Word - Babraham_Institute - Discovery Biology for Biomedicine
PhD Student Opportunities 2011
The Babraham Institute is an international focus for innovative research in post-genomics
studying gene function in cells, organs and systems, supported principally by the Research
Councils. It is a recognised postgraduate teaching Department of the University of
Cambridge. Starting October 2011 a number of Research Council Quota studentships will be
available at Babraham leading to a University of Cambridge PhD degree. These studentships
can be awarded for up to 4 years. In addition, we will be continuing a new Babraham
European Studentship scheme, funded jointly by the Babraham Institute and the Cambridge
Home and European Scholarship Scheme (CHESS), which will provide full funding for three
further 3 year studentships.
Please see our website (www.babraham.ac.uk) and the BBSRC website
(http://www.bbsrc.ac.uk/funding/training/eligibility.pdf) for details of eligibility and
funding. Non-EU nationals must find funding for academic fees and personal support. In
cases where applicants must find their own funding, we will require evidence that the level
of funding is at least equal to the standard BBSRC/MRC PhD funding package. Students will
join a thriving scientific community situated on an attractive parkland campus near
Cambridge. Our 70 students are all members of Cambridge Colleges and participate fully in
University social and academic life (www.biomed.cam.ac.uk/gradschool/).
Details of our interactive scientific programmes can be found on www.babraham.ac.uk. The
Institute is fully equipped for state-of-the-art biological research including: innovative
molecular biology, stem cell manipulation and transgenics, epigenetics, structural studies on
chromatin, real-time laser scanning confocal microscopy, calcium imaging, fluorescence
sorting of cells, gene targeting and knockouts, mouse models of disease, mouse behavioural
testing, proteomics and lipidomics. The Institute PhD Recruitment Day will be held on
JANUARY 2011 to which selected students will be invited to attend
interviews, discuss their research interests and view the Institute’s facilities.
Full details of potential projects and supervisors are given below; our supervisors welcome
Potential projects (supervisor/title):
Michael Coleman (firstname.lastname@example.org): Mechanisms regulating mitochondrial
trafficking in axons
Anne Corcoran (email@example.com): Does non-coding RNA regulate nuclear
Sarah Elderkin (firstname.lastname@example.org): Understanding regulation of Polycomb
Repressor Complex 1 in embryonic stem cell self renewal and cellular proliferation
Peter Fraser (email@example.com): Long non-coding RNAs and their role in nuclear
compartmentalization, genome organization and epigenetic regulation of gene expression
Jon Houseley (firstname.lastname@example.org): Investigating the roles of non-coding RNA in
Gavin Kelsey (email@example.com): Gender-specificity of imprinting or How sex
dictates gene expression
Nicholas Ktistakis (firstname.lastname@example.org): Functional proteomics of autophagy
Llew Roderick (email@example.com): Signalling to chromatin to control cardiac
hypertrophic gene transcription
Len Stephens (firstname.lastname@example.org): Unraveling the signals that coordinate pathogen
killing in phagosomes using a genome-wide RNAi screen
Martin Turner (email@example.com): Novel pathways for the regulation of
Patrick Varga-Weisz (firstname.lastname@example.org): Muscling into chromatin: Role for
myosin and actin in chromatin remodeling
Marc Veldoen (email@example.com): The maintenance and function of lymphocytes
in the skin
Sonja Vermeren (firstname.lastname@example.org): Analysing ARAP3 in angiogenesis
Michael Wakelam (email@example.com): Regulation of mTOR signalling by
phospholipase D during ageing
Heidi Welch (firstname.lastname@example.org): Targeting Rac-GEF activity
Travel expenses will be paid to those invited to attend our Institute Recruitment Open Day.
Applicants should submit a full Curriculum Vitae with a covering letter indicating the two
projects in which they are most interested, in order of preference, and arrange for two
referees to write to the Institute on their behalf before the deadline; please include your
contact details for 3-19 January. Our website also provides a checklist of the information
required to be provided in your application before it can be considered. Incomplete
applications will not be considered.
Please send your applications to: Ms Caroline Coursol, Graduate Studies Programme, The
Babraham Institute, Babraham, Cambridge CB22 3AT, Tel: 01223 496324, Fax: 01223
496046 or email email@example.com by Friday 17th December 2010
An Equal opportunities employer. An Institute supported by the Biotechnology and
Biological Sciences Research Council
Checklist of Information required for application
- Full Curriculum Vitae including
o Nationality and Residence in UK information
o Details of Schooling including GCSE and A Level results (or other
o Details of University Education including courses taken and results of any
examinations to date
o Degree result (if already known)
o Details of any lab based projects or laboratory placements
o Details of any industrial placements
o Details of any previous employment
- Covering Letter giving the details of the two projects in which you are most
interested and your reasons for choosing them. These projects should be chosen
from different Group Leaders.
