Nerve cells are connected into neuronal networks which constitute the cellular basis of brain function. Within these network, long thin cellular protrusions called axons convey neuronal messages and pass them on at synapses to other neurons, muscles or gland cells. The growth of axons is therefore a key process during brain development and regeneration. The molecular machinery underlying axonal growth provides key drug targets for the treatment of stroke or paralysis patients, or of impaired nerve regeneration in diseases (e.g. diabetes). This project aims to decipher the molecular mechanisms of this machinery, thus addressing a key challenge to modern neurobiology.
Extracellular signalling factors line the path of growing axons and guide them towards their target areas in the brain. But the actual growth of axons is executed by the cytoskeleton, composed of actin and microtubules. You will investigate the molecular mechanisms mediating between signalling factors and cytoskeleton. To this end you will use unique strategies available for the genetic model organism Drosophila, based on a neuronal cell culture system established in our group. In this system, regulatory mechanisms of axonal growth can be dissected with an unparalleled repertoire of genetic and pharmacological means. Given the universal requirements of cytoskeletal dynamics for most cell functions, your work will have further implications in other relevant areas of investigation, such as cancer biology, neurodegenerative diseases (e.g. Alzheimer's) or pathologies, such as mental retardation.
During this project you will gain excellent training in biotechnology. You will generate cell cultures from neural embryonic stem cells or dissociated brains, use sophisticated genetic strategies and molecular biology techniques, generate transgenic animals, employ drugs for pharmacological manipulations, and use advanced microscopy including live imaging. The postgraduate training programme of Manchester's Faculty of Life Sciences will enable you to prepare for all aspects of your future career.
 

• Lowery & van Vactor, 2009, Nat Rev Mol Cell Biol 10, 332ff.
• Sánchez-Soriano et al., 2007, Neural Develop 2, 9ff.
• Sánchez-Soriano et al., 2010, Dev. Neurobiol. 70, 58ff.
• Sánchez-Soriano et al., 2009, J Cell Sci 122, 2534ff. 

• Animal Biology
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Genetics
• Molecular and Cellular Neuroscience
• Molecular Biology
• Neuroscience

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Adult stem cells reside in a variety of niches, including the bone marrow. Bone marrow-derived cells (BMDCs) contain a subpopulation of multipotent stem cells that can migrate to peripheral tissues and, once there, differentiate and contribute to the maintenance of that tissue. BMDCs also appear to play an extensive role in repair and regeneration. For example, in skin, a small number of BMDCs routinely migrate to the dermis and contribute to many resident cell populations. This process is dramatically ‘ramped up’ in response to injury, and then returns to normal as wound healing resolves and homeostasis is achieved.

Previously we demonstrated that the transcription factor, Hoxa3, significantly promotes angiogenesis during tissue repair and regeneration (Mace et al., 2005 J Cell Sci). Subsequent analysis of GFP bone marrow chimeras during wound repair in mice with attenuated Hoxa3 expression revealed that Hoxa3 can modulate the recruitment of different bone marrow-derived cell (BMDC) types to the site of injury. For example, directed Hoxa3 expression in the wound promotes the recruitment of endothelial progenitor cells, while reducing the number of inflammatory cells recruited. The balance of different BMDC types present in the injured tissue can profoundly affect the repair and regeneration process.

This project may involve the identification of which BMDCs are recruited to the wound at different times, experimental manipulation of these populations in vitro and in vivo and the analysis of BMDC differentiation at the site of injury.

• Mace KA, Hansen SL, Myers C, Young DM, Boudreau N, (2005) HOXA3 induces cell migration in endothelial and epithelial cells promoting angiogenesis and wound repair. Journal of Cell Science 118: 2567-77.
• Yaojiong Wu MD, PhD, JianFei Wang DVM, PhD, Paul G. Scott PhD, Edward E. Tredget MD, MSc, FRCSC (2007) Bone marrow-derived stem cells in wound healing: a review. Wound Repair and Regeneration 15: S18–S26.

• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Gene Expression
• Immunology
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The Bone Morphogenetic Protein (BMP) signalling pathway has critical roles in human development. Disruption of BMP signalling leads to many human diseases including cancer, bone disorders, kidney disease and vascular disorders. In addition, the BMP signalling pathway has wide-ranging roles in various stem cell systems. In my lab we are using the genetically tractable Drosophila model organism to investigate how the BMP signalling pathway is regulated to ensure correct embryonic development and maintenance of germline stem cells. Various projects exist in this area including 1) identification of target genes on a genome-wide scale; 2) analysis of transcriptional and translational control; 3) role of the SUMO post-translational modification; 4) links to the miRNA pathway; 5) role of the extracellular matrix. We use cutting edge genomics approaches and state-of-the-art microscopy, combined with molecular biology, biochemical and cell/developmental biology techniques. Results from our findings are directly relevant to BMP signalling in human development and its misregulation in diseases such as cancer.

Harris, R.E., Pargett, M., Sutcliffe, C., Umulis, D. and Ashe, H.L. Brat promotes stem cell
differentiation via control of a bistable switch that restricts BMP signalling. Submitted.

Wang, X., Harris, R.E., Bayston, L.J.and Ashe, H.L. (2008). Type IV collagens regulate BMP
signalling in Drosophila. Nature 454, 72-78.

Miles, W.O., Jaffray, E., Campbell, S.G., Takeda, S., Bayston, L.J., Basu, S.P., Li, M., Raftery, L.A.,
Ashe, M.P., Hay, R.T. and Ashe H.L. (2008). Medea SUMOylation restricts the signaling range of
the Dpp morphogen in the Drosophila embryo. Genes and Development 22, 2578-90..

Ashe, H. L. (2008). Type IV collagens and Dpp: positive and negative regulators of signaling. Fly
2, 313-315.

Ashe, H. L. and Briscoe, J. (2006). The Interpretation of Morphogen Gradients. Development 133,
385-394.
 

• Animal Biology
• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Gene Expression
• Genetics
• Molecular Biology
• Molecular Cancer Studies
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

When cell migration goes wrong, it can have catastrophic consequences, for example resulting in cancer cell invasion. Understanding how cell migration is regulated at the molecular level is therefore important for the development of novel disease treatments and therapeutic agents. Live imaging of embryonic development, wound healing and immune responses has revealed the incredible importance of cell migration, whilst providing tools to study its role and regulation. Using these techniques we have found that cell type specific motility and adhesion during development requires the correct regulation of a small GTPase (Rap1) and the cell matrix associated protein Filamin. In this project, you will use a combination of genetics (mutagenesis), biochemistry (proteomics) and live cell imaging (3D imaging of cell movement) to identify novel genes that regulate Rap1 and Filamin complex activity, cell adhesion and cell migration.

• Parkinson K., Bolourani P., Traynor D., Kay R.R., Weeks G. and *Thompson C.R.L. (2008) Cell Type Specific Regulation of Rap1 Activity is Required for Patterning and Morphogenesis in Dictyostelium. Journal of Cell Science, in press
• Keller T. and *Thompson C.R.L. (2008) Cell type specificity of a diffusible inducer is determined by a GATA family transcription factor. Development, vol 1.35, p 1635-1645 
   

• Biochemistry
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Evolutionary Biology
• Gene Expression
• Genetics
• Immunology
• Microbiology
• Molecular Biology
• Molecular Cancer Studies

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The aim of this project is to determine the function of non-coding RNAs (ncRNAs) in the Hox complex, in particular how they affect gene expression and function during differentiation of the anterior-posterior axis. The Hox complex is clustered set of related transcription factors that establish positional identity on the anterior-posterior axis in all animals. We have used a combination of deep-sequencing and tiling microarray expression analysis to identify more than 20 ncRNAs in the Hox complexes of the fly, beetle, and honeybee. We are interested in understanding how these ncRNAs function and how they evolve. Many of these transcripts have unique, Hox-like expression patterns and some correlate with classically described homeotic mutations or genetically identified regions controlling the temporal and/or spatial regulation of Hox gene expression. We are using a combination of genetic and bioinformatic approaches to study both potential cis and trans functions of these ncRNAs. We are taking advantage of a comparative approach to identify the analogues and homologues of these ncRNAs to determine if there is a pattern of conservation in the sequence or structure that may hint at the function. The results of this work will begin to answer questions regarding how the evolution of these ncRNAs may have contributed to diversification of metazoan bodyplans.

Shippy TD, Ronshaugen M, Cande J, He J, Beeman RW, Levine M, Brown SJ, Denell RE. (2008). Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters. Development genes and evolution, 218, 127-39.

Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC. (2005). The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes & development, 19, 2947-52.

Ronshaugen M, Levine M. (2004). Visualization of trans-homolog enhancer-promoter interactions at the Abd-B Hox locus in the Drosophila embryo. Developmental cell, 7, 925-32.
 

• Animal Biology
• Bioinformatics
• Developmental Biology
• Evolutionary Biology
• Gene Expression
• Genetics
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Each year 1,000,000 women worldwide develop breast cancer and 400,000 women die from the disease. There has, however, been a marked improvement in the survival of women with breast cancer over the last three decades, with many more women living five or more years after diagnosis before finally succumbing to the disease. This improvement has come from screening programmes, leading to earlier diagnosis, and the use of new therapies. The development of new therapeutics has been driven by the realisation that breast cancer is not just one disease but rather several that can be distinguished by the combination of the oestrogen, progesterone and Her2 receptors expressed. This gives three recognised subtypes (hormone receptor positive cancers that express oestrogen and progesterone receptors, Her2 positive cancers, and triple negative cancers that lack all three proteins). Targeted therapies have been developed that disrupt the function of these receptors, such as tamoxifen which inhibits oestrogen receptor and Herceptin which blocks Her2. These therapies have significantly improved treatment of hormone receptor positive and Her2 positive tumours respectively.
However there are still no targeted therapies for patients with triple negative breast cancer. These cancers constitute 15% of all breast cancers and they are often the most aggressive and difficult to treat. We are looking for new therapies for these cancers and in particular we are focussing on the Notch signalling pathway. We have shown that signalling through this pathway is elevated in breast cancer and that sustained Notch signalling makes breast epithelial cells become cancerous, preventing their death following treatment with chemotherapeutics. Others have shown that Notch signalling is particularly strong in triple negative breast cancer. This project will continue our work on the role of Notch signalling in breast cancer, ultimately looking to target the pathway therapeutically for the treatment of triple negative breast cancer.
The project fee will either be at a University Band 2 or Band 3, and will be confirmed with the candidate during the application process.
 

• Brennan, K. and Brown, A. M. C. (2003). Is there a role for Notch signalling in human breast cancer? Breast Cancer Res 5, 69-75.

• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Molecular Cancer Studies

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Our laboratory is within the North West Embryonic Stem Cell Centre (NWESCC www.manchester.ac.uk/nwescc) which has the remit to generate human embryonic stem cells (hESc) at clinical grade for therapy including possible therapies for diseases of endodermal derivatives ( e.g. type1 diabetes, liver disease etc).
We have robust protocols to target differentiation of hES cells to endoderm the precursor of pancreatic β-cells and hepatocytes. The project student will focus on endoderm development using a combination of genetic manipulation, cell culture, biochemistry and imaging techniques. For the pancreatic endocrine project, we have already developed a number of constucts containing reporter genes driven by promoter sequences of key endoderm and endocrine genes which will be used to monitor in vitro development of these cells within the project. The project will investigate the signalling pathways involved in transition from pluripotent hESc to commited endodermal progenitor and endocrine precursors and the cross talk between these pathways. By working out the key elements of the developmental pathway by which cells develop along this lineage we will be able to mimic it more closely in therapeutic protocols. .In this respect we are developing protocols which allow us to conduct real-time analysis of cell differentiation along these lineages using marker analysis and reporter gene expression.. Cells will be monitored by Realtime fluorescence microscopy and lineage marker analysis by Q- PCR as well as FACs. The student will be trained in scientific method, feeder and feeder-free human ES cell culture, molecular cloning, transgenesis, Real-time video microscopy , qualitative and Q-PCR, as well as FACs analysis.
 

Camarasa MV, Kerr R, Sneddon S, Brison DR & Kimber SJ (2010) Derivation of human embryonic stem cell lines from clinically unusable eggs in Manchester. J In Vitro Laboratory Science E-pub ahead of print

Baxter M, Caramasa M, Bates N, Small F, Murray P, Edgar D & Kimber SJ (2009) Analysis of feeder cell- and serum-free tissue culture conditions for the maintenance of self-renewing human embryonic stem cell lines. Stem Cell Research 3 28-38.

DeSousa PA , Gardner J, Sneddon S, Pells S, Tye B , Collins PD, Collins DM , Sewart K, Shaw L, Pryzborski, S, Cooke M, McLaughlan J, Kimber S J, Lieberman B, Wilmut I & Brison DR (2009) Clinically failed eggs as source of normal human embryo stem cells. Stem Cell Research 2, 188-199.
 

• Biochemistry
• Cell Biology
• Developmental Biology
• Gene Expression
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Our laboratory as part of the North West Embryonic Stem Cell Centre (NWESCC) has generated a number of human embryonic stem cells (hESc) lines and has a remit to generate lines suitable for clinical therapy. The Centre provides a focus for research projects on pluripotency, generation of mesodermal and endodermal differentiated derivatives and the stem cell niche. HESc can form all tissues of the body and have excellent potential as agents for tissue regeneration. As the extracellular matrix is known to regulate hESc status, the aim of this project is to elucidate the mechanisms whereby adhesion through integrins influences hESc differentiation status and lineage choice. The extracellular matrix and integrin profile assembled by hES cells (before and after differentiation along various specific pathway) has already been partially analyzed in the lab and the student will build on this information to investigate how integrin signalling influences the transition form pluripotency to early differention states and in longer targeted differentiation protocols how specific integrin signalling the cell fate decisions to cartilage and bone. In this context we have developed well defined protocols for generation of chondrogenic and osteogenic cells from hESc These comparisons will reveal key targets for functional analyses by e.g. RNAi knock-down and over-expression of molecules which are fundametal to matrix-signalling and influence expression of genes associated with pluripotency or specific differentiation states.. Techniques will include hESc culture, immunofluorescence, immunoprecipitation, Western blotting. Real-Time fluorescence and confocal microscopy, FACs analysis, both qualitative and quantitative RT-PCR, lentiviral mediated genetic manipulation and other techniques depending on the results obtained.

Baxter M, Caramasa M, Bates N, Small F, Murray P, Edgar D & Kimber SJ (2009) Analysis of feeder cell- and serum-free tissue culture conditions for the maintenance of self-renewing human embryonic stem cell lines. Stem Cell Research 3 28-38.
Hamidouche Z, Fromigué O, Ringe J, Häupl T, Vaudin P, Pagès JC, Srouji S, Livne E, Marie PJ.Priming integrin alpha5 promotes human mesenchymal stromal cell osteoblast differentiation and osteogenesis.Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18587-91
 

• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Gene Expression
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The placenta plays a crucial role in transporting nutrients and oxygen to the fetus and maintaining fetal homeostasis. Seriously problematic pregnancies are common (fetal growth restriction (FGR) ~5% in the UK; preeclampsia 1 in 30 first pregnancies with 50,000 maternal deaths worldwide per year) and both syndromes are primarily due to failure in normal placental development. FGR is a well-established cause of postnatal and subsequent adult ill health, with high cost impacts on the NHS.

The cells which drive placental invasion and form the front line for gas and nutrient exchange in placental villi are the trophoblast, and deficiency in trophoblast occurs in the major diseases of pregnancy. There are no interventions available to correct placental insufficiency or animal models to replicate the structure and function. An in vitro model of human trophoblast in which differentiation pathways can be controlled and functions derived that reflect events in normal placental development would allow us to study disease in pregnancy in new ways.

In this project we will develop protocols to generate trophoblast stem cells from human embryonic stem cells based on the known growth and transcription factor pathways influencing placental development. These cells will be characterised by marker analysis and epigenetic profiling (microarray analysis in comparison with normal and diseased trophoblast) and by functional assays, 2D/3D invasion models and nutrient transport assays). We will establish differentiation protocols to derive different trophoblast lineages, identify key genes with altered expression, and couple knockdown and overexpression studies with function assays to identify their properties. We will compare expression patterns in PE, FGR and diabetic placentas and other early high risk specimens. Furthermore the project will feed into an existing programme to develop non-genetic therapies including RNAi and membrane-permeable proteins for rescue of placental abnormality which may become suitable for human therapy.
 

El-Hashash AHK, Warburton D and Kimber SJ. (2010) Genes and Signals Regulating Murine Trophoblast Cell Development. Mechanisms of Development 127,1-20

Baxter M, Caramasa M, Bates N, Small F, Murray P, Edgar D & Kimber SJ (2009) Analysis of feeder cell- and serum-free tissue culture conditions for the maintenance of self-renewing human embryonic stem cell lines. Stem Cell Research 3 28-38.

Forbes K, West G, Garside R, Aplin JD, Westwood M (2009). The protein-tyrosine phosphatase, SHP-2, is a crucial mediator of exogenous IGF signalling to human trophoblast. Endocrinology. 150:4744-54.

Karen Forbes, Melissa Westwood*, Philip N Baker & John D Aplin (2008) Insulin-like growth factor-I and –II regulate the life cycle of trophoblast in the developing human placenta. Am J Physiol, 294:C1313-22.

El-Hashash AHK & Kimber SJ. (2006) PTHrP induces changes in cell cytoskeleton and E-cadherin and regulates Eph/Ephrin kinases and RhoGTPases in murine secondary trophoblast cells. Dev Biol 290, 13-31
 

• Animal Biology
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Gene Expression
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

When stem cells are placed in a uniform signaling environment not all cells respond in the same way, and some cells do not respond at all. It is thought that this is because different cells within a seemingly uniform population are be biased or primed to respond due to their ‘epigenetic signaling history’. Understanding this priming may improve our ability to exploit stem cells in therapeutic treatments. However, little is known about the molecular basis underlying this phenomenon.
One way to address this is to use is through studies of cell fate choice during multicellular development, especially case where cells differentiate seeming at random or stochastically in response to developmental signals. This is clearly seen in examples ranging from the early mouse embryo to the social amoeba D. discoideum. Indeed, we have recently discovered that the retinoblastoma (Rb) tumour suppressor and the Ras oncogene bias cell fate choice in the model organism D. discoideum. In this project you will study the interplay between Ras and retinoblastoma, how their activity is controlled and how these differences affect responses to the signals regulating cell fate. Two experimental approaches are possible (1) You will use cutting edge genome wide mutagenesis using a barcoded set of mutants to identify novel genes that affect bias and the regulation of Ras/retinoblastoma activity (2) You will use proteomic and genomic (transcriptome/next generation sequencing) to identify novel regulators of Ras and retinoblastoma and to establish how they exert their affects.
The role of novel genes will be defined in D. discoideum and mammalian cells using molecular genetic (e.g. transformation, knockout GFP-fusion) and microscopy approaches (live cell imaging). Your studies, will lead to a better understanding of why cells adopt a particular fate and how this may be manipulated.
 

• Animal Biology
• Biochemistry
• Cell Biology
• Developmental Biology
• Evolutionary Biology
• Gene Expression
• Genetics
• Microbiology
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Vertebrate haematopoiesis is a highly sophisticated system; it comprises various specialised cell types functioning in gas transport, blood clotting and immune response, while the varieties of these cells are differentiated from only one type of haematopoietic stem cells (HSC). Although the progress of molecular and developmental biology in the last decade has revealed the molecular mechanism of this process, little is known about its evolutionary origin. This is mainly because most data have come from experiments using model vertebrates such as mouse, chicken or zebrafish. Although recent studies of Drosophila haematopoiesis show that some fundamental mechanisms are conserved between Drosophila and vertebrates, we still do not know how the multiple lineages of vertebrate blood cells and HSC system were established in evolution.
In this project, we will analyse the haematopoiesis and its ontogeny in the basal vertebrates, namely lampreys and hagfish. These jawless-fishes are known as the extant representatives of the oldest lineage of vertebrates and are in the best phylogenetic positions to address the evolutionary origin of vertebrate haematopoiesis. As these animals have not been studied in detail like other model vertebrates, we will first describe the developmental and the differentiation process of blood cells and then analyse their underlying molecular mechanisms and compare them with the data from model vertebrate animals or Drosophila in order to study how this elaborate system has been established during the early evolutionary history of the vertebrate.
This project will use molecular, developmental and haematological techniques including isolation of genomic and cDNA sequences, developmental analyses, in situ hybridisation, cytochemistry, flowcytometry as well as comparative genomics.
 

• Adaptive Organismal Biology
• Animal Biology
• Cell Biology
• Developmental Biology
• Evolutionary Biology
• Genetics
• Immunology
• Molecular Biology
• Physiology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Effective wound healing and timely restoration of skin functions is essential to prevent infection. As we age our skin’s ability to heal diminishes. Indeed, in many older individuals the process of wound healing fails entirely, leading to disease phenotypes such as leg ulcers or bed sores. Current treatments for poor wound healing are ineffective. Thus, there is an urgent need to develop new tharapies. We have identified a key role for estrogen deficiency in delayed wound healing, an effect that can be reversed by estrogen treatment. More recently we have discovered differential roles for the two murine estrogen nuclear hormone receptors during skin wound healing. Further, our comparative gene expression studies have identified numerous associated estrogen-regulated genes and processes that represent potential new targets for therapeutic manipulation to promote wound healing in elderly humans.

You will be embedded within a leading tissue regeneration research group based in new state of the art laboratory facilities in the Faculty of Life Sciences. You will be exposed to and trained in varied techniques, ranging from gene expression profiling, nano-structural quantitative data anaysis, surgery and mouse phenotyping to analysis of clinical samples and proof-of-principle clinical studies. We have strong collaborations with colleagues in the Faculty of Medicine and world-leading experts in estrogen signalling. Ultimately, this work should lead to the development of new therapies to accelerate healing.
 

