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Research students are welcomed to Brunel as valued members of our thriving, research-intensive community. Find out more about Research Degrees in Brunel. A research degree provides the opportunity to investigate a topic in depth, and contribute new knowledge to your discipline. We are particularly interested in supervising students' research in the following areas: 

  • Environmental Health and Ecosystems
  • Biological Pathways and Systems
  • Environmental Change
  • Environmental Solutions
  • Environmental Policy and Communication

Proposed PhD Projects

Radiation risks to patients treated with Radium-223

Bone related cancers are common and represent a wide spectrum of malignant disease. Radium-223 (223Ra) is a form of ionising radiation which selectively targets to bone-cancer sites where it very effectively causes the malignant cancer cells to die. The success of this new therapy in improving patient survival in prostate cancer patients is creating a great deal of excitement whereby its therapeutic use may be broadened to include other cancers with bone disease including those in younger patients. Immature blood cells, which mature into all of the different cell types of the peripheral blood, reside in the bone marrow (BM). Immature blood cells therefore sit close to radioactive-targeted cells of the bone which means that they are potentially at risk of radiation exposure as a consequence of this treatment. To date, the risks of such exposure on long-term BM complications such as secondary, treatment-related leukaemia are unknown.

Key objectives of the proposed research are (i) whether cells of the haemopoietic system are directly (or indirectly) exposed to 223Ra upon uptake into bone metastases and (ii), whether there is any evidence for the occurrence of radiation-induced genomic instability. These will be addressed in two ways. Firstly, whole blood will be sampled from prostate cancer (PCa) patients treated with 223Ra and secondly, we will irradiate a human 3D tissue culture model of BM in vitro. A range of cytogenetic techniques will be employed including multiplex fluorescence in situ hybridisation (M-FISH) to ascertain the frequency of transmissible radiation-induced chromosome aberrations. This will provide evidence of previous 223Ra (α-particle) exposure to the BM. Additional techniques employed may include the quantification of micronuclei, DNA damage foci and inflammatory cytokine secretion to examine for any radiation-induced bystander effect. Findings from this study will be used to determine whether 223Ra treatment results in any exposure to the BM and if so, to make estimations of the radiation dose and also, any potential long-terms risks of this.

Contact supervisor: Dr Rhona Anderson

Understanding effects and mechanisms of anti-depressant drug pollution on molluscs

Pharmaceuticals, persisting in the environment are becoming a growing concern for wildlife health.  Antidepressants act by modulating the action of neurotransmitters such as serotonin. Because many biological mechanisms are conserved throughout evolution compounds may have unintended effects in non-target organisms. In molluscs serotonin is involved in important behaviours such as feeding, locomotion, reproduction and predator avoidance. Recent research has highlighted that molluscs, often under-represented in toxicology research, could be extremely sensitive to antidepressant drugs compared to standard vertebrate test species (e.g. fish). Understanding how sensitive molluscs are to this type of pollution, and if important population levels effects might occur, is necessary to adequately regulate pollution and protect ecologically important groups of animals. Detailed investigations into why such differences might occur between vertebrates and mollusc have yet to be conducted. Therefore the student will develop their research in this emerging field of toxicology. 
This project will require a multidisciplinary (e.g. ecology, physiology, toxicology, analytical chemistry, molecular biology etc.) approach to answer the research questions surrounding how and why molluscs might be more sensitive to anti-depressant drugs, and importantly, what the impacts of pollution might be to wild populations of molluscs. The students would be expected to develop the research project with the support and guidance of the supervisory team. Likely methodologies will include: some basic biology, in vivo experimentation as well as in vitro and in silico techniques, other methods such as field work and modelling may also be used depending on research outcomes.