- The names and contact information of the two referees you have asked to write to
the Institute supporting your application for a PhD position
- Your contact details between 3rd and 19th January 2011
Projects for 2011 (full description)
Michael Coleman (firstname.lastname@example.org)
Mechanisms regulating mitochondrial trafficking in axons
This project will investigate mechanisms that regulate the trafficking of mitochondria along
axons. Axons face unique intracellular transport challenges as they must deliver proteins
and organelles to their sites of function many centimeters from their origins, and remove
them to sites of degradation when they become non-functional.
Mitochondrial dysfunction contributes to several neurodegenerative disorders including
Parkinson’s disease and peripheral neuropathies. We have developed live imaging methods
and new software (Andrews, Gilley and Coleman, submitted) to quantify mitochondrial
transport both in primary culture and explanted tissue. By combining these methodologies
with Babraham’s extensive resources of PI3 kinase inhibitors and subunit-specific genetically
modified mice, we will test the hypothesis that a specific PI3 kinase subunit regulates axonal
transport of mitochondria. We will then use appropriate inhibitors or mouse strains to
investigate how this is altered in ageing and disease.
Our group works at the forefront of studies into axon degeneration mechanisms, having
identified a mutant protein that greatly delays axon degeneration (Mack et al., 2001) and a
wild-type protein that influences the same pathway (Gilley and Coleman, 2010; Coleman
and Freeman, 2010). Recently we studied the roles of axon pathology in Alzheimer’s disease
(Adalbert et al., 2009) and Huntington’s disease as well as developing new methods for
imaging axonal structure and transport that will be used in this project.
1. Andrews, S., Gilley, J. & Coleman, M.P. Difference Tracker: ImageJ plugins for fully-
automated analysis of multiple axonal transport parameters J Neurosci. Meth.
2. Coleman, M.P. and Freeman, M.R. (2010) Wallerian degeneration, WldS
and Nmnat. Ann
Rev Neurosci. 33: 245-67.
3. Gilley, J. & Coleman, M.P. (2010) Endogenous Nmnat2 is an essential survival factor for
maintenance of healthy axons. PLOS Biol 8: (1) e1000300.
4. Adalbert, R., et al (2008) Severely dystrophic axons at amyloid plaques remain
continuous and connected to viable cell bodies. Brain 132: 402-16.
5. Mack, T.G.A.,, et al (2001) Wallerian degeneration of injured axons and synapses is
delayed by a Ube4b/Nmnat chimeric gene Nature Neuroscience 4: 1199-1206
Anne Corcoran (email@example.com)
Does non-coding RNA regulate nuclear structure?
Recombination of multiple genes in the immunoglobulin and T cell receptor DNA loci
generates the vast repertoire of antibodies and T cell receptors required for a functional
immune system. The focus of our research is to understand the chromatin remodelling
mechanisms that regulate these antigen receptor loci, to facilitate V(D)J recombination in
lymphocytes. Since these DNA loci are the largest in the genome, containing hundreds of
genes that must colocalise, they have evolved several dynamic processes, including nuclear
relocalisation (movement within the nucleus), histone modification, non-coding RNA
transcription, 3D DNA looping (to bring distal genes together). Thus they also provide an
excellent paradigm for chromatin regulation of all multigene loci. In particular, eukaryotic
genomes have recently been shown to produce an enormous number of conserved non-
coding RNAs, which are thought to play a vital role in many nuclear processes, including
developmental regulation of gene expression, gene silencing and formation of functional
nuclear substructures. However, the mechanisms are poorly understood. We have shown
that large non-coding RNA transcripts are generated in the immunoglobulin heavy chain
(Igh) locus prior to V(D)J recombination and are strongly implicated in regulation of
recombination. This project will determine the function of these transcripts. In particular we
will test the hypothesis that these transcripts contribute to movement of the Igh locus and
formation of nuclear substructures that facilitate V(D)J recombination. We will also
investigate a putative role for these transcripts in trafficking of key histone modifying
enzymes to targets in the Igh. State-of-the-art techniques including high-throughput
fluorescence in situ hybridization (FISH), chromatin immunoprecipitation (CHIP), genome-
wide next generation sequencing (NGS) and bioinformatics will be used.
1. Bolland et al 2004, Nature Immunology 5: 630-637
2. Bolland et al 2007, Mol Cell Biol 27:5523-33
3. Featherstone et al 2010, J Biol Chem 285: 9327-38
Sarah Elderkin (firstname.lastname@example.org)
Understanding regulation of Polycomb Repressor Complex 1 in embryonic stem cell self
renewal and cellular proliferation
Polycomb-group (PcG) repressor proteins are key epigenetic regulators involved in both
establishing gene expression patterns and maintaining long-term cellular memory.