• Campbell L, Emmerson E, Davies F, Gilliver SC, Krust A, Chambon P, Ashcroft GS and Hardman MJ. (2010) Estrogen promotes cutaneous wound healing via ER beta independent of anti-inflammatory activities. J Exp Med. Epub – Aug 23
• Emmerson E, Campbell L, Ashcroft GS and Hardman MJ. (2010) The phytoestrogen genistein promotes wound healing by multiple independent mechanisms. Mol Cell Endocrinol 321:184-93.
• Emmerson E, Campbell L, Ashcroft GS, Hardman MJ. (2009) Unique and synergistic roles for 17beta-estradiol and MIF during cutaneous wound closure are cell type specific. Endocrinology. 150:2749-57.
• Hardman MJ, Ashcroft GS. (2008) Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly. Genome Biol. 9:R80.
   

• Animal Biology
• Biochemistry
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Genetics
• Immunology
• Molecular Biology
• Physiology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Non-protein-coding RNA genes produce a functional RNA product, rather than a translated protein. An unexpectedly large number of non-coding RNAs are found in the animal genome – over 5000 functional RNAs can be easily annotated in human, including around 1000 microRNAs, 400 small nucleolar RNAs (snoRNAs), 500 transfer RNAs, and 60 spliceosomal RNAs – and computational prediction hints at as many as 30000 structured RNAs. Many RNA transcripts appear to make multiple functional products; for example microRNAs and snoRNAs are often located in introns of protein-coding genes, and many primary microRNA transcripts are processed to produce multiple mature microRNAs. These genomic relationships highlight fundamental questions regarding RNA function:

1. Are functional intronic RNAs co-transcribed with host genes?
2. Do linked RNA and protein products function in common pathways?
3. Are patterns of co-transcription and common function conserved between related species?

This project will make use of a wide range of computational biology and comparative genomics techniques, resources and algorithms to approach the above questions. The work will involve generation and analysis of RNA deep sequencing data as well as mining existing publicly available datasets. Fundamental insights will be gained into the genomic context, transcriptional regulation and function of non-protein-coding RNAs in the animal genome.
 

[1] Griffiths-Jones S. (2007). Annotating noncoding RNA genes. Annu Rev Genomics Hum Genet. 8:279-298.
[2] Bartel D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-97.
[3] Saini H.K., Enright A.J. and Griffiths-Jones S. (2008) Annotation of mammalian primary microRNAs. BMC Genomics 9:564.
 

• Bioinformatics
• Developmental Biology
• Evolutionary Biology
• Gene Expression

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Long bones in the skeleton grow by endochondral ossification, a complex process in which chondrocytes form a cartilage template known as a growth plate. Growth plate chondrocytes undergo a coordinated and tightly regulated process of proliferation and maturation prior to mineralisation of the newly formed bone matrix. Disruptions to this process result in a group of genetic bone diseases known as the skeletal dysplasias.
The skeletal dysplasias are an extremely diverse group of disorders and their aetiology is both varied and complex. Although individually rare, as a group of conditions they have an overall prevalence of at least 4 per 10,000 and amount to a huge burden in pain and very often crippling disability. The majority of skeletal dysplasia cannot as yet be cured and for this very reason emphasis must be placed on research activities that are focused on determining the molecular mechanisms that underpin their pathophysiology so that effective therapies can be developed.
We have recently shown using genetically engineered mouse models that the induction of ER stress and the unfolded protein response (UPR) in chondrocytes, through the expression of mutant cartilage proteins, can affect cell phenotype and cause growth plate dysplasia and skeletal dysplasia. We hypothesise that in these diseases the UPR is functioning in a beneficial manner and that by genetically ablating the different pathways of the UPR we will increase disease severity.
In this context, the aims of this project are to genetically dissect relative contribution of the different UPR pathways to growth plate dysplasia. This will be achieved by crossing mouse models of chondrodysplasia onto mice that are conditional nulls for X-bp1, eIF2??or ATF6. The resulting phenotypes and quantitative markers of growth plate dysplasia will be studied to determine if activation of the different branches of the UPR is chondrocyte protective or a fundamental cause of dysplasia.
 

•  An unfolded protein response is the initial cellular response to the expression of mutant matrilin-3 in a mouse model of multiple epiphyseal dysplasia. Nundlall S, Rajpar H, Bell PA, Zeeff LAH, Gardner B, Thornton DJ, Boot-Handford RP and Briggs MD. Cell Stress Chaperones. 2010 Apr 30. In press.
• Piróg KA, Jaka O, Katakura Y, Meadows RS, Kadler KE, Boot-Handford RP, Briggs MD. A mouse model offers novel insights into the myopathy and tendinopathy often associated with pseudoachondroplasia and multiple epiphyseal dysplasia. Hum Mol Genet. 2010 Jan 1;19(1):52-64.
• Boot-Handford RP, Briggs MD. The unfolded protein response and its relevance to connective tissue diseases. Cell Tissue Res. 2010 Jan;339(1):197-211. Epub 2009 Oct 23.
• Rajpar MH, McDermott B, Kung L, Eardley R, Knowles L, Heeran M, Thornton DJ, Wilson R, Bateman JF, Poulsom R, Arvan P, Kadler KE, Briggs MD, Boot-Handford RP. Targeted induction of endoplasmic reticulum stress induces cartilage pathology. PLoS Genet. 2009 Oct;5(10):e1000691.
• Tompson S, Merriman B, Funari VA, Fresquet M, Lachman RS, Rimoin DL, Nelson SF, Briggs MD, Cohn DH, Krakow D. A novel recessive skeletal dysplasia, SEMD-aggrecan type, results from a missense mutation affecting the C-type lectin domain of aggrecan. A J Hum Genet. 2009 Jan;84(1):72-9. 

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Genetics
• Molecular Biology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Many tissues, including skin, undergo major structural and functional changes with age, losing both elasticity and the ability to repair following injury. We have shown that fibrillin microfibrils, important components of the elastic fibre system, are degraded in aged skin and that estrogen deprivation is associated with a significant loss of microfibril tensile strength. Although estrogen is known to protect against age-associated changes in skin both the causative mechanisms and influence of this hormone on the elastic fibre system remain poorly understood.

You will be co-supervised by Dr Matthew Hardman (Faculty of Life Sciences) and Dr Mike Sherratt (Faculty of Medicine) and embedded within a leading tissue regeneration research group based in new state of the art laboratory facilities in the Faculty of Life Sciences. Your project will investigate the molecular and cellular mechanisms underlying a) accelerated skin ageing in the absence of estrogen and b) estrogen’s protective and restorative effects on skin structure and function. To achieve this you will employ a wide range of techniques including transgenic and surgical models, physiological, cellular, molecular and nano-structural analysis and clinical studies.
 

• Campbell L, Emmerson E, Davies F, Gilliver SC, Krust A, Chambon P, Ashcroft GS and Hardman MJ. (2010) Estrogen promotes cutaneous wound healing via ER beta independent of anti-inflammatory activities. J Exp Med. Epub – Aug 23
• Emmerson E, Campbell L, Ashcroft GS and Hardman MJ. (2010) The phytoestrogen genistein promotes wound healing by multiple independent mechanisms. Mol Cell Endocrinol 321:184-93.
• Sherratt MJ, Bayley CP, Reilly SM, Gibbs NK, Griffiths CE, Watson RE. (2010) Low-dose ultraviolet radiation selectively degrades chromophore-rich extracellular matrix components. J Pathol. 222:32-40
• Emmerson E, Campbell L, Ashcroft GS, Hardman MJ. (2009) Unique and synergistic roles for 17beta-estradiol and MIF during cutaneous wound closure are cell type specific. Endocrinology. 150:2749-57.
• Hardman MJ, Ashcroft GS. (2008) Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly. Genome Biol. 9:R80.
   

• Animal Biology
• Biochemistry
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Genetics
• Immunology
• Molecular Biology
• Physiology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Adhesion provides a mechanism for cells of multicellular organisms to sense their location and respond to the environment. My lab determines how cellular adhesion regulates key aspects of epithelial cell behaviour, particularly proliferation, differentiation, and polarity. We use this knowledge to identify better strategies for treating breast cancer.

The physical interaction between cells and the extracellular matrix (ECM) occurs at specialized sites within the plasma membrane called adhesion complexes. The central components of adhesion complexes are integrins, which are transmembrane receptors that link the ECM on the outside of the cell to structural molecules and signalling enzymes on the inside. Integrins convey signals from the local environment of the cell to determine how cells behave. They are essential for cell cycle, expression of tissue-specific genes, and for the morphogenesis of tissues during development. We use in vivo genetic strategies, together with shRNA knockdown, sophisticated culture techniques with breast epithelial cells and stem cells, and real time 3D imaging to elucidate how integrin-mediated adhesion regulates breast epithelial cell function.

This project will determine how integrins control the function of breast epithelial stem cells. Integrins are classic markers of epithelial stem cells, but no one knows what their role is in either normal or breast cancer stem cells. Using lentiviruses that express inducible shRNAs, you will transduce epithelial cells from normal or cancerous breast tissue, isolate the stem cells, and then determine if perturbing integrins alters the ability of precursor cells to form breast ducts or tumours, both in culture models and in vivo. The outcome will lead to an understanding of how integrins determine stem cell fate decisions in normal development and in breast cancer.
 

• Naylor MJ, Li N, Cheung J, Lowe ET, Lambert E, Marlow R, Wang P, Schatzmann F, Wintermantel T, Schuetz G, Clarke AR, Mueller U, Hynes NE, Streuli CH. 2005. Ablation of beta1 integrin in mammary epithelium reveals a key role for integrin in glandular morphogenesis and differentiation. Journal of Cell Biology 171:717-728
• Akhtar N, Marlow R, Lambert E, Scatzmann F, Lowe ET, Cheung J, Katz E, Li W, Wu C, Dedhar S, Naylor MJ, Streuli CH. 2009. Molecular dissection of integrin signalling proteins in the control of mammary epithelial development and differentiation. Development 136:1019-1027
• Streuli CH. 2009. Integrins and cell-fate determination. Journal of Cell Science. 122:171-177
• Muschler J, Streuli CH. 2010. Cell-matrix interactions in mammary gland development and breast cancer. Cold Spring Harbor Perspectives in Biology Series. doi:10.1101/cshperspect.a003236
   

• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Molecular Cancer Studies
• Stem Cell Research

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Cardiovascular disease represents a significant threat to health globally. In addition to adult cardiac disease, congenital heart defects are a major source of infant mortality. Although these defects have a genetic basis, the specific genes that underlie many cases remain unknown. Additional genes that contribute to human cardiovascular developmental defects can be identified from mouse models. In this project, we will study a mouse mutant, L11Jus8, which has abnormal yolk sac vasculature, cardiac morphology, and haemorrhage leading to death after mid-gestation. Because the L11Jus8 mutant was isolated from a balancer chromosome mutagenesis screen, the specific genetic mutation that causes the phenotype is unknown, although the mutant phenotype has been mapped to a 5.3Mb interval on mouse chromosome 11. No similar defects have been reported for mutations of genes in this region of the genome. However, several developmentally expressed genes are located in the candidate interval. By combining meiotic mapping, candidate gene analysis, and genomic sequencing we will identify the L11Jus8 mutation. Further characterisation of the mutants will define the developmental processes that are regulated by this gene. We will investigate whether cardiac or vascular defects are the primary cause of the mutant phenotype. In addition, we will examine marker genes to identify genetic pathways that are affected in the mutants. We will assess cardiac function in mutant embryos using whole embryo culture. The identification of the L11Jus8 gene and its functions during cardiovascular development will have a strong impact on modelling congenital heart defects.