Supervisors:
Prof. Susan Jobling
Dr. Alice Baynes

Development of clean-up and clean technologies for the treatment of industrial waste streams 

The main focus of my research is on process innovations in various industries, for example, chemical, petrochemical, textile, plating, and leather manufacturing processes. I work on the development of treatment system which can be subdivided into end-of-pipe technologies and clean technologies. The end-of-pipe technologies are basically designed for installation at the end of the production process, without altering the chemical reactions manufacturing the main product. The clean technology, on the other hand, is a type of technology with which pollution is eliminated from within the production process, meaning that pollutants do not form in the first place. Thus, clean technologies are frequently seen as being superior to end-of-pipe technologies for both environmental and economic reasons. The selection of these technologies to combat the problems associated with the management of pollution control largely depends on the nature of the environmental problems and the type of regulations involved.

The development of clean-up technologies involves the use of various types of solvents to remove toxic materials from both solid and liquid waste streams. The main focus of my research is to prepare and characterise different types of ionic liquids (ILs) and evaluate their performances for the selective extraction of metals from mixed waste samples. The specific objectives are: 1) to synthesis ILs using solvent-free methods, 2) to characterise these ionic liquids and 3) to investigate the solubility of heavy metals, rare earth metals, and metal oxides in these ILs. The development of clean technologies involves optimisation and improved control of chemical reactions in existing processes and the development of new processes to achieve environmentally clean reactions. In particular, I work on the development of a concentrator cell to improve metal recovery systems from dilute solutions for the control of industrial pollution received the Queen’s Award for Environmental Achievement.

Supervisor: Dr Abdul Jabbar Chaudhary

Persian Gulf Oasis hypothesis: an environmental paradise in hyperarid periods

Archaeological evidence from the Persian Gulf (PG) suggests that early humans were able to survive hyperarid climatic oscillations by occupying environmental refugia. Geological models propose that during past periods of low global sea-level, linked to regional aridity, the PG may have functioned as a wetland ‘oasis’ environment. Both models suggest the establishment of a freshwater wetland in what is now the deeper part of the PG. This would have favoured human population survival during arid periods by providing stable and predictable sources of freshwater and food.

This proposal aims to yield unique palaeoenvironmental evidence (from pollen, dinoflagellate cysts and charcoal) to test the ‘Gulf Oasis’ hypothesis, by studying existing sediment cores taken in and around the PG. The focus is to elucidate the relationship between climate, the environment and ancient population dynamics within this crucial region. The project is multidisciplinary as it requires the close collaboration of geologists, archaeologists and palaeo-environmentalists. The objectives are double: I. to produce the first high-resolution spatiotemporal (centennial-scale) palaeoecological records (terrestrial and marine) around the PG for the last 28,000 years, using micropalaeontological methods. II. to integrate palaeoecology and archaeological findings, assessing climate-environment-human relationships in the PG, whilst testing the Gulf Oasis hypothesis.

Supervisor: Prof. Suzanne Leroy

The ‘Trojan Horse’ - transfer of chemicals in the environment to animals by microplastics

In Greek Mythology, the Trojan Horse (hiding a select force of men), enabled the Greeks to gain entrance into Troy during the Trojan War.  Metaphorically a "Trojan Horse" has come to mean any act of subterfuge that causes the target to invite a foe into a securely protected place; a phrase that isnow associated with tiny pieces of plastics (microplastics) that find their way into our urban rivers every day.  Microplastics are believed to influence the movement of chemicals in the aquatic environment by mobilising chemicals contained within sediments by binding them onto their surfaces. The plastics, being small and mobile, may be ingested by a range of benthic organisms, and release their biologically active payload inside the body to affect health. 

This project will combine state-of-the-art methodology and expertise from Brunel University London to (i) understand how microplastics influence the mobility, partitioning and bioavailability of aquatic pollutants, and (ii) to determine whether exposure to microplastic ‘Trojan Horses’ can alter the behaviour, reproduction and expression of relevant biomarker genes in live snails.  Laboratory exposures, using the mud snail Potamopyrgus antipodarum, will be used to develop a greater understanding of the role of microplastics on the distribution and bioavailability of known sediment-bound contaminants.  There may also be opportunities to utilise field studies and catchment modelling approaches to determine the best management options through working with project partners Thames21 and other external stakeholders.

Supervisors:

Are retinoid-like chemicals prevalent in the environment and do they pose an ecotoxicological risk?