Maintenance of cellular gene expression memory is an important process in regulation of
embryonic stem cell self renewal, cell identity, cell proliferation and tumor development
(Sparmann and van Lohuzin 2006).
PcG proteins form large multi-protein complexes. The Polycomb Repressor Complex 1
(bmiPRC1) containing the Bmi1 subunit has been shown to be an E3 ubiquitin ligase that
modifies chromatin by mono-ubiquitylation of histone H2A lysine 119. This epigenetic
modification has been associated with gene repression (Wang et al. 2004). In mammalian
cells multiple paralogues for the core PRC1 subunits have been identified. Recently we have
identified a novel PRC1-like complex melPRC1 which contains the Bmi1 paralogue Mel-18.
Additionally we have found that melPRC1 mediates gene repression through mono-
ubiquitylation of H2A lysine 119 is regulated by phosphorylation (Elderkin et al. 2007).
We are particularly interested in understanding how epigenetic modifying PRC1-like
complexes are potentially regulated by different signalling pathways and how specific
genomic loci are silenced by different polycomb complexes to maintain specific transcription
profiles in mammalian cells.
The PhD project in our laboratory will involve understanding mechanistically how different
genomic loci are regulated by specific polycomb complexes in embryonic stem cells. This
project will provide strong training in embryonic stem cell and epigenetics research, protein
and chromatin biochemistry, molecular biology and bioinformatics.
Peter Fraser (email@example.com)
Long non-coding RNAs and their role in nuclear compartmentalization, genome
organization and epigenetic regulation of gene expression
We have identified a number of novel, long non-coding RNAs (ncRNA) that are enriched in,
or restricted to, the nuclei of cells. This project will use various state-of-the-art fluorescence
in situ hybridization (FISH) and imaging techniques to investigate the nuclear positioning
and potential compartmentalization of these ncRNAs (Nagano et al., 2008). The applicant
will use RNA TRAP (Carter et al., 2002; Nagano et al., 2008) adapted for high-throughput
sequencing to comprehensively investigate and identify in vivo chromatin/gene targets of
the most interesting of these ncRNAs. Potential ncRNA roles in chromatin modification,
packaging, locus sequestration and nuclear genome organization (Nagano and Fraser, 2009)
will be investigated using ChIP, 3C, 4C and Hi-C techniques. The successful applicant will join
have the enthusiasm and intellectual qualities needed to generate and analyze large
datasets, with the aim to understand novel gene regulatory mechanisms.
1. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R and Fraser P (2008)
The Air non-coding RNA epigenetically silences transcription by targeting G9a to
chromatin. Science 322,1717-1720.
2. Carter, D., Chakalova, L., Osborne, C.S., Dai, Y-F, Fraser, P. (2002) Long-range chromatin
regulatory interactions in vivo. Nat. Genet., 32,623-626.
3. Nagano T, Fraser P. (2009) Emerging similarities in epigenetic gene silencing by long
noncoding RNAs. Mamm Genome 20:557–562
Jon Houseley (firstname.lastname@example.org)
Investigating the roles of non-coding RNA in meiotic recombination
Only a tiny fraction of the human genome encodes proteins, but recent studies show that
almost the entire genome is transcribed into RNA. This means that many more genes
produce RNA than produce proteins, and the key aim of my research is to find functions for
these non-protein coding RNAs.
We are particularly interested in the potential roles of non-coding RNAs in coordinating
genome rearrangements. Although genomes are often thought of as largely unchanging,
they undergo extensive recombination during meiosis, the specialised cell division required
for sexual reproduction. These recombination events are vital for successful meiosis and are
responsible for most of the mixing of parental traits in children.
We and others have found evidence that non-protein coding RNAs and their associated
enzymes can influence DNA recombination. This raises the fascinating possibility that non-
coding RNAs can influence genome changes, and therefore that organisms have the ability
to control how traits are assorted between progeny during reproduction. Furthermore,
studies of meiotic recombination are medically important as cells that undergo too little
recombination or recombination in the wrong place end up aneuploid, leading to
miscarriages and conditions such as Down Syndrome.
The aim of this PhD project is to investigate the roles of non-coding RNAs in coordinating
meiotic recombination. It will particularly focus on the changes in chromosome structure
that precede recombination and the importance of these changes to the initiation of
The realisation that cells produce so much non-coding RNA provides new areas of
fundamental biology to explore, and non-coding RNAs are of considerable pharmaceutical
interest. This project will provide much sought-after experience in this fast-moving area of
biology, which should be very beneficial to the successful candidate's future scientific
1. Houseley, J., Kotovic, K., El Hage, A. & Tollervey, D. Trf4 targets ncRNAs from telomeric
and rDNA spacer regions and functions in rDNA copy number control. Embo J 26, 4996-
2. Kobayashi, T. & Ganley, A. R. Recombination regulation by transcription-induced cohesin
dissociation in rDNA repeats. Science 309, 1581-1584 (2005).
