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Professor Jane Endicott <Jane by O2F4Xm

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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                    Dr James Allen

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/allen/
                         james.allen@bioch.ox.ac.uk

   Research              Assembly of cytochrome c in the African sleeping sickness parasite. The
   area:                 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.
   Research              Rotation: Microbiological culture (bacterial and eukaryotic); Protein
   methods:              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.

   PI                    Professor Judith P. Armitage

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/armitage/
                         judith.armitage@bioch.ox.ac.uk

   Research              E.coli chemosensing is the best understood sensory system in biology,
   area:                 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              All aspects of cloning, fluorescence microscopy, protein:protein
   methods:              interaction measurement (in vivo by FRET, in vitro by SPR and yeast two
                         hybrid), bioinformatics, behavioural analysis.

   PI                    Professor Fraser Armstrong

   URL                   http://www.chem.ox.ac.uk/researchguide/faarmstrong.html
                         fraser.armstrong@chem.ox.ac.uk

   Research              Biological oxidation and reduction. Mechanistic studies on long-range
   area:                 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.
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   Research              Many electrochemical techniques including ‘protein film volatmmetry’
   methods:              and potential step kinetic methods. Rapid solution kinetics (stopped
                         flow). Electron paramagnetic resonance (EPR). Anaerobic (glovebox
                         techniques. Microbiology, molecular biology and protein chemistry.

   PI                    Professor Hagan Bayley

   URL                   www.chem.ox.ac.uk/bayleygroup/
                         hagan.bayley@chem.ox.ac.uk

   Research              Membrane protein folding, assembly and function; membrane protein
   area:                 engineering; rapid screening of membrane proteins; Bionanotechnology

   Research              Research methods: molecular genetics, protein chemistry, organic
   methods:              synthesis, biophysical measurements including single-channel recording

   PI                    Dr Ben Berks

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/berks/
                         ben.berks@bioch.ox.ac.uk

   Research              Mechanism of an unusual protein transport system; molecular basis of
   area:                 bacterial sulfur oxidation; membrane protein structural biology

   Research              Protein chemistry (protein purification, antibody methodology, in vitro
   methods:              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                    Professor Benjamin G. Davis

   URL                   http://www.chem.ox.ac.uk/researchguide/bgdavis.html
                         http://users.ox.ac.uk/~dplb0149/
                         Ben.Davis@chem.ox.ac.uk

   Research              Chemical Glycobiology, Biocatalysis and Mechanistic Enzymology,
   area:                 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              Mechanistic Enzymology, Synthetic Methodology, Inhibitor and Small-
   methods:              Molecule 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                    Professor Stuart Ferguson

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/ferguson/
                         stuart.ferguson@bioch.ox.ac.uk

   Research              Structure, function, molecular mechanism, biogenesis and assembly of
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   area:                 bacterial respiratory proteins of the Nitrogen cycle.

   Research              Molecular and structural biology; spectroscopy and other biophysical
   methods:              methods; enzymology; protein biochemistry; recombinant protein
                         expression, purification and characterisation

   PI                     Dr Nicholas Lakin

   URL            http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=585
   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.


   Research               Recombinant DNA technology (gene cloning/manipulation), mammalian
   methods:               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                     Professor Chris Schofield

   URL                    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               Molecular and cellular biology, protein purification and characterisation,
   methods:               proteomics (including MS based methodology and techniques for
                          studying protein-protein interactions), structural biophysics, especially
                          crystallography and MS, organic synthesis especially of enzyme
                          inhibitors.

   PI                     Dr Mark Wallace

   URL                    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)

   Research               Single-molecule fluorescence techniques; Laser spectroscopy;
   methods:               Microscopy; Single-channel electrical recording; Protein expression,
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                          purification, and chemical modification.


                         2. SECONDARY 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 and rotation training, thus
                         broadening the research experience and opportunities for creativity
                         of successful candidates.

   PI                    Professor Harry L. Anderson

   URL                   http://users.ox.ac.uk/~hlagroup/
                         harry.anderson@chem.ox.ac.uk

   Research              Design, synthesis and testing of dyes for a wide range of applications,
   area:                 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              Organic synthesis; fluorescence spectroscopy; NMR; mass
   methods:              spectrometry; HPLC; tissue culture experiments.

