutant constructs that have already been generated and transfect them into a cell line containing the partner chains of LAMA5. Mutant and wild type chains will be transfected, and a positive control for ER stress, Western blots and immunofluorescence (IF) will then be used to determine the presence of ER stress in these cells and post mortem samples. To assess the effect of the mutation on the GBM structure we will employ immunofluorescence and scanning TEM/SEM analysis. Other techniques may include, PCR, cloning, Western Blotting and immunofluorescence.

For further information contact Dr Paul K Potter: ppotter@brookes.ac.uk

Requirements:
Applicants should have a first or upper second class honours degree in a relevant area of biology or a related subject from a Higher Education Institution in the UK or acceptable equivalent qualification. EU Applicants must have a valid IELTS Academic test certificate (or equivalent) with an overall minimum score of 7.0 and no score below 6.0 issued in the last 2 years by an approved test centre.  

How to apply:
Applications should be sent to hlsapplications@brookes.ac.uk and should include the following form

Application form »

If you wish to apply to the DTP via Oxford Brookes University please complete the Faculty of Health and Life Sciences PhD Research Studentship Application Form.

Application and CV must be emailed to the addresses shown on the application form.

The Oxford Interdisciplinary Bioscience Doctoral Training Partnership (DTP) programme is a 4-year DPhil*/PhD programme that aims to equip a new generation of researchers with the skills and knowledge needed to tackle the most important challenges in bioscience research.

We provide an innovative, individually-tailored training programme that includes taught courses in interdisciplinary skills and the opportunity for students to undertake two exploratory research projects with prospective supervisors in their first year before choosing their main 3-year research project. Students also undertake a 12-week professional internship to gain direct experience of the areas of work into which they can apply their skills.

Oxford Brookes University is offering a place on the BBSRC funded DTP within the Department of Biological & Medical Sciences in the areas of plant cell biology, virology, insect and spider development, mammalian cell biology, molecular biology, metabolic modelling/systems biology, parasitology and bioimaging. The successful candidate will enjoy access to our state of the art facilities, including newly refurbished laboratories and bioimaging suite.

In addition to their choice of PhD project at Oxford Brookes University, the student will be able to undertake their exploratory research projects at any of the seven world-class research institutions that make up the DTP:

• University of Oxford, coordinators of the DTP
• Oxford Brookes University, a partner with the University of Oxford in developing regional excellence in bioscience research
• Pirbright Institute, the UK’s national centre of research into viral diseases of livestock and viruses that spread from animals to humans
• Diamond Light Source, the UK’s national synchrotron science facility
• ISIS, which provides national capabilities for neutron science
• STFC Central Laser Facility, which provides state-of-the-art laser technology for experiments in physics, chemistry and biology
• The Research Complex at Harwell (RCaH), is a multidisciplinary laboratory specialising in research using Diamond, ISIS and the Central Laser Facility at Harwell

The programme is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) with additional support from within the Partnership. Please see below for potential supervisors and instructions on how to apply.

We have many projects available which can be taken as a short term (3-month) rotation or a full PhD project. The following supervisors are offering exciting projects; for further information click on the link to visit their lab website.

Alison Forhead - Endocrine regulation during fetal growth

Alistair McGregor - Evolution of animal development and morphology

Andy Jones - Functional studies of insect nicotinic acetylcholine receptors.

Barbara Jennings - Investigating the mechanism of Groucho-mediated repression

Casper Breuker - Butterfly Ecological Evolutionary Developmental Biology

Maria Santos-Nunes - Phenotypic evolution and adaptation

Dave Carter - Extracellular Vesicle biology

David Meredith - Membrane Transporter function

Dianne Newbury - The Genetics of Language Disorders

Hee-Jeon Hong - Microbial genetics and antibiotic resistance

Isabel Bermudez - Molecular Neuropharmacology

Jack Sunter - Understanding cell morphogenesis in Leishmania

Jon Lees - Deep Learning for protein function prediction

Jordi Solana - The use of single-cell RNA-seq to identify stem cells

Katja Graumann - Nuclear envelope in plants

Linda King - Molecular Virology

Maike Kittelmann - Synapse formation in neurons

Mark Poolman - Cell systems modelling

Ravinder Kanda - The Role of Endogenous Retroviruses in Immunity

Ryan Pink - Cell signalling

Saad Arif - Evolutionary Genetics and Genomics

Sue Vaughan - Cell Biology of Trypanosomes

Verena Kriechbaumer - Endoplasmic reticulum structure and function

Deadline for receipt of applications for the first round is 12 noon on 24 January 2020.

Eligibility criteria: Only open to UK applicants (who must be resident in UK)

Start date: September/October 2020

The Bursary is approximately £15,609 for academic year 2020/2021

Applicants require a good Honours degree level equivalent to a UK degree BSc (minimum 2.1 or higher).

Any queries please contact:
Prof David Carter: dcarter@brookes.ac.uk