ERC FUNDED PROJECTS

Asymmetric cell division is a key mechanism for the generation of cell diversity in eukaryotes. During this process, a polarized mother cell divides into non-equivalent daughters. These may differentially inherit fate determinants, irreparable damages or age determinants. Our aim is to decipher the mechanisms governing the individualization of daughters from each other. In the past ten years, our studies identified several lateral diffusion barriers located in the plasma membrane and the endoplasmic reticulum of budding yeast. These barriers all restrict molecular exchanges between the mother cell and its bud, and thereby compartmentalize the cell already long before its division. They play key roles in the asymmetric segregation of various factors. On one side, they help maintain polarized factors into the bud. Thereby, they reinforce cell polarity and sequester daughter-specific fate determinants into the bud. On the other side they prevent aging factors of the mother from entering the bud. Hence, they play key roles in the rejuvenation of the bud, in the aging of the mother, and in the differentiation of mother and daughter from each other. Recently, we accumulated evidence that some of these barriers are subject to regulation, such as to help modulate the longevity of the mother cell in response to environmental signals. Our data also suggest that barriers help the mother cell keep traces of its life history, thereby contributing to its individuation and adaption to the environment. In this project, we will address the following questions: 1 How are these barriers assembled, functioning, and regulated? 2 What type of differentiation processes are they involved in? 3 Are they conserved in other eukaryotes, and what are their functions outside of budding yeast? These studies will shed light into the principles underlying and linking aging, rejuvenation and differentiation.

2 200 000 €

Start date: 2010-05-01, End date: 2015-04-30

Cells use circuits of interacting proteins to respond to their environment. In the past decades, molecular biology has provided detailed knowledge on the proteins in these circuits and their interactions. To fully understand circuit function requires, in addition to molecular knowledge, new concepts that explain how multiple components work together to perform systems level functions. Our lab has been a leader in defining such concepts, based on combined experimental and theoretical study of well characterized circuits in bacteria and human cells. In this proposal we aim to find novel principles on how circuits resist fluctuations and errors, and how they can be controlled by drugs: (1) Why do key regulatory systems use bifunctional enzymes that catalyze antagonistic reactions (e.g. both kinase and phosphatase)? We will test the role of bifunctional enzymes in making circuits robust to variations in protein levels. (2) Why are some genes regulated by a repressor and others by an activator? We will test this in the context of reduction of errors in transcription control. (3) Are there principles that describe how drugs combine to affect protein dynamics in human cells? We will use a novel dynamic proteomics approach developed in our lab to explore how protein dynamics can be controlled by drug combinations. This research will define principles that unite our understanding of seemingly distinct biological systems, and explain their particular design in terms of systems-level functions. This understanding will help form the basis for a future medicine that rationally controls the state of the cell based on a detailed blueprint of their circuit design, and quantitative principles for the effects of drugs on this circuitry.

2 261 440 €

Start date: 2010-03-01, End date: 2015-02-28

The ribosome is a large cellular organelle that plays a central role in the process of protein synthesis in all organisms. Currently, structural information at atomic resolution exists only for bacterial ribosomes and some of their functional complexes. Eukaryotic ribosomes are larger and significantly more complex than their bacterial counterparts. They consist of two unequal subunits with a combined molecular weight of approximately 4 million Daltons and contain 70-80 different protein molecules and four different RNAs. Currently the only structural information on eukaryotic ribosomes is available from cryo electron microscopic reconstructions in the nanometer resolution range, which is insufficient to derive information about the function of the eukaryotic ribosome at the atomic level. The aim of this proposal is to use X-ray crystallography to obtain structural and functional information on the eukaryotic ribosome and its functional complexes at high resolution. The key targets of the structural work will be: i) the structure of the small ribosomal subunit, ii) the structure of the large ribosomal subunit, and iii) structures of complexes involved in the initiation of protein synthesis. Besides the obvious fundamental importance of this research for understanding protein synthesis in eukaryotes the proposed studies will also be the prerequisite for understanding the structural basis of the regulation of protein synthesis in normal cells and how it is perturbed in various diseases. Finally, comparing the structures of bacterial and eukaryotic ribosomes is important for understanding the specificity of various clinically used antibiotics for the bacterial ribosome.

