ERC FUNDED PROJECTS

A significant advance in the field of development has been the appreciation that radial glial cells are progenitors and give birth to neurons in the brain. In order to advance this exciting area of biology, we need approaches that combine structural and functional studies of these cells. This is reflected by the emerging realisation that dynamic interactions involving radial glia may be critical for the regulation of their proliferative behaviour. It has been observed that radial glia experience transient elevations in intracellular Ca2+ but the nature of these signals, and the information that they convey, is not known. The inability to observe these cells in vivo and over the course of their development has also meant that basic questions remain unexplored. For instance, how does the behaviour of a radial glial cell at one point in development, influence the final identity of its progeny? I propose to build a research team that will capitalise upon methods we have developed for observing individual radial glia and their progeny in an intact vertebrate nervous system. The visual system of Xenopus Laevis tadpoles offers non-invasive optical access to the brain, making time-lapse imaging of single cells feasible over minutes and weeks. The system s anatomy lends itself to techniques that measure the activity of the cells in a functional sensory network. We will use this to examine signalling mechanisms in radial glia and how a radial glial cell s experience influences its proliferative behaviour and the types of neuron it generates. We will also examine the interactions that continue between a radial glial cell and its daughter neurons. Finally, we will explore the relationships that exist within neuronal progeny derived from a single radial glial cell.

1 284 808 €

Start date: 2010-02-01, End date: 2015-01-31

RNA interference (RNAi) is a conserved sequence-specific, gene-silencing mechanism that is induced by double-stranded RNA (dsRNA). One of the functions of this pathway is the defense against parasitic nucleic acids: transposons and viruses. Previous results demonstrated that viral infections in Drosophila melanogaster are fought by an antiviral RNAi response and that components of the endocytic pathway are required for dsRNA entry to initiate the RNAi response. Recently we have shown that infected insect cells spread a systemic silencing signal that elicits a protective RNAi-dependent immunity throughout the organism. This suggests that the cell-autonomous RNAi response is insufficient to control a viral infection and that flies also rely on systemic immune response to fight against such infections. As a junior group leader, I will study the mechanisms that mediate the RNAi-based antiviral response in insects. By combining biochemical, cellular, molecular and genomic approaches, both in vivo and in cell culture, I will analyze the mechanisms underlying viral tropism, systemic propagation of the antiviral signal and the basis of the persistence of the antiviral state. Furthermore, I will examine whether the dsRNA-uptake pathway is conserved in mosquitoes and its relationship with viral immunity in that host. This comprehensive approach will tackle how this nucleic acid-based immunity works in insects to generate an anti-viral stage. A better understanding of the role of RNA silencing in insects during virus infection will allow the exploitation of this pathway for improvement of public health related problems such as arbovirus infection and disease.

1 900 000 €

Start date: 2009-10-01, End date: 2014-12-31

Telomeres are heterochromatic nucleoprotein complexes located at the end of linear eukaryotic chromosomes. Contrarily to a longstanding dogma, we have recently demonstrated that mammalian telomeres are transcribed into TElomeric Repeat containing RNA (TERRA) molecules. TERRA transcripts contain telomeric RNA repeats and are produced at least in part by DNA-dependent RNA polymerase II-mediated transcription of telomeric DNA. TERRA molecules form discrete nuclear foci that co-localize with telomeric heterochromatin in both interphase and transcriptionally inactive metaphase cells. This indicates that TERRA is an integral component of telomeres and suggests that TERRA might participate in maintaining proper telomere heterochromatin. We will use a variety of biochemistry, cell biology, molecular biology and microscopy based approaches applied to cultured mammalian cells and to the yeast Schizosaccharomyces pombe, to achieve four distinct major goals: i) We will over-express or deplete TERRA in mammalian cells in order to characterize the molecular details of putative TERRA-associated functions in maintaining normal telomere structure and function; ii) We will locate TERRA promoter regions on different human chromosome ends; iii) We will generate mammalian cellular systems in which to study artificially seeded telomeres that can be transcribed in an inducible fashion; iv) We will identify physiological regulators of TERRA by analyzing it in mammalian cultured cells where the functions of candidate factors are compromised. In parallel, taking advantage of the recent discovery of TERRA also in fission yeast, we will systematically analyze TERRA levels in fission yeast mutants derived from a complete gene knockout collection. The study of TERRA regulation and function at chromosome ends will strongly contribute to our understanding of how telomeres are maintained and will help to clarify the general functions of mammalian non-coding RNAs.