* Kile, B.T.*, Hentges, K.E.*, Clark, A.T.*, Nakamura, H., Salinger, A.P., Liu, B., Box, N., Stockton, D.W., Johnson, R.L., Behringer, R.R., Bradley, A., and Justice, M.J. (2003) Functional genetic analysis of mouse chromosome 11. Nature 425:81-86. *co-first authors.
* Hentges, K.E., and Justice, M. J. (2004) Checks and Balancers: Balancer Chromosomes to Facilitate Genome Annotation. Trends in Genetics 20:252-9.
 

• Cell Biology
• Developmental Biology
• Genetics
• Molecular Biology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

From genome sequences, the total number of genes in several organisms can now be predicted. However, the functions of many of these genes remain unknown. The number and percentage of genes that are required for development and classified as essential varies among organisms. The percentage of genes required for human survival is unknown. However, studies in the mouse allow mammalian essential genes to be identified from experimental data. From these data a subset of essential and non-essential genes have been discovered. The task that remains is to identify all the genes that are likely to be required for mammalian development using the mouse as a model, and comparative genomics to then characterise essential human genes. Incorporating a machine learning approach, we seek to identify characteristics that are over-represented in genes known to be required for development. This will allow us to develop criteria for essential genes. By applying these criteria to the mouse genome, we can then identify regions of the genome that contain high numbers of essential genes, as well as identify the individual genes that are likely to be required for mammalian development.

Hentges KE, Pollock DD, Liu B, Justice MJ. Regional variation in the density of essential genes in mice. PLoS Genet. 2007 May 4;3(5):e72.

Lovell SC, Li X, Weerasinghe NR, Hentges KE. Correlation of microsynteny conservation and disease gene distribution in mammalian genomes. BMC Genomics. 2009 Nov 12;10:521.
 

• Bioinformatics
• Developmental Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

A major challenge in cancer research lies in the difficulty to satisfactorily model in vitro the interaction between host and tumour that is desirable for identifying physiologically relevant signalling molecules that could be used as targets to develop better therapies. To circumvent this problem, my laboratory has created novel genetically modified mouse models in which components of the mitogen-activated protein kinase (MAPK) pathways can be specifically deleted to understand the molecular mechanisms underlying the development of tumours that occur in situ. For example, we have discovered that skin-specific MKK4-deficient mice are resistant to tumourigenesis associated with oncogenic activation of the c-Ha-ras gene. These results provide a strong genetic demonstration that signalling downstream of MKK4 is essential for tumour formation in the skin. Based on these data, this project aims at defining the role of MKK4 in tumour progression under normal conditions and in response to anticancer therapies. More specifically, we will delineate the role of MKK4 with respect to tumour initiation, progression and maintenance (aim 1). This information is crucial to validate MKK4 as a valuable drug target for cancer therapy. We will elucidate the role of MKK4 in the response of transformed cells to anticancer drug treatment (aim 2). The results of this study will determine whether MKK4 is involved in the development of chemoresistance by promoting the expression of membrane drug transporters. Finally, we will test whether these results are transferable to another epithelial cancer model, pancreatic cancer, to elucidate whether MKK4 has a general pro-oncogenic role downstream of Ras (aim 3). One potential important outcome of this project is the demonstration that MKK4 is a drug target for the treatment of cancers. In particular, combined with conventional DNA-damaging chemotherapeutics, inhibitors of MKK4 may provide a new strategy to overcome resistance of tumours to the current therapies.

Finegan KG, Tournier C (2010) The mitogen-activated protein kinase kinase 4 (MKK4) has a pro-oncogenic role in skin cancer. Cancer Res (accepted for publication)

Manning AM, Davis RJ. Targeting JNK for therapeutic benefit: from junk to gold? Nat Rev Drug Discov 2003 2:554-65.

Wang X, Destrument A, Tournier C. Physiological roles of MKK4 and MKK7: insights from animal models. Biochim Biophys Acta 2006 1773:1349-57.

Weston CR, Davis RJ. The JNK signal transduction pathway Curr Opin Cell Biol 2007 19:142-9.

Whitmarsh AJ, Davis RJ. Role of mitogen-activated protein kinase kinase 4 in cancer. Oncogene. 2007 26:3172-84.
 

• Cell Biology
• Molecular Biology
• Molecular Cancer Studies 

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Cooperative or social behaviour occurs when cells or organisms help one another. But why would it be beneficial to sacrifice yourself to help others. Why not cheat and not pay your fair share of the cost? Understanding why cooperation has evolved and is stable is a major unanswered problem in the biological sciences. We know that genes regulate social behaviour, but which ones? We also know that it must be costly to lose genes that promote cooperation, but why? Microorganisms give us the chance to answer these questions as they are often not only social, but can also be studied in the lab using post genomic or molecular genetic approaches. The social amoeba Dictyostelium discoideum is one such organism. In my lab we have begun to isolate social mutants in Dictyostelium. The aims of this project will be to identify and study the disrupted genes in one or more of these mutants. You will use cutting edge genetic (mutagenesis), biochemical (proteomic), genomic (transcriptome analysis) and microscopy approaches (live cell imaging). Through your studies, you will identify novel genes that regulate social behaviour and characterise the roles that they play.

• Buttery N.J., Rozen D.E., Wolf J.B., *Thompson C.R.L. (2009)Quantification of social behavior in D. discoideum reveals complex fixed and facultative strategies. Current Biology, vol 19 p. 1373-7
• Foster K.R., Parkinson K. and *Thompson C.R.L. (2007)What can microbial genetics teach sociobiology?  Trends in Genetics, vol. 23, p. 74-80

• Adaptive Organismal Biology
• Animal Biology
• Biochemistry
• Cell Biology
• Developmental Biology
• Environmental Biology
• Evolutionary Biology
• Gene Expression
• Genetics
• Microbiology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Integrins are receptors for the extracellular matrix (ECM) which provide cells with spatial information within a tissue and act to coordinate signalling pathways downstream of growth-factor and cytokine receptors. Integrins are internalised from the cell surface, and traffic through endosomal compartments from which they can be recycled back to the plasma membrane. The trafficking of integrins can take place in a spatially restricted manner within the cell, and it is now clear that recycling integrins can contribute to the progression of cancer by influencing the trafficking of growth-factor receptors. However, very little is known about integrin trafficking in normal epithelial cells, the cell type of origin of most solid cancers.

This project will focus on the role of integrin trafficking in regulating cytokine receptor signalling in epithelial cells as they differentiate. Using a combination of biochemical techniques alongside advanced microscopy and live cell imaging we will identify the cellular mechanisms through which integrins coordinate signalling pathways in normal cells, and further the understanding of cancer development by studying how these pathways are co-opted in cancer. 

Caswell, P.T., Vadrevu, S. & Norman, J.C (2009). Integrins: masters and slaves of endocytic transport. Nature Reviews Molecular Cell Biology, 10(12), 843-53.

Muller, P.A., Caswell, P.T., Doyle, B., Iwanicki, M.P., Tan, E.H., Karim, S., Lukashchuk, N., Gillespie, D.A., Ludwig, R.L., Gosselin, P., Cromer, A., Brugge, J.S., Sansom, O.J., Norman, J.C. & Vousden, K.H (2009). Mutant p53 drives invasion by promoting integrin recycling.  Cell, 139(7), 1327-41.

Caswell, P.T., Chan, M., Lindsay, A.J., McCaffrey, M.W., Boettiger, D. & Norman, J.C (2008). Rab-coupling protein coordinates recycling of alpha5beta1 integrin and EGFR1 to promote cell migration in 3D microenvironments. The Journal of Cell Biology, 183(1), 143-55.

Akhtar N, Marlow R, Lambert E, Schatzmann F, Lowe ET, Cheung J, Katz E, Li W, Wu C, Dedhar S, Naylor MJ, Streuli CH. (2009).
Molecular dissection of integrin signalling proteins in the control of mammary epithelial development and differentiation.
Development , 136(6):1019-27.
 

• Cell Biology
• Cell Matrix Research
• Membrane Trafficking
• Molecular Cancer Studies

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Female fertility is dependent on successful ovulation, where a fertilisable oocyte is released from an ovarian follicle. Two proteins, namely TSG-6 and inter-alpha-inhibitor (I alpha I), have been identified as having essential roles in ovulation, where mice that don't express either one of these proteins are severely female sub-fertile (see [1,2]). We have shown that TSG-6 catalyses the modification of the polysaccharide hyaluronan (HA) by transferring the heavy chain (HC) components of I alpha I onto HA to form covalent HC•HA complexes [3]. During ovulation HA and TSG-6 are produced by the cumulus cells that surround the oocyte leading to the formation of HC•HA, which is essential for the generation of a jelly-like matrix around the oocyte. This cumulus extracellular matrix is required for successful ovulation and fertilisation. Aside from their roles in formation of the cumulus matrix, TSG-6 and I alpha I might also contribute to other aspects of female fertility e.g. by controlling breakdown of the follicle wall during ovulation (via regulation of the protease network [4]).

This project will form part of ongoing work to fully understand the contributions of TSG-6 and I alpha I to female fertility and the underlying molecular mechanisms, which might lead to improvements in the treatments available for infertility. Since TSG-6-catalysed HC•HA formation also occurs during inflammation (see [1,2,4]), this work might also lead to better understanding of inflammatory disease processes. A broad range of techniques will be utilised, including immunhistochemistry, protein functional characterisation and molecular biology.
 

[1] Milner, C.M. & Day, A.J. TSG-6: a multifunctional protein associated with inflammation. (2003) J. Cell Sci. 116: 1863-1873.
[2] Milner, C.M., Higman, V.A. & Day, A.J. TSG-6: a pluripotent inflammatory mediator? (2006) Biochem. Soc. Trans. 34 (part 3): 446-450.
[3] Rugg, M.S., Willis, A.C., Mukhopadhyay, D., Hascall, V.C., Fries, E., Fülöp, C., Milner, C.M. & Day, A.J. Characterization of complexes formed between TSG-6 and inter-?-inhibitor as intermediates in the covalent transfer of heavy chains onto hyaluronan. (2005) J. Biol. Chem. 280: 25674-25686.
[4] Milner, C.M., Tongsoongnoen, W., Rugg, M.S. and Day, A.J. The molecular basis of inter-?-inhibitor heavy chain transfer onto hyaluronan. (2007) Biochem. Soc. Trans. 35 (part 4): 672-676.
[5] Mahoney, D.J., Mulloy, B., Forster, M.J., Blundell, C.D., Fries, E., Milner, C.M. & Day, A.J. Characterization of the interaction between tumor necrosis factor-stimulated gene-6 and heparin: implications for the inhibition of plasmin in extracellular matrix microenvironments. (2005) J. Biol. Chem. 280: 27044-27055.
 