2 446 725 €

Start date: 2010-07-01, End date: 2015-06-30

Immunological memory confers long term protection against pathogens and is the basis of successful vaccination. Following antigenic stimulation long lived plasma cells and memory B cells are maintained for a lifetime, conferring immediate protection and enhanced responsiveness to the eliciting antigen. However, in the case of variable pathogens such as influenza virus, B cell memory is only partially effective, depending on the extent of similarity between the preceding and the new viruses. The B cell response is dominated by serotype-specific antibodies and heterosubtypic antibodies capable of neutralizing several serotypes appear to be extremely rare. Understanding the basis of broadly neutralizing antibody responses is a critical aspect for the development of more effective vaccines. In this project we will explore the specificity and dynamics of human antibody responses to influenza virus by using newly developed technological platforms to culture human B cells and plasma cells and to analyze the repertoire of human naïve and memory T cells. High throughput functional screenings, structural analysis and testing in animal models will provide a thorough characterization of the human immune response. The B cell and T cell analysis aims at understanding fundamental aspects of the immune response such as: the selection and diversification of memory B cells; the individual variability of the antibody response, the mechanisms of T-B cooperation and the consequences of the original antigenic sin and of aging on the immune response. This analysis will be complemented by a translational approach whereby broadly neutralizing human monoclonal antibodies will be developed and used: i) for passive vaccination against highly variable viruses; ii) for vaccine design through the identification and production of recombinant antigens to be used as effective vaccines; and iii) for active vaccination in order to facilitate T cell priming and jump start the immune responses.

1 979 200 €

Start date: 2010-09-01, End date: 2015-08-31

Over the last decade epigenetic gene regulation has become a major focus of scientific research as it was shown to play an important role in normal plant and animal development, but also in the ontogeny of human disease. A role of epigenetic processes in evolution, however, has found little general support to date. The goal of this project is to understand the complex interplay of epigenetic mechanisms in plant development and evolution. Many of the approaches we use rely on the recent advances in sequencing technologies, which allow the analysis of molecular characters at an unprecedented level and speed. To achieve our goal, we will focus on two epigenetic paradigms. In Program A, we will focus on dissecting the mechanisms of genomic imprinting at the MEDEA (MEA) locus in Arabidopsis, which we will investigate using genetic, molecular, and innovative biochemical approaches to gain a comprehensive picture of the complex interplay of various epigenetic pathways. In program B, we will analyze the role of epigenetic change in adaptation and evolution using (i) an experimental selection approach in Arabidopsis, where genome-wide analyses of epigenetic modifications have become possible, and (ii) a stable, heritable, epigenetic change occurring in Mimulus populations. In this system, an epigenetic switch of the pollinator syndrome leads to reproductive isolation and, therefore, has an effect on population structure and thus the evolutionary trajectory. These experimental systems each offer unique opportunities to shed light onto the underlying mechanisms controlling epigenetic states. In combination with the new methodologies used, these analyses promise to provide step change in our understanding of epigenetic processes at the level of genes, organisms, and populations.

2 496 641 €

Start date: 2010-04-01, End date: 2015-12-31

We describe here an innovative strategy for understanding the so-called magnetostrophic regime of fluid flow in the Earth s core, and thus the mechanisms by which the Earth s magnetic field is sustained over time. The magnetostrophic regime is the state in which Lorentz (magnetic) forces are balanced by Coriolis (rotational) forces and pressure gradients and is thought to be the zeroth order force balance in the core. We propose a series of ground-breaking experiments using liquid sodium contained in a rapidly rotating sphere containing a differentially rotating solid inner sphere. For the first time electric current is injected into the fluid in different configurations in order that the Lorentz force is everywhere significant. Various other magnetic fields can be applied from the exterior and the interior. The influence of turbulence, viscous and magnetic boundary layers will be examined. The presence of instabilities and wave motion will be studied, and the existence of steady solutions will be naturally determined. Diagnostic measurements of magnetic fields and electrical potentials, and Doppler velocimetry will characterise the experiment. These unique experiments are backed by numerical calculations. Complementary studies will analyse the observed magnetic field over the last 400 years in the same magnetostrophic framework. An inverse method will be developed to find the initial state of the field that evolves in a manner compatible with observations. This will elucidate the interior structure of the magnetic field for the first time, determining the amplitude and morphology of the field. The importance of magnetic diffusion (Joule heating) will arise naturally, and fluid motion in the entire core will be found, allowing comparison with geodetic observations.

3 116 900 €

Start date: 2010-05-01, End date: 2016-04-30

How does the assembly of neuronal circuits contribute to the emergence of function controlling dedicated animal behaviors? Finding answers to this question requires a deep understanding of the connectivity map of neuronal circuits controlling a behavior as well as the mechanisms involved in the generation of these specific circuit maps. In the project outlined here, I propose the analysis of the neuronal circuits involved in the generation of motor output, a behavior representing the ultimate output of nearly all nervous system activity. Studying the mouse motor output system will allow the analysis of neuronal circuit connectivity at an exquisite degree of specificity. Owing to the anatomical arrangement of motor neuron pools innervating individual muscles, this system offers the possibility to combine genetic, anatomical and physiological analysis of synaptic specificity with a direct link to a behavioral output. Generation of coordinated motor behavior is functionally linked to the high degree of specificity in presynaptic connections controlling the activation of individual motor neuron pools, yet knowledge on the specificity map of premotor circuits is currently missing. The aim of this research project is to acquire information on the general principles guiding the acquisition, maintenance and developmental plasticity of neuronal connectivity between premotor neurons and functionally defined subpopulations of motor neurons. This project is now possible due to the unique combination of our detailed know-how of the motor system in mice including a variety of genetic animal models, and the application of novel viral circuit tracing technology revealing monosynaptically connected premotor neurons, which we have recently applied successfully to the motor system in mice in vivo. Together, our project will elucidate the anatomical connectome of the motor output system as well as the principles governing the specificity with which motor circuits assemble.