3. Houseley, J. & Tollervey, D. The many pathways of RNA degradation. Cell 136, 763-776
4. Nowacki, M. et al. RNA-mediated epigenetic programming of a genome-rearrangement
pathway. Nature 451, 153-158 (2008).
5. Wahls, W. P., Siegel, E. R. & Davidson, M. K. Meiotic recombination hotspots of fission
yeast are directed to loci that express non-coding RNA. PLoS ONE 3, e2887 (2008).
Gavin Kelsey (email@example.com)
Gender-specificity of imprinting or How sex dictates gene expression
Genomic imprinting is a form of epigenetic regulation that results in the alleles of certain
genes being expressed with a legacy of their parental origin, and is profoundly important for
embryonic growth and development in mammals. This parental-allele dependent gene
activity is determined by primary imprint marks (at imprinting control regions, ICRs) which
are laid down in gametes and stably maintained in somatic cells (Reik & Walter, 2001). A
fundamental question is what is the mechanism responsible for germline-specific marking?
Most known ICRs are marked by DNA methylation in oocytes, fewer acquire methylation
specifically in male germ cells. Our work has identified components necessary for targeting
DNA methylation to ICRs in oocytes (Chotalia et al., 2009), and shown that: it requires the
ICR promoter to be quiescent; it depends on transcription across the ICR from an upstream
promoter; and is likely to require an appropriate set of histone modifications (e.g., lack of
H3K4methylation; Ciccone et al., 2009). Transcription through ICRs may down-regulate ICR
promoters to be methylated and/or establish a permissive histone modification pattern.
Although we have a model for maternal germline marking, we also need to account for why
these sequences are resistant to methylation in male germ cells. This project addresses the
crucial question of gender-specificity in imprint establishment. We shall apply the logic
underlying female germline ICR marking to male germ cells at the time of methylation
establishment to discover why these ICRs are specifically protected. Analysis will be done at
several imprinted loci using FACS-purified populations of male germ cells. Genome-wide
studies employing next generation sequencing could be undertaken to extend to other
sequences methylated specifically in oocytes that we have identified in genome-wide
studies. The results of these analyses will lead to mechanistic studies, utilising transgenic,
knock-down or targeting approaches, to examine the role of specific factors implicated in
protection from methylation.
1. Chotalia et al., (2009) Transcription is required for establishment of germline
methylation marks at imprinted genes. Genes & Dev. 23:105-117.
2. Ciccone et al., (2009) KDM1B is a histone H3K4 demethylase required to establish
maternal genomic imprints. Nature 461:415-418.
3. Reik & Walter (2001) Genomic imprinting: parental influence on the genome. Nat. Rev.
Nicholas Ktistakis (firstname.lastname@example.org)
Functional proteomics of autophagy
Autophagy is an important cellular response to nutrient availability and stress. It is
frequently altered in many disease models including cancer and neurodegeneration.
Autophagy is also required for life span extension. Autophagosomes are novel organelles
formed during autophagy that mediate the autophagic response. We have recently
proposed that autophagosomes are formed within omegasomes, novel membrane
compartments enriched in phosphatidylinositol 3-phosphate and connected to the
endoplasmic reticulum. Previous work in my lab has led to the isolation of omegasomes and
the characterization of some of the proteins that are found there. This project will explore
the function of these proteins during autophagosome formation.
1. Axe EL, Walker SA, Manifava M, Chandra P, Roderick HL, Habermann A, Griffiths G and
N.T. Ktistakis 2008. J Cell Biol 182: 685-701
2. Burman C, Ktistakis NT. 2010 FEBS Lett 584: 1302-1312 Special Issue on Autophagy, N.
3. Burman C, Ktistakis NT. 2010 Seminars in Immunopathology, in press.
Llew Roderick (email@example.com)
Signalling to chromatin to control cardiac hypertrophic gene transcription
Cardiovascular diseases including heart failure and cardiac hypertrophy are the greatest
causes of morbidity and mortality in the UK. Although, hypertrophy (heart muscle growth
without cell division) induced by injury, genetic factors or prolonged hypertension are a
precursor of heart failure, cardiac hypertrophy induced by exercise or pregnancy, for
example, improve cardiac function. Moreover, whereas, physiological hypertrophy is
reversible, pathological hypertrophy is not. Understanding the mechanisms underlying the
induction and progression of cardiac hypertrophy as well as the differences between the
beneficial and the pathological forms of hypertrophy are therefore key steps to the
development of future therapy. Research in our laboratory has pinpointed nuclear-localised
calcium signals acting via specific transcription factors including NFAT as key to the
induction of hypertrophy (Mol Cell 2009). Although modulation of histone acetylation is
now also known to play a key role in the activation of hypertrophic gene phosphorylation,
the role of other epigenetic modifications including methylation and phosphorylation is not
determined. We hypothesise that histone methylation is instrumental in the transcriptional
reprogramming. Moreover, we predict that different hypertrophic stimuli cause a
characteristic signature of histone modifications and that this code determines the
hypertrophic phenotype. To test these hypotheses, using animal and cell models of
hypertrophy, the student will analyse the effect of pathological and physiological
hypertrophic stimuli on methylation of histones of different hypertrophic gene markers
(pathological and physiological), investigate the role of epigenetic modifiers in this process
(histone methylases/demethylases) and analyse the signal transduction pathways involved.
