ERC FUNDED PROJECTS

The human genome is highly transcribed, with over 90% of sequences contributing to the production of RNA. The function of the vast majority of these RNAs is unknown. Evidence over many years has revealed that transcription factors and chromatin regulators are associated with a variety of non-coding (nc)RNAs, but their function remains largely unknown. There are a few cases where a role has been ascribed for ncRNAs in transcription, but no clear mechanistic insight has been defined yet. We predict that many of the newly identified ncRNAs emanating from the genome will play a role in transcriptional processes. We intend to identify and characterise such ncRNAs. This will take place in two phases. In the first phase we will use biochemical approaches to identify ncRNAs involved in the regulation of chromatin and transcription. Our investigations will focus on proteins leading to the induction of pluripotency and oncogenesis. ncRNAs associated with such proteins will be identified using targeted screens. In the second phase, the importance of these RNAs in determining pluripotency and oncogenesis will be analysed. In addition, a variety of molecular approaches will be used to investigate the mechanism by which these ncRNAs regulate the function of the proteins or complexes they associate with. One particular hypothesis we will explore is that such ncRNAs play a role in guiding proteins to DNA sequences, via the formation of RNA/DNA triplexes. This concerted and focused analysis will provide mechanistic insights into the functions of ncRNAs in transcriptional regulation and validate their role in key biological processes. The identification of such new ncRNA-regulated pathways may open up new avenues for therapeutic intervention.

2 141 470 €

Start date: 2011-05-01, End date: 2017-04-30

The study of host-pathogen systems is of central importance to the control of infectious disease, but also provides unique opportunities to observe evolution in action. Many pathogen species have diversified under selection pressures from the host; conversely, genes that are important in host defence also exhibit high degrees of polymorphism. This proposal divides into two parts: (1) the evolution of pathogen diversity under host immune selection, and (2) the evolution of host diversity under pathogen selection. I have developed a body of theoretical work showing that discrete population structures can arise through immune selection rather than limitations on genetic exchange. The predictions of this framework concerning the structure and dynamics of antigenic, metabolic and virulence genes will be empirically tested using three different systems: the bacterial pathogen, Neisseira meningitidis, the influenza virus, and the malaria parasite, Plasmodium falciparum. The current theory will also be expanded and modified to address a number of outstanding questions such whether it can explain the occurrence of influenza pandemics. With regard to host diversity, we will be attempting to validate and extend a novel framework incoporating epistatic interactions between malaria-protective genetic disorders of haemoglobin to understand their intriguing geographical distribution and their mode of action against the malarial disease. We will also be exploring the potential of mechanisms that can organise pathogens into discrete strains to generate patterns among host genes responsible for pathogen recognition, such as the Major Histocompatibility Complex. The co-evolution of hosts and pathogens under immune selection thus forms the ultimate theme of this proposal.

1 670 632 €

Start date: 2011-06-01, End date: 2017-05-31

Biopharmaceutical proteins are typically produced in cultivated mammalian cells, a costly process with limited scalability. Thus products such as monoclonal antibodies are very expensive and often beyond the reach of the world’s poor. The problem is compounded by the fact that important strategies for preventing diseases such as HIV and rabies typically involve large doses of multiple antibodies and other virucidal proteins. Plants have emerged as alternative production platforms for biopharmaceutical proteins because they are less expensive, more scalable and potentially could be transferred to developing countries. Recently, the first products have reached the clinic, but many of them are follow-on products already manufactured in mammalian cells. Here, Prof Julian Ma (St George’s Hospital Medical School, London, UK) and Prof Dr Rainer Fischer (RWTH Aachen University, Germany) aim to develop innovative ways to use plants for the economical, safe and sustainable production of combinations of active pharmaceutical ingredients (APIs) based on recombinant proteins, thereby pushing the boundaries of what can be achieved in plants beyond current capabilities with fermenter-based systems. We will focus on the production of antibodies and lectins against HIV and rabies, with the aim of generating GMP-compliant microbicidal cocktails for evaluation in human trials. Key aspects of the project will include the production of APIs both individually and as combinations in plants, the development of technologies allowing the introduction of transgenes into pre-determined genomic loci, the use of click chemistry to optimize the production and stoichiometry of recombinant protein cocktails, the development of candidate products for both topical and parenteral administration and the development of downstream processing concepts that are transferrable to developing countries, such as minimal processing and processing trains based on pre-assembled disposable modules. We will complete one Phase I clinical trials, each testing a plant-derived product that advances the field in a significant way

3 488 863 €

Start date: 2011-08-01, End date: 2019-01-31

Our recent discovery, that large integral membrane protein complexes can survive intact in the mass spectrometer, prompts many new experiments to understand the mechanism of their release from micelles and to maximise the impact of this finding. We propose to examine the structure of membrane complexes after their release from micelles in the gas phase. We will apply ion mobility mass spectrometry to extract collision cross sections of membrane complexes of known structure and compare these with those calculated form atomic coordinates. Conditions will be optimised to minimise the distortion of structure. More controlled release of membrane complexes from micelles will be investigated using photo-activation. To do this we will explore properties of detergents incorporating chromophores, with infra red laser activation to activate the micelle selectively without perturbing the membrane protein complex. We also propose to develop methods for determining structures of lipids bound specifically in membrane protein interfaces and assess their effects on the stability and stoichiometry of the complex. To visualise these complexes in the absence of micelles we propose to 'soft land' membrane protein complexes on electron microscopy grids, targeting components by virtue of their mass to charge. We will apply these methods to some of the most challenging and controversial membrane protein complexes including EmrE, the intact ATP synthases, the M2 proton channel of the influenza A virus, the P-type ATPases and the ATP-sensitive potassium channel. Overall, through this ambitious program of research, we plan to shed new light on membrane protein complexes and the role of lipids and small molecules in stabilising and modifying their properties.

2 100 155 €

Start date: 2011-06-01, End date: 2016-05-31