Retinoids have a significant role in many vital biological processes such as regulation of skin function and neuronal development.  There are over 2,500 retinoid related compounds used in cosmetic products and as anti-acne therapeutic agents. There is increasing concern about the presence of retinoids and synthetic chemicals with retinoid-like properties entering the environment. Retinoid activity has been detected in wastewater effluent, pulp mill effluents, and from unknown/diffuse sources, suggesting that a variety of chemicals exist in nature (natural and/or man-made) that mimic the activity of natural endogenous retinoids. There is little information on what these chemicals might be, or where they come from, and identifying these chemicals is now on the OECD agenda.

The complete identity of retinoid like chemicals or the risks they pose to natural systems is unknown. Identification of the most active components and an assessment of their potential impact on the environment can be used to determine treatment strategies and to inform policy makers.  This project will develop bioassay directed methods to determine the identity of retinoid chemicals and investigate if retinoid-like chemicals are prevalent in the environment and if they pose an ecotoxicological risk.   

Supervisors:

Elucidating the molecular mechanisms of parasite-host interactions between snails and schistosomes

The parasitic disease Schistosomiasis affects 243 million people worldwide. Having hatched from human urine or faeces contaminating water-bodies, the parasite must seek and infect a compatible water snail before developing further to infect humans. Recent research conducted at Brunel has identified an attractant released by snails that is used by the parasite to find and infect the snail intermediate host.

Now that we have isolated the attractant released by snails into the water that schistosomes use to find and infect snails, we
propose to investigate the genes and synthetic pathways relevant to snail schistosome attraction using genomic approaches.  It is hoped that this fundamental information will help in the development of novel intervention strategies for disease transmission.

Supervisors:

Regulation of Brk/PTK6 Expression in Breast Cancer Cell Lines

Brk/PTK6 is an intracellular tyrosine kinase whose expression is up-regulated in many breast cancers and high expression has been linked to higher tumour grade. It has been shown to potentiate EGF, IGF and MET signalling pathways resulting in increased
signalling up-regulating several processes that are required for tumour development such as cellular proliferation, anchorage-independent cell growth and migration. Brk expression also results in decreased cell death. Much of the current research focuses on identifying new substrates and elucidating Brk's potential role in tumour progression and chemotherapy resistance. However, to
date there is little known about the processes that lead to Brk expression. Identification of a HIF-response element upstream of the ptk6 gene indicates that hypoxia could play a role in regulating expression, although this is unlikely to be the only mechanism. Understanding how Brk expression is regulated may lead to the identification of new targets for therapeutic intervention.

This project will focus on identifying transcription factors that are known to be involved in tumourigenesis and investigating whether they play a role in regulating Brk expression. Expression analysis will be carried out to identify transcription factor expression patterns in breast cancer cell lines which can then be correlated to Brk expression. Once individual transcription factors (or their families) have been identified, RNA interference and over expression techniques will be used to down regulate transcription factor expression and the effects on Brk expression will be determined.  In addition methylation of the Brk promoter in breast cancer cells with varied Brk expression will be examined The main techniques for this study will be cell culture, RNA interference, RT-PCR, RNA extraction, reverse transcription, western blotting and epigenetic analysis.

Supervisors:

  • Dr Amanda Harvey
  • Dr Mark Pook

Brk and mTOR signalling: implications for Taxol resistance

One of the major causes of death amongst breast cancer patients is due to the development of distal metastases and the acquisition of resistance to chemotherapeutic agents. There is a scientific and clinical need to understand the alterations in cellular signalling pathways that could contribute to chemotherapeutic resistance in breast cancer. Our preliminary data implicates both that Brk expression and mTOR signalling are up-regulated in resistance to Taxol, a chemotherapeutic drug that is widely used in treating breast cancer. This project seeks to investigate the involvement of Brk, a kinase over expressed in up to 86% of breast cancers, in regulating mTOR signalling in the development of drug resistance.

