Department of Biochemistry University of Oxford Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU

Tel: +44 (0)1865 613200
Fax: +44 (0)1865 613201
Image showing the global movement of lipids in a model planar membrane
Matthieu Chavent, Sansom lab
Anaphase bridges in fission yeast cells
Whitby lab
Lactose permease represented using bending cylinders in Bendix software
Caroline Dahl, Sansom lab
Epithelial cells in C. elegans showing a seam cell that failed to undergo cytokinesis
Serena Ding, Woollard lab
Collage of Drosophila third instar larva optic lobe
Lu Yang, Davis lab
First year Biochemistry students at a practical class
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Postgraduate Research Studentships

Department of Biochemistry Studentships

In collaboration with the Medical Sciences Division and Colleges, the Department awards a number of Postgraduate Research Studentships each year. These are full awards that will cover University and College Fees and funding for living expenses. All applicants that apply by the early January deadline will automatically be considered for one of these awards.

 


Group Leader and Project-specific Studentships

In addition to Department of Biochemistry Studentships, we occassionally advertise studentships that are associated with a specific Group Leader or Project. Details about these studentships are given below.

There are four Group Leader/Project-specific Studentships currently available in the Department:

Project title:                                                                                                    

Marie Curie Innovative Training Network Studentship: Development of next generation 3D super-resolution imaging of fixed and live tissues for biomedical application

3 year PhD studentship covering the cost of tuition and college fees and approximately €44,000 (before taxes) per year for living expenses, with additional resources to visit conferences and project meetings.

The Schermelleh Lab is part of the Micron Bioimaging Unit, developing and refining quantitative super-resolution imaging methods and tools for application in cell biology. Our biological interest focuses on the three-dimensional (3D) chromation organisation and dynamics in response to epigenetic signals, and in relation to gene function. As we seek to expand our studies from 2D mammalian cell culture to 3D tissues and into organismic contexts, we are looking for a highly motivated student with a major in Biomedical or Bioengineering sciences who has a strong interest in multidisciplinary research at the interface of biology, biophysics and optical engineering. Your research project will be embedded in the Marie Curie ITN (Innovative Training Network) project called DeLIVER ("Super-resolution optical microscopy of nanosized pore dynamics in endothelial cells"). The network is an international consortium involving 6 academic beneficiaries, 4 SMEs, 1 large international Pharmaceutical Enterprise, and 4 Partners who will provide unique research environments and complementary skills training.

The DeLIVER project

DeLIVER is a European Marie Curie Actions Project (H2020, MSCA-ITN) that aims to train a new generation of early-stage researchers (ESRs) in the development and application of newly developed high speed and high-resolution imaging tools in biomedical research. ESRs will be cross-pollinated with concepts and skills in physics and biomedicine. These skills are applied to reveal for the first time the function and dynamics of nanosized pores in endothelial cells (EC) that present the main barrier between the blood and vital organs for human physiology, such as the liver, brain, kidneys , and the eyes.

Aim

The prime goal of this project will be establish a novel imaging modality for fast 3D super-resolution imaging of fixed and live tissues. To this end, Micron (in collaboration with Prof. Martin Booth, Uni. Oxford) has been developing a bespoke structured illumination microscopy setup (Deep-SIM) that implements 'adaptive optics' to enable ultra-fast aberration-free 3D-SIM imaging. The first task of the ESR will be to (1) adapt and refine the biological application of the Deep-SIM instrument, in close collaboration with optics & software engineers at Micron. The biological application should then be centred around the following goals: (2) to provide an optical and molecular characterisation of liver sinussoidal endothelial cells (LSECs) in healthy and diseased liver tissue; (3) to perform high-resolution and high-speed SR-SIM imaging of 3D structure of LSECs in 3D cell culture in vitro interactions of small molecules and nanoparticles with LSECs in perfused sinusoids; in linking with our core research theme (4) to investigate functional chromatin organisation and dynamics in different developmental and replicative stages in embryonic stem cell bodies and differentiated tissue. 

Your profile

-Master degree in Biology, Biomedical sciences, Biophysics or equivalent

-Ability and motivation to work independently as well as collaboratively in an interdisciplinary team

-Exceptional communicative and intercultural skills

-Excellent English writing and presenting skills

-Willingness for significant mobility throughout Europe and stakeholder interactions.

The main responsibilities of the candidate will be:

-To manage and carry out an independent, cell biology based, research project in close collaboration with partners in DeLIVER

-To actively participate in research and training activities within the DeLIVER network

-To contribute to writing articles for scientific journals

-To disseminate research results in the scientific community (via international conferences) and in the non-scientific community (via outreach and public engagement).