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Developmental Biology
• Immunology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The human protein TSG-6 is secreted by many cell types (including mesenchymal stem cells) in response to inflammation and has been detected in the context of diseases such as arthritis (see [1]). TSG-6 has been shown to limit inflammation and tissue damage when it is administered to mice with inflammatory arthritis (see [1]) and when it is secreted by stem cells during the treatment of myocardial infarction [2]. We have shown recently that neutrophils store TSG-6 protein in granules and release it in response to inflammatory stimuli [3], indicating that it is an endogenous regulator of inflammation. We have also shown that TSG-6 is involved in regulating the balance between the formation and breakdown of bone and that it can inhibit bone erosion by osteoclasts during inflammation [4]. These properties of TSG-6 might be beneficial in the development of new drugs, e.g. for the treatment of bone diseases.

This project will form part of ongoing work to understand the mechanisms that underlie the anti-inflammatory and tissue-protective effects of TSG-6. In particular it will focus on the molecular interactions that are responsible for the effects of TSG-6 on bone erosion. A combination of site-directed mutagenesis and interaction analyses, coupled with structural and biophysical methods, will be used in addition to protein expression and functional characterisation.
 

[1] Milner, C.M. & Day, A.J. TSG-6: a multifunctional protein associated with inflammation. (2003) J. Cell Sci. 116: 1863-1873.
[2] Lee, R.H., Pulin, A.A., Seo, M.J., Kota, D.J., Ylostalo, J. Larson, B.L., Semprun-Prieto, L., Delafontaine, P. & Prockop, D.J. Intravenous hMSCs improve myocardial infarction in mice because cells embolized in the lung are activated to secrete the anti-inflammatory protein TSG-6. (2009) Cell Stem Cell 5: 54-63.
[3] Maina, V., Cotena, A., Doni, A., Nebuloni, M., Pasqualini, F., Milner, C.M., Day, A.J., Mantovani, A. & Garlanda, C. Co-regulation in leukocytes of the long pentraxin PTX3 and TSG-6, two co-operating molecules involved in the assembly of hyaluronan-rich extracellular matrices. (2009) J. Leukocyte Biology 86:123-132.
[4] Mahoney, D.J., Mikecz, K., Ali, T., Mabilleau, G., Benayahu, D., Plaas, A., Milner, C.M., Day, A.J. & Sabokbar, A. TSG-6 regulates bone remodeling through inhibition of osteoblastogenesis and osteoclast activation. (2008) J. Biol. Chem. 283: 25952-25962.
 

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Cell Matrix Research
• Immunology
• Molecular Biology
• Stem Cell Research
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Synapses are the points of contact where neurons transmit signals to other neurons, glands or muscles. They are key regulators of information flow in the nervous system, acting to filter and modify the information passing through them. For this reason the precise control of synapse formation and function crucially underlies cognitive abilities, such as learning and memory. Aberrant control of synapse development has been implicated in causing neurological disorders including autism, mental retardation, schizophrenia and epilepsy. Understanding how synapses develop remains a prime challenge in modern neurobiology.
The cytoskeleton, composed of actin and microtubules, is a key component for the formation of synapses. However, the mechanisms regulating the synaptic cytoskeleton remain little understood. To decipher these mechanisms, we have established unique strategies in the genetic model organism Drosophila. These strategies are based on a novel primary neuronal cell culture system, which is amenable to systematic genetic and pharmacological manipulations. Using this system, you will carry out pioneering work on cytoskeletal regulation of synapses, within a laboratory specialised in cytoskeletal regulators and with a long standing expertise on synapse formation. Given the universal requirements of cytoskeletal dynamics for almost every cell function, your work will have further implications in other relevant areas of investigation, ranging from Alzheimer's research to cancer biology.
During this project you will gain excellent training in biotechnology. You will generate cell cultures from neural embryonic stem cells or dissociated brains. You will also use sophisticated genetic strategies, molecular biology techniques, generate transgenic animals, employ drugs for pharmacological manipulations, and use advanced microscopy including live imaging. The postgraduate training programme of Manchester's Faculty of Life Sciences will enable you to prepare for all aspects of your future career.
 

• Dillon & Goda, 2005, Annu Rev Neurosci 28, 25ff.
• Sánchez-Soriano et al., 2010, Dev. Neurobiol. 70, 58ff.
• Küppers-Munther et al., 2004, Dev. Biol. 269, 459ff.
• Prokop & Meinertzhagen, 2006, Semin Cell Dev Biol 17, 20ff.

• Animal Biology
• Biomolecular Science
• Cell Biology
• Developmental Biology
• Genetics
• Molecular & Cellular Neuroscience
• Molecular Biology
• Neuroscience

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Human Embryonic stem cells (hESc) hold tremendous promise for generation of cellular therapies because they can give rise to progenitors of all cell types of the body. However to exploit this promise we have to be able to control and monitor their differentiation. In early human embryos and hESc metabolic activity and dominant metabolic pathways change during differentiation. To obtain high quality cells for therapy we need to tailor our culture medium to support the specific metabolic pathways conducive to each of hESc expansion, differentiated intermediates and specific differentiated cell types, and to be able to monitor differentiation. We have developed an efficient directed differentiation protocol to produce chondrogenic cells from hESc lines with a view to providing a therapy for osteoarthritis. Provisional novel data show that specific metabolites and pathways (e.g. amino acids) are indeed associated with this chondrogenic differentiation. Therefore the aims of this project are:

1) To establish a unique metabolic profile for hESc
2) To determine the metabolic profiles during a defined chrondrogenesis differentiation protocol
3) To determine the metabolome of chondrogenic precursor cells
4) To use this information to develop stage-specific media appropriate to metabolic status and identify novel non-invasive metabolic markers of differentiation

This will lead us to refine methods of culture for hESc and their derivatives and to monitor differentiation non-invasively, crucial for ES-scale up for tissue regeneration. Manchester has state of the art metabolomics facilities (installed 2010). We will start with IR and Ramen spectroscopy in collaboration with Professor Goodacre and Dr Dunn, School of Chemistry, followed by gas chromatography-mass spectrometry (GC-MS) to analyze the metabolic footprint of different hES lines as the best metabolomics platform for unequivocal identification/quantification of metabolites The results will provide enhanced understanding of metabolic pathways in hES cells and their relation to cell function and differentiation.

This project will be co-supervised by Dr Sue Kimber and Dr Daniel Brison.

• Brison et al., 2004 Hum.Reprod. 19:2319
• Ellis & Goodacre, 2006 Analyst 131, 875
• Goodacre Genome Biol. 2005; 6(11): 354.
   

• Biochemistry
• Biotechnology
• Cell Biology
• Developmental Biology
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

During neurogenesis, neural stem cells undergo self-renewal to replenish the progenitor population and at the same time generate neurons in a controlled manner. MicroRNAs are a class of small non-coding RNAs, which have been shown to play key roles in many developmental processes including stem cell proliferation and differentiation. mir-9 is a highly conserved microRNA, which is expressed primarily in the Central Nervous System. We have found that mir-9 is required for neuronal differentiation and limits the proliferation of neural stem cells. In this project, we will examine the regulation of mir-9 and the interaction with downstream targets in Xenopus tropicalis frog tadpoles and in neuroblastoma cell lines. This project will employ techniques of molecular biology, imaging and is also suitable for mathematical modelling.

• Cell Biology
• Developmental Biology
• Gene Expression
• Molecular & Cellular Neuroscience
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Development of the lip and palate involves a complex series of highly integrated events that are frequently disrupted resulting in the congenital disoders cleft lip and cleft palate. Collectively, cleft lip and cleft palate have an estimated incidence of 1 in 500-2500 live births depending on geographic origin, racial and ethnic variation, and socio-economic status and result in considerable morbidity to affected families as individuals who exhibit this condition may experience problems with eating, speaking and hearing which can be corrected to varying degrees by surgery, dental treatment, speech therapy and psychosocial intervention. The frequent occurrence and significant burden imposed by cleft lip and cleft palate highlight the need to dissect the aetiology and molecular pathogenesis of this distressing condition.

Sonic hedgehog (Shh) has been shown to be a key regulator of palatal development. In this project, we will generate two high-throughput systems databases. First, we will determine Shh targets in the palatal mesenchyme by generating a highly filtered dataset. To enrich for direct Shh targets, we will compare palatal mesenchyme conditional Smoothened (Smo) loss- and gain-of-function microarrays and filter this dataset through a Gli Chromatin Immuno-Precipitation (ChIP) database. We will verify these targets in Smo mutant mice.

This project will therefore increase our understanding of the Shh signalling pathway during development of the secondary palate.

• Dixon MJ, Marazita ML, Beaty TH, Murray JC (2011) Cleft lip and palate: understanding genetic and environmental influences. Nature Reviews Genetics 12:167-178.
• Gritli-Linde A (2007) Molecular control of secondary palate development. Developmental Biology 301:309-326.
• Lan Y, Jiang R (2009) Sonic hedgehog signaling regulates reciprocal epithelial-mesenchymal interactions controlling palatal outgrowth. Development 136:1387-1396.

• Animal Biology
• Biomolecular Sciences
• Developmental Biology
• Gene Expression
• Genetics
• Molecular Biology

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Epithelial cells are typically polarised along an apical-basal axis. Cell polarity and the cell-cycle are two fundamental processes regulating embryonic development. They are also involved in stem cell maintenance as neural stem cells are also polarised in vivo. Around 90% of the human cancers are of epithelial origin, and are often marked by the concomitant loss of cell polarity and enhanced cellular proliferation. Although this indicates that there may be an intrinsic connection between cell cycle and cell polarity, the mechanistic basis linking them is not understood. We have recently shown that the apically localised serine/threonine kinase aPKC, well known for establishing and maintaining epithelial polarity, affects cell fate and proliferation in Xenopus ectoderm. In this project we will identify the phosphorylation targets of aPKC and define their role on cell proliferation, differentiation and fate decisions. This investigation will establishe a so far elusive, direct link between cell polarity and cell cycle.

Saberwhal, N., Tsutsui, A, Hodge, S., Wei, J., Chalmers, A.D. and Papalopulu, N. (2009). The apical-basal polarity kinase aPKC functions as a nuclear determinant and regulates cell proliferation and fate during Xenopus neurogenesis Development 136: 2767-77 (highlighted paper).

• Cell Biology
• Developmental Biology
• Gene Expression
• Molecular Biology
• Molecular Cancer Studies
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The mechanisms that integrate extracellular signals with intracellular pathways to determine the fate of neural cells in the brain during development and disease remain largely uncharacterised. This is due, in part, because the mutation of genes involved in key signal transduction cascades, such as c-Jun NH2-terminal protein kinase (JNK) signalling, often causes early embryonic lethality. To circumvent this problem, my laboratory has created a novel mouse model in which the activity of JNK can be temporally and selectively blocked in the neural cell lineage where JNK is found constitutively active. These mice will be used to discover novel regulatory mechanisms underlying neurogenesis and programmed cell death during development (a physiological process) and in response to oxidative stress (a major pathological challenge). More specifically, this project will aim at testing the hypothesis that active JNK is essential for regulating critical neuronal processes including cell cycle exit of neural stem cells, cell migration, initiation of neuronal differentiation and neuronal death.