This project seeks to investigate the involvement of Brk, a kinase over expressed in up to 86% of breast cancers, in regulating mTOR signalling in the development of Taxol resistance. You will examine the gene expression of mTOR components by real-time Q-PCR in Brk-suppressed and Brk-overexpressing breast cancer cells. Relative phosphorylation levels will also be determined using phospho-specific antibody arrays. To determine whether mTOR, is a Brk substrate, we will immunoprecipitate Brk and western blot for members of the mTOR pathway. We will also examine whether Brk influences the effects of mTOR inhibitors and whether combinations of Brk and mTOR inhibitors alter sensitivity to Taxol in Taxol-resistant cells.

Supervisors:

  • Dr Amanda Harvey
  • Dr Emmanouil Karteris

Novel regulation of glucose metabolism

Glucose can be degraded by two fundamental metabolic pathways, glycolysis and the pentose phosphate pathway (PPP). There have been extensive studies of feedback and feed-forward mechanisms and regulation by hormones such as insulin. However, environmental factors and internal signals can also affect these pathways and the mechanisms by which this happens are not well understood - for example, how the pathways respond to oxidative stress and how they change in tumour cells. We have recently identified two novel regulators which will be characterised in this project. We will use budding yeast as a model organism. Yeast cells are much easier to manipulate than mammalian cells and most molecules and mechanisms are conserved from yeast to man. As a consequence much of our understanding of glycolysis and the PPP is derived from studies with budding yeast.

The aim of this project is the analysis of the role of the novel regulators of glucose metabolism. It will be established which glycolytic and PPP enzymes bind to the regulator proteins. Since the regulators are protein kinases, phosphorylation of these enzymes will be examined. We will also use enzyme assay and determine concentration of metabolites to understand how the regulators control glucose metabolism.
Molecular biological techniques will be employed to generate strains and plasmids required for the project. Protein-protein interaction will be analysed by co-immunoprecipitations and the split-ubiquitin system. The phosphorylation status of proteins will be examined by immunoblotting. The concentration of glycolytic and PPP metabolites will be determined by mass spectrometry in collaboration with the University of Cambridge.

Supervisor: Dr Thomas Höfken

Regulation of nuclear mRNA export

The export of mRNA from the nucleus to the cytoplasm is a key step in the regulation of gene expression in eukaryotic cells. This process is therefore important for most if not all biological functions in eukaryotes. This is illustrated by a range of human diseases, including cancer, caused by defects in mRNA export. Several components involved in nuclear mRNA export have been described but we are only beginning to understand the regulation of this process. Budding yeast is an ideal system to study this fundamental cell biological process. Yeast cells are much easier to manipulate than mammalian cells and most molecules and mechanisms are conserved from yeast to man. As a consequence much of our understanding of mRNA export is derived from studies with budding yeast.

We have recently identified a kinase as a novel regulator of mRNA transport. The aim of this project is the analysis of the role of this kinase in the regulation of mRNA export. It will be examined under which conditions this protein mediates mRNA export. Potential regulatory mechanisms will be analysed. It will for example be tested whether the kinase regulates the localisation or protein-protein interactions of mRNA export factors. Furthermore, phosphorylation of mRNA export factors will be analysed.
Molecular biological techniques will be employed to generate strains and plasmids required for the project. Fluorescence in situ hybridisation (FISH) and GFP tagging will be used to determine the intracellular localisation of mRNA and proteins, respectively. Protein-protein interaction will be analysed by co-immunoprecipitations and the split-ubiquitin system. The phosphorylation status of proteins will be examined by immunoblotting.

Supervisor: Dr Thomas Höfken

Development of an in vitro 3D tissue culture model to study the effects of environmental contaminants on the human fetal-placental unit

Endocrine disrupting chemicals (EDCs) are environmental chemicals that interfere with physiological systems, adversely affecting hormone balance (endocrine system) and disrupting the normal function of organs heavily regulated by hormones, such as those of the female reproductive system. They include a variety of classes of chemicals, such as industrial by-products, pesticides and plasticisers. A common chemicals detected in human tissues is xenoestrogen bisphenol A (BPA), a plasticiser. BPA is present at levels that are 5-fold higher in the amniotic fluid than the maternal sera, due to its active transport across the placenta. Also, there is a positive correlation between BPA and miscarriages, and a link with the onset of preeclampsia; a leading cause of maternal and perinatal morbidity and mortality. Exposure to EDCs play a critical role not only in placentation but also in embryonic development and can impact later on in adult life.

