PhD Studentships currently available:

PhD Studentship on "Speciation genomics, adaptation and gene transfer networks in bacteria"

Imperial College London in partnership with the University of Reading are pleased to announce a 3.5-year PhD studentship starting in October 2019. The project is titled "Speciation genomics, adaptation and gene transfer networks in bacteria" and is co-supervised by Tim Barraclough (Dept of Life Sciences, Imperial College London) and Richard Everitt (Dept of Mathematics and Statistics, University of Reading).

Project Summary: 

Bacteria constitute a massively diverse radiation of life, but the mechanisms of diversification remain less well understood than in sexual eukaryotes. In particular, although all bacteria reproduce clonally, many engage in a wide variety of mechanisms of recombination that can transfer DNA between individuals and divergent species. We still lack detailed understanding of how recombination influences both the ability of bacteria to diverge into distinct species and the way that bacteria adapt to environmental change.

This project will use genomic data to infer networks of gene transfer in bacteria and to determine the consequences of transfer events for speciation and adaptation. Alternative models for the structure of recombination will be compared – for example, a model of gradually declining gene transfer with genetic distance versus a model of discrete species units defined by mechanisms preventing gene transfer between them. The results will be used to test recent models for alternative mechanisms of bacterial speciation. A key component will be to develop computational methods that are feasible for large datasets and flexible enough to encode alternative sets of evolutionary mechanisms.

Population genetic models will then be used to determine how the shape of gene transfer networks affects evolutionary responses to contemporary environmental change. For example, do multiple species tend to evolve independently and in parallel or do beneficial mutations arising in one species spread through a wider clade or community? Does adaptation involve sequential beneficial mutations in a clonal background or recombination of beneficial variants from different genomic backgrounds? Which mechanisms of gene transfer are most effective in responding to different kinds of environmental change?  Results will be applied to antibiotic resistance in waste water communities in order to improve management actions for limiting the spread of environmental antibiotic resistance.

The project will involve computational modelling, Bayesian statistics, Monte Carlo methods, bioinformatics, evolutionary analysis and genomics. Depending on your interests, it may also include evolution experiments on speciation or whole community responses in the laboratory. We are keen to shape the exact focus and range of approaches to match the student’s own experience and interests.

The student would join the Centre for Doctoral Training in Quantitative and Modelling Skills in Ecology and Evolution (QMEE),, which provides training in the quantitative and modelling skills needed to address real-world problems by connecting theory, data, and practice. You could be a life sciences student interested in quantitative methods or a mathematics, computing or physical sciences student interested in applying your skills to evolutionary problems.

How to apply:  Please send your CV, a covering letter explaining why you are interested in the CDT and that project, and the names and e-mail addresses of two academic referees to At least one referee should have supervised you on a previous research project. Closing date 16th January 2019

Funding: The PhD funding will be for 3.5 years and provides a stipend of £16,999, which includes London weighting.

ICR Funded Studentship

Key information

Supervisor: Dr Masahiro Ono (Life Sciences) & Prof Alan Melcher (ICR)

Project Title: Understanding systems and molecular mechanisms underlying cancer immunotherapy for the development of precision immunotherapy with informed strategies

Recent breakthroughs in immunotherapy development have established that anti-tumour immunity is a major exploitable mechanism to fight cancer [1]. Notably, immune checkpoint inhibitors such as anti-PD-1 and anti-CTLA-4 antibodies abrogate negative regulatory mechanisms in the T cell system and enhance anti-tumour immune response, and have been clinically approved for various cancer patients including melanoma, renal cell carcinoma, ovarian cancer, and Hodgkin’s disease [2]. Our recent investigation using a single cell technology identified PD-1 and regulatory T cells (Treg) as two major suppressive mechanisms in tumour-infiltrating T cells from melanoma patients (malignant skin cancer) [3]. PD-1 is a surface protein that has a role in suppressing T cell receptor (TCR) signalling and thereby inhibiting T cell activation. PD-1 is highly expressed in overactivatedT cells (often called ‘exhausted T cells’), and inhibits their reactions to antigen. Thus the blocking of PD-1 and its ligand PD-L1/L2 can release the activity of tumourspecific T cells [4]. Treg specifically express the transcription factor Foxp3 and suppress anti-cancer immunity, and are a promising target for cancer immunotherapy [5]. Importantly, the immune check point inhibitor anti-CTLA4 antibody not only blocks costimulatory signalling (precisely, CD28 signalling), but also depletes regulatory T cells (Treg). However, anti-CTLA-4 increases the T cell responsiveness to not only cancer antigens but also self-antigens, inducing autoimmune reactions [2, 6]. In order to understand these dynamic processes during anti-tumour immune response,
Masahiro Ono and his group used Fluorescent Timer protein, which changes its emission spectrum spontaneously and irreversibly, and thereby developed a new tool for analysing time-dependent changes in antigen-reactive effector T cells and Treg, designated as Timer-of-Cell-Kinetics-and-Activity,Tocky [7, 8]).

The proposed project aims to increase the precision of cancer immunotherapy by improving the understanding of T cell regulation in animal models and clinical samples using a multidisciplinary approach. Under this major aim, the project has the following objectives.

Objective 1: To understand differential effects of immunotherapy on T cells from tumour tissues using the Tocky technology. In order to understand dynamic changes in these cells upon immunotherapy, the project will use computational codes that have been developed in the Ono lab, and the student will be trained for both experimental methods (multicolour flow cytometry) and computational analysis. Immunotherapy models include immune checkpoint inhibitors and viral immunotherapies, which have been developed in the Melcher lab [9].

Objective 2: To investigate new T cell subpopulations in tumour tissues that have unique 2 immunological functions. Multidimensional methods [3] will be used to identify effector, regulatory, and activated T cell subpopulations in tumour tissues. Objective 3: To identify clinically meaningful T cell subpopulations using clinical samples. The student will analyse tumour-infiltrating T cells using multicolour flow cytometry, gene expression analysis, and the multidimensional methods and other statistical methods.

Full details & How to Apply: 

BBSRC DTP 2019 Studentship: 1. Structural Basis of Selective Protein Degradation by the Plant Autophagy Cargo Receptor NBR1

Supervisors: Dr Doryen Bubeck (Dept of Life Sciences, ICL) & Dr Tolga Bozkurt (Dept of Life Sciences, ICL)

Project Description: Autophagy is an intracellular self-eating machinery central to cellular homeostasis and stress responses. In plants, autophagy cargo receptor NBR1 mediates selective degradation of protein aggregates and contributes to immunity. NBR1 mediated selective autophagy relies on interactions of NBR1 with the ubiquitin and the core autophagy adaptor, ATG8. However, molecular basis of selective autophagy and how NBR1 contributes to cell-autonomous immunity are poorly understood.The aim of this proposal is to dissect the functional principles of NBR1-targeted autophagy in plants. Specifically, it uses a multifaceted approach, integrating cryo-electron microscopy and plant molecular biology to characterize NBR1 mediated selective autophagy in plants.

Deadline: Tuesday, 15 January 2019 at 23:59UTC

BBSRC DTP Programme & Application Process

2. Phenoscopes: A high-throughput Platform for Phenotypical Typing of Insect Strains for the “Insects as Source of Proteins” Industry

Supervisors: Dr Giorgio Gilestro (Dept of Life Sciences, ICL) and Dr Nikolai Windblicher (Dept of Life Sciences, ICL)

Project Description: Creating sustainable, carbon neutral, protein-rich food sources is one of the leading priorities of this century, worldwide. The aim of this project is to create a repertoire of genetically selected and/or engineered insects, possibly aimed at mass scale production for the food industry for animal and, eventually human, consumption. The project will be carried in collaboration with N. Windblicher (expert in genetic manipulation of non-model-organism species) and BetaBugs, a small but promising UK startup. The project will consist of three work packages: 

  • WP1: Evolve a device we recently developed for sleep analysis in Drosophila (the ethoscope, Geissmann et al. PLoS Biology 2017) into a device that can be used for large scale phenotypical analysis of Hermetia illucens (Black Soldier flies), the most commonly used insect species in the food industry. Ethoscopes employ video-based machine-learning technology to detect activity and behaviour in fruitflies and phenoscopes, our proposed evolution, will also be able to detect metabolic features such as growth rate, body size, preferential temperature and humidity conditions of growth. 
  • WP2: Establish H. illucens as genetically amenable organism, using CRISPR-based homologous recombination techniques. 
  • WP3: Study the metabolism and behaviour of H. illucens

 More information on

BBSRC DTP 2019: 3. Imaging and modelling oomycetes invasion of plant roots

Supervisors: Dr GIovanni Sena (Dept of Life Sciences, ICL) & Dr Tolga Bozkurt (Dept of Life Sciences, ICL)

Project Description: Oomycetes such as the Phytophthora species are aggressive filementous pathogens responsible for major disruption of crops around the world. The mechanism adopted by these fungus-like organisms to track, attack and invade plant roots in soil is a paramount example of the complex physical and molecular interaction between roots and soil-living organisms. Remarkably, oomycetes zoospores are attracted to crop roots at least in part by the endogenous electrostatic field generated by root tips [1-2].The Sena group has recently studied important aspects of the interaction between roots and external electric fields and is developing new fluorescence tools to image and quantify the dynamics of membrane potentials in vivo in Arabidopsis roots. 

In this project you will learn to use state-of-the-art live imaging and quantitative methods to reveal the physical and molecular mechanisms guiding the invasion of root tissue by motile oomycete spores, at cellular resolution. As part of this study, you will analyse the interaction between oomycetes and root endogenous bioelectric fields, using state-of-the-art genetic tools to identify molecular components in Phytophtora essentials for root interaction and invasion. 

[1] van West P, et al. Oomycete plant pathogens use electric fields to target roots. Mol Plant Microbe Interact. 2002, 15(8):790–8.

[2] Staples RC. Zoospores use electric fields to target roots. Trends in Plant Science 2002, 7(11):484.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process


BBSRC DTP 2019: 4. Structural Basis of Nitrogenase Assembly and Oxygen Protection

Supervisors: Dr James Murray (Dept of Life Sciences, ICL) and Dr A William Rutherford

Project Description: Biological nitrogen fixation is catalysed by nitrogenase. Nitrogenase is a complex enzyme, with three subunits, binding several cofactors. The best studied nitrogenase has molybdenum in the active site, and is encoded by nif genes. The nif operon encodes other assembly factors and conserved proteins of unknown function. Two alternative nitrogenases, with vanadium or iron instead of molybdenum, encoded by vnf and anf clusters, are even less well-characterised. Nitrogenase is inactivated by oxygen, and this vulnerability, combined with the complicated assembly, makes heterologous expression of nitrogenase challenging. However, expression of nitrogenase in crop plants could revolutionise agriculture, by ending the need for polluting nitrogenous fertilizers.

We have recently biochemically and structurally characterised the Anf3 protein, which protects the iron-only nitrogenase from oxygen. Anf3 is associated with two other conserved genes anf12, which are of unknown function but also essential for iron-only nitrogenase. Our work on the oxygen-protective FeSII protein (PDB 5FRT), is a prerequisite to determining the mechanism of nitrogenase protection. In this project we will structurally and functionally characterise the remaining nif and alternative nitrogenase genes. This will require biochemistry and X-ray crystallography in the Murray group, and biophysical techniques such as EPR and spectroelectrochemistry for the bioinorganic chemistry in the Rutherford group.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 5. Biotechnological Carbon Capture and Conversion

Supervisors: Dr John Heap (Dept of Life Sciences, ICL) & Dr Karen Polizzi (Dept of Chemical Engineering, ICL)

Project Description: Greenhouse gas (GHG) emissions must be rapidly reduced to limit climate change. Special microorganisms can capture carbon from industrial waste gases, and can be genetically modified to convert this captured carbon into valuable products, unlike conventional carbon capture and storage.

This exciting new project builds on the expertise and ongoing research of the Heap lab (Life Sciences) and Polizzi lab (Chemical Engineering). Synthetic biology, metabolic engineering and process engineering approaches will be developed and applied to the development of sustainable biotechnological carbon capture and conversion of methane and CO2, both major waste products of widespread industrial processes.

OBJECTIVE 1. METHANE BIOCONVERSION: Methane is a potent GHG, so its release must be avoided, and it is usually burnt. This project will develop a new engineered methanotrophic biological system to convert waste methane into valuable products.

OBJECTIVE 2. PHOTOAUTOTROPHIC BIOCONVERSION OF CO2: We recently developed and applied combinatorial metabolic engineering for the first time in cyanobacteria, achieving efficient conversion of CO2 to the target product and genetic stability, key challenges in this field. This project will build on this success and develop the approach to biologically convert CO2 to further products, including terpenoids and diols.

OBJECTIVE 3. HYBRID CARBON CAPTURE AND BIOCONVERSION: The above processes will be linked to capture and convert first methane, then the CO2 exhaust from methane bioreactors.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 6. Bacterial Outer Membrane Proteins: The First Line of Defense Against Antibiotic Entry

Supervisors: Dr Konstantinos Beis (Dept of Life Sciences, ICL) & Prof Gad Frankel (Dept of Life Sciences, ICL)

Project Description: Antibacterial resistance is a rising global crisis. Resistance occurs by modification of drug targets, antibiotic degradation, efflux out of the cell or reduction of drug passage through the outer membrane (OM) into the cell. Porins at the OM facilitate the uptake of small polar nutrients and are the main entry route for many antibiotics. Clinical studies have shown that altering the expression of porins or mutations that alter their charge profile can contribute to antibiotic resistance. To-date, there are limited structural and functional studies of clinically-resistant bacteria with modified porins. In this project, we will work with clinical ESKAPE strains, which are the leading cause of nosocomial infections throughout the world, isolated from Imperial College Healthcare NHS trust, characterise their antibiotic resistant profile and underpin the role of porin in resistance using structural and functional methodologies.

This is a collaborative project between the Beis and Frankel labs. The structural work will be undertaken at the Research Complex at Harwell situated next to the Diamond Light Source synchrotron facility, Oxfordshire, whereas the Beis lab is based. The functional studies will be performed at the Frankel lab located at the MRC Centre for Molecular Bacteriology and Infection, Imperial College London.

This studentship will suit an enthusiastic student with background in either microbiology, biochemistry or structural biology.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 7. Imaging G-quadruplex DNA in Telomeres of Live Cells Using FLIM

Supervisors: Dr Marina Kuimova (Dept of Chemistry, ICL) & Prof Ramon Vilar (Dept of Chemistry, ICL)

Project Description: This project will focus on the development of novel probes and imaging techniques to monitor the formation of non-canonical DNA structures termed G-quadruplexes. Over the past few years, mounting experimental evidence suggested that these non-canonical DNA structures play essential biological roles. However, to date there is still little direct evidence that G-quadruplexes are functional in live cells. This work will build on our ‘proof of concept’ study using Fluorescence Lifetime Imaging Microscopy (FLIM) that has been published in [A. Shivalingam, et al, Nature Commun., 2015, 6, 8178]. 

The successful applicant will perform cellular imaging including FLIM and spectroscopic characterisation of new fluorescent probes and their interaction with various DNA topologies. The main focus will be to use these techniques to study G-quadruplex formation and its relationship to cell function. There is also scope to design and synthesise optical probes, provided the applicant has the right expertise and an aptitude for synthesis.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 8. Zinc Finger-based Gene Therapy in Huntington’s Disease

Supervisors:  Prof Mark Isalan (Dept of Life Sciences, ICL) & Prof Steven Brickley (Dept of Life Sciences, ICL)

Project Description: Huntington's disease (HD) is an inherited neurodegenerative disorder, caused by a CAG repeat expansion in the HTT gene, leading to toxic gene products. The disease has a high prevalence for an inherited disorder, affecting approximately 700,000 people worldwide (one in 10,000). Suffering is high for both patients and carers, with death generally occurring within 10 - 20 years of diagnosis. In this study, we will repress the leading therapeutic target in HD (mutant HTT) using cutting-edge imaging to observe the consequences in the CNS. We will use a synthetic designed zinc finger (ZF) against mutant HTT to attack HD pathology at its source (1,2). We will use our established AAV2- and AAV9-based delivery system, while exploring new delivery strategies (Isalan). The efficacy will be measured by biochemical (metabolomic, transcriptomic) and phenotypic effects, especially ex vivo 2 photon whole-brain imaging in mice (3,4) (Brickley). Overall, we aim to develop a practical therapeutic strategy that is based on gene therapy, which will lead to clinical applications in HD, as well as providing detailed imaging data on HD development.

1. Agustín-Pavón C, Mielcarek M, Garriga-Canut M & Isalan M. Deimmunization for gene therapy: host matching of synthetic zinc finger constructs enables long-term mutant Huntingtin repression in mice. Molecular Neurodegeneration 11(1):64 (2016).
2. Garriga-Canut, M., et al. & Isalan M. Synthetic zinc finger repressors reduce mutant Huntingtin expression in the brain of R6/2 mice. Proc Natl Acad Sci USA 109 (45):E3136-E3145 doi:10.1073/pnas.1206506109 (2012).
3. Song JH, Lucaci D, Calangiu I, Brown MTC, Park JS, Kim J, Brickley SG, Chadderton P (2018) Combining mGRASP and Optogenetics Enables High-Resolution Functional Mapping of Descending Cortical Projections. Cell Reports 24(4):1071-1080 24.
4. Houston CM, Diamanti E, Diamantaki M, Kutsarova E, Cook A, Sultan F, Brickley SG (2017) Exploring the significance of morphological diversity for cerebellar granule cell excitability. Scientific Reports 7, 46147

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 9. Stochasticity of Gene Expression in the C. elegans Epidermal Stem Cell Network

Supervisors: Dr Michalis Barkoulas (Dept of Life Sciences, ICL) & Dr Vahid Shahrezaei (Dept of Mathematics, ICL)

Project Description: Biological systems face constant fluctuations and perturbations, such as inherent stochasticity in their molecular processes or changes in the environment, yet tend to show robust and reliable behaviour. However, our knowledge on the mechanisms underlying biological robustness is still very limited. Among all multicellular organisms, Caenorhabditis elegans offers a unique experimental system to study robustness because of its remarkably reproducible development. The aim of this project is to reveal the extent of gene expression variability between genetically identical animals, as well as understand its functional implications. To this end, this project integrates experimental and theoretical work (the balance of which depends on the interests of the selected student) focusing on key transcription factors that constitute the C. elegans epidermal stem cell gene network. On the experimental side, the student will use molecular biology and single molecule microscopy to compare gene expression and protein dynamics between different cells and animals, both in wild-type development and upon delivering perturbations known to break the limits of stem cell robustness. On the theoretical side, the student will employ stochastic mathematical modelling of genetic networks driving stem cell fate decisions to interpret the observed interplay between noise and robustness in C. elegans development. 

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 10. Sustainable Sunlight-driven Bioproduction of Multi-purpose Chemicals

Supervisors:  Dr Patrik Jones (Dept of Life Sciences, ICL) & Prof Klaus Hellgardt (Dept of Chemical Engineering, ICL)

Project Description: Are you interested in biotechnology, sustainability and startups? Join our multi-disciplinary team and learn-by-doing the process of translating fundamental knowledge into real-world application with impact on societal sustainability.

With the practical aim of realizing sustainable commercial bioproduction of fossil fuel replacement chemicals using engineered cyanobacteria, this project will engineer continuous sunlight-driven bioreactors using synthetic metabolism. The work builds upon recent publications in our joint PHOTOFUEL project demonstrating biosynthesis of multi-purpose chemicals using engineered photosynthetic algae1, 2, 3, 4 and is supported by industrial collaboration.

The work will involve three steps. (a) Construction of synthetic metabolic pathways, through searching and engineering enzymes, followed by in vitro and/or in vivo implementation, and optimization of both the strain and the introduced pathway. (b) Construction and optimization of a continuous bench-scale bioreactor and capture system. (c) Mentored development of a pre-incorporation startup including pitching. Time permitting, we will also consider implementing non-native substrate based systems proven to minimize the threat of microbial contamination.

A suitable background would include at least 2 of the following: (1) molecular/synthetic biology, (2) biochemistry/enzymology, (3) bioreactor engineering. A passion for entrepreneurship and sustainability questions in general would also be valuable.

(1) Yunus and Jones (2018) Photosynthesis-dependent biosynthesis of medium chain-length fatty acids and alcohols. Metabolic Engineering 49, 59-68.

(2) Yunus, Wichmann, Wördenweber, Lauersen, Krue and Jones (2018) Synthetic metabolic pathways for photobiological conversion of CO2 into hydrocarbon fuel. Metabolic Engineering 49, 201-211.

(3) Harun, I., Del Rio-Chanona, E. A., Wagner, J. L., Lauersen, K. J., Zhang, D., & Hellgardt, K. (2018). Photocatalytic Production of Bisabolene from Green Microalgae Mutant: Process Analysis and Kinetic Modeling. Industrial & Engineering Chemistry Research, 57(31), 10336-10344.

(4) Dechatiwongse, P., Maitland, G., & Hellgardt, K. (2015). Demonstration of a two-stage aerobic/anaerobic chemostat for the enhanced production of hydrogen and biomass from unicellular nitrogen-fixing cyanobacterium. Algal Research, 10, 189-201.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 11. Engineering Glycoprotein Therapeutics

Supervisors: Dr Stuart Haslam (Dept of Life Sciences, ICL) & Dr Cleo Kontoravdi (Dept of Chemical Engineering)

Project Description: Biopharmaceuticals, new medical drugs produced using industrial biotechnology processes, are one of the fastest growing sectors of the pharmaceutical industry. Many important biopharmaceuticals, such as therapeutic antibodies with commercial sales in the billions of pounds are glycoproteins. The type of sugar molecule on the biopharmaceuticals can greatly affect their functional properties. This can greatly affect the potential therapeutic value of the products.

The project will fundamentally involve the development and application of new bioprocesses to improve the production of consistent, high-quality glycoprotein therapeutics. This will include glycoengineering of CHO cells, altering the expression of glycosyltransferases, glycosidases and other key biosynthetic enzymes and transporters to both control and homogenize glycosylation patterns. Also, the development of a cell free artificial Golgi with a defined and tunable glycosylation machinery to reduce glycosylation variability. The impact of these approaches on glycoprotein glycosylation will be defined by mass spectrometric analysis, the data from which will be fed back to facilitate integrative design improvements.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 12. Unravelling the importance of mitochondrial DNA variability for cell competition during embryonic development

Supervisors: Dr Tristan Rodriguez (National Heart & Lung Institute, ICL) & Dr Nick Jones (Dept of Mathematics, ICL)

Project Description: During embryogenesis and tissue homeostasis growth relies on the proper balance of proliferation and cell death. The mechanisms that control this balance also act later in the adult during tissue homeostasis and repair. Manipulating these pathways to induce cell replacement is therefore an important drive for regenerative medicine. Cell competition is a quality control that acts at the tissue level to compare cell fitness within a population and then remove and replace those cells that are less-fit than their neighbours. We have recently found that small non-pathogenic changes in mitochondrial DNA (mtDNA) sequence are sufficient to alter the competitive ability of embryonic stem cells, allowing them to colonise the pluripotent niche.  In this project the student will test the hypothesis that cell competition acts as purifying selection to select the cells with the fittest mitochondria. This will be done by studying experimentally as well as by modelling mathematically the dynamics of the competitive behaviour of cells with different mitochondrial DNAs. Additionally, the student will screen for the signalling pathways that mediate this competitive behaviour and analyse their importance for mitochondrial activity in the developing heart.  Together these studies will provide valuable insight into the selection mechanisms that act to optimise fitness during tissue homeostasis.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

BBSRC DTP 2019: 13. Host Proteins Targeted by the CSEP family 21 Effectors from the Biotrophic Pathogenic Fungus Blumeria Graminis

Supervisors: Dr Laurence Bindschedler (Biological Sciences, RHUL) & Dr Tolga Bozkurt (Life Sciences, ICL) 

Project Description: Fungi are major actors in spoiling crops and reducing food yield. Among them, powdery mildews are a class of obligate fungal pathogens affecting major agricultural and horticultural crops such as cereals, grape, zucchini or strawberry, thus having a major impact on food production, in the UK and globally. 

The barley powdery mildew, Blumeria graminis f.sp. hordei is a typical example, that is also used as a molecular model. Blumeria possess 500+ candidate secreted effector proteins (CSEPs) that are likely virulence determinants (Pederson et al, 2012). Little is known about them except that many have 3D structure resembling RNAses. All 4 candidates from CSEP family 21 have now been validated for their virulence role during infection of barley.
One of the member of CSEP family 21, CSEP0064 (BEC1054) was shown to interact with 2 barley pathogenesis related (PR) proteins and two elongation factors (eEF) proteins (Pennington et al, 2016, 2018). This project will investigate the molecular function of the remaining 3 effectors, as well as the resistance role of barley proteins interacting with CSEP064. The objectives are:

1. Identifying barley proteins interacting with the remaining 3 effectors from CSEP family 21 using in vitro and in planta systems for protein-protein interaction techniques (protein pull down and mass spectrometry). This will allow to understand whether effector proteins from the same families target different host proteins to highjack the host immune system.
2. Validating interactors with targeted molecular approaches (BiFC or Y2H)
3. Validating BEC1054 four interactors (2 PRs and 2 eEFs) function in resistance using a RNAi derived gene silencing transient assay set up to work with biotrophic pathogens.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

Additional Project Information


BBSRC DTP 2019: 14. Green perfect: allocation of resources for chloroplast biogenesis

Supervisors: Dr Enrique López-Juez (Biological Sciences, RHUL) & Prof Peter Nixon (Life Sciences, ICL) 

Project Description: Plant biology has arguably never been as relevant as it is today. The biology of chloroplasts underpins the biology of whole plants, and the two most-important impacts of plants for humanity: as food source and as carbon sink. Yet a surprising number of aspects of chloroplast biology remain poorly understood.
Like the solar cells of man-made panels, chloroplasts first need to be built, which requires not only energy but also abundant nutrients for the synthesis of proteins and nucleic acids - chloroplasts are very protein-rich and possess their own DNA. This process requires nitrogen for both and phosphate mostly for the latter. Hence chloroplasts are "expensive" organelles, and both nutrients limit chloroplast development. Nitrogen supplementation in particular is energy costly, environmentally damaging, and its loss an important source of greenhouse gases.
Chloroplasts develop from pro-plastids in plant "stem cells" during cellular differentiation. We have carried out a detailed analysis of cell and chloroplast differentiation during development of wheat, which exhibits an ideally-suited full range of cellular developmental stages within a single leaf. That analysis, using quantitative microscopy and examining global gene expression, resolved elementary cellular processes, monitored known chloroplast development regulators, and provided the basis for the search for novel regulators.

The current project will explore how nutrient limitations alter the "total chloroplast compartment" of wheat leaf cells, whether they do so through altering previously known or novel regulators, whether the "expensive" chloroplast genetic machinery (transcription and translation capacity) in particular becomes altered, and what is the impact on photosynthetic performance.

Through targeted alteration of homologues of those chloroplast regulators in the genetic model plant, Arabidopsis thaliana, the project will examine whether the impacts of altered nutrient availability on productivity can be minimised, establishing the basis for future, rational improvement.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

Additional Project Information

BBSRC DTP 2019: 15. Validating the Use of Curcumin in Health and Disease

SupervisorsProf Robin SB Williams (Biological Sciences, RHUL) & Dr Olivier E Pardo (Dept of Surgery & Cancer, ICL) 

Project Description: Developing new therapeutic strategies for cancer offers the best hope of continued good health for many people in our society. The natural product curcumin, derived from the spice turmeric, has been effective in several clinical trials relating to cancer and inflammation. However, its use remains limited partially due to a lack of understanding of its therapeutic mechanism. To address this our research has provided new insights to the mechanisms of action of curcumin in a simple biomedical model system that we have used extensively as a pharmacogenetic model in the analysis of many diseases including epilepsy (Chang et al., 2012; Kelly et al., 2018; Xu et al., 2007), Alzheimer’s disease (Ludtmann et al., 2014; Otto et al., 2016) and bipolar disorder (Kelly et al., 2018; Williams et al., 1999; Williams et al., 2002), successfully translated to pre-clinical models (Chang et al., 2013; Chang et al., 2014; Chang et al., 2015a; Chang et al., 2015b; Williams et al., 2002). Using this model provides range of experimental approaches that are not possible in mammalian models, enabling rapid advances in research (Warren et al., 2018; Williams et al., 2006). In our recent study of curcumin (Cocorocchio et al., 2018), we have identified a potential target protein for curcumin that is deregulated in many forms of cancer, suggesting this may be how curcumin blocks cancer progression. Using this model, we have further unpublished data describing this novel mechanism in regulating a related pathway involved in both cancer and inflammation (called the mTOR pathway) (Kim et al., 2017). The proven success of this model, the demonstrated mechanisms, and our new data provides an excellent basis for research discovery relating to curcumin mechanistic insight and cancer treatment.

This project will undertake a detailed characterization of this novel mechanism of curcumin action at a molecular level, providing a unique insight into how curcumin may function in the treatment of cancer and inflammation. Discoveries will then be validated and translated to relevant animal/human models, through collaboration with Dr Pardo at Imperial College, who provides world-leading expertise in translational research relating to mTOR signalling in cancer. The data collected here will therefore provide synergistic advances in biomedical and translational research to help improve cancer treatment and ultimately societal health.

The project will provide advanced training in a multidisciplinary range of techniques, including cell and developmental biology, biochemistry, pharmacology, and pharmacogenetics. The student will also develop expert knowledge in traditional (mammalian) cell models, providing an integrated approach for 3Rs research. Skills in scientific writing and oral presentation at international meetings will also be developed. Through collaboration with Dr Pardo and his group at the Department of Surgery and Cancer Imperial College, the project will also provide training on cutting edge pre-clinical studies in mammalian model for translational impact.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

Additional Project Information

BBSRC DTP 2019: 16. Controlling the Switch between Centrosomes and Cilia: How Cells Prevent Ciliogenesis When It’s Not Required

Supervisors: Dr Christopher J Wilkinson (Biological Sciences, RHUL) & Dr David Mann (Life Sciences, ICL) 

Project Description: Cilia are hair-like organelles that project from the surface of many cells. They act as signalling masts, housing receptors that are essential for communication and environmental sensing. The cilium consists of hundreds of components and many of them are required for cilium construction and maintenance. Cilia employ many of the same components as centrosomes and these two organelles are, in fact, mutually exclusive with only one type present in cells at any one time.  Thus, switching between cilia and centrosomes is critical, particularly during the cell cycle. We identified BCAP as a dedicated ciliogenesis inhibitor and hypothesise that BCAP is a key intermediary linking ciliogenesis with proliferative control. This project will investigate the precise mechanism by which BCAP achieves inhibition, exploiting the expertise at Royal Holloway and Imperial. Roles in autophagy and vesicle trafficking will be tested. We will determine the protein partners of BCAP through proteomic studies. We will investigate how BCAP is subject to cell cycle control through phosphorylation by protein kinases known to control ciliogenesis using biochemical, proteomic and chemical genetic approaches. These experiments will uncover the roles and regulation of BCAP, elucidating the linkage between ciliogenesis and proliferative control, a fundamental aspect of human cell biology.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

BBSRC DTP Programme & Application Process

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BBSRC DTP 2019: 17. Exploring the Effects of Decanoic Acid on Ion Channel Function and Synaptic Network Activity

Co-Supervisors: Dr Philip Chen (Biological Sciences, RHUL) & Prof Robin Williams (Biological Sciences, RHUL)

Additional Supervisor: Prof Stephen Brickley (Dept of Life Sciences, ICL) 

Project Description: Most anti epileptic drugs modify synaptic transmission or neuronal excitability and act on ionotropic receptors for the main excitatory (glutamate) or inhibitory (GABA) neurotransmitters or ion channels within the mammalian CNS. We have recently discovered a straight chain ten-carbon fatty acid (decanoic acid, DA) which displays non-competitive antagonism for the AMPA (AMPAR) subtype of glutamate receptor (Chang et al., 2016). Plasma levels of decanoic acid rise in patients prescribed the medium chain triglyceride (MCT) ketogenic diet and have been shown to have antiseizure effects in vitro and in vivo at clinically relevant concentrations. Despite our pharmacological characterization of DA action at AMPARs, there is little information on the molecular basis for DA’s inhibitory activity at AMPARs and the effect of DA on other glutamate receptors such as NMDA receptors or other ion channels. Furthermore we have little understanding of how DA’s inhibitory activity would influence synaptic network activity within the brain.

We will investigate the action of DA on other ion channels by using recombinant heterologous expression systems such as Xenopus oocytes to express ion channel RNA transcribed in vitro. Furthermore we will use structure-function studies and generate and express mutant channels to identify the amino acid residues contributing to the site of action. We will also try to understand how DA modifies synaptic activity within a neuronal network and we will use patch-clamp electrophysiology in brain slices to investigate the actions of DA.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

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BBSRC DTP 2019: 18. Stimuli-responsive Biopolymers for Life Science, Materials and Therapeutic Applications

Supervisors: Dr Mikhail Soloviev (Biological Sciences, RHUL) & Prof Xiao Yun Xu (Chemical Engineering, ICL) 

Project Description: The scientific motivation behind this project is to generate remotely controlled molecularly defined systems capable of changing their physical or molecular properties in response to external stimuli. New smart materials and preparations are being increasingly used in biotechnology and biomedical applicators, particularly for targeted drug delivery. The majority of stimuli-responsive materials reported to date rely on polymers, composites and nano-scale macromolecular assemblies. These include liposomal formulations, colloids, micelles, nanoparticles, and other polymeric drug delivery systems. Such composite nano-medicines often possess new biophysical and pharmacological traits, including stimuli sensitivity, where rapid physicochemical transitions could be triggered by small changes of the surrounding environment. However, such therapeutically useful and sought after attributes have to be generated through careful formulation and preparation of multicomponent macromolecular particulates. Such combinations are difficult to engineer rationally and to guarantee their reproducibility during manufacturing. Whilst such macromolecular assemblies are most suitable for the delivery of small molecule drugs, combining synthetic nano-composite materials with biologically derived therapeutic molecules, such as proteins, presents a substantial additional challenge. The complexity of such composite nano-medicines makes them difficult to manufacture reproducibly.

The key aim of this project is to engineer protein based functional equivalents of polymer nano-composites, where the key functionalities, such as targeting, (multi)stimuli-sensitivity and therapeutic functionality, are combined in a molecularly defined protein or protein complex. To this end we have already developed and partially characterized a polypeptide system capable of self-assembly and stimuli-responsive controlled disassembly in response to changes in temperature or pH. The protein vector developed allows reversible combining of different protein functionalities into a defined multi-subunit protein complex through a simple self-assembly process in solution. The project will built on these foundations to further expand the range of stimuli-sensitive modules to include sensitivity to pressure, light, electrical, mechanical or chemical stimulation. The student will further explore our combinatorial approach to protein molecular engineering, with a particular focus on devising flow-sensitive and multi-stimuli-sensitive protein modules and will characterize newly developed preparations biochemically and biophysically. A collaboration with Prof Xu (Imperial College London) will further advance this research through multi-scale modelling of cardiovascular fluid mechanics and drug delivery. Our system will yield an ultimate protein vector for targeted and controlled delivery and stimuli-controlled release of protein therapeutics delivered intravenously.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

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BBSRC DTP 2019: 19.The Application of Modern Synthetic Biology Techniques to Address the Production of Nutritional and Industrial Speciality Chemicals

Co-Supervisors: Prof Paul Fraser (Biological Sciences, RHUL) & Dr Genny Enfissi (Biological Sciences, RHUL) 

Additional Supervisor: Dr Rodgrigo Ledesma-Amaro (Bioengineering, ICL) 

Project Description: Isoprenoids, also known as terpenoids represent the largest and oldest class of natural products documented. In crop plants intense efforts have been made to increase nutritional isoprenoids such as carotenoids (carotene provitamin A) and tocopherols (vitamin E) as a means of nutritional enhancement. Commercially isoprenoids are used in cosmetics and fragrances, and as colorants and nutritional supplements in foods and feeds. The present production platforms are either plants and/or microorganisms. Biosynthetically all isoprenoids are related via a common five carbon building block (isopentenyl pyrophosphate; IPP). Different isoprenoid classes can utilise the same isoprenoid precursors, which are preferentially used or channeled at different developmental stages. Through the creation of enzyme fusions a means of altering/optimising metabolite challenging can been achieved. These fusions which utilise flexible peptide linkers have the potential to optimise the flow of precursors from one class of isoprenoid into the desired products. In effect create an artificial metabolon. Proof of concept work has proven the potential of the system both in terms of enzymatic function and high throughput screening. In the proposed project fusions between isoprenoid enzymes metabolising geranylgeranyl (C20) or farnesyl (C15) diphosphate will be created and tested in plants and yeasts.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

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BBSRC DTP 2019: 20. Sensing and Memorising Abiotic Stress through the DNA Integrity Pathway in Plants

SupervisorsProf Laszlo Bogre (Biological Sciences, RHUL) & Dr Jie Song (Life Sciences, ICL) 

Project Description: How plants cope with environmental stresses is a fundamental question for sustainable agriculture. We recently discovered that in parallel to the canonical DNA damage signalling pathway, the RETINOBLASTOMA RELATED (RBR) together with the E2F transcription factors play important transcriptional and non-transcriptional roles to signal DNA damage on the plant chromatin. Evidence is accumulating that this signaling mechanism is also used to sense biotic and abiotic stresses. The model is that these stress signals evoke disruption and arrest in DNA synthesis that recruits RBR to the stalling DNA replication sites together with chromatin modifiers, which could be involved both in evoking adaptation responses as well as in stress memory. Within this project we will investigate how and where on chromosomes the RBR complexes become recruited upon environmental stresses and how the chromatin landscape is modified to facilitate environmental adaptation.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

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BBSRC DTP 2019: 21. Social Epidemiology: Interactions, Networks, and Disease Spread in a Key Pollinator

Supervisors: Prof Mark J F Brown (Biological Sciences, RHUL) & Prof Matthew Fisher (School of Public Health, ICL) 

Project Description: Disease spread – in humans, domesticated animals and plants, and wildlife – is a major threat to health and ecosystem services. However, how diseases spread – their epidemiology – in complex social organisms, like humans and bees, is poorly understood. Determining how diseases spread in social networks is key to understanding and controlling them. Bumblebees and their parasites provide a model system in which to develop an understanding of such epidemiology. In addition, bumblebees are key pollinators that are undergoing decline across the globe, and one reason for these declines is parasites and the diseases they cause. Consequently, understanding disease spread in bumblebees also has significant applied conservation value.

This project will use the bumblebee Bombus terrestris and its parasites Crithidia bombi and Nosema bombi, both of which have significant impact on bumblebee colonies, to ask how social structures affect parasite epidemiology. Importantly, it will combine both empirical experiments and modelling work to understand parasite dynamics. Empirical research will range from controlled laboratory experiments, through controlled semi-field experiments, to observations in wild field populations of parasite dynamics. Modelling work will use the classic Susceptible-Infected modelling framework for parasite epidemiology to explore, explain, and predict the empirical data.

The results of the project will provide a detailed insight into how social networks impact disease epidemics, and specifically how these occur in bumblebees. In addition to its scientific impact, it will feed into policy and management of pollinators in the UK, and globally.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

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BBSRC DTP 2019: 22. Increasing Fitness Potential of Plants through Chromatin Landscape Analysis during Stress Responses

Supervisors: Dr Alessandra Devoto (Biological Sciences, RHUL) & Dr Colin Turnbull (Life Sciences, ICL) 

Project Description: Stress responses under water scarcity are induced to enable survival and simultaneously shoot growth is reduced to limit water loss. It is therefore of paramount importance to analyze the molecular mechanisms regulating stress response and tolerance in higher plants to enhance stress-survival. The interplay between abscisic acid (ABA) and jasmonates (JAs) stress hormone signalling pathways is central to align plant growth with the environment. JAs evokes a transient growth arrest in an ambivalent, so called, READY-TO-GO state, followed by the reset of growth rate. Methyl jasmonate (MeJA) and ABA levels increase during drought stress and MeJA plays an important role in drought-induced loss of grain yield. The process of priming or hardening involves previous experience of a biotic or an abiotic stress making a plant more resistant to future exposure. Chromatin remodelling is emerging as an important factor to regulate environmental response genes. Exposure to a priming agent could modify an epigenetic mark such histone modification, enhancing responses to subsequent stress.

This project will establish the molecular mechanism by which plants memorize information on stress exposure to overcome the limits that biotic and abiotic stresses impose on agricultural production due to down-regulation of yield. The successful candidate will learn high-throughput functional genomics, plant physiology and biochemistry and techniques of wide applicability working in a vibrant internationally competitive environment.

Deadline: Tuesday, 15 January 2019 at 23:59 UTC

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