1. Higazi, D.R., Fearnley, C.J., et al., (2009) Endothelin-1-stimulated InsP3-induced Ca2+
release is a nexus for hypertrophic signaling in cardiac myocytes. Mol Cell, 33, 472-482.
Len Stephens (firstname.lastname@example.org)
Unraveling the signals that coordinate pathogen killing in phagosomes using a genome-
wide RNAi screen
Phagocytes such as neutrophils and macrophages are responsible for the detection,
phagocytosis and destruction of many bacterial and fungal pathogens. These pathogens are
detected by a range of cell-surface receptors that either recognise characteristic foreign
molecules or host-derived complexes specifically decorating the pathogen surface. Once
engaged the pathogens are drawn in and engulfed by the process of phagocytosis that
culminates in the pathogen being sealed inside the phagocyte in a structure called the
phagosome. Once created the phagosome changes rapidly, other intracellular membranes
fuse and digestive enzymes, ions and reactive oxygen species (ROS) are pumped inside to kill
and digest the contents. These processes are crucial to health, a number of life-threatening
diseases result either from their dysfunction or from pathogens capable of evading this
We have shown that a key event coordinating this process is the production of the signaling
lipid phosphatidylinositol 3-phosphate (PI3P) in the phagosomal membrane by the class III
. This event leads to the movement of a ROS-generating protein complex, via
the ability of one of its components (p40PHOX) to specifically bind PI3P through its PX
domain, to the cytosolic surface of the phagosome and hence drive transport of ROS into
. In keeping with this, mutations in the PX domain of p40PHOX, that prevent
PI3P binding, cause a human immunodeficiency syndrome4
and in mice reduce their ability
to kill pathogenic bacteria such as Staphylococcus aureus5,6
. Furthermore, it is likely that
there are further PI3P binding proteins involved in this pathway.
Despite our detailed understanding of components of this pathway, the signals between the
pathogen-recognition receptors and the engagement of VPS34 with the phagosome are
unknown. VPS34 is also known to be a regulator of other important cell responses, such
nutrient-stimulated cell growth and intracellular trafficking of proteins, in organisms from
yeast to man. In none of these settings, however, do we have a detailed molecular
understanding of how VPS34 activity is controlled. Hence an explanation of how VPS34 is
regulated during phagocytosis would have very broad significance.
We have model cell lines that can phagocytose defined pathogens and express a fluorescent
GFP-PX domain reporter construct that will dynamically localize to phagosomes in response
to the accumulation of PI3P. Using fluorescence microscopy it is possible to visualize and
quantify the accumulation of the reporter around phagosomes as an indirect measure of
VPS34 activity in this compartment. In the context of our existing robotic liquid handling
machines, high-throughput confocal microscope and image analysis software it is possible to
perform such assays in 96-well tissue culture plates very rapidly. Hence we propose to use a
genome-wide RNAi library (Dharmacon, 22,000 targets) to test the effects of individually
suppressing the expression of all human genes on the ability of the reporter to decorate
We expect a wide variety of hits, including activators and inhibitors and both novel and
known molecules, that will need to be validated, classified and prioritized for further study
as potential members of the network of molecules that control VPS34 and the maturation of
1. Anderson, K.E., et al. CD18-dependent activation of the neutrophil NADPH oxidase
during phagocytosis of Escherichia coli or Staphylococcus aureus is regulated by class III
but not class I or II PI3Ks. Blood 112, 5202-5211 (2008).
2. Ellson, C.D., et al. Phosphatidylinositol 3-phosphate is generated in phagosomal
membranes. Curr Biol 11, 1631-1635 (2001).
3. Ellson, C.D., et al. PtdIns(3)P regulates the neutrophil oxidase complex by binding to the
PX domain of p40(phox). Nat Cell Biol 3, 679-682 (2001).
4. Matute, J.D., et al. A new genetic subgroup of chronic granulomatous disease with
autosomal recessive mutations in p40 phox and selective defects in neutrophil NADPH
oxidase activity. Blood 114, 3309-3315 (2009).
5. Ellson, C., Davidson, K., Anderson, K., Stephens, L.R. & Hawkins, P.T. PtdIns3P binding to
the PX domain of p40phox is a physiological signal in NADPH oxidase activation. Embo J
25, 4468-4478 (2006).