   PI                    Dr Phil Biggin

   URL                   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              Ionotropic Glutamate Receptors, Nicotinic Acetylcholine Receptors,
   area:                 Neurotransmission, Anti-viral agents, Lipid-drug interactions, Drug-
                         receptor binding, Conformational change in proteins

   Research              Structural Bioinformatics, Molecular Dynamics, Free Energy
   methods:              Calculations, Homology Modelling, Normal Mode Analysis.

   PI                    Professor Raymond Dwek with Dr Nicole Zitzmann

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/zitzmann/
                         nicole.zitzmann @bioch.ox.ac.uk

   Research              Development of antiviral therapeutics for Hepatitis C virus, Hepatitis B
   area:                 virus, and HIV. Biophysical and structural studies of the ion channels.
                         Antiviral drug discovery, ion channel inhibitors and sugar-based anti-HIV
                         therapeutics

   Research              Molecular biology; cell culture; ion channel studies in black lipid
   methods:              membranes; structural and biophysical techniques including
                         crystallography, NMR, circular dichroism, differential scanning
                         calorimetry.

   PI                    Professor T.J. Donohoe
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   URL                   http://www.chem.ox.ac.uk/researchguide/tjdonohoe.html
                         timothy.donohoe@chemistry.oxford.ac.uk

   Research              Synthetic Methodology for Complex Molecules with Biological Activity
   area:
   Research              Synthetic organic chemistry: development of new methodologies for
   methods:              synthetic organic chemistry and asymmetric synthesis, and application to
                         synthesis of biologically important natural products.

   PI                    Professor Jane Endicott

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/endicott/
                         Jane.Endicott@bioch.ox.ac.uk

   Research              Structural and biochemical characterisation of the Plasmodium
   area:                 falciparum protein kinase family.

   Research              Molecular biology, protein purification and characterisation, X-ray
   methods:              crystallography, principles in structure-aided inhibitor design,
                         biophysical techniques to characterise protein-protein interactions, to
                         include SPR and ITC.

   PI                    Dr Antony Fairbanks

   URL                   http://users.ox.ac.uk/~dplb0070/index.html
                         antony.fairbanks@chemistry.oxford.ac.uk

   Research              Glycochemistry; carbohydrate based drug discovery e.g. anti-fungals
   area:                 and antibiotics; glycoprotein and glycopeptide chemistry

   Research              Synthetic methodology, sugar chemistry.
   methods:
   PI                    Dr Elspeth Garman

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/garman/
   Research              Structural Biology Methodology, Crystallography. Macromolecular
   area:                 Crystallography. Methods development. Cryo-techniques and
                         understanding of radiation damage. Metal identification in proteins.
                         Structural studies on neuraminidases.

   Research              Crystallography, microPIXE.
   methods:
   PI                    Professor Penny Handford

   URL                   http://www.bioch.ox.ac.uk/aspsite/research/brochure/handford/
                         penny.handford@bioch.ox.ac.uk

   Research              Molecular Mechanisms of Biological Systems focussing on structural and
   area:                 functional consequences of Notch-ligand interactions; and intra- and
                         inter-molecular interactions of calcium-dependent extracellular matrix
                         proteins

   Research              General molecular biology (DNA and protein analytical methods),
   methods:              specific expertise in vitro refolding of disulphide-rich proteins,
                         measurement of weak, moderate and high affinity calcium binding sites
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                         in proteins, prokaryotic and eukaryotic protein expression, biophysical
                         methods (NMR, crystallography, surface plasmon resonance)

   PI                    Professor Peter J. Hore

   URL                   http://www.chem.ox.ac.uk/researchguide/pjhore.html
                         peter.hore@chemistry.oxford.ac.uk

   Research              Real-time kinetic NMR studies of protein folding
   area:                 Structural studies of partially folded proteins using photo-CIDNP

   Research              High resolution NMR
   methods:              Laser kinetics
                         Photo-CIDNP (Chemically Induced Dynamic Nuclear Polarization)

   PI                     Dr Mark Howarth

   URL                    http://www.bioch.ox.ac.uk/aspsite/research/brochure/howarth/
                          mark.howarth@bioch.ox.ac.uk

   Research               Bionanotechnology and its application to cell signalling and disease
   area:

   Research               Molecular and cellular biology, protein engineering and selection,
   methods:               microscopy, organic synthesis


   PI                     Dr Petros Ligoxygakis

   URL                    http://www.bioch.ox.ac.uk/aspsite/research/brochure/ligoxygakis/
                          petros.ligoxygakis@bioch.ox.ac.uk

