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stalliongrapevineBiotechnology

Oct 1, 2013 (3 years and 6 months ago)

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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

D
r J
ames Allen


URL

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
chara
cterize the proteins that do this job in trypanosomes.


Research
methods:


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); Memb
rane 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
area:


E.coli

chemose
nsing 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 spe
cies 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 th
e 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

Professor Fraser Armstrong


URL

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

Professor Hagan Bayley


URL

www.chem.ox.ac.uk/bayleygroup/

hagan.bayley@chem.ox.ac.uk



Research
area:

Membrane protein fo
lding, 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

Dr Ben Berks


URL

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

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
area:

Chemical Glycobiology, Biocatalysis and Mechanistic Enzymology,
Protein and Glycoprotei
n 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, Synthet
ic Methodology, Inhibitor and Small
-
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 S
urfaces, 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
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

Dr Mark Howarth


URL

http://users.ox.ac.uk/~bioc0756/MyWebs/activesite/

mark.howarth@bioch.ox.ac.uk


Research area

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.


Research
m
ethods

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



PI

URL

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 criti
cal 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 an
d signalled to in
i
tiate
the DDR and (ii) how repair of DNA double strand breaks is

regulated.


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

Dr Christina Redfield


URL

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

christina.redfield@bioch.ox.ac.uk



Research
area:

NMR metho
ds 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

Professor Carol Robinson


URL

http://research.chem.ox.ac.uk/carol
-
robinson.aspx

carol.robinson@chem.ox.ac.uk



Research
area:

Study
of membrane protein complexes

3D models of protein complexes


Research
methods:


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

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 i
mpossible
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 bas
ed 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 detecti
on of membrane proteins

(Bionanotechnology, Molecular Mechanisms of Biological Systems,



Physical Biochemistry)



Research
methods:


Single
-
molecule fluorescence techniques; Laser spectroscopy;



Microscopy; Single
-
channel electrical recording; Protein e
xpression,



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
.



PI

Professor Harry L. Anderson


URL

http://users.ox.ac.uk/~hlagroup/

harry.anderson@chem.ox.ac.uk


Research
area:

Design, synthesis and testing of dyes for a wide range of applications,
partic
ularly 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.





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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
area:

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



Research
methods:

Structural Bioinformatics, Molecular Dynamics, Free Energy
Calculatio
ns, 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
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

Professor T.J. Donohoe


URL

http://www.chem.ox.ac.uk/researchguide/tjdonohoe.html

timothy.donohoe@chemistry.oxford.ac.uk



Research
area:

Synthetic Methodology for Complex Molecules with Biological Activity


Research
methods:


Synthetic organic chemistry: development of new
methodologies for
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
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.




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PI

Dr Antony Fairbanks


URL

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

Dr Elspeth Garman


URL

http://www.bioch.ox.ac.uk/aspsite/research/brochure/garman/



Research
area:


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

Professor Penny Hand
ford


URL

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 molec
ular 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, biophysi
cal
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
area:


Real
-
time kinetic NMR studies of protein folding

Structural studies of partially folded proteins using photo
-
CIDNP


Research
methods:


High resolut
ion NMR

Laser kinetics

Photo
-
CIDNP (Chemically Induced Dynamic Nuclear Polarization)






PI

Dr Petros Ligoxygakis


URL

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 p
urification, 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
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

Dr
James Parker


URL

http://www.bioch.ox.ac.uk/aspsite/research/brochure/parker/



Research
area:

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
ultrac
entrifugation)



PI

Dr Jason Schnell


URL

http://spincore.com/nmrjobs/pos09_08.html



Research
area:


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, Time
-
Resolved Spectroscopies, Structure
-
Based Drug Design, Combina
torial
Library Screening.



PI

Dr Lorna Smith


URL

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.


Research
methods:


Protein NMR Spectroscopy
-

2D and 3D techniques

Theoretical mo
lecular dynamics simulations.



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PI

Dr Christiane R. Timmel


URL

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

Dr George Wadhams


URL

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

george.wadhams@bioch.ox.ac.uk




Research
area:


Bacterial motil
ity 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 mo
dular
biochemical components, development of rationally designed signalling
pathways for use as biosensors.



Research
methods:


Microbiology, molecular biology, protein purification, fluorescence
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
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 resonanc
e 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

Dr
L.
-
L Wong


URL

luet.wong@chemistry.oxford.ac.uk



Research
area:


Biocatalysis, Redox Enzymes, Biosensors


Research
methods:



Biological Chemistry