6. Ellson, C.D., et al. Neutrophils from p40phox-/- mice exhibit severe defects in NADPH
oxidase regulation and oxidant-dependent bacterial killing. J Exp Med 203, 1927-1937
7. Herre, J., et al. Dectin-1 uses novel mechanisms for yeast phagocytosis in macrophages.
Blood 104, 4038-4045 (2004).
Martin Turner (email@example.com)
Novel pathways for the regulation of lymphocyte development
B lymphocytes develop in the mammalian bone marrow and T lymphocytes develop in the
thymus after passing through a well-characterised series of intermediate stages. The
progression and phenotype of cells can be assessed by their cell surface phenotype and
their transcriptional profile. This type of approach has led to the emergence of a concept of
transcriptional networks controlling lymphocyte development, with one or a few
transcription factors acting as “master regulators”. Work from our group has placed
emphasis on post-transcriptional processes and their impact on the development and
function of lymphocytes.
Post-transcriptional processes affect the handling of RNA after transcription and can
influence the expression of genes by altering the stability of the mRNA or by changing the
rate at which the mRNA is translated into protein. Small RNAs called microRNAs are one
aspect of this level of control. RNA binding proteins are also key regulators of mRNA
stability and translation. In the project the student will examine the role and mechanism of
RNA binding protein function using conditional gene expression mouse models of
1. Hodson et al. Nature Immunology 2010 Aug; 11(8):717-24 and comment in Nat
Immunol. 2010 Aug; 11(8):697-8.
Patrick Varga-Weisz (firstname.lastname@example.org)
Muscling into chromatin: Role for myosin and actin in chromatin remodeling
Actin and myosin are force-generating molecules that have many important functions in cell
mobility and cell shape. Over the last few years, it has become clear that these factors also
have roles in the nucleus and are important cofactors for transcription. What these proteins
do in the nucleus precisely and how they exert their function is largely an enigma. Actin and
actin-related proteins are stable components of several chromatin remodeling factors. We
will study what is the link between myosin and actin-containing chromatin remodeling
factors in transcription regulation, DNA replication and repair. Our hypothesis is that myosin
targets remodeling factors in response to environmental signals to control chromatin shape
and position. We will combine yeast genetics with genome-wide binding maps to analyze
the role of myosin in nuclear processes. We will use chromosome conformation capture
technology and live cell imaging to map how the myosin-actin interaction dynamically
shapes chromosomes in the living cell. We will study how the interaction between myosin
and chromatin is regulated. Initially, these studies will be done in yeast, but if successful, we
will test principles in mammalian cells in culture.
1. Fission yeast Iec1-ino80-mediated nucleosome eviction regulates nucleotide and
phosphate metabolism. Hogan CJ, Aligianni S, Durand-Dubief M, Persson J, Will WR,
Webster J, Wheeler L, Mathews CK, Elderkin S, Oxley D, Ekwall K, Varga-Weisz PD. Mol
Cell Biol. 2010 Feb;30(3):657-74.
2. Regulation of higher-order chromatin structures by nucleosome-remodelling factors.
Varga-Weisz PD, Becker PB. Curr Opin Genet Dev. 2006 Apr;16(2):151-6. Review.
Marc Veldoen (email@example.com)
The maintenance and function of lymphocytes in the skin
The mammalian host is engaged in continuous mutual communication with its environment,
which provide invaluable signals that maintain a healthy state of being. These interactions
often involve small chemical messenger molecules some of which can be derived from the
abundantly present and diverse comensal microbiota that occupy the epithelial sites, the
skin and gastro-intestinal tract (Hooper et al., 2002). But interestingly, other factors can be
more directly derived from the physical world around us, e.g. the direct exposure to sunlight
activates a cholesterol precursor, resulting in the production of cholecalciferol (Vitamin D3).
Its converted products, not only regulate concentration of calcium and phosphate in the
blood stream but can also function as a cytokine, enhancing the body's defensive
mechanisms against invading microorganisms (Adams and Hewison, 2010).
Epithelial sites, contain their own specialised subsets of lymphocytes. These cells are
thought to have specialised functions in host-defence mechanisms, epithelial barrier
formation and in the maintenance of a healthy microbiota (Swamy et al., 2010). Preliminary
results in our lab indicate that a close relationship exists between some populations of
lymphocytes in the skin and external factors that together impact the maintenance of a
healthy and well functioning epithelial barrier.
The successful applicant will study the development and maintenance of skin lymphocytes
under carefully managed conditions, and will investigate the consequences of altered
environmental circumstances on the functioning of the epithelial barrier as well as the
1. Adams, J.S., and Hewison, M. (2010). Update in vitamin D. J Clin Endocrinol Metab 95,
2. Hooper, L.V., Midtvedt, T., and Gordon, J.I. (2002). How host-microbial interactions
shape the nutrient environment of the mammalian intestine. Annu Rev Nutr 22, 283-
3. Swamy, M., Jamora, C., Havran, W., and Hayday, A. (2010). Epithelial decision makers: in
search of the 'epimmunome'. Nat Immunol 11, 656-665.