   Research               Pathogen recognition by the innate immune system, using a genetically
   area:                  tractable organism (Drosophila melanogaster.) as a model system

   Research               Standard molecular biology (cloning, PCR, RNA work), protein
   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                     Professor Martin Noble

   URL                    http://www.bioch.ox.ac.uk/aspsite/research/brochure/noble/
                          martin.noble@bioch.ox.ac.uk

   Research               Structural studies on regulatory proteins; Adhesive interactions, the cell
   area:                  cycle, and NAT enzymes

   Research               Protein X-ray crystallography and other biophysical methods; drug
   methods:               design; visualization/analysis; protein binding interactions

   PI                     Dr James Parker
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   URL                    http://www.bioch.ox.ac.uk/aspsite/research/brochure/parker/
   Research               Research area: Structural and molecular biology of RNA silencing: RNA
   area:                  interference, microRNAs, piRNAs, Argonaute, Dicer, Slicer -
                          fundamental biology and basic molecular mechanisms

   Research               Molecular biology, protein biochemistry, X-ray crystallography,
   methods:               biophysical methods (isothermal titration calorimetry, analytical
                          ultracentrifugation)

   PI                     Dr Christina Redfield

   URL                    http://www.bioch.ox.ac.uk/aspsite/research/brochure/redfield/
                          christina.redfield@bioch.ox.ac.uk

   Research               NMR methods for characterising partly folded and unfolded proteins
   area:                  and study of ligand-binding protein systems

   Research               Protein NMR methods including double and triple resonance 2D and 3D
   methods:               NMR, 15N relaxation studies and residual dipolar couplings

   PI                     Dr Jason Schnell

   URL                    http://spincore.com/nmrjobs/pos09_08.html
   Research               Structure, function, and inhibition studies of ion channels that are of
   area:                  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               Molecular Biology, Protein Biochemistry, NMR spectroscopy,
   methods:               Mass Spectrometry, Surface Plasmon Resonance, Calorimetry, Time-
                          Resolved Spectroscopies, Structure-Based Drug Design, Combinatorial
                          Library Screening.

   PI                     Dr Lorna Smith

   URL                    http://www.chem.ox.ac.uk/researchguide/ljsmith.html
                          lorna.smith@chem.ox.ac.uk

   Research               Experimental and theoretical methods to characterise partially folded
   area:                  and misfolded proteins. NMR studies of protein structure, dynamics and
                          ligand binding.
   Research               Protein NMR Spectroscopy - 2D and 3D techniques
   methods:               Theoretical molecular dynamics simulations.

   PI                     Dr Christiane R. Timmel

   URL                    http://www.chem.ox.ac.uk/researchguide/crtimmel.html
                          timmel@physchem.ox.ac.uk

   Research               Investigations of stable and transient radicals in chemical and biological
   area:                  systems, Electron Paramagnetic Resonance (EPR), Magnetic Field
                          Effects (MFEs)
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   Research               Continuous and pulsed Electron Paramagnetic Resonance,
   methods:               Magnetically Affected Reaction Yields (MARY)
                          Oscillating Magnetic Field Effects (OMFE)
                          Reaction Yield Detected Magnetic Resonance (RYDMR)
                          Laser Flash Photolysis

   PI                     Dr George Wadhams

   URL                    http://www.bioch.ox.ac.uk/aspsite/research/brochure/armitage/
                          george.wadhams@bioch.ox.ac.uk

   Research               Bacterial motility and chemotaxis, Synthetic biology, Biosensor design
   area:                  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               Microbiology, molecular biology, protein purification, fluorescence
   methods:               microscopy (including TIRF).

   PI                     Professor Anthony Watts

   URL                    http://www.bioch.ox.ac.uk/aspsite/research/brochure/watts/
                          anthony.watts@bioch.ox.ac.uk

   Research                Ligand activation of GPCRs, Membrane protein expression, Membrane
   area:                  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                Membrane biochemistry and molecular biology, surface plasmon
   methods:               resonance, solid state NMR, computational simulations, multifrequency
                          electron spin resonance, bioorganic chemistry for labelling biomolecules

   PI                     Dr L.-L Wong

   URL                    luet.wong@chemistry.oxford.ac.uk

   Research               Biocatalysis, Redox Enzymes, Biosensors
   area:

   Research                Biological Chemistry
   methods:

								
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