Additional Marie Curie eligibility requirements that you have to meet are:

*  you must not have more than 4 years fulltime research experience and must not yet have a PhD)

*  you must not have lived for more than 12 months in the UK over the last 3 years.

*  you must be a UK or EU national and lived all of your life in the EEA or Switzerland.

To apply, please contact Dr Lothar Schermelleh (lothar.schermelleh@bioch.ox.ac.uk) initially for informal discussion.

 

4-YEAR EPSRC CASE Studentship: Multiscale Molecular Simulations to Probe Lipid Bilayer Modifications Causing Antimicrobial Resistance

Department of Biochemistry, University of Oxford

Industrial Sponsor: IBM

Main academic supervisor: Professor Mark Sansom

Please quote Studentship Source Code: EPSRC1

PROJECT DESCRIPTION

Molecular simulations allow us to probe the physical properties of increasingly complex and bio-realistic models of cell membranes. This will allow us to probe the role of lipid modifications to bacterial membranes which render bacteria resistance to 'last defence' antibiotics such as daptomycin and to new generation antimicrobial peptides (AMPs). Multiscale molecular dynamics simulations will be used to explore lipids bilayers of various compositions, analysing their physical properties and calculating free energy landscapes for interaction of antibiotics and related compounds with wild type vs. modified (i.e drug resistant) membranes. This studentship will involve a collaboration between the groups of Mark Sansom and Phillip Stansfeld (Oxford Biochemistry), who have expertise in multiscale modelling of complex cell membranes, of Maike Bublitz (Oxford Biochemistry), who conducts experimental biochemistry and structural biology of cell membranes and their proteins, and IBM Research, Hartree Centre, with expertise in Big Data and cognitive systems approaches to molecular simulations. The project will provide the student with training in molecular simulations and advanced approaches to analysis of large simulation datasets. There will also be opportunities for exposure to and collaboration with experimentalists in bacterial membrane systems. The outcome will be simulation toolkit for analysis of antibiotic interactions with complex models of bacterial membranes, providing physical insights into mechanisms of current and future antimicrobial resistance.

Further information and background reading:

http://sbcb.bioch.ox.ac.uk

Students with a chemistry, biophysics of biochemistry background, ideally with some relevant undergraduate computational experience, would be preferred.

Informal enquiries are welcome: mark.sansom@bioch.ox.ac.uk

The project is supported by a 4-year CASE PhD studentship covering fees at home/EU rate plus a living allowance of not less than £14,777 per annum plus an additional supplement paid by the industrial sponsor.

To apply for this EPSRC-funded studentship, please submit an online application to the University of Oxford for admission to the D.Phil. in Biochemistry (course code: RD_BC1) by the deadline 12.00 noon (UK time) 13th April 2018. It is very important that you quote Studentship Source Code EPSRC1. No research proposal is required as part of the application. Instead you are required to upload a personal statement no more than 1000 words, describing your motivation and aptitude for this position, and your CV. Please arrange that three referees directly submit references for you.

Eligibility: ONLY students who have established UK residency are eligible to apply. For further details about residence requirements follow link:

Admissions policy and requirements

 

 

4-Year MRC ITTP Studentship: Novel genetic approaches to predictive developmental and reproductive toxicology

Main academic supervisors: Prof. Catherine Pears and Prof. Alison Woollard

Industrial Collaborator: Syngenta

Project Description:

The project explores the use of invertebrate model organisms for toxicity testing of compounds destined to be released into the environment and exploits their genetic tractability to faciliate product design while minimising toxic effects. Toxicity testing of chemicals released into the environment is an essential component of risk assessment that prevents adverse effects on human health. It is particularly relevant in the agrochemical sector, where crop protection chemicals (for plant disease, pest and weed control) are used in the environment and low levels of pesticide residues may be present in the edible crop at harvest. Developmental and reproductive toxicity (DART) is particularly challenging to assess because a whole organism approach is required, standardly involving cost-and time intensive tests in rats and rabbits, and knowledge of mechanisms of toxicity is limited. This project will exploit the genetic tractability of two prominent invertebrate model organisms, the social amoeba Dictyostelium and the nematode worm C elegans , to optimise a promising alternative testing platform in which the use of vertebrate animals is avoided. The platform will be used to probe the molecular basis of DART for selected compounds, ultimately presenting important opportunities to design better products combining high efficacy with low toxicity. This studentship, based in Oxford, is a collaboration between Catherine Pears and Alison Woollard based in the Department of Biochemistry and Kathryn Wolton in Syngenta, Jealott's Hill. The proposed work combines the disciplines of developmental biology and toxicology, exploiting recent advances in genetic analysis and biomaker development. This is an interdisciplinary project aligning a large variety of experimental and bioinformatic techniques in developmental biology, genetics and toxicology. It offers unique training opportunities for the student in the use of both C. elegans and Dictyostelium as model organisms for developmental biology, including systems approaches, genetic manipulation, biomaker imaging and bioinformatics. Training will include attendance at an annual residential course to interact with other relevant scientists. In addition, the student will gain expertise in toxicology in an industrial setting, including experimental approaches such as large scale screening and comparative data mining. Overall, the work aims to address this emerging challenge in predictive toxicology of particular relevance to the agrochemical sector, due to the pressing need to develop new crop protection products in an increasingly demanding regulatory environment.

Students with a biology, toxicology or biochemistry background, ideally with some  relevant undergraduate experience, would be preferred.

Informal enquiries are welcome: catherine.pears@bioch.ox.ac.uk

The project is supported by a 4 year MRC PhD studentship covering fees at Home/EU rate plus a living cost allowance of not less than £14,777 per annum.

To apply for this studentship, please submit an online application to the University of Oxford for admission to the D.Phil. in Biochemistry (course code RD_BC1) by the deadline noon (UK time) 25th May 2018. No research proposal is required as part of the application. Instead you are required to upload a personal statement of no more than 1000 words, describing yourmotivation and aptitude for this position, and your CV. Please arrange three referees directly submit references for you.

Eligibility: ONLY students who have established UK residency are eligible to apply. For further details of about residence requirements follow link:

Admission policy and requirements

 

4-Year PhD Studentship: Structural analysis of cell guidance receptors in cortical development

Main academic supervisor: Dr Elena Seiradake

Project description:

Background. Brain development depends on the concerted actions of cell guidance receptors that act as context-recognisers by forming functionally distinct cell surface assemblies. Adhesion GPCRs are particularly good examples, as these contain large extracellular domains that act as platforms for diverse ligand interactions. Acting as hubs for receptor interactions, they perform key roles in guiding cell migration, polarisation and synapse formation, the process underlying brain wiring. How these receptors bind their multiple ligands and how signals are generated in the cell is just beginning to emerge.

Project. The project involves X-ray crystallography and cryo-electron microscopy to determine the structues of adhesion GPCRs and their ligands, and cell biology to investigate how structurally distinct complexes determine neuronal cell functions. We will provide training in the required techniques such as protein expression and purification from large-scale mammalian expression systems, biophysical analysis, and use of our advanced microscopy and crystallography facilities. The project also involves collaborations with the groups of Mark Sansom (Oxford Biochemistry),who has expertise in multiscale modelling of complex cell membranes, Carol Robinson (Oxford Chemistry), who investigates protein-protein and protein-lipid complexes using mass spectrometry and Ruediger Klein (Max-Planck Institute of Neurobiology, Munich), who uses advanced genetic tools to investigate nervous system development.

Outcomes. The project will provide the student with training in protein biochemistry, structural biology and basic cell biology. There will also be opportunities for exposure to and collaboration involving molecular modelling, mass spectrometry and specialised experiments to study protein function in situ. The primary outcome will be a molecular level insight into the currently unknown structures and functions of the target receptors in brain development. The results will underpin the development of new drugs and treatments for neurodevelopmental disorders that caused by malfunction of these receptors.

Further information and background reading: https://www.bioch.ox.ac.uk/research/seiradake

Students with molecular biology, cell biology or biochemistry background,ideally some relevant practical undergraduate experience, would be preferred.

The project is supported by a 3 year PhD studentship covering fees (at the Home/EU rate) plus a living cost allowance of not less than £14,777 per annum.

To apply for this funded studentship, please submit an online application to the University of Oxford for admission to the DPhil in Biochemistry (course code: RD_BC1) by the deadline 12.00 noon (UK time) 25th May 2018. No research proposal is required as part of the application. Instead you are required to upload a personal statement of no more than 1000 words, describing your motivation and aptitude for this position, and your CV, plus including official transcripts of your undergraduate marks and degrees. Please arrange that three referees directly submit references for you.


 

College Scholarships

College Scholarships include:

E.P. Abraham Scholarship in the Chemical, Biological/Life and Medical Sciences at St Cross College

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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