Sonja Vermeren (firstname.lastname@example.org)
Analysing ARAP3 in angiogenesis
A vascular system is crucial for the provision of nutrients and oxygen to the developing
organism. Initially, precursors fuse to form a primitive vascular plexus as well as the dorsal
aorta by a process termed vasculogenesis. Later, this primitive plexus is remodelled by
angiogenesis to form a mature network of arteries and veins, which are connected by
capillaries . This involves the formation of new vessels by sprouting, by splitting of
existing vessels, and by pruning of the pre-existing primitive plexus. Angiogenesis requires
tight co-ordination of multiple important processes including cell growth, differentiation
and motility. Outside of development, angiogenesis is also important for a number of
pathological situations, one example being tumour growth.
ARAP3 is a GTPase activating protein for the small GTPases RhoA and Arf6, which is
regulated by phosphoinositide 3-OH kinase (PI3K) and the small GTPase Rap [2-4]. The
catalytic function of PI3Ka is absolutely required for angiogenesis . We showed recently
in vivo and ex vivo that PI3K signalling through ARAP3 is essential for developmental
angiogenesis . However, Rap has also been shown to be required for angiogenesis .
Aim of this project is to address, whether ARAP3 might act as a co-incidence detector for
signals from Rap and PI3K, to regulate Arf and Rho GTPases in angiogenesis. To address this,
you will analyse angiogenesis in a variety of assays both in vitro and in vivo, focusing on
sprouting of new vessels, which in turn depends on cell motility. You will use primary
endothelial cells in which ARAP3 has been knocked down retrovirally using siRNA to perform
motility and sprouting assays. In addition, you will analyse sprouting angiogenesis in murine
hindbrain and retina samples.
The successful candidate should be a highly motivated and enthusiastic individual. He or she
will join a young and dynamic group. You will acquire diverse skills in the fields of cell
biology, molecular biology, immunohistochemistry, imaging, as well as in vitro assays.
1. Adams & Alitalo (2007) Molecular regulation of angiogenesis and lymphangiogenesis.
Nat Rev Mol Cell Biol 8,464.
2. Krugmann et al. (2002) Identification of ARAP3, a PI3K effector regulating both Arf and
Rho GTPases, by selective capture on phosphoaffiinity matrices. Mol Cell 9, 95.
3. Krugmann et al. (2004) ARAP3 is a PI3K and Rap-regulated GAP for RhoA. Curr Biol 14,
4. Craig et al. (2010) ARAP3 binding to phosphatidylinositol-(3,4,5)-trisphosphate depends
on N-terminal tandem PH domains and adjacent sequences. Cell Signal 22, 257.
5. Graupera et al. (2008) Angiogenesis selectively requires the p110a isoform of PI3K to
control endothelial cell migration. Nature 453, 662.
6. Gambardella et al. (2010) PI3K signalling through ARAP3 is essential for developmental
7. Chrzanowska-Wodnicka et al. (2008) Defective angiogenesis, endothelial migration,
proliferation, and MAPK signaling in Rap1b-deficient mice. Blood 111, 2647.
Michael Wakelam (email@example.com)
Regulation of mTOR signalling by phospholipase D during ageing
Rapamycin is a potent antifungal metabolite that inhibits proliferation of mammalian cells
and possesses immunosuppressive properties. The mammalian target of Rapamycin, mTOR,
is a serine/threonine kinase that is present in all eukaryote organisms, and has been
implicated in regulating life span. During development, mTOR primarily regulates growth,
but in the adult, where there is relatively little growth, mTOR controls ageing.
mTOR integrates signals received from growth factors, nutrients, stress and the energy
status of cells, to regulate cellular growth, autophagy, proliferation and shape. Aberrant
mTOR activity results in the initiation and progression of several age-related diseases. These
include human cancers, the development of autoimmune disorders such as rheumatoid
arthritis and Parkinson’s disease, cardiac hypertrophy and type II diabetes. Consequently,
mTOR inhibitors such as Rapamycin may be useful therapeutic agents for several age-
related human diseases.
The Ras-related small G protein, Rheb, activates mTOR and has been shown to induce
oncogenic transformation in vitro, and to produce the rapid development of lymphomas
and prostate tumours in vivo. The tumourigenic activity of Rheb is dependent on mTOR
Rheb activates mTOR in response to growth factors and nutrients by two distinct
mechanisms; (1) Rheb binds to an endogenous inhibitor of mTOR, FKBP38, thereby
antagonising the inhibition of mTOR by FKBP38, and (2) Rheb binds to and activates
phospholipase D1 (PLD1), thereby elevating the levels of the lipid second messenger
phosphatidic acid (PA), a direct activator of mTOR.
