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: Are bee viruses driving heritable symbiont success?
Eligibility: Home UK/EU applicants who must be permanently resident in UK/EU

Closing date: 31 December 2019

Start date:  September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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. Michael Gerth, Prof Stewart Thompson, Dr. Daniela Nunes, Dr. Andrew Jones

Project:

Background

Inherited microbes are bacteria that live in close association with various animals, and are transmitted from mother to offspring. It is estimated that more than half of all terrestrial arthropod species carry one or more inherited symbionts, but it is not fully understood how the bacteria can reach such high incidence rates. In order to be successful, the symbionts must not only be able to shift hosts, but also to establish in novel hosts without imposing high fitness costs. Recently, it has been demonstrated that inherited symbionts may protect their hosts from certain pathogens. Such protective phenotypes are potentially beneficial in terms of host fitness, and thus could aid symbiont establishment. This prediction is supported through ecological modeling, but has rarely been tested in natural settings.

Aims

1) To determine if symbiont mediated pathogen blocking can drive the evolutionary success of inherited microbes.

2) To determine symbiont factors that contribute to pathogen blocking phenotypes.

Workplan

Solitary bees and Wolbachia bacteria will be used as model host/symbiont system. The candidate will investigate natural populations of bees and measure symbiont and viral titres in different species collected in and around Oxfordshire. These data will be used to determine if symbiont infection status predicts viral loads. Further, the candidate will characterize symbiont genomes through Nanopore and Illumina sequencing and use pool-Seq to determine which genomic features of the symbionts correlate negatively with viral presence. Further, novel viruses potentially interacting with symbionts will be described through viral metagenomics of solitary bee samples.

For informal inquiries about the project and the application process please contact Dr Michael Gerth: mgerth@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 biological science or related discipline. 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 application form:

http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc

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: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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.uk or 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
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc)

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

3 Year, full-time PhD studentship

Project title: Long-term effects of pesticides on environmental health – how does exposure of a female egg-laying insect to pesticides affect subsequent generations?

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

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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 Casper J. Breuker, Dr Andrew Jones, and Dr Melanie Gibbs

Although controls are in place for pesticide use, including banning certain pesticides from outdoor use (e.g. various neonicotinoids in the EU), most of these measures are based on evidence from research on the short-term effects of continuous use. Little is known of the long-term effects of pesticide use, and how much variation there is between insect species in their response. In this project we aim to gain an understanding of the molecular basis underlying a specific type of long-term effect; transgenerational effects. If a parent is exposed to pesticides how does that affect subsequent generations of offspring, even when they are not directly exposed themselves? In order to address this important and topical environmental health question, research is required on a broader range of insect species to complement the on-going studies that use commercially important pollinators such as bees. Many other insects, like butterflies, that are beneficial to the environment and fulfil important eco-system functions, are known to also be negatively affected by pesticide use. In our research group we have used butterflies to characterise maternal regulation of embryonic development (e.g. https://doi.org/10.1371/journal.pone.0144471), and also reviewed the large gaps in our knowledge on the effects of pesticides on butterflies (https://doi.org/10.1016/j.envpol.2018.06.100). In this project, we wish to elucidate how embryonic insect development is affected by maternal pesticide exposure (e.g. thiacloprid and acetamiprid). We will collect transcriptomic as well as fitness data, and the project will involve insect stock maintenance, experimental rearing, molecular work, and bioinformatics. Although the project will focus primarily on butterflies (e.g. Bicyclus anynana and Pararge aegeria), the project does offer scope to expand into comparative molecular work on other beneficial insect species, insect pests (that are often pesticide targets), and powerful insect lab systems for molecular work on transgenerational effects e.g. the fruit fly.

For further information contact Dr Casper J. Breuker (cbreuker@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 Life Sciences discipline. 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 application
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc).