1 602 600 €

Start date: 2009-10-01, End date: 2014-09-30

The biomembrane is a prerequisite of life. It enables the cell to maintain a controlled environment and to establish electrochemical gradients as rapidly accessible energy stores. Biomembranes also provide scaffold for organisation and spatial definition of signal transmission in the cell. Crystal structures of membrane proteins are determined with an increasing pace. Along with functional studies integral studies of individual membrane proteins are now widely implemented. The BIOMEMOS proposal goes a step further and approaches the function of the biomembrane at the higher level of membrane protein complexes. Through a combination of X-ray crystallography, electrophysiology, general biochemistry, biophysics and bioinformatics and including also the application of single-particle cryo-EM and small-angle X-ray scattering, the structure and function of membrane protein complexes of key importance in life will be investigated. The specific targets for investigation in this proposal include: 1) higher-order complexes of P-type ATPase pumps such as signalling complexes of Na+,K+-ATPase, and 2) development of methods for structural studies of membrane protein complexes Based on my unique track record in structural studies of large, difficult structures (ribosomes and membrane proteins) in the setting of a thriving research community in structural biology and biomembrane research in Aarhus provides a critical momentum for a long-term activity. The activity will take advantage of the new possibilities offered by synchrotron sources in Europe. Furthermore, a single-particle cryo-EM research group formed on my initiative in Aarhus, and a well-established small-angle X-ray scattering community provides for an optimal setting through multiple cues in structural biology and functional studies

2 444 180 €

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

My lab is interested in the development of the tissue that gives rise to vertebrae and skeletal muscles called the paraxial mesoderm. A striking feature of this tissue is its segmental organization and we have made major contributions to the understanding of the molecular control of the segmentation process. We identified a molecular oscillator associated to the rhythmic production of somites and proposed a model for vertebrate segmentation based on the integration of a rhythmic signaling pulse gated spatially by a system of traveling FGF and Wnt signaling gradients. We are also studying the differentiation of paraxial mesoderm precursors into the muscle, cartilage and dermis lineages. Our work identified the Wnt, FGF and Notch pathways as playing a prominent role in the patterning and differentiation of paraxial mesoderm. In this application, we largely focus on the molecular control of paraxial mesoderm development. Using microarray and high throughput sequencing-based approaches and bioinformatics, we will characterize the transcriptional network acting downstream of Wnt, FGF and Notch in the presomitic mesoderm (PSM). We will also use genetic and pharmacological approaches utilizing real-time imaging reporters to characterize the pacemaker of the segmentation clock in vivo, and also in vitro using differentiated embryonic stem cells. We further propose to characterize in detail a novel RA-dependent pathway that we identified and which controls the somite left-right symmetry. Our work is expected to have a strong impact in the field of congenital spine anomalies, currently an understudied biomedical problem, and will be of utility in elucidating the etiology and eventual prevention of these disorders. This work is also expected to further our understanding of the Notch, Wnt, FGF and RA signalling pathways which are involved in segmentation and in the establishment of the vertebrate body plan, and which play important roles in a wide array of human diseases.