2 499 354 €

Start date: 2010-03-01, End date: 2016-02-29

Oligomers are toxic in an array of protein misfolding and aggregation (PMA) disorders. However, the chain of events from protein aggregation to dysfunction is poorly understood. Prion diseases are marked by accumulation of PrPSc, a misfolded variant of wild-type PrPC. PrPC mediates PrPSc neurotoxicity and counteracts toxic PrPC mutants, indicating that a subversion of normal PrPC function may underlie neurodegeneration, and this may not be limited to prion disease. Here, we propose to explore these newly discovered physiological functions of PrPC in three paradigms. We show that PrPC assembles into a multiprotein complex containing a protease; neurotoxic PrPC mutants generate a smaller complex that is uncleaved. We show that neuronal expression of PrPC is required in trans for long-term myelin maintenance in peripheral nerves. We will therefore investigate the hypothesis that a fragment of PrPC transmits signals crucial for axomyelinic integrity. We show that PrPC physically interacts with both amyloid b and islet amyloid polypeptide and attenuates functional impairment mediated by these peptides. We therefore propose to test whether subversion of normal PrPC function is involved in diverse PMA disorders. We developed an ex vivo model that accurately reproduces major features of prion infections, most notably neurodegeneration. We have identified several unexpected PrPSc-induced cellular stress pathways which may be common to other PMA disorders. Using this model system, we will clarify the role of PrPC in cell survival pathways and determine the requirement for PrPC in the pathology of other PMA disorders. This proposal capitalizes on provocative recent results and, if successful, will provide valuable insights into PMA toxicity that will go far beyond prion diseases.

2 500 000 €

Start date: 2010-05-01, End date: 2015-04-30

Signal representations with Fourier and wavelet bases are central to signal processing and communications. Non-linear approximation methods in such bases are key for problems like denoising, compression and inverse problems. Recently, the idea that signals that are sparse in some domain can be acquired at low sampling density has generated strong interest, under various names like compressed sensing, compressive sampling and sparse sampling. We aim to study the central problem of acquiring continuous-time signals for discrete-time processing and reconstruction using the methods of sparse sampling. Solving this involves developing theory and algorithms for sparse sampling, both in continuous and discrete time. In addition, in order to acquire physical signals, we plan to develop a sampling theory for signals obeying physical laws, like the wave and diffusion equation, and light fields. Together, this will lead to a sparse sampling theory and framework for signal processing and communications, with applications from analog-to-digital conversion to new compression methods, to super-resolution data acquisition and to inverse problems in imaging. In sum, we aim to develop the theory and algorithms for sparse signal processing, with impact on a broad range of applications.

1 839 174 €

Start date: 2010-05-01, End date: 2015-04-30

One of the central mysteries of immunology is self-tolerance. How does the human body select ~10e12 T lymphocytes, that are reactive to foreign pathogens but tolerant to normal cellular constituents of the host? Over the last few years, my laboratory identified 2 fundamental mechanisms used by thymocytes to establish T cell tolerance. We demonstrated that the affinity threshold for negative selection is a constant for all thymocytes expressing MHC I restricted TCRs. This binding affinity threshold (KD H 6 ¼M; estimated T1/2 H 2 sec) is the fundamental biophysical parameter used by TCRs to delete autoimmune T cells. We also established how the TCR generates distinct signals for positive and negative selection. At the selection threshold, a small increase in ligand affinity for the T-cell antigen receptor leads to a marked change in the activation and subcellular localization of Ras and mitogen-activated protein kinase (MAPK) signaling intermediates. The ability to compartmentalize signaling molecules differentially within the cell endows the thymocyte with the ability to convert a small change in analogue input (affinity) into a digital output (positive versus negative selection) and provides the molecular basis for central tolerance. In the present application, we plan to fully understand 1-how the biophysical events during antigen binding to the TCR initiate an intracellular signal; 2-how these signals program an unambiguous cell fate and 3-how the system fails, when an autoimmune T cell is generated and activated. We will use a combination of transgenic and knockout mice, biochemistry and molecular imaging to fully define how the TCR functions as a molecular switch.

1 930 000 €

Start date: 2010-04-01, End date: 2015-03-31