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

3 Year, full-time PhD studentship

Project title: And along came two spider genomes: Investigating the developmental consequences of whole genome duplication in spiders

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

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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

Supervisors: Professor Alistair McGregor, Dr Anna Schoenauer and Dr Lauren Sumner-Rooney

Project:

Whole genome duplication is arguably the largest single mutational event that a genome can experience. The retained duplicated genes, or ohnologs, are thought to contribute to the evolution of gene regulatory networks and phenotypic diversification. Like vertebrates, some spiders have experienced multiple whole genome duplications in their evolutionary history. However, the consequences of whole genome duplication in spiders, and how these compare to independent events in vertebrates, are poorly understood.  This project will first explore the repertoire of ohnologs in spiders with sequenced genomes, including the common house spider (Parasteatoda tepidariorum), a social spider (Stegodyphus mimosarum) and the brown recluse (Loxosceles reclusa). The project will then investigate the expression and function of ohnologs during spider development compared to single copy genes in other arthropods that have not had a whole genome duplication. This will provide an excellent opportunity to test whether the outcomes of whole genome duplication are similar between vertebrates and invertebrates, and to reassess the contribution of these events to the evolution of animal genomes and diversity in a broader sense.

This project will provide training at the nexus of bioinformatics, bioimaging, and wet lab biology. The student will learn to reconstruct and analyse genomes and transcriptomes, study embryogenesis, gene expression and gene function, and examine morphology using high-powered X-ray imaging techniques.

For further information contact Professor Alistair McGregor: amcgregor@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 application form
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc).

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

3 Year, full-time PhD studentship

Project title: Respiratory control and sensation in neurological patients
Eligibility: Home UK/EU applicants who must be permanently resident in UK/EU

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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. Shakeeb H Moosavi (Clinical Physiology), Professor Alex Green (Clinical Neuroscience/neurosurgery), Dr. Sanjay Kumar (Clinical Psychology)

Project:

This multidisciplinary project brings together overlapping concerns within respiratory medicine and neurology. The neurophysiological mechanisms of breathlessness (‘dyspnoea’) in cardiopulmonary disease is poorly understood, there remains a need for effective treatments to improve quality of life. In neurology, the respiratory consequences of neurological conditions and neurosurgical interventions are neglected and cardiorespiratory dysfunction under-appreciated.

Various neurological patients will be studied, including those with Parkinson’s and Myaesthenia Gravis. Novel techniques will be employed to stimulate the brain using deep brain stimulation (DBS) via surgically implanted electrodes and by repetitive transcranial magnetic stimulation (rTMS). Local field potentials (LFPs) will be recorded from implanted electrodes. Training will also be provided in conventional lung function, magnetoencephalography and brain imaging techniques.

The project builds on a developing collaboration between the cardiorespiratory research group at Brookes and Oxford University’s Clinical Neurosciences department at John Radcliffe Hospital. Recent publications from this collaboration have reported a substantial reduction in ‘air hunger’ with DBS of the motor thalamus (Green et al., 2019, Brain Stimul 12: 827-828) and improvements in upper airway function with DBS of the pedunculopontine region in patients with Parkinson’s (Hyam et al., 2019, Ann Clin Transl Neurol 6: 837-847). Other, unpublished data has demonstrated differential changes in LFPs in the left and right anterior cingulate cortex that vary according to the respiratory paradigm.

The broad aim is to elucidate the role of various brain nuclei in respiratory function/dysfunction, and provide insight into whether this knowledge can translate into therapies for chronic respiratory conditions. The work would extend current knowledge of cerebral mechanisms of dyspnoea and may shed new light on the extent to which multi-morbidity can account for respiratory dysfunction and breathlessness in neurological patients.