Here, we propose the use of inter-connecting chambers 3D placental/umbilical cord/fetal cell models as platform to study how EDCs.  Therefore, during the 3-year PhD studentship we will:
Aim 1: Establish and validate a 3D in vitro model to study fetal-placental function. We will grow commercially available placental, umbilical cord and fetal cells on a 3D matrix of inter-connecting chambers.
Aim 2:  Study the effects of EDCs (e.g. BPA) using tanscriptomics and proteomics. Following treatments, we will investigate changes in the entire genome and proteome of these cells.
Aim 3: Ases the best biomarkers in terms of specificity and specificity for endocrine disruption in the feto-placental model. Using a combination of proteomic and transcriptomic arrays the most predictive biomarkers will be identified for EDCs.
All techniques are well established, so no caveats are anticipated.

Supervisors:

  • Dr Emmanouil Karteris
  • Dr Elisabete Silva

Investigating the effects of surfactant proteins in ovarian cancer progression

Ovarian cancer is one of the most common types of cancer in in women; every year 7,000 women are diagnosed in UK. It is the second most common occurring in the reproductive tract and the fifth overall. It is associated with very high mortality; after 5 years typically less than one third of patients diagnosed are still surviving. The cure rate for women with ovarian cancer has not significantly changed over the past 10 years. Surfactant proteins are important for clearing pathogens, maintaining pulmonary homeostasis and survival. These proteins have been localised in various parts of the human reproductive tract, including the ovaries. Surfactant protein D (SP-D) has recently been implicated in cancer and has been reported to have an inhibitory role. Tumour cells can be affected by the inflammatory environment and that can have an effect on tumour proliferation and metastasis, thus making surfactant proteins’ role even more important.

We hypothesised that SP-D has a potential inhibitory role in ovarian cancer progression since it is expressed in various parts in the reproductive tract. The main objectives are:
1. Identify the effects of intrauterine tissue secreted proteins on cancer cell proliferation. For this, conditioned media from myometrial and endometrial cells treated with SP-D will be used to treat 3 distinct human ovarian cancer cell lines.
2. Study the effects of SP-D on gene expression of surfactant proteins and mTOR pathway components.
3. Elucidate the effects of SP-D on cell proliferation as well as apoptosis or involvement in any other cytotoxic or cytostatic events.
For this project we will employ a wide repertoire of molecular, cellular and biochemical techniques. All techniques are well established, so no caveats are anticipated.

Supervisors:

  • Dr Emmanouil Karteris
  • Dr Uday Kishore

Targeting TERT and the MYCN gene network as a novel therapeutic approach for high-risk neuroblastoma.

MYCN belongs to a small family of transcription factors implicated in fundamental cellular processes. There are 3 members of the MYC family in mammalian cells, c-MYC, MYCN and L-MYC. They interact with DNA through a consensus sequence called the E-box (CANNTG) and in concert with the partner MAX facilitate gene transcription. The importance of MYC in cell biology is vast. MYC controls key cellular processes including proliferation, survival and metabolism. Critical to this proposal is the fact that one of the genes positively regulated by MYC is the catalytic subunit of the telomerase complex, TERT . A recent study has shown that genomic rearrangements near the TERT gene are frequent in high-risk neuroblastomas and activation of TERT is particularly frequent in MYCN amplified tumours. These results are supported by our own analysis suggesting that the expression of TERT is significantly predictive of poor prognosis in multiple neuroblastoma datasets.