2 500 000 €

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

Energy, supplied in the form of oxygen and glucose in the blood, is essential for the brain s cognitive power. Failure of the energy supply to the nervous system underlies the mental and physical disability occurring in a wide range of economically important neurological disorders, such as stroke, spinal cord injury and cerebral palsy. Using a combination of two-photon imaging, electrophysiological, molecular and transgenic approaches, I will investigate the control of brain energy supply at the vascular level, and at the level of individual neurons and glial cells, and study the deleterious consequences for the neurons, glia and vasculature of a failure of brain energy supply. The work will focus on the following fundamental issues: A. Vascular control of the brain energy supply (1) How important is control of energy supply at the capillary level, by pericytes? (2) Which synapses control blood flow (and thus generate functional imaging signals) in the cortex? B. Neuronal and glial control of brain energy supply (3) How is grey matter neuronal activity powered? (4) How is the white matter supplied with energy? C. The pathological consequences of a loss of brain energy supply (5) How does a fall of energy supply cause neurotoxic glutamate release? (6) How similar are events in the grey and white matter in energy deprivation conditions? (7) How does a transient loss of energy supply affect blood flow regulation? (8) How does brain energy use change after a period without energy supply? Together this work will significantly advance our understanding of how the energy supply to neurons and glia is regulated in normal conditions, and how the loss of the energy supply causes disorders which consume more than 5% of the costs of European health services (5% of ~1000 billion euro/year).

2 499 947 €

Start date: 2010-04-01, End date: 2016-03-31

Eukaryotic cells inherit much of their genomic information in the form of chromosomes during cell division. Centimetre-long DNA molecules are packed into micrometer-sized chromosomes to enable this process. How DNA is organised within mitotic chromosomes is still largely unknown. A key structural protein component of mitotic chromosomes, implicated in their compaction, is the condensin complex. In this proposal, we aim to elucidate the molecular architecture of mitotic chromosomes, taking advantage of new genomic techniques and the relatively simple genome organisation of yeast model systems. We will place particular emphasis on elucidating the contribution of the condensin complex, and the cell cycle regulation of its activities, in promoting chromosome condensation. Our previous work has provided genome-wide maps of condensin binding to budding and fission yeast chromosomes. We will continue to decipher the molecular determinants for condensin binding. To investigate how condensin mediates DNA compaction, we propose to generate chromosome-wide DNA/DNA proximity maps. Our approach will be an extension of the chromosome conformation capture (3C) technique. High throughput sequencing of interaction points has provided a first glimpse of the interactions that govern chromosome condensation. The role that condensin plays in promoting these interactions will be investigated. The contribution of condensin s ATP-dependent activities, and cell cycle-dependent post-translational modifications, will be studied. This will be complemented by mathematical modelling of the condensation process. In addition to chromosome condensation, condensin is required for resolution of sister chromatids in anaphase. We will develop an assay to study the catenation status of sister chromatids and how condensin may contribute to their topological resolution.

2 076 126 €

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

Cellular clearance is a fundamental process required by all cells in all species. Important physiological processes, such as aging, and pathological mechanisms, such as neurodegeneration, are strictly dependent on cellular clearance. In eukaryotes, most of the cellular clearing processes occur in a specialized organelle, the lysosome. This project is based on a recent discovery, made in our laboratory, of a gene network, which we have named CLEAR, that controls lysosomal biogenesis and function and regulates cellular clearance. The specific goals of the project are: 1) the comprehensive characterization of the mechanisms underlying the CLEAR network, 2) the thorough understanding of CLEAR physiological function at the cellular and organism levels, 3) the development of strategies and tools to modulate cellular clearance, and 4) the implementation of proof-of-principle therapeutic studies based on the activation of the CLEAR network in murine models of human lysosomal storage disorders and of neurodegenerative diseases, such as Alzheimers s and Huntington s diseases. A combination of genomics, bioinformatics, systems biology, chemical genomics, cell biology, and mouse genetics approaches will be used to achieve these goals. Our goal is to develop tools to modulate cellular clearance and to use such tools to develop therapies to cure human disease. The potential medical relevance of this project is very high, particularly in the field of neurodegenerative disease. Therapies that prevent, ameliorate or delay neurodegeneration in these diseases would have a huge impact on human health.