The project would suit those with a background in systems physiology, neuroscience, biological psychology, or with medical training specialising in respiratory medicine or neurology (or related speciality). For further information contact Dr Shakeeb Moosavi (smoosavi@brookes.ac.uk) and/or visit the following websites: /bms/about/staff/?wid=&op=full&uid=p0076413

https://www.ndcn.ox.ac.uk/team/alex-green

Requirements:
Applicants should have a first or upper second class honours degree from a Higher Education Institution in the UK. 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 application form
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc)

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

3 Year, full-time PhD studentship

Project title: Investigating the genetic and evolutionary mechanisms facilitating the rapid divergence of male genitalia in Drosophila

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

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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. Maria Daniela Santos Nunes

Project:

Male genitalia evolve rapidly in many animal groups but the genetic basis of this fast evolution have eluded biologists for decades. Recently we uncovered a gene, tartan, that contributes to differences in the size of a secondary genital structure between two Drosophila species. This project aims to understand the genetic and evolutionary mechanisms facilitating the rapid divergence of male genitalia taking advantage of our recent findings.  Specifically, in this project we will take a multidisciplinary approach, bridging behavioural genetics, high-resolution microscopy, machine-learning, neuroscience and evolutionary genomics. These are some of the questions we aim to address:

1)   Do the evolved genetic changes in trn affect mating behaviour and genital coupling in these species? This will include setting up and video recording high-throughput behavioural experiments and manual and automated measurements of standard behavioural parameters.

2)   What are the mechanisms through which these changes affect reproductive fitness? This will include the study of the neural circuitry regulating the female response to mating and how this is modified in flies mated to males carrying heterospecific alleles of trn.

3)  Did selection play a role in the evolution of this gene? This will include analysis of genomic data from populations of D. simulans and D. mauritiana, as well as direct tests of selection on the species-specific tartan alleles.

 The results of this Project will provide fundamental insight into the mechanisms through which morphological changes affect behavioural phenotypes and the evolution of reproductive isolation between species and speciation more generally.

For further information contact Dr Maria Daniela Santos Nunes: msantos-nunes@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 follow application form
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc).

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

 3 Year, full-time PhD studentship

 Project title: The role of extracellular vesicles and glycosylation in breast cancer metastasis

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

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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

Supervisors: Prof Dave Carter, Prof Susan Brooks, Dr Ryan Pink

Project:

The way in which cancer cells metastasise to other parts of the body is highly complex and not fully understood. Unravelling the molecular mechanisms of the metastatic process is crucially important, as there are currently no ways to block the spread of cancer and it is the metastatic form of cancer that patients tend to succumb to.

Extracellular vesicles (EVs) are small cargo-carrying lipid-enclosed vesicles released by cells into the extracellular space. EVs play a number of important biological roles and can be deregulated in pathological conditions, including cancer metastasis. However, the ways in which they contribute to metastasis has not been fully explored.

We have shown that EVs released by some breast cancer types carry specific proteins with an altered glycosylation pattern. These EVs interact with a cognate receptor on the surface of target tissues, which leads to the seeding of a ‘pre-metastatic niche’, helping the tumour cells to colonise the new tissue.

The aim of this project is to test the mechanisms by which these breast cancer cells use EVs to seed the pre-metastatic niche. To establish the effect of EVs on the target tissue the candidate will use techniques including mass spectroscopy, flow cytometry, migration assays, invasion assays, and cell-cell adhesion assays. The project will involve the use of mammalian cell culture and may include in vivo experiments. The candidate will also explore the potential of EVs as a diagnostic/prognostic in breast cancer metastasis, and test the therapeutic potential of blocking these.

We are seeking a motivated and talented student to join our vibrant team on this fascinating project. Experience in EVs, cell culture and the other techniques described above would be beneficial but is not required, though experience in lab-based experimental design, execution and analysis is essential.