Kriegstein AR, Noctor SC. Patterns of neuronal migration in the embryonic cortex. Trends Neurosci 2004; 27:392.

Burek MJ, Oppenheim RW. Programmed cell death in the developing nervous system. Brain Pathol 1996 6:427.

Davis RJ. Signal transduction by the JNK group of MAP kinases. Cell 2000 103:239.

Wang X, Nadarajah B, Robinson AC, McColl BW, Jin JW, Dajas-Bailador F, Boot-Handford RP, Tournier C. Mitogen-activated protein kinase kinase 4 is an essential activator of the c-Jun N-terminal protein kinase during brain development. Mol Cell Biol 2007 27:7935.

Wang X, Destrument A, Tournier C. Physiological roles of MKK4 and MKK7: insights from animal models. Biochim Biophys Acta 2006 1773:1349. 
 

• Cell Biology
• Developmental Biology
• Genetics
• Molecular & Cellular Neuroscience
• Molecular Biology
• Neuroscience

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The shapes of organisms are integrated so that functionally and developmentally interacting parts vary together. Morphological integration is often clearly structured, so that there are modules that are tightly integrated internally and relatively independent of other modules. Such integration and modularity is thought to be the result of adaptive evolution and, in turn, it also influences the potential for further evolution. My lab uses the methods of geometric morphometrics to address various questions concerning integration and modularity of shapes in diverse study systems including fly wings and mammalian skulls. We also have developed new methods for examining patterns of integration, for testing hypotheses of modularity and for inferring the developmental basis of morphological integration.

Your project will expand on this work. Current challenges in the field concern the evolution of integration and its genetic basis. Accordingly, your project could either use a comparative approach or the methods of quantitative genetics. Depending on these choices, your research could be lab-based or primarily use museum collections. It is also possible to include a component of methods development into the project in addition to the empirical work. The precise topic of your project will be decided after discussion, and so it is possible to take into account your previous background and experience as well as your interests and personal preferences.
 

• Klingenberg, C. P. 2010. Evolution and development of shape: integrating quantitative approaches. Nature Reviews Genetics 11:623–635. doi:10.1038/nrg2829
• Klingenberg, C. P., and N. A. Gidaszewski. 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Systematic Biology 59:245–261. doi:10.1093/sysbio/syp106

• Adaptive Organismal Biology
• Animal Biology
• Developmental Biology
• Evolutionary Biology
• Genetics

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

To understand the causes of early pregnancy pathologies and miscarriages we need to increase our understanding of early mammalian development. Moreover, knowledge about how the first lineages in the mammalian embryo are formed is elemental for defining the optimal conditions for maintaining pluripotent embryonic stem (ES) cells in a stable undifferentiated state and inducing them to differentiate. This in turn is critical to provide safe and effective cell therapies in regenerative medicine.

This project aims to understand when and how the epiblast – a pluripotent cell lineage that gives rise to the whole fetus (and is a source of ES cells) – arises within the developing preimplantation embryo. In particular we want to determine whether the signals initiating epiblast specification come from cell-cell and cell-environment interactions or whether the process remains under the genetic control of transcriptional factors. We also want to clarify what factors are crucial for the stabilisation of the epiblast lineage during development.

In this project a student will have chance to learn basic molecular biology methods as well as more advance methods used in experimental embryology and IVF clinics, such as embryo handling and culture, microinjection and micromanipulation.
 

• Cell Biology
• Developmental Biology
• Stem Cell Research

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Phosphoinositide 3-kinases (PI3Ks) are a family of enzymes that generate lipid signals which regulate key aspects of cell physiology and metabolism. Hence they have been linked to diseases of development and aging and are major therapeutic targets because of their role in cancer and diabetes. We are dissecting the mechanisms by which these enzymes are involved in signalling processes using fluorescently tagged lipid binding domains to visualise the lipid signals in vivo and a range of genetic reagents to manipulate the levels of the PI3Ks.

• Skwarek LC and Boulianne GL (2009): Great expectations for PIP: Phosphoinositides as regulators of Signaling during development and disease. Dev Cell 16: 12-20.
• MacDougall LK, Gagou ME, Leevers SJ, Hafen E, Waterfield MD (2004): Targeted expression of the class II phosphoinositide 3-kinase in Drosophila melanogaster reveals lipid kinase-dependent effects on patterning and interactions with receptor signaling pathways. Mol Cell Biol. 24:796-808.

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Genetics
• Membrane Trafficking
• Molecular Biology
• Molecular Cancer Studies

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Notch receptors are transmembrane glycoproteins that are of fundamental importance in multiple cell-fate decisions, such as occur during stem cell maintenance and cell differentiation. Notch receptors interact with membrane-tethered ligands (Delta, Serrate, Jagged) presented on neighbouring cells, resulting in downstream events that lead to control over the receiving cell’s differentiation programme. Dysregulation of Notch has been implicated in a myriad of disease states, including cancers. To achieve a signal, the Notch receptor must undergo three proteolytic cleavage events that enable release of the Notch intracellular domain into the cytosol, whereupon it translocates to the nucleus to act as a transcription factor. The second proteolytic cleavage, at a site ‘S2’, is key to Notch activation, triggered by ligand binding. This S2 site is housed with a part of the Notch extracellular domain called the Notch Regulatory Region (NRR). A crystal structure of the NRR reveals that the S2 site is normally buried and that Notch is thus autoinhibited. This S2 site needs to be unmasked to activate Notch. We explore the hypothesis that ligand binds to the extracellular domain of Notch and then exerts sufficient force (upon its endocytosis) to cause exposure of the S2 site through conformational change. Mechanical force has indeed emerged as a factor driving a number of cell processes.

Bridging physics and biology disciplines, we will measure the degree of force required to induce structural changes in the NRR to facilitate protease cleavage, and compare these to the forces that are actually exerted during ligand endocytosis. Using force microscopy on recombinant NRR, we have already demonstrated unfolding of protein domains. This PhD will continue the single molecule work, using AFM to establish whether mechanical unfolding does increase protease susceptibility at the S2 site. The work will extend to analysis of Notch mechanical unfolding and activation on live cells, ideally followed by detection of signalling in the nucleus (new method development). Furthermore, the student will initiate experiments aimed at measuring the force exerted on the Serrate ligand upon its endocytosis, in order to correlate this force with that recorded as sufficient to unravel Notch to expose the S2 site. Such an investigation of endocytic force is unprecedented and will involve both AFM and laser tweezer experimentation.
At the end of the PhD, the intended outcomes are to have proven mechanotransduction of the Notch signal, induced by ligand binding, and to thus provide new insight that could in turn lead to new routes to targeting Notch in anti-cancer (or other Notch-related disease) therapy. Indeed, scope for successful targeting of Notch proteolytic processing at a third (S3) site has recently been demonstrated; inhibitors of S3 (?-secretase) cleavage having reached phase II clinical trials. The skills training will encompass molecular biology, protein expression in bacteria and eukaryotic systems, cell culture, protein chemistry, atomic force microscopy, optical trapping (laser tweezers), spectroscopy and microscopy. Hence, multidisciplinary training is a key feature of the project, supported by the supervisory team.
 

• Hansson EM, Lendahl U, Chapman G (2004) Notch signaling in development and disease . Semin Cancer Biol. 14:, 320-8.
• Chen J, Zolkiewska A (2011) Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing. PLoS One 6: e22837.
• Gordon WR, Vardar-Ulu D, Histen G, Sanchez-Irizarry C, Aster JC, Blacklow SC. (2007) Structural basis for autoinhibition of Notch . Nat Struct Mol Biol. 14:, 295-300.
• Malecki MJ, Sanchez-Irizarry C, Mitchell JL, Histen G, Xu ML, Aster JC, Blacklow SC. (2006) Leukemia-associated mutations within the NOTCH1 heterodimerization domain fall into at least two distinct mechanistic classes. Mol Cell Biol. 26:, 4642-51.
• Vogel V (2006) Mechanotransduction involving multimodular proteins: converting force into biochemical signals. Annu. Rev Biophys Biomol Struct 35:, 459-488

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Molecular Biology
• Molecular Cancer Studies
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Ion channels represent one of the major therapeutic drug targets for wide ranging diseases. For example ion channel driven cellular responses to ATP regulate diverse physiological processes in mammals, including inflammation and pain. ATP signaling by P2X receptors therefore represents a novel target for disease involving pain and inflammation, with several pharmaceutical companies actively pursuing this potential. Understanding how P2X receptors are regulated will therefore be important for the further development of such drugs. Recently we have developed a novel approach to identify such regulators due to our discovery of a novel P2X receptor in the model organism Dictyostelium discoideum. You will use the unique combination of genetic (mutageneis), biochemistry (proteomic), live cell imaging and post-genomic tools available in Dictyostelium to identify novel genes that regulate P2X receptor function. Your studies will lead to a better understanding of the role and regulation of this pharmacologically important class of molecule. 

• Fountain S.J., Parkinson K., Young M.T., Cao L., *Thompson C.R.L., North R.A. (2007)
• An intracellular P2X receptor required for osmoregulation in Dictyostelium discoideum.Nature, vol. 448, p. 200-3

• Adaptive Organismal Biology
• Animal Biology
• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Channels & Transports
• Environmental Biology
• Evolutionary Biology
• Genetics
• Membrane Trafficking
• Microbiology
• Molecular & Cellular Neuroscience
• Molecular Biology
• Neuroscience
• Organelle Function
• Pharmacology
• Physiology
   

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

A central goal in developmental neuroscience is to elucidate the cellular and molecular mechanisms behind the formation, refinement, and maintenance of neural networks. Indeed, both during embryonic development and in diseases, failure to form adequate neural connections may result in severe disabilities. A critical event in the setting up of neuronal circuits is axonal branching. Indeed, control of axonal branching formation and retraction allows neurons to make connection with several targets, therefore playing an important in the formation of neuronal circuits.
We have recently identified a novel gene in the lab involved in axonal branching, Sprouty3. Specifically, we have found that (i) spry3 is expressed in spinal motor and sensory neurons in a BDNF-dependant manner (ii) in a biochemical assay, Spry3 prevents calcium release downstream TrkB (BDNF receptor) signalling and (iii) knock-down of Spry3 expression causes an excess of axonal branching in spinal cord motor neurons.
The goal of this project is to elucidate the mechanisms by which Spry3 regulate axonal branching. In particular, we want to understand the relation between calcium signalling and cytoskeleton. To this end, we will use in vivo imaging of both calcium and components of the cytoskeleton (such as Actin and microtubule) to analyse how their dynamics is affected by Sprouty3. Because Spry3 is specifically expressed in motor neurones, this work will have important implication for our understanding of the physiopathology of motor neurones diseases such Amyotrophic Lateral Sclerosis (ALS).
This project will be done in the very stimulating environment of the Healing Foundation Centre and in the Developmental Biology grouping of the Faculty of Life Sciences. The student will therefore have access to a wide-range of facilities and expertise to achieve world-class science.