2 100 000 €

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

How do we understand the actions and intentions of others? Hereby we intend to address this issue by using a multidisciplinary approach. Our project is subdivided into four parts. In the first part we investigate the neural organization of monkey area F5, an area deeply involved in motor act understanding. By using a new set of electrodes we will describe the columnar organization of the area F5, establish the temporal relationships between the activity of F5 mirror and motor neurons, and correlate the activity of mirror neurons coding the observed motor acts in peripersonal and extrapersonal space with the activity of motor neurons in the same cortical column. In the second part we will assess the neural mechanism underlying the understanding of the intention of complex actions , i.e. actions formed by a sequence of two (or more) individual actions. The focus will be on the neurons located in ventrolateral prefrontal cortex, an area involved in the organization of high-order motor behavior. The rational of the experiment is that, while the organization of single actions and the understanding of intention behind them is function of parietal neurons, that of complex actions relies on the activity of the prefrontal lobe. In the third and fourth parts of the project we will delimit the cortical areas involved in understanding the goal (the what) and the intention (the why) of the observed actions in individuals with typical development (TD) and in children with autism and will establish the time relation between these two processes. Our hypothesis is that the chained organization of intentional motor acts is impaired in children with autism and this impairment prevents them from organizing normally their actions and from understanding others intentions.

1 992 000 €

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

Reasoning, to derive conclusions from facts, is a fundamental task in Artificial Intelligence, arising in a wide range of applications from Robotics to Expert Systems. The aim of this project is to devise new efficient algorithms for real-world reasoning problems and to get new insights into the question of what makes a reasoning problem hard, and what makes it easy. As key to novel and groundbreaking results we propose to study reasoning problems within the framework of Parameterized Complexity, a new and rapidly emerging field of Algorithms and Complexity. Parameterized Complexity takes structural aspects of problem instances into account which are most significant for empirically observed problem-hardness. Most of the considered reasoning problems are intractable in general, but the real-world context of their origin provides structural information that can be made accessible to algorithms in form of parameters. This makes Parameterized Complexity an ideal setting for the analysis and efficient solution of these problems. A systematic study of the Parameterized Complexity of reasoning problems that covers theoretical and empirical aspects is so far outstanding. This proposal sets out to do exactly this and has therefore a great potential for groundbreaking new results. The proposed research aims at a significant impact on the research culture by setting the grounds for a closer cooperation between theorists and practitioners.

1 421 130 €

Start date: 2010-01-01, End date: 2014-12-31

CoralWarm will generate for the first time projections of temperate and subtropical coral survival by integrating sublethal temperature increase effects on metabolic and skeletal processes in Mediterranean and Red Sea key species. CoralWarm unique approach is from the nano- to the macro-scale, correlating molecular events to environmental processes. This will show new pathways to future investigations on cellular mechanisms linking environmental factors to final phenotype, potentially improving prediction powers and paleoclimatological interpretation. Biological and chemical expertise will merge, producing new interdisciplinary approaches for ecophysiology and biomineralization. Field transplantations will be combined with controlled experiments under IPCC scenarios. Corals will be grown in aquaria, exposing the Mediterranean species native to cooler waters to higher temperatures, and the Red Sea ones to gradually increasing above ambient warming seawater. Virtually all state-of-the-art methods will be used, by uniquely combining the investigators expertise. Expected results include responses of algal symbionts photosynthesis, host, symbiont and holobiont respiration, biomineralization rates and patterns, including colony architecture, and reproduction to temperature and pH gradients and combinations. Integration of molecular aspects of potential replacement of symbiont clades, changes in skeletal crystallography, with biochemical and physiological aspects of temperature response, will lead to a novel mechanistic model predicting changes in coral ecology and survival prospect. High-temperature tolerant clades and species will be revealed, allowing future bioremediation actions and establishment of coral refuges, saving corals and coral reefs for future generations.

3 332 032 €

Start date: 2010-06-01, End date: 2016-05-31

Following a long history of quantitative genetics in crop plants, it now becomes feasible to use naturally-occuring variation contained in Arabidopsis thaliana accessions (lines isolated from natural populations) as the source of quantitative genomics approaches, designed to map QTLs and resolve them at the gene level. Apart from being able to exploit in multiple genetic backgrounds allelic variation that cannot be easily generated by conventional mutagenesis, the (relatively few) success of the QTL studies has often been because of the use of quantitative phenotyping, as opposed to the qualitative gauges used in typical mutant screens. Among the various genetic mechanisms responsible for natural variation that have just started to be revealed, cis-acting regulation is potentially of large impact, despite remaining more difficult to recognize and confirm. The objective of this project is to apply genome-wide quantitative molecular genetics to both, a very integrative and classical quantitative trait (growth in interaction with the environment) and a molecular trait a priori more directly linked to the source of variation (gene expression under cis-regulation). We propose to use a combination of our unique high-troughput phenotyping robot, fine-mapping, complementation approaches and association genetics to pinpoint a significant number of QTLs and eQTLs to the gene level and identify causative polymorphisms and the molecular variation controlling natural diversity. Working at an unprecedented scale should finally allow to resolve enough quantitative loci and pay a significant contribution to drawing a general picture as to how and where in the pathways adaptation is shaping natural variation and improve our understanding of the transcriptional cis-regulatory code.

1 742 113 €

Start date: 2010-02-01, End date: 2016-01-31

The innovation of DELPHINS application will consist in building a generic multi-sensor design platform for embedded multi-gas-analysis-on-chip, based on a global modelling from the individual NEMS sensors to a global multiphysics NEMS-CMOS VLSI (Very large Scale Integration) system. The latter constitute a new research field with many potential applications such as in medicine (specific diseases recognition) but also in security (toxic and complex air pollutions), in industry (perfumes, agribusiness) and environment control. As an example, several studies in the last 10 years have demonstrated that some specific combination of biomarkers in breath above a given threshold could indicate early stage of diseases. More generally, patterns of breathing gas could constitute a virtual fingerprint of specific pathologies. NEMS (Nano-Electro-Mechanical Systems) based sensor is one of the most promising technologies to get the required resolutions and sensitivities for few molecules detection. We will focus on the analytical module of the system (sensing part + embedded electronics processing) that will include ultra-dense (more than thousands) NEMS arrays with state-of the art CMOS transistors. We will obtain integrated nano-oscillators individually addressed within an innovative architecture inspired from memory and imaging technologies. Few molecules sensitivity will be achieved thanks to suspended resonant nanowires co-integrated locally with their closed-loop and reading electronics. This would make possible the analysis of complex gases within an integrated portable system, which does not exist yet.

1 723 206 €

Start date: 2009-11-01, End date: 2014-10-31

What is the fundamental unit of computation in the brain? Answering this question is crucial not only for understanding how the brain works, but also for building accurate models of brain function, which require abstraction based on identification of the essential elements for carrying out computations relevant to behaviour. We will directly test the possibility that single dendritic branches may act as individual computational units during behaviour, challenging the classical view that the neuron is the fundamental unit of computation. We will address this question using a combination of electrophysiological, anatomical, imaging, molecular, and modeling approaches to probe dendritic integration in pyramidal cells and Purkinje cells in mouse cortex and cerebellum. We will define the computational rules for integration of synaptic input in dendrites by examining the responses to different spatiotemporal patterns of excitatory and inhibitory inputs. We will use computational modeling to extract simple rules describing dendritic integration that captures the essence of the computation. Next, we will determine how these rules are engaged by patterns of sensory stimulation in vivo, by using various strategies to map the spatiotemporal patterns of synaptic inputs to dendrites. To understand how physiological patterns of activity in the circuit engage these dendritic computations, we will use anatomical approaches to map the wiring diagram of synaptic inputs to individual dendrites. Finally, we will manipulate dendritic function using molecular tools, in order to provide causal links between specific dendritic computations and sensory processing. These experiments will provide us with deeper insights into how single neurons act as computing devices, and how fundamental computations that drive behaviour are implemented on the level of single cells and neural circuits.