Mammalian cells express a second isoform of phospholipase D, PLD2, which has also been
reported to also regulate mTOR. However, in contrast to PLD1, PLD2 does not appear to be
regulated by Rheb, but instead binds to Raptor, an mTOR-interacting protein that is required
for mTOR signalling.
The aim of this studentship is to: (1) investigate the physiological significance of the
Rheb/PLD1/mTOR and PLD2/Raptor/mTOR pathways in regulating mTOR signalling in
response to growth factors, nutrients, stress and the energy status of the cell; (2) determine
if the tumourigenic activity of Rheb is also dependent on PLD activity; and (3) elucidate the
mechanism(s) of PLD/PA regulation of mTOR activity and the importance of these pathways
in controlling autophagy.
These aims will be achieved through the use of a set of novel isoform-specific PLD1 and
PLD2 inhibitors in established model cell lines, and the use of primary cells isolated from
mice that no longer express PLD1 and/or PLD2. The possible importance of PLD acting as a
scaffolding protein in regulating these pathways will be investigated by transfection of
catalytically inactive PLD1 or PLD2 into cells isolated from the knockout mice. Plan B will
focus upon determining the molecular regulation of the mTOR complex in vitro – the
proteins and lipids are available in the lab.
Heidi Welch (firstname.lastname@example.org)
Targeting Rac-GEF activity
The small G protein Rac is a key regulator of cytoskeletal structure (and hence cell shape,
adhesion, motility, phagocytosis, regulated secretion), gene expression and oxygen radical
formation. Dysregulated Rac activity is implicated in a broad range of human disorders
ranging from cancer metastasis to inflammatory conditions. Hence, the ability to control Rac
activity with drugs would be useful tool in the fight against a range of clinically important
human pathologies. However, targeting of Rac activity itself does not seem a good idea,
because of the plethora of functional roles which Rac fulfils and the therefore likely
devastating side-effects of any such direct drugs.
Like all small G proteins, Rac is activated by guanine-exchange factors (GEFs), and just like
Rac itself, Rac-GEFs are implicated in a variety of human diseases, mainly immune disorders,
cancer and developmental disorders. Rac-GEFs greatly outnumber Rac isoforms, and
different types of GEFs couple Rac to different signalling pathways. Therefore, it seems
more promising to target the activities of specific Rac-GEFs rather than Rac activity itself.
For activation of Rac, the catalytic domain of Rac-GEFs forms a transient protein / protein
interaction with Rac. Largely due to structural complexity, this interaction between GEFs
and Rac has, until recently, not received much attention as a potential target for novel
therapeutics. However, several groups have recently succeeded in identifying small
molecule inhibitors that target this interaction specifically, notably NSC23766 and EHT1864
(Gao Y et al, 2004, PNAS 18:7618; Shutes A, et al, 2007, 282:35666), although the potency of
these early compounds is low.
Our lab focuses on one particular family of Rac-GEFs that we discovered a few years ago, the
P-Rex family (Welch HC et al, 2002, Cell 108:809). The P-Rex family controls the function of
neutrophils (cell of the innate immune system that clear bacterial and fungal infections;
Welch HC et al, 2005, Curr Biol) and of Purkinje neurons (cells in the cerebellum which
regulate fine motor control; Donald S et al, 2008, PNAS 105:4483). There is also exciting
recent evidence for P-Rex family involvement in cancer metastasis (Fine et al, 2009, Science
325:1261; Qin et al, 2009, Oncogene 28:1853; and unpublished results). Hence, P-Rex family
Rac-GEFs seem valid targets for the development of novel therapeutics.
We have very recently embarked on developing inhibitors for the P-Rex family, starting with
a basic modeling approach to identify possible candidate compounds that may inhibit the P-
Rex-dependent activation of Rac. Quite surprisingly, we have obtained very encouraging
preliminary results in vitro, notably regarding the potency of our compounds (unpublished).
This PhD project is the detailed characterisation of these early lead P-Rex inhibitors for their
potency and specificity in vitro and in vivo. It involves in vitro and in vivo GEF assays with a
range of GEFs (P-Rex, isolated P-Rex domains, other types of GEFs) and substrates (Rac and
other GTPases) as well as assays for Rac-dependent cell functions in transfected cell lines
(e.g. cell shape, motility, invasion assays) and in primary cells, such as isolated neutrophils
that either express or lack P-Rex. Depending on the data obtained on specificity and potency
of the compounds in the early phases of characterisation, there is also a possibility of
further testing of the inhibotors in murine models of inflammatory disorders and metastasis
later on. This project has the potential to move P-Rex inhibition towards a translation phase
and render the compounds commercially exploitable for the development of anti-
inflammatory or anti-metastatic drugs in the future.