Techniques for this project: basic molecular and biochemical techniques (cloning, RT-PCR, western blot); work with Xenopus embryos and generation of transgenics animals; primary culture of neurons; advanced imaging (live imaging, calcium imaging).
 

• Animal Biology
• Biochemistry
• Cell Biology
• Developmental Biology
• Molecular & Cellular Neuroscience
• Molecular Biology
• Neuroscience

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Epithelia are sheets of cells that line the surfaces and cavities of our bodies and act as barriers protecting us against infection, toxins and dehydration. Epithelia can be damaged by injury, surgery and disease and this damage must be rapidly repaired to restore the barrier function of the epithelium. We are investigating how epithelial repair occurs at a molecular level. Our work is carried out using the fruitfly Drosophila as a model system. The process of epithelial wound healing is remarkably similar in Drosophila and humans, and Drosophila has the advantage that we can readily use genetic techniques to explore the molecular and genetic basis of the process. We have developed a range of fluorescent molecules that allow us to image the process of epithelial repair in live Drosophila embryos.

Epithelial repair is achieved by movement of intact epithelial cells across wounded area until it is completely covered. In order for this to occur the epithelial cells have to change from being static to being motile. This is similar to the process of metastasis that occurs in cancer. How does this change from static to motile occur? The goal of this project is to identify the signals that are activated in wounded epithelia and how these trigger changes in epithelial cells. In this project you will investigate the role of a number of genes that we believe are important signals in triggering the shift of epithelial cells from static to motile. You will use genetics and live imaging techniques to explore how these genes influence epithelial cell behaviour and wound healing. This research may ultimately lead to new therapies that improve the ability of our bodies to heal wounds.
 

• Millard TH, Martin P. Dynamic analysis of filopodial interactions during the zippering phase of Drosophila dorsal closure. Development (2008) 135 621-626.
• Jacinto A, Martinez-Arias A, Martin P. Mechanisms of epithelial fusion and repair. Nat Cell Biol. (2001) 3 E117-23.

• Cell Biology
• Developmental Biology
• Genetics

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Using GFP bone marrow chimeras, we are analyzing the behaviour of inflammatory cells in different wound environments, such as chronic wounds and acute (normal) wounds. Sustained expression of Hoxa3 during tissue repair and regeneration reduces inflammation and accelerates healing, however, it is unclear if this is direct or indirect (whether Hoxa3 function is required in the wound resident cells, the inflammatory cells, or both). We would like to better understand the regulation of inflammatory cell gene expression in response to injury.

Current projects include:

• the development of an in vitro co-culture model system which will allow fast and efficient assays of inflammatory cell behaviour under a variety of conditions
• the development of fluorescence activated cell sorting (FACS) and reporter assays to study populations of inflammatory cells isolated form wounds at different time points, as well as from chronic v acute wounds

• Mace KA, Hansen SL, Myers C, Young DM, Boudreau N, (2005) HOXA3 induces cell migration in endothelial and epithelial cells promoting angiogenesis and wound repair. Journal of cell science 118(Pt 12): 2567-77.

• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Gene Expression
• Immunology
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The control of cell differentiation during development requires communication between cells via diffusible growth factors and cell-cell adhesion mediated signalling molecules. The Notch receptor is an example of the latter class and regulates the timing and outcome of cell differentiation decisions in many different tissues during development and the regulation of stem cells. The Notch signal must be precisely regulated to prevent inappropriate signalling since misactivation of Notch can cause cancer. Notch was first identified in Drosophila but has subsequently been identified in a range of vertebrate species, including four versions of the gene in humans. The activity of Notch in vivo has to be precisely controlled spatially and temporally. Using the Drosophila model system, our group has identified s novel mechanisms of Notch signal regulation which involve directing Notch to different locations in the endocytic trafficking pathway, depending on the activity of different ubiquitin ligase proteins. We are using genetic, biochemical, cell biological and computational analyses to investigate the regulation of Notch endosomal sorting and activity and the role this regulation plays in determining correct development and in avoiding cancer.

• Wilkin M, Tongngok P, Gensch N, Clemence S, Motoki M, Yamada K, Hori K, Franklin E, Taniguchi-Kanai M, Matsuno K, Baron M. (2008) Drosophila HOPS and AP-3 complex genes are required for a Deltex-regulated activation of notch in the endosomal trafficking pathway. Dev Cell 15:762-72.
• Cordle J, Johnson S, Tay JZY, Roversi P, Wilkin M, Hernandez B, Shimizu H, Jensen S, Whiteman P, Boquan J, Redfield C, Baron, M, Lea SM, Handford PA. (2008) A conserved face of the Jagged/Serrate DSL Domain is involved in Notch Trans-Activation and Cis-Inhibition. Nat Struct Mol Biol: 15:849-57.

• Biochemistry
• Cell Biology
• Developmental Biology
• Genetics
• Membrane Trafficking
• Molecular Biology
• Molecular Cancer Studies
• Organelle Function
• Stem Cell Research
• Structural Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Adult tissues are in a constant state of renewal to replace damaged and aged cells. A reservoir of stem cells is required to maintain this production of new tissue. Stem cells have the property both of cell renewal and ability to give rise to precursor cells, which have the potential to adopt many different cell fates. Reduction in stem cell activity has recently been linked to problems in tissue repair during aging. Misregulation of stem cells has also shown to be involved in origin of cancerous cells. It is important therefore to understand the fundamental mechanisms that control stem cell function in vivo in order to understand the different ways in which they can become misregulated. The ideal approach is to investigate stem cell regulation in vivo i.e. in the intact organism, because removal of stem cells from their niche to grow them in tissue culture can change their properties. The Drosophila melanogaster ovary has been well characterised as a model system to study stem cells in vivo because egg production has to be maintained throughout the lifespan of the adult fly. Different populations of stem cells reside in the ovary, giving rise to the germ line and to the somatic follicle cells which surround and separate each developing cyst. We have recently identified several novel genes, which are responsible for regulating stem cell function in the Drosophila ovary. This project will utilise molecular, biochemical and transgenic expression approaches to understand the mechanism by which one of these genes regulates the maintenance, proliferation and differentiation of the ovary stem cells.

• Animal Biology
• Cell Biology
• Developmental Biology
• Genetics
• Molecular Biology
• Molecular Cancer Studies
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

A long-standing problem for biologist is to understand how cell fate is established and maintained during development. To unravel this mystery could have a significant impact on cancer and stem cell research.

Our general strategy is to use the simple, but powerful model organism, C. elegans, and study how signalling pathways such as RAS and Notch can generate specific epigenetic landscapes during development.

The project is based on the finding that post-translational modifications of histone tails and the recognition of these modifications by specialised factors are critical to prevent excess RAS or Notch signalling.

At the conclusion of the project, the student will have developed an expertise in high throughput technology, genetics, GFP imaging, biochemistry, and basic molecular biology skills. In addition, the student will acquire an understanding of the role of model organisms in cancer research.
 

• Dev Biol. Fisher K, Southall SM, Wilson JR, Poulin GB. 2010
• Genes Dev. Wang JK, Tsai MC, Poulin G, Adler AS, Chen S, Liu H, Shi Y, Chang HY. 2010
• EMBO J. Poulin G, Dong Y, Fraser AG, Hopper NA, Ahringer J. 2005
• Oncogene. Poulin G, Nandakumar R, Ahringer J. 2004
• Nature. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, Welchman DP, Zipperlen P, Ahringer J. 2003

• Cell Biology
• Developmental Biology
• Gene Expression
• Genetics
• Molecular Cancer Studies
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Complex epithelia are endowed with the ability to modulate ion transport and homeostasis. Failure of ionic regulation is a hallmark of many human diseases. For ion transporting epithelia, such as those found in kidney and epididymis failure of ionic regulation leads to abnormalities such as distal renal tubular acidosis and male sterility. In other epithelia, such as secretory and mucociliary epithelia found in the gut and lung, failure of ionic regulation leads to diseases such as cystic fibrosis, associated with abnormalities in mucus consistency and secretion. Most epithelia consist of several cell types and the challenge is to understand how different cell types co-operate to form a functional organ and how abnormalities in one may affect the function of the others. Since such epithelia are difficult to study in vivo, in mammals, there is a great need for model systems that will recapitulate the complexity of the epithelia while being amenable to non-invasive observation and experimental manipulation.

The frog embryonic (larval) skin possesses mucus secreting goblet cells and multiciliated cells. We have shown that in addition, the epidermis of the Xenopus tropicalis larva, contains a population of ionocytes that express high levels of ion channels, enzymes and transporters such as V-ATPase, Carbonic anhydrase 12, pendrin and others. Thus, they are remarkably similar to the intercalated cells found in the mammalian kidney. We find that when ionocytes are genetically deleted, surprisingly, this has a deleterious effect on the development of ciliated cells, which show fewer cilia per cell. This project will aim to elucidate the molecular mechanism by which ionocytes influence the development of ciliated cells. We will use molecular biology, cell biology and imaging, including live confocal microscopy and Electron Microscopy. This is a powerful system to model complex epithelial diseases and in the future, to test potential therapeutic strategies.
 

• Cell Biology
• Channels & Transporters
• Developmental Biology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Evi3 is a large zinc-finger protein found to be up-regulated in B-cell leukaemia. We are investigating the mechanism by which Evi3 causes B-cell transformation. We are also interested in determining how Evi3 is regulated during normal B-cell differentiation. Using a haematopoietic stem cell assay system, we will test the hypotheses that Evi3 functions to direct cell differentiation into the B-cell lineage, and that excess Evi3 expression causes transformation of haematopoietic stem cells into leukaemic states. We will use this stem cell culture system to investigate gene expression defects and cell proliferation defects that are hallmarks of B-cell leukaemia. By identifying downstream targets of Evi3 we will gain greater insights into the genetic defects that cause leukaemia. Additionally, by studying Evi3 regulation, we will make progress towards understanding the requirements for Evi3 during B-cell differentiation, and determine how mis-regulation of Evi3 contributes to B-cell leukaemia.

Hentges et al., Evi3, a zinc-finger protein related to EBFAZ, regulates EBF activity in B-cell leukaemia. Oncogene. 2005 24(7):1220-30.

• Cell Biology
• Developmental Biology
• Genetics
• Molecular Biology
• Stem Cell Research

This project has a Band 3 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

The filamentous fungus Neurospora crassa is a well-known model eukaryote used for studying numerous phenomena including; gene silencing, light signal transduction and the circadian clock. The Neurospora genome is fully sequenced and contains almost 10 000 genes many of which encode proteins of unknown function. Investigations into the role of these proteins of unknown function will not only throw light on Neurospora growth and survival strategies but also inform studies on other industrially important fungi, cultivated strains, and plant and animal pathogens.

We are interested in the role of two genes encoding proteins similar to heat shock transcription factors. We found that hsf1 is an essential gene and that hsf2 is required for asexual sporulation (Thompson et al., 2008). The aim of this project is to identify targets of HSF1 and HSF2 and determine their importance for the organisms’ development and its ability to respond to temperature change.
 

Thompson S, Croft NJ, Sotiriou A, Piggins HD, Crosthwaite SK. (2008) Neurospora crassa heat shock factor-1 is an essential gene; a second heat shock factor-like gene, hsf2, is required for asexual spore formation. Eukaryot. Cell 7, 1573-1581. 

 

 

 

 

 

 

  

• Adaptive Organismal Biology
• Biochemistry
• Bioinformatics
• Developmental Biology
• Gene Expression
• Microbiology
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Lead Supervisor: Dr Shane Herbert (informal enquiries can be sent to Shane Herbert)

Sprouting of new capillaries from pre-existing vessels (angiogenesis) promotes the formation of almost all blood vessels during development, growth and tissue regeneration. Furthermore, imbalances in angiogenesis contribute to numerous disease states, including cancer, blindness, arthritis and ischemic disorders. Recent studies have determined that angiogenesis involves coordinated sprouting of specialized endothelial cells with distinct cell-fate specifications and behaviours. Endothelial “tip cells” lead sprouting vessels, extend filopodia and migrate in response to gradients of the soluble ligand, vascular endothelial growth factor (VEGF). In contrast, “stalk cells” trail behind tip cells, do not actively migrate and generate a vascular lumen. The induction of specific endothelial cell phenotypes and angiogenesis involves the tight spatiotemporal control tip/stalk cell-specific gene expression. However, the cell-type-specific transcriptional mechanisms that control gene expression during angiogenesis are unclear. Combining advanced genomic and in vivo cell biological approaches in the zebrafish model system we have identified various tip/stalk cell-specific genes that play key roles during angiogenesis in zebrafish. This project will define the cis regulatory elements controlling expression of these tip/stalk cell-restricted genes in vivo. Furthermore, these cis-regulatory elements will be exploited to develop zebrafish transgenic tools that will allow the genetic manipulation tip/stalk cell gene expression and angiogenesis in vivo. This project will use molecular biological, cell biological, advanced genomic, zebrafish transgenic and in vivo live imaging approaches. Ultimately, this project aims to uncover a detailed transcriptional framework for the control of angiogenic sprouting in vivo.

1) Herbert, S. & Stainier, D (2011). Molecular control of endothelial cell behaviour during blood vessel morphogenesis. Nat Rev Mol Cell Biol, 12(9), 551-64.
2) Herbert, S., Huisken, J., et al. (2009). Arterial-venous segregation by selective cell sprouting: an alternative mode of blood vessel formation. Science, 326(5950), 294-8.
3) Siekmann, A. & Lawson, N (2007) Notch signalling limits angiogenic cell behaviour in developing zebrafish arteries. Nature, 445(7129), 781-4
4) Hellstrom, M., Phng, L., et al. (2007) Dll4 signalling through Notch1 regulates formation of tip cells during angiogenesis. Nature, 445(7129), 776-80

• Biochemistry
• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Gene Expression
• Membrane Trafficking
• Molecular Biology

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Several Hox transcription factors are upregulated in response to injury. These transcription factors, in turn, regulate downstream target genes which influence cell function and cell behaviour. Microarray analysis of Hoxa3 target genes during wound repair in vivo identified a number of genes regulated by Hoxa3 during tissue repair and regeneration. In particular, we are interested in a subset of genes which may influence bone marrow-derived cell trafficking to injured tissue, or the engraftment and differentiation of those cells.

Current projects include:

• characterization of these target genes during tissue repair at different time points
• enhancer/reporter analysis to define regulatory elements controlling their expression

• Mace KA, Hansen SL, Myers C, Young DM, Boudreau N, (2005) HOXA3 induces cell migration in endothelial and epithelial cells promoting angiogenesis and wound repair. Journal of cell science 118(Pt 12): 2567-77.

• Biomolecular Sciences
• Cell Biology
• Developmental Biology
• Gene Expression
• Immunology
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

A major goal in regenerative medicine is to understand and ultimately facilitate our body’s ability to repair itself following injury. Unlike adults, embryos have the remarkable capacity to heal wounds quickly and completely, without leaving scars. For this reason, we have begun to investigate the molecular and cellular basis of embryonic wound healing. In a recent paper, published in Nature (reference below), it was shown that embryos produce H2O2 immediately after wounding, and this small molecule is involved in the fast recruitment of inflammatory cells to the wounds. In our lab, we recently performed a series of microarray experiments during embryonic wound healing and inflammation. These experiments uncovered many genes involved in the production or removal of H2O2 (such as myeloperoxidase, ncf1, ncf2, catalase, etc.). The aim of this rotation project will be to determine the role of H2O2 during embryonic wound healing and the recruitment of inflammatory cells to wounds, using a variety of gain and loss of function experiments in Xenopus embryos. The level of H2O2 in embryonic wounds will be assayed using confocal fluorescence microscopy and a H2O2 fluorecence sensor. Affects on wound healing efficiency and recruitment of inflammatory cells will be assayed using time-lapse microscopy and whole mount in situ hybridization to myeloid specific genes.

Key words: Inflammation, wound healing, tissue regeneration, stem cells
 

Chen, Y., Costa, R.M.B., Love, N.R., Soto, X., Roth, M., Paredes R. and Amaya, E. (2009) C/EBP? initiates primitive myelopoiesis in pluripotent embryonic cells. Blood 114:40-48.

Niethammer P, Grabher C, Look AT, Mitchison TJ. (2009) A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish. Nature 459:996-999.

Costa, R.M.B., Soto, X., Chen, Y., Zorn, A.M. and Amaya, E. (2008) spib is required for primitive myeloid development in Xenopus. Blood 112(6):2287-2296.
 

• Cell Biology
• Developmental Biology
• Immunology
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Inflammatory cells, macrophages and neutrophils in particular, play a pivotal role in orchestrating different phases of adult wound healing. We are currently characterizing the development of the primitive myeloid lineages, such as the primitive macrophage, and have begun to investigate their potential roles during embryonic wound healing. One big question that remains unanswered is what are the signals that mediate the recruitment of embryonic inflammatory cells to wounds? While in adults, recruitment of inflammatory cells to wounds appear to be mediated by cytokines and chemokines, the embryo does not express the genes encoding these proteins. In a recent series of microarray experiments during embryonic wound healing and inflammation, we identified Alox5, which is a gene involved in the production of leukotrienes, which are fatty molecules involved in inflammation. Therefore, the aim of this rotation project will be to determine whether Aox5 and leukotrienes are important during the inflammatory response in embryonic wound healing, using a variety of gain and loss of function experiments in Xenopus. The recruitment of inflammatory cells following wounding will be assessed using time-lapse microscopy and whole mount in situ hybridization to myeloid specific genes.

Key words: Inflammation, wound healing, tissue regeneration, stem cells
 

Chen, Y., Costa, R.M.B., Love, N.R., Soto, X., Roth, M., Paredes R. and Amaya, E. (2009) C/EBP? initiates primitive myelopoiesis in pluripotent embryonic cells. Blood 114:40-48.

Costa, R.M.B., Soto, X., Chen, Y., Zorn, A.M. and Amaya, E. (2008) spib is required for primitive myeloid development in Xenopus. Blood 112(6):2287-2296.
 

• Cell Biology
• Developmental Biology
• Immunology
• Molecular Biology
• Stem Cell Research

This project has a Band 2 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.

Although the Darwinian idea of ‘survival of the fittest’ is central to our understanding of the diversity of life on this planet, the evolution and maintenance of cooperative behaviour remains a conundrum. This is because when cooperating individuals perform some sort of costly act to help one another, they run the risk of disruptive cheaters that do not pay their fair share of the cost. In other words, if cheating is a better strategy, how is cooperative behaviour maintained within populations.

To address these problems, we use a simple system for the study of cooperative behaviour, the soil dwelling social amoeba D. discoideum. Under favourable conditions, D. discoideum amoebae exist as single celled individuals that grow and divide by feeding on bacteria. Upon starvation, however, up to 100,000 amoebae aggregate and cooperate to make a multicellular fruiting body consisting of hardy spores supported by dead stalk cells. Stalk cells thus sacrifice themselves to help the dispersal of spores, raising the question of why selection does not lead to unchecked cheating by individuals that do not pay their fair share of the cost of stalk production. Indeed, we have recently found that even within a small number of different D. discoideum strains, different social strategies, including facultative partner specific cheating and coercion, could be detected.

However, the key will be to extend this work to address patterns of genetic variation at the molecular genomic level in natural populations.

Through this PhD studentship we aim to reach this important goal. The project will have 3 stages:

1. Genome sequencing: Whole genome sequence data will be generated for many different naturally occurring D. discoideum isolates

2. Bioinformatic analysis of this sequence data: This will allow you to test whether genetic variation is associated with patterns of phenotypic variation. Through this you will identify ‘social genes’ and the potential role of all of these genes as generators of biodiversity. Finally, these data will allow broader questions regarding the selective forces driving genome evolution and the emergence of social traits to be addressed.

3. Molecular genetics: Using cutting edge developmental genetics techniques (e.g. transformation, knockouts and forced expression of functional variants) you will test hypotheses about the functional consequences of sequence variation on social behaviour.

In summary, this project will address major questions in evolutionary, developmental and environmental ecology. It will utilise hugely multidisciplinary approach by combining next generation sequencing, bioinformatic exploration of sequence variation, together with molecular and developmental genetics. Consequently it will undoubtedly provide an unprecedented opportunity for training in multidisciplinary approaches to biological questions.
 

• Parkinson K., Buttery N.J., Wolf J.B. and Thompson C.R.L (2011) A simple mechanism for complex social behaviour. PLoS Biology, vol9 e1001039
• Buttery N.J., Thompson C.R.L, Wolf J.B. (2010) Complex genotype interactions influence social fitness during the developmental phase of the social amoeba Dictyostelium discoideum. Journal of Evolutionary Biology, vol 23 p.1664-71.
• Buttery N.J., Rozen D.E., Wolf J.B., Thompson C.R.L. (2009) Quantification of social behavior in D. discoideum reveals complex fixed and facultative strategies. Current Biology, vol 19 p. 1373-7
• Santorelli L., Thompson C.R.L., Villegas E., Svetz J, Dinh C., Parikh A., Sucgang R., Kuspa A., Strassman J.E., Queller D.C., Shaulsky G. (2008) Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae. Nature, vol 451, p 1107-10
• Foster K.R., Shaulsky G., Strassmann J.E., Queller D.C., Thompson C.R.L. (2004) Pleiotropy as a mechanism to stabilize cooperation.. Nature, vol. 431, p. 693-6

• Adaptive Organismal Biology
• Developmental Biology
• Environmental Biology
• Evolutionary Biology
• Genetics
• Microbiology
• Molecular Biology

This project has a Band 1 fee. Details of different fee bands are available for UK/EU or International applicants. See: Fees.