2 416 078 €

Start date: 2010-06-01, End date: 2016-05-31

Chronic pain syndromes are to a large extent due to maladaptive plastic changes in the CNS. A CNS area particularly relevant for such changes is the spinal dorsal horn, where inputs from nociceptive and non-nociceptive fibers undergo their first synaptic integration. This area harbors a sophisticated network of interneurons, which function as a gate-control unit for incoming sensory signals. Several different types of interneurons can be distinguished based e.g. on their neurotransmitter and neuropeptide content. Despite more than 40 years of research, our knowledge about the integration of these neurons in dorsal horn circuits and their contribution to sensory processing is still very limited. This proposal aims at a comprehensive characterization of the dorsal horn neuronal network under normal conditions and in chronic pain states with a focus on inhibitory interneurons. A genome-wide analysis of the gene expression profile shall be made from defined dorsal horn interneurons genetically tagged with fluorescent markers and isolated by fluorescence activated cell sorting. A functional characterization of the connectivity of these neurons in spinal cord slices and of their role in in vivo sensory processing shall be achieved with optogenetic tools (channelrhodopsin-2), which permit activation of these neurons with light. Finally, behavioral analyses shall be made in mice after diphteria toxin-mediated ablation of defined interneuron types. All three approaches shall be applied to naïve mice and to mice with inflammatory or neuropathic pain. The results from these studies will improve our understanding of the malfunctioning of sensory processing in chronic pain states and will provide the basis for novel approaches to the prevention or reversal of chronic pain states.

2 467 000 €

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

Epigenetic gene regulation is of central importance for development and disease. Despite dramatic progress in epigenetics during the past decade, DNA demethylation remains one of the last big frontiers and very little is known about it. DNA demethylation is a widespread phenomenon and occurs in plants as well as in animals, during development, in the adult, and during somatic cell reprogramming of pluripotency genes. The molecular identity of the DNA demethylase in animal cells remained unresolved and has hampered progress in the field for decades. In 2007 we published that Growth Arrest and DNA Damage 45 a (Gadd45a) is a key player in active DNA demethylation, which opened new avenues in the study of this elusive process. The goal of this project is to further analyze the mechanism of DNA demethylation as well as the role played by Gadd45 in development. Given the many unresolved questions in this burgeoning field, our work promises to be ground-breaking and therefore have a profound impact in unraveling one of the least understood processes of gene regulation. Specifically we will address the following points. I) The biological role of Gadd45 mediated DNA demethylation in mouse embryos and adults is unknown. We have obtained mouse mutants for Gadd45a,b, and g and we will analyze them for developmental defects and dissect the methylation regulation of relevant genes. II) The targeting mechanism by which Gadd45 is binding to and demethylating specific sites in the genome is a central unresolved issue. We have identified a candidate DNA binding protein interacting with Gadd45 and we will analyze its role in site specific targeting of DNA demethylation in vitro and in mouse. III) We found that Gadd45 is an RNA binding protein and we will therefore analyze how non-coding RNAs are involved in targeting and/or activating Gadd45 during DNA demethylation.

2 376 000 €

Start date: 2010-06-01, End date: 2015-05-31

Swarm intelligence is the discipline that deals with natural and artificial systems composed of many individuals that coordinate using decentralized control and self-organization. In this project, we focus on the design and implementation of artificial swarm intelligence systems for the solution of complex problems. Our current understanding of how to use swarms of artificial agents largely relies on rules of thumb and intuition based on the experience of individual researchers. This is not sufficient for us to design swarm intelligence systems at the level of complexity required by many real-world applications, or to accurately predict the behavior of the systems we design. The goal of the E-SWARM is to develop a rigorous engineering methodology for the design and implementation of artificial swarm intelligence systems. We believe that in the future, swarm intelligence will be an important tool for researchers and engineers interested in solving certain classes of complex problems. To build the foundations of this discipline and to develop an appropriate methodology, we will proceed in parallel both at an abstract level and by tackling a number of challenging problems in selected research domains. The research domains we have chosen are optimization, robotics, networks, and data mining.

2 016 000 €

Start date: 2010-06-01, End date: 2015-05-31

150 years from the Origin and we have yet to unravel how ecological speciation works, and how it leads to spectacular adaptive radiations. The process has two components: adaptation to ecological niches and production of new species. My aim is to make breakthroughs in understanding ecological speciation by the study of geographically parallel adaptive radiations in mycalesine butterflies that have yielded some 250 extant species in the Old World tropics. More empirical studies are needed because few radiations have been examined from many different perspectives (including in insects). It is not fully understood either how exactly radiation occurs or how exactly selection leads to speciation. This proposal provides a unique opportunity, outside a few vertebrate clades, to resolve this by fully integrating several lines of evidence and methodologies. My approach will be to study patterns of diversity and disparity in morphospace for several sets of key traits: 1) wing patterns, 2) larval host plant choice especially with respect to C3 and C4 photosynthesis, and 3) male secondary sexual traits and sex pheromones. We will collect phenotypic, genetic, developmental, and ecological data. Application of phylogenetic comparative methods to the relationships of all traits among all species will make inferences about the biological mechanisms that have driven diversification and speciation. The combination of surveys of morphospace, the use of comparative methods, and microevolutionary studies using laboratory models will provide a unique comprehensive view. Our analyses will distinguish among alternative patterns of adaptive radiations, test predictions from models, and move us forward in identifying the drivers of observed patterns.

2 474 128 €

Start date: 2010-10-01, End date: 2016-06-30

X-chromosome inactivation (XCI) represents a classic example of epigenetics in mammals. In this process, one of the two X chromosomes in females is converted from an active into a clonally heritable, inactive, state during early embryonic development, to ensure dosage compensation between the sexes. This process is also remarkable in that an entire chromosome is silenced while its homologue, present in the same nucleus, remains active. Thus, in addition to being an epigenetics paradigm, XCI also represents a powerful model for monoallelic gene expression and could provide important insights into the mechanisms underlying other examples of random, monoallelic regulation. The key locus underlying the initiation of XCI is the X-inactivation centre (Xic). The Xic ensures the induction and monoallelic expression of a non-coding RNA (Xist) that is responsible for triggering chromosomal silencing in cis during development. We would like to understand the mechanisms underlying the Xic's functions and define whether other, Xic-like loci exist in the genome. Once XCI is established, the inactive state is initially reversible but becomes progressively locked in as development proceeds due to numerous epigenetic marks such as DNA methylation and histone modifications, as well as nuclear compartmentalization and asynchronous replication. In the proposed program, we will exploit our expertise in XCI to develop new lines of research and use novel technologies to investigate monoallelic gene expression, nuclear organization and epigenetics during development. Our main objectives are (1) to understand how monoallelic expression states are established and maintained during early development and (2) to assess how chromosome dynamics and nuclear architecture can impact on these states.

2 860 000 €

Start date: 2010-05-01, End date: 2015-10-31

Living organisms exhibit great variation in size and shape, and display many morphological innovations. Recent progress has been made in identifying the genetic basis for the evolution of some traits but there remains a paucity of knowledge concerning the evolution of complex morphological traits, and how the underlying changes arose and spread in populations. This proposal will address this by establishing a research program to investigate the genetic basis for the evolution of intra- and inter- specific differences in a complex sensory organ, the insect compound eye. Drosophila mauritiana has significantly larger eyes than its sibling species D. simulans. However, there is also considerable eye size variation between D. simulans populations. Taking advantage of our knowledge of eye development in flies, this proposal will describe the developmental basis for eye size differences and investigate the number and distribution of photoreceptor subtypes (which are sensitive to different light wavelengths) between species and populations with eye size variation. In addition, the proposal will take advantage of cutting edge methods to map the molecular basis for eye size evolution between D. mauritiana and D. simulans, and compare this to the genetic architecture of eye size differences within D. simulans. Population genetic approaches will then be applied to test evolved sequences for directional selection. Thus, this project will not only reveal the genetic changes in development underlying the evolution of eye size and resolve the contribution of standing genetic variation for eye size differences within species to differences between species, but also establish this trait as a model for future studies of morphological evolution.

1 225 040 €

Start date: 2010-01-01, End date: 2014-12-31

In each cell cycle, eukaryotic cells must faithfully replicate large genomes in a relatively short time. This is accomplished by initiating DNA replication from many replication origins distributed along chromosomes. Ensuring that each origin is efficiently activated once and only once per cell cycle is crucial for maintaining the integrity of the genome. Recent evidence indicates that defects in the regulation of origin firing may be important contributors to genome instability in cancer. Strict once per cell cycle DNA replication is achieved by a two-step mechanism. DNA replication origins are first licensed by loading an inactive DNA helicase (Mcm2-7) into pre-replicative complexes (pre-RCs). This can only occur during G1 phase. Initiation then occurs during S phase, triggered by cyclin dependent kinases (CDKs) and Dbf4-dependent kinase (DDK), which promote recruitment of proteins required for helicase activation and replisome assembly. Research proposed herein will lead to a deeper understanding of the mechanism and regulation of DNA replication. We have reconstituted the licensing reaction with purified proteins which will be used to characterise the mechanism of licensing and the mechanism by which licensing is regulated in the cell cycle. We will also use this system to reconstitute events leading to the initiation of DNA replication. We will use genetic and biochemical approaches to characterise the mechanisms by which perturbed licensing causes gross chromosome rearrangements. We will also explore mechanisms involved in regulating the temporal programme of origin firing and how origin firing is regulated in response to DNA damage. Work in budding yeast and mammalian cells will be pursued in parallel to exploit the specific advantages of each system.

2 449 999 €

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

Our ability to control infectious diseases relies on a better understanding of epidemiological and evolutionary dynamics of pathogens. I will develop a research program combining theoretical and experimental approaches. First, I will extend the theoretical framework of evolutionary epidemiology into several new directions to study (1) the evolution of host and pathogen key life-history traits (parasite virulence, host resistance and host manipulation by the parasite) and, (2) the dynamics of adaptation of pathogens in constant and variable environments. This part of the project will be grounded on both mathematical epidemiology and population genetics. Second, I will use two biological models to test some of these theoretical predictions both in the laboratory and in the field: (1) I will study the interaction between the avian malaria parasite (Plasmodium relictum) and its mosquito vector (Culex pipiens) to test some of the predictions generated on life-history evolution, and in particular on host manipulation by the parasite. (2) I will study the evolutionary dynamics of the coliphage phix174 under different scenarios of environmental heterogeneity to test the predictions issued from models on the dynamics of adaptation in variable environments. In addition, I will measure patterns of adaptation across space and time using natural samples of viral and bacterial communities. The originality of this project lays in the combination of different perspectives on the dynamics of infectious diseases, ranging from theoretical population genetics to experimental behavioural ecology and evolution. Combining these different perspectives will yield a more comprehensive view of the dynamics of infectious diseases and contribute to the improvement of public-health interventions.

1 308 660 €

Start date: 2010-01-01, End date: 2014-12-31

In spite of considerable work in artificial intelligence, machine learning, and pattern recognition in the past 50 years, we have no machine capable of adapting to the physical and social environment with the flexibility, robustness and versatility of a 6-months old human child. Instead of trying to simulate directly the adult s intelligence, EXPLORERS proposes to focