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1. CORE RESEARCH AREAS CURRENTLY FUNDED BY THE
BBSRC. These areas have attracted generous funds from the
BBSRC. Candidates interested in doing a PhD in one or more of
these areas are strongly encouraged to apply.
PI
URL
Dr James Allen
http://www.bioch.ox.ac.uk/aspsite/research/brochure/allen/
james.allen@bioch.ox.ac.uk
Research
area:
Assembly of cytochrome c in the African sleeping sickness parasite. The
genome of the African sleeping sickness parasite Trypanosoma brucei
reveals a typical mitochondrial respiratory chain but none of the known
proteins for cytochrome c assembly. We are seeking to identify and
characterize the proteins that do this job in trypanosomes.
Rotation: Microbiological culture (bacterial and eukaryotic); Protein
purification; Bacterial molecular biology; Various protein chemistry
methods; Mass spectrometry; Gel electrophoresis; Absorption
spectroscopy; Bioinformatics/genome analysis; Enzymology;
Immunoprecipitation. DPhil project: Advanced molecular biology
(bacterial & eukaryotic – e.g. cloning and expression, constructing
trypanosome gene knockouts, RNAi); Membrane protein expression,
purification, etc.; Advanced enzymology (e.g. detailed characterization,
inhibitor studies, etc.); Protein crystallography; Advanced spectroscopic
methods.
Research
methods:
PI
URL
Professor Judith P. Armitage
http://www.bioch.ox.ac.uk/aspsite/research/brochure/armitage/
judith.armitage@bioch.ox.ac.uk
Research
area:
E.coli chemosensing is the best understood sensory system in biology,
with transmembrane chemoreceptors regulating the activity of a histidine
kinase which determines the phosphorylation state of the flagellar motor
binding response regulator. However, in most other species sensing is
more complex, with several pathways controlling behaviour. Research
will centre on (a) identifying whether signalling pathways are linear or
parallel and (b) the dynamics of the sensory proteins which are localised
to specific regions of the bacterial cell.
Research
methods:
All aspects of cloning, fluorescence microscopy, protein:protein
interaction measurement (in vivo by FRET, in vitro by SPR and yeast two
hybrid), bioinformatics, behavioural analysis.
PI
URL
Professor Fraser Armstrong
http://www.chem.ox.ac.uk/researchguide/faarmstrong.html
fraser.armstrong@chem.ox.ac.uk
Research
area:
Biological oxidation and reduction. Mechanistic studies on long-range
electron transfer and proton transfer in enzymes. Investigations of
enzymes containing metal cofactors. Studies and exploitation of
oxidases and hydrogenases, including oxidation and production of
hydrogen by enzymes and the applications to ‘smart’ hydrogen and
novel fuel cell technologies.
Research
methods:
Many electrochemical techniques including ‘protein film volatmmetry’
and potential step kinetic methods. Rapid solution kinetics (stopped
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flow). Electron paramagnetic resonance (EPR). Anaerobic (glovebox
techniques. Microbiology, molecular biology and protein chemistry.
PI
URL
Professor Hagan Bayley
www.chem.ox.ac.uk/bayleygroup/
hagan.bayley@chem.ox.ac.uk
Research
area:
Membrane protein folding, assembly and function; membrane protein
engineering; rapid screening of membrane proteins; Bionanotechnology
Research
methods:
Research methods: molecular genetics, protein chemistry, organic
synthesis, biophysical measurements including single-channel recording
PI
URL
Dr Ben Berks
http://www.bioch.ox.ac.uk/aspsite/research/brochure/berks/
ben.berks@bioch.ox.ac.uk
Research
area:
Mechanism of an unusual protein transport system; molecular basis of
bacterial sulfur oxidation; membrane protein structural biology
Research
methods:
Protein chemistry (protein purification, antibody methodology, in vitro
transcription-translation, protein modification, enzymology, protein
biophysics); membrane biology; recombinant DNA methodology;
structural biology (X-ray crystallography, single particle electron
microscopy, high throughput expression methods, molecular dynamics);
single cell and single molecule fluorescence methods.
PI
URL
Professor Benjamin G. Davis
http://www.chem.ox.ac.uk/researchguide/bgdavis.html
http://users.ox.ac.uk/~dplb0149/
Ben.Davis@chem.ox.ac.uk
Research
area:
Chemical Glycobiology, Biocatalysis and Mechanistic Enzymology,
Protein and Glycoprotein Chemistry, Inhibitor and Small-Molecule Probe
Design, Antivirals, Chemical Genetics, Synthetic Methodology,
Glycoimmunology, Drug Delivery, In Vivo imaging, Therapeutic
Strategies, Biopharmaceuticals.
Research
methods:
Mechanistic Enzymology, Synthetic Methodology, Inhibitor and SmallMolecule Probe Design, Sugar Chemistry, Asymmetric Small Molecule
Chemistry, Peptide Synthesis, Molecular Biology, Protein Expression,
Forced Evolution, Structural Biology, Mass Spectrometry, Novel
Chemistry on Protein Surfaces, In Vivo Methods.
PI
URL
Professor Stuart Ferguson
http://www.bioch.ox.ac.uk/aspsite/research/brochure/ferguson/
stuart.ferguson@bioch.ox.ac.uk
Research
area:
Structure, function, molecular mechanism, biogenesis and assembly of
bacterial respiratory proteins of the Nitrogen cycle.
Research
methods:
Molecular and structural biology; spectroscopy and other biophysical
methods; enzymology; protein biochemistry; recombinant protein
expression, purification and characterisation
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PI
URL
Research area
Research
methods
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Dr Mark Howarth
http://users.ox.ac.uk/~bioc0756/MyWebs/activesite/
mark.howarth@bioch.ox.ac.uk
Bionanotechnology:
Discovery of new types of post-translational modifications involved in
bacterial infection and cancer. Use of protein chemistry to design infinite
affinity antibodies for imaging and diagnosis. Protein “superglue” and
padlocks from pathogenic bacteria.
Molecular and cellular biology, protein engineering and selection,
fluorescence microscopy, X-ray crystallography, basic organic
synthesis, mammalian cell culture, small-molecule probe design, mass
spectrometry, proteomics, bioinformatics
Dr Nicholas Lakin
http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=585
nicholas.lakin@bioch.ox.ac.uk
Research area: Maintenance of genome integrity: The detection signalling and repair of
DNA damage. Repair of DNA damage is critical to maintain genome
integrity. As such, the cell has developed a DNA damage response
(DDR) that detects and signals DNA damage to facilitate cell cycle
arrest and DNA repair. Our research exploits mammalian cell culture
and the genetic model organism Dictyostelium to decipher how the DDR
is regulated at the molecular level. Research areas include (i)
Understanding how DNA damage is detected and signalled to initiate
the DDR and (ii) how repair of DNA double strand breaks is regulated.
PI
URL
Research
methods:
Recombinant DNA technology (gene cloning/manipulation), mammalian
and Dictyostelium cell culture, genetics/chemical genetics (gene
disruption, siRNA, small molecule inhibitors of DNA repair), biochemistry
(protein expression, purification and analysis), cell biology (microscopy
and immunofluorescence).
PI
URL
Dr Christina Redfield
http://www.bioch.ox.ac.uk/aspsite/research/brochure/redfield/
christina.redfield@bioch.ox.ac.uk
Research
area:
NMR methods for characterising partly folded and unfolded proteins
and study of ligand-binding protein systems
Research
methods:
Protein NMR methods including double and triple resonance 2D and 3D
NMR, 15N relaxation studies and residual dipolar couplings
PI
URL
Professor Carol Robinson
http://research.chem.ox.ac.uk/carol-robinson.aspx
carol.robinson@chem.ox.ac.uk
Research
area:
Research
methods:
Study of membrane protein complexes
3D models of protein complexes
We are interested in all aspects of protein complexes and their
properties in the gas phase of a mass spectrometer. Although not the
traditional role of this analytical tool, recent developments enable mass
spectrometry to probe large intact protein assemblies, providing
knowledge of their stoichiometry, topology and interaction partners
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PI
URL
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Professor Chris Schofield
http://www.chem.ox.ac.uk/researchguide/cjschofield.html
christopher.schofield@chemistry.oxford.ac.uk
Research area: Molecular understanding of the mechanisms behind the hypoxic
response (how cells counteract the effect so low oxygen, e.g. at altitude
or in tumours), the biosynthesis of antibiotics, the structures and
mechanisms of enzymes that catalyse synthetically impossible
reactions, functional assignment and selective inhibition of human
enzymes, regulating transcription by small molecules.
Research
methods:
Molecular and cellular biology, protein purification and characterisation,
proteomics (including MS based methodology and techniques for
studying protein-protein interactions), structural biophysics, especially
crystallography and MS, organic synthesis especially of enzyme
inhibitors.
Dr Mark Wallace
http://www.chem.ox.ac.uk/researchguide/mwallace.html
mark.wallace@chemistry.oxford.ac.uk
Research area: Single-molecule detection of membrane proteins
(Bionanotechnology, Molecular Mechanisms of Biological Systems,
Physical Biochemistry)
PI
URL
Research
methods:
Single-molecule fluorescence techniques; Laser spectroscopy;
Microscopy; Single-channel electrical recording; Protein expression,
purification, and chemical modification.
2. Additional Research Areas for rotation projects and collaborative
dphil projects. These areas may not currently supported by BBSRC
research grants but fall within the remit of BBSRC, and therefore
would provide interesting possibilities for collaborative projects in
collaboration with the main areas above.
Research
area:
Professor Harry L. Anderson
http://users.ox.ac.uk/~hlagroup/
harry.anderson@chem.ox.ac.uk
Design, synthesis and testing of dyes for a wide range of applications,
particularly using porphyrins and rotaxanes; drugs for two-photon excited
photodynamic therapy; membrane-probes based on second harmonic
generations; nonlinear optics; molecular recognition; supramolecular
chemistry and chromophore engineering.
Research
methods:
Organic synthesis; fluorescence spectroscopy; NMR; mass
spectrometry; HPLC; tissue culture experiments.
PI
URL
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PI
URL
Dr Phil Biggin
http://sbcb.bioch.ox.ac.uk/biggin.php
http://www.bioch.ox.ac.uk/aspsite/research/brochure/biggin/
Philip.biggin@bioch.ox.ac.uk
Research
area:
Ionotropic Glutamate Receptors, Nicotinic Acetylcholine Receptors,
Neurotransmission, Anti-viral agents, Lipid-drug interactions, Drugreceptor binding, Conformational change in proteins
Research
methods:
Structural Bioinformatics, Molecular Dynamics, Free Energy
Calculations, Homology Modelling, Normal Mode Analysis.
PI
URL
Professor Raymond Dwek with Dr Nicole Zitzmann
http://www.bioch.ox.ac.uk/aspsite/research/brochure/zitzmann/
nicole.zitzmann @bioch.ox.ac.uk
Research
area:
Development of antiviral therapeutics for Hepatitis C virus, Hepatitis B
virus, and HIV. Biophysical and structural studies of the ion channels.
Antiviral drug discovery, ion channel inhibitors and sugar-based anti-HIV
therapeutics
Research
methods:
Molecular biology; cell culture; ion channel studies in black lipid
membranes; structural and biophysical techniques including
crystallography, NMR, circular dichroism, differential scanning
calorimetry.
PI
URL
Professor T.J. Donohoe
http://www.chem.ox.ac.uk/researchguide/tjdonohoe.html
timothy.donohoe@chemistry.oxford.ac.uk
Research
area:
Research
methods:
Synthetic Methodology for Complex Molecules with Biological Activity
PI
URL
Professor Jane Endicott
http://www.bioch.ox.ac.uk/aspsite/research/brochure/endicott/
Jane.Endicott@bioch.ox.ac.uk
Research
area:
Structural and biochemical characterisation of the Plasmodium
falciparum protein kinase family.
Research
methods:
Molecular biology, protein purification and characterisation, X-ray
crystallography, principles in structure-aided inhibitor design,
biophysical techniques to characterise protein-protein interactions, to
include SPR and ITC.
Synthetic organic chemistry: development of new methodologies for
synthetic organic chemistry and asymmetric synthesis, and application to
synthesis of biologically important natural products.
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PI
URL
Dr Antony Fairbanks
http://users.ox.ac.uk/~dplb0070/index.html
antony.fairbanks@chemistry.oxford.ac.uk
Research
area:
Glycochemistry; carbohydrate based drug discovery e.g. anti-fungals
and antibiotics; glycoprotein and glycopeptide chemistry
Research
methods:
Synthetic methodology, sugar chemistry.
PI
URL
Research
area:
Dr Elspeth Garman
http://www.bioch.ox.ac.uk/aspsite/research/brochure/garman/
Structural Biology Methodology, Crystallography. Macromolecular
Crystallography. Methods development. Cryo-techniques and
understanding of radiation damage. Metal identification in proteins.
Structural studies on neuraminidases.
Research
methods:
Crystallography, microPIXE.
PI
URL
Professor Penny Handford
http://www.bioch.ox.ac.uk/aspsite/research/brochure/handford/
penny.handford@bioch.ox.ac.uk
Research
area:
Molecular Mechanisms of Biological Systems focussing on structural and
functional consequences of Notch-ligand interactions; and intra- and
inter-molecular interactions of calcium-dependent extracellular matrix
proteins
Research
methods:
General molecular biology (DNA and protein analytical methods),
specific expertise in vitro refolding of disulphide-rich proteins,
measurement of weak, moderate and high affinity calcium binding sites
in proteins, prokaryotic and eukaryotic protein expression, biophysical
methods (NMR, crystallography, surface plasmon resonance)
PI
URL
Professor Peter J. Hore
http://www.chem.ox.ac.uk/researchguide/pjhore.html
peter.hore@chemistry.oxford.ac.uk
Research
area:
Real-time kinetic NMR studies of protein folding
Structural studies of partially folded proteins using photo-CIDNP
Research
methods:
High resolution NMR
Laser kinetics
Photo-CIDNP (Chemically Induced Dynamic Nuclear Polarization)
PI
URL
Dr Petros Ligoxygakis
http://www.bioch.ox.ac.uk/aspsite/research/brochure/ligoxygakis/
petros.ligoxygakis@bioch.ox.ac.uk
Research
area:
Pathogen recognition by the innate immune system, using a genetically
tractable organism (Drosophila melanogaster.) as a model system
Research
Standard molecular biology (cloning, PCR, RNA work), protein
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methods:
biochemistry (expression, purification), bacterial cell wall chemistry
(peptidoglycan purification, isolation of smaller fragments with HPLC),
Drosophila genetics (mutagenesis, genetic transformation, crosses),
study of the interaction between immune receptors and the bacterial cell
wall using confocal microscopy.
PI
URL
Professor Martin Noble
http://www.bioch.ox.ac.uk/aspsite/research/brochure/noble/
martin.noble@bioch.ox.ac.uk
Research
area:
Structural studies on regulatory proteins; Adhesive interactions, the cell
cycle, and NAT enzymes
Research
methods:
Protein X-ray crystallography and other biophysical methods; drug
design; visualization/analysis; protein binding interactions
PI
URL
Research
area:
Dr James Parker
http://www.bioch.ox.ac.uk/aspsite/research/brochure/parker/
Research area: Structural and molecular biology of RNA silencing: RNA
interference, microRNAs, piRNAs, Argonaute, Dicer, Slicer fundamental biology and basic molecular mechanisms
Research
methods:
Molecular biology, protein biochemistry, X-ray crystallography,
biophysical methods (isothermal titration calorimetry, analytical
ultracentrifugation)
PI
URL
Research
area:
Dr Jason Schnell
http://spincore.com/nmrjobs/pos09_08.html
Structure, function, and inhibition studies of ion channels that are of
high medical relevance. Structural analysis of ion channel systems by
high-resolution solution NMR and other the tools of biophysics (e.g.
fluorescence, and ultracentrifugation) and molecular biology in
combination with functional assays (e.g. liposomal ion flux assays) to
elucidate the molecular details of activity.
Research
methods:
Molecular Biology, Protein Biochemistry, NMR spectroscopy,
Mass Spectrometry, Surface Plasmon Resonance, Calorimetry, TimeResolved Spectroscopies, Structure-Based Drug Design, Combinatorial
Library Screening.
PI
URL
Dr Lorna Smith
http://www.chem.ox.ac.uk/researchguide/ljsmith.html
lorna.smith@chem.ox.ac.uk
Research
area:
Experimental and theoretical methods to characterise partially folded
and misfolded proteins. NMR studies of protein structure, dynamics and
ligand binding.
Protein NMR Spectroscopy - 2D and 3D techniques
Theoretical molecular dynamics simulations.
Research
methods:
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PI
URL
Dr Christiane R. Timmel
http://www.chem.ox.ac.uk/researchguide/crtimmel.html
timmel@physchem.ox.ac.uk
Research
area:
Investigations of stable and transient radicals in chemical and biological
systems, Electron Paramagnetic Resonance (EPR), Magnetic Field
Effects (MFEs)
Research
methods:
Continuous and pulsed Electron Paramagnetic Resonance,
Magnetically Affected Reaction Yields (MARY)
Oscillating Magnetic Field Effects (OMFE)
Reaction Yield Detected Magnetic Resonance (RYDMR)
Laser Flash Photolysis
PI
URL
Dr George Wadhams
http://www.bioch.ox.ac.uk/aspsite/research/brochure/armitage/
george.wadhams@bioch.ox.ac.uk
Research
area:
Bacterial motility and chemotaxis, Synthetic biology, Biosensor design
and construction. Molecular understanding of the processes governing
signal amplification and gain in the bacterial chemotaxis system,
synthesis of novel bacterial signalling pathways from existing modular
biochemical components, development of rationally designed signalling
pathways for use as biosensors.
Research
methods:
Microbiology, molecular biology, protein purification, fluorescence
microscopy (including TIRF).
PI
URL
Professor Anthony Watts
http://www.bioch.ox.ac.uk/aspsite/research/brochure/watts/
anthony.watts@bioch.ox.ac.uk
Research
area:
Ligand activation of GPCRs, Membrane protein expression, Membrane
protein reconstitution, Solid state NMR of membrane receptors, Single
molecule studies of membrane receptors, computational approaches to
drug docking, multifrequency electron spin resonance of membrane
proteins.
Research
methods:
Membrane biochemistry and molecular biology, surface plasmon
resonance, solid state NMR, computational simulations, multifrequency
electron spin resonance, bioorganic chemistry for labelling biomolecules
PI
URL
Dr L.-L Wong
luet.wong@chemistry.oxford.ac.uk
Research
area:
Biocatalysis, Redox Enzymes, Biosensors
Research
methods:
Biological Chemistry