For further information contact Prof Dave Carter: dcarter@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 Biological Science or related discipline. Experience in lab-based experimental design, execution and analysis 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
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc)

Oxford Brookes University

Faculty of Health and Life Sciences

Department of Biological and Medical Sciences

3 Year, full-time PhD studentship

Research title: Investigating Antibiotic Resistance in Bacteria using Functional Genomics

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

PhD Start date: September 2020

Application Closing Date: 31 December 2019

Interview: w/c 13 January 2020

Bursary p.a: Bursary equivalent to UKRI national minimum stipend plus fees (2019/2020 bursary rate is £15,009)

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

Main supervisor: Dr Hee-Jeon Hong

2nd supervisors: Dr Victor Bolanos-Garcia, Dr Andy Jones, Dr Andy Hesketh (University of Brighton)

Project Summary: Our research focuses on characterization of bacterial responses to antibiotics using Actinomycetes as model system. Actinomycetes produce about 70% of known antibiotics and are the ultimate source of genes involved in sensing and responding to extracellular antibiotics including antibiotic resistance system and are therefore an ideal system to use for furthering the understanding of the processes involved. Antibiotics that target the bacterial cell envelope, such as penicillin and vancomycin, are particularly clinically important in treatment of infectious diseases but many inducible resistance systems in pathogens have evolved that reduce their effectiveness with an example of vancomycin-resistant MRSA. Our research will involve a diverse range of functional genomic approaches such as RNA sequencing analysis, genetic modification, cell wall analysis and susceptibility assay in conjunction with bioinformatics and systems biology. The fundamental aim of our research is to extend our knowledge of the functions and systems that are important for bacterial resistance/tolerance to the antibiotic, and open ways by which these can be exploited in future antibiotic therapies. We also aim to progress this research into pathogens responsible for hospital acquired infections. This work has direct implications for public health, contributing to efforts to understand the molecular basis of defensive responses and resistance to antibiotics in bacteria. The Department of Biological and Medical Sciences has excellent research groups and facilities in this area of study and so there will be good opportunities for the student to have multidisciplinary collaborations. As part of your training you will be required to assist in demonstrating on undergraduate practical during semesters without further remuneration.

For further information, please contact Dr Hee-Jeon Hong (hee-jeon.hong@brookes.ac.uk).

Entry Requirements: A good Honours degree minimum 2.1 from a UK university or acceptable equivalent from a recognised 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.

How to apply: Please complete the Application Form, which you can download from

http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc

With your application please enclose a CV, scanned copy of your degree certificates and transcripts. Additionally, if appropriate, a valid IELTS Academic test score certificate.

Applications only accepted by e-mail to hlsapplications@brookes.ac.uk.

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

3 Year, full-time PhD studentship

Project title: Time to be born: the role of thyroid hormones in the development of the hypothalamic-pituitary axis before birth
Eligibility: Home UK/EU applicants who must be permanently resident in UK/EU

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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 Alison Forhead, Dr Laura Gathercole, Dr Helen Christian

Project:

Thyroid hormones and cortisol are important hormonal regulators of fetal growth and development.  Thyroid hormone deficiency before birth delays maturation of fetal organs and prolongs gestation, possibly via effects on the fetal hypothalamic-pituitary-adrenal (HPA) axis.  Our recent research in an animal model shows that hypothyroidism reduces circulating cortisol and adrenocorticotropin (ACTH), and impairs the growth and steroidogenic capacity of the fetal adrenal cortex.  The effects of thyroid hormone deficiency on the structure and functional development of the fetal hypothalamic-pituitary axis, however, are unknown.  The aim of this PhD studentship is to investigate the mechanisms by which hypothyroidism in utero suppresses the activity of the fetal HPA axis.

In collaboration with colleagues at the Universities of Oxford and Cambridge, the structure of neuronal networks and relative numbers of pituitary cell types may be determined by immunohistochemistry and stereological techniques.  Studies may also be carried out to examine the sensitivity of the fetal pituitary to secrete ACTH in vitro, both basal and in response to regulatory factors.  Protein and mRNA abundance of molecules important for pituitary hormone synthesis and secretion may be quantified by Western blotting and qRT-PCR.  This project will determine the role of thyroid hormones in the growth and development of the fetal HPA axis, with implications for the control of fetal maturation and the timing of birth.

For further information contact Dr Alison Forhead: aforhead@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 physiology or related cognate discipline.  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 application form
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc).

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

 3 Year, full-time PhD studentship

 Project title: Genetic regulation of stem cell differentiation in vivo by single-cell sequencing of planarian cells
Eligibility: Home UK/EU applicants who must be permanently resident in UK/EU

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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 Jordi Solana

Project:

Single-cell sequencing methods will revolutionize the functional and comparative study of stem cells. The flatworm Schmidtea mediterranea is a very promising model for in vivo stem cell biology thanks to its large number of stem cells that continuously differentiate to all adult cell types and that enable its amazing regenerative capacities. We have previously used single-cell transcriptomics to in silico reconstruct the differentiation lineage tree of planarian stem cells. However, the mechanisms that orchestrate this differentiation in vivo are not well understood. There is strong evidence that these mechanisms are conserved at least in part from planarians to humans. The use of model organisms such as planarians will therefore be key to study the fundamental biology of stem cells and their evolution. We will use RNAi-mediated gene knockdown in combination with single-cell transcriptomics. Whole worm systemic RNAi is a powerful and scalable tool to knockdown gene expression in planarians. Subsequently, single-cell sequencing will allow profiling stem cells, progenitors as well as fully differentiated cells and studying the effects of the knockdown at the single-cell level. This will allow elucidating the effect of several transcriptional, posttranscriptional and epigenetic regulators in the self-maintenance and differentiation output of planarian stem cells.

For further information contact Dr Jordi Solana: jsolana@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 or related discipline (knowledge of research design and statistics 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 or show evidence of fluency in English.

How to apply:
Applications should be sent to hlsapplications@brookes.ac.uk and should include the following form
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc)

Oxford Brookes University

Faculty of Health and Life Sciences,

Department of Biomedical and Medical Sciences

3 Year, full-time PhD studentship

Project title: Assembly and function of basal bodies in Trypanosoma brucei

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

Closing date: 31 December 2019

Start date: September 2020

Interview: w/c 13 January 2020

Bursary p.a.: Bursary equivalent to UKRI national minimum stipend plus fees (2019/20 bursary rate is £15,009)

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

Supervisor: Prof. Sue Vaughan.

Project:

Eukaryotic flagella/cilia are complex microtubule based organelles that are assembled from basal bodies. These organelles are required for motility and carry out many different sensory functions in a wide variety of cells. Most cells in Humans can produce a primary cilium which are used in sensory functions as well as modulating flow and for motility. There are a group of genetic diseases called ciliopathies in Humans that result from defects in cilia/flagella function. Many unicellular eukaryotic organisms including protozoan parasites also use flagella for motility. The African sleeping sickness parasite Trypanosoma brucei, requires the flagellum and motility in all of its life cycle stages and is essential for pathogenicity.

The Vaughan laboratory is part of a large collaborative Wellcome Trust Project to produce a genome-wide localisation study in Trypanosomes. A total of 307 proteins were localised to the basal body area. Trypanosomes have excellent molecular biology tools including RNAi, knockouts, endogenous tagging of proteins to interrogate the function of these proteins. The aim of this project is to dissect the assembly and maturation process of basal bodies in Trypanosomes. This project will give key insights into basal body biogenesis and discover which proteins are part of core-conserved functions in mammalian cells and which are unique to unicellular organisms and parasites. This project will use a range of different techniques including molecular biology, tissue culture and bioimaging. Prof. Vaughan is the Bioimaging Lead and the project will use cutting edge 3D microscope techniques including cellular electron tomography and serial block face scanning electron microscopy.

For further information contact Prof. Sue Vaughan Svaughan@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 biological science or related discipline. 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
(http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc)

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 30th April 2019.

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

Start date: September/October 2019

The Bursary for academic year 2019/20 is approximately £15,009.

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