The central objective of the study is to verify whether inhibition of TERT by a clinically viable inhibitor called Imetelstat and using Fluoxetine-Prozac to inhibit the MYCN signalling network can cause synergistic killing of high-risk, MYCN amplified neuroblastoma cells. In vitro studies: neuroblastoma cell lines will be exposed to increasing concentrations of Imetelstat, Prozac and drug combinations for 24-72 hours and the IC50 will be calculated using MTT/MTS assays. The different cell lines will also be subjected to immunofluorescence analysis with activated caspase-3 antibody, propidium iodide staining and FACS analysis to determine the cell cycle and apoptosis status. In vivo studies: it will be verified if Imetelstat can cause regression of human neuroblastoma tumours transplanted into immunocompromised mice.

Supervisor: Prof Arturo Sala

Modelling the t(6:9) translocation and MYB-NFIB gene fusion using the Crispr/Cas9 technology: implications for adenoid cystic carcinoma.

Recent advances in genomic technologies have revealed frequent MYB rearrangements in human malignancies. MYB, MYBL1 and MYBL2 belong to a small gene family encoding transcription factors whose role in oncogenesis has always been suspected, but never fully demonstrated. The main goal of the project is to validate the hypothesis that the t(6:9) chromosomal translocation, and formation of the MYB-NFIB fusion gene, is the leading cause of Adenoid Cystic Carcinoma (ACC), a rare and incurable tumour of exocrine glands that will be used as a model of MYB-addicted malignancy. The establishment of animal and cellular models of ACC will be critical for the validation of MYB targeting molecules. A further aim is the understanding of the signalling pathways downstream of MYB that could lead to the identification of new biomarkers and targets for therapy.

Specific Objectives:

1. To create mouse and cellular models of ACC implementing genomic editing technology. The mouse and cellular models will be used to study the molecular pathogenesis of the disease and in preclinical experiments. 2. To study signalling pathways and kinases activated as a result of oncogenic mutation of MYB that could be used as pharmacological targets. 3. To use genomic approaches to distinguish gene signatures common to mouse and human ACCs that could serve as prognostic biomarkers to predict the clinical outcome of ACC patients. 4. To identify and refine MYB small molecule inhibitors and develop them into drugs for the treatment of ACC and other MYB driven cancers.

Supervisor: Prof Arturo Sala

Differential expression patterns associated with the development of systemic sclerosis

Systemic sclerosis is a chronic autoimmune rheumatic disease, characterised by excessive scarring and fibrosis which causes thickening and tightening of the connective tissues of the skin and damage to major organs, including lungs, heart, kidneys, and the gastrointestinal tract. In collaboration with clinicians at the Royal Free Hospital in London we are using microarray profiling of control and disease tissues to identify changes in protein expression.

The main aim of the project is to establish the defects in membrane traffic and signalling that are at the basis of disease progression in systemic sclerosis. Identification of proteins involved in disease progression will help the development of novel therapeutic targets to halt this debilitating disease.
Microarray analysis and characterisation of proteins that show altered expression levels in diseased samples will be used to identify candidate proteins. These proteins will be further selected by gene ontology profiling and their importance in disease progression tested in our in vitro systems, using novel imaging techniques (e.g. total internal reflection microscopy).

Supervisor: Dr Gudrun Stenbeck

Involvement of the matrix protein SPARC in the dynamic interaction between tumour and host cells

Tumour growth depends on the crosstalk between malignant and surrounding stromal cells (fibroblasts, osteoblasts, endothelial cells and inflammatory cells). Malignant cells secrete soluble proteins that reach neighbouring stromal cells, forcing them to provide a suitable 3D environment for their growth and spreading (metastasis). Different studies, including expression array analysis, identified the matrix protein SPARC as a marker of poor prognosis in different types of cancer.

Growth factors, like TGFbeta and PTHrP, play a role in tumour progression by modulating protein expression. However, little is known of how these external factors modulate the intracellular trafficking machinery to stimulate secretion of proteins such as SPARC.

The main aim of the project is to elucidate how aberrant growth factor signalling alters protein secretion. To investigate the effects of TGFbeta and PTHrP on SPARC secretion, we plan to use tumour cells and primary osteoblastic cells known to naturally express SPARC. We will study secretion of endogenous SPARC by immunoprecipitation as well as by measuring secretion of Green Fluorescent Protein-SPARC chimerae in response to treatment with TGFbeta and PTHrP. TGFbeta and PTHrP signalling most likely stimulates GTP exchange factors (GEF) that are specific for the small GTPases  of the ARF and Rab family. We will therefore study SPARC secretion before and after knockdown of selected GTP-exchange proteins with small interfering RNA.

Supervisor: Dr Gudrun Stenbeck

Differential expression patterns and transport characteristics of aged cells

Ageing is associated with a number of diseases and manifests itself at the organ level (e.g. the morphological changes in the skin) as well as cellular level. Cellular function is dependent on correct delivery of proteins to their destinations, which is especially apparent in the ageing brain where axonal and dendritic transport is impaired. The underlying causes of this impairment most likely are due to changes to intracellular organelles, which are processing the proteins for secretion, i.e. the Golgi apparatus. Fragmentation of the Golgi has been implicated in functional and structural impairments of axons, presynaptic terminals and postsynaptic dendritic spines, which have been observed in neurodegenerative diseases and ageing.

The project aims to analyse key components of the intracellular trafficking machinery in aged cells to identify alterations associated with ageing. Special attention will be given to the analysis of protein lipid modifications in aged cells with the long-term aim of finding intervention possibilities. We have evidence that budding of transport vesicles from the Golgi apparatus in aged cells is altered and will use advanced imaging techniques to establish Golgi transport kinetics in control and aged cells in addition to biochemical Golgi transport assays. Furthermore, we have a system established in our laboratory to purify intracellular organelles and transport vesicles. We will use these purified fractions to analyse alterations in protein modifications by nano liquid chromatography - tandem mass spectrometry (Nano LC-MS/MS).

Supervisors:

  • Dr Gudrun Stenbeck
  • Dr Ian Kill

Nanoparticles in drug delivery

Nanoparticles (NPs) are materials with overall dimensions in the nano scale range (5nm-100nm). Due to their unique physicochemical properties, they have found a wide range of applications and are currently explored as drug and gene delivery vehicles. The mechanism by which NPs are taken up by cells has important implications for their fate and their impact on biological systems. After uptake, NPs can either become trapped in the cells and their cellular organelles or are recycled back to the extracellular space. The routes taken by a specific NP depend on surface charge and shape and determine if NP have inflammatory or toxic effects. Awareness of these effects is an important aspect in the use of NPs in biomedical applications and tailoring the particles for drug delivery ensuring their biosafety.

The aim of the project is to analyse the uptake and intracellular routes of NPs in clinical relevant cell types to establish their potential as drug delivery vehicles. Carbon nanotubes, magnetic particles and gold nanoparticles uptake by immune and cancer cells will be studied by measuring the NPs’ interaction with the cell membrane, their intracellular fate and their effect on signal transduction by high-resolution live cell microscopy, total internal reflection microscopy, Raman spectroscopy and quantitative ELISA. Cytokine release will be measured by microarray and qPCR. Cellular organelles containing NPs will be purified after uptake and their protein content analysed by mass spectrometry. RNAi technology will be employed to verify candidate proteins involved in NP uptake.

Supervisors:

  • Dr Gudrun Stenbeck
  • Dr Uday Kishore

The impact of chromosomal rearrangements on the genome organisation of leukaemia cells.

Chromosomal rearrangements are a hallmark of leukaemia. It is well known that specific chromosomal rearrangements are associated with certain leukaemia subtypes and that can predict clinical outcome. What is not well understood, is how these chromosomal rearrangements influence the genome organisation within the nuclear architecture of leukaemia cells.  The study of genome organisation is an emerging field of research in pathologies such as cancer. It has been shown that gene repositioning in the nuclei of cancer cells may be associated with abnormal gene expression. We and others have previously shown that gene repositioning may be due to chromosomal rearrangements affecting a particular locus. What exactly dictates the gene repositioning is matter of investigation.
Useful background reading:
1. Bourne et al. (2013) Interphase Chromosome Behaviour in Normal and Diseased Cells, In: Yurov Y, Vorsanova SG, Iourov IY, editors. Human Interphase Chromosomes: the Biomedical Aspects, Springer, p. 9-33.
2. Ballabio et al. (2009) Ectopic expression of the HLXB9 gene is associated with an altered nuclear position in t(7;12) leukaemias. Leukemia 23:1179-1182
3. Roukos and Misteli (2014) The biogenesis of chromosome translocations. Nat Cell Biol 16:293-300.

This project aims at clarifying the contribution of chromosomal rearrangements to the genome organisation of leukaemic cells and at exploring the effects that gene repositioning might have on gene expression. As part of this project, leukaemia derived cell lines will be selected on the basis of specific chromosomal rearrangements. Fluorescence in situ hybridisation will be applied to those cell lines in order to map chromosomal breakpoints accurately and to identify specific loci of interest. Specific genes will be investigated for their expression levels using Quantitative Real Time PCR and for their radial nuclear positioning using specialised software.

Supervisors

  • Dr Sabrina Tosi
  • Dr Joanna Bridger

Repo-Man function in embryogenesis and differentiation

Repo-Man (CDCA2) is a Protein Phosphatase 1 (PP1) targeting subunit that has been shown to be an important regulator of cell division. Recent studied from our laboratory have also shown that that Repo-Man is important for the correct assembly and maintenance of heterochromatin by an epigenetic mechanism. Since genome-wide profiling of pluripotent cells and differentiated cells suggests global chromatin remodelling during differentiation which results in a progressive transition from a fairly open chromatin configuration to a more compact state, we want to address the importance of this complex during early embryogenesis using zebrafish as a model system.

The aim of the project is to knock-down CDCA2 in zebrafish and analyse the early development  by imaging and immunofluorescence staining.  The student will conduct both whole animal gene knock out or tissue-specific gen knock-out selecting the tissues where CDCA2 is highly expressed in adults. Moreover, the in vivo function of this complex will be investigating by generating specific mutants using the newly developed CRISPR/Cas9 mediated genome engineering.

Supervisor: Dr Paola Vagnarelli

Role of CDCA/PP1 in Triple Negative Breast Cancer (TNBC)

Estrogen, progesterone, and HER2 receptor-negative (triple-negative breast cancers TNBC) encompass the most clinically challenging subtype for which targeted therapeutics are lacking.  To identify critical therapeutic targets, a better understanding of the biology of triple-negative breast cancer is therefore needed.
We have identified a phosphatase complex CDCA2/PP1 that acts as an epigenetic modifier and it is overexpressed in breast cancer cells, more specifically in TNBC, and its overexpression correlates with bad prognosis. Interestingly, depletion of CDCA2 in the TNBC cell lines blocks the ability of these cells to proliferate in wound healing assays suggesting that decreasing CDCA2 level could be an avenue for therapy. However the detailed molecular mechanisms for this are not known.

The project aims to identify the molecular pathways that are controlled by CDCA2 in TNBC and to develop small molecules or cyclic peptides that interfere with the formation or activity of this complex. For this, the student will use biochemical and molecular biology tools to identify the key molecules that are subjected to differential regulation in TNBC cells (Mass spectrometry and Reverse Phase Protein Array) before and after depletion of CDCA2.
In collaboration with Prof Manfred Auer at Edinburgh University, the student will use a phage display library to isolate cyclic peptides that bind specifically to the complex and then will test their efficacy on arresting proliferation of TNBC cells.

Supervisor: Dr Paola Vagnarelli

 

Funding for doctoral studies

A number of studentships and other research funding opportunities are available at Brunel. Please see full list here: Research degree funding

Choosing your supervisor

Our researchers create knowledge and advance understanding, and equip versatile graduates with the confidence to apply what they have learnt for the benefit of society. Browse the list of the members of our Theme to select your potential supervisor here. You are welcome to approach your potential supervisor directly to discuss your research interests.

All research degrees are administered by the Postgraduate Programmes Office in Colleges. Once you have identified your area of research and a potential supervisor, please use the contact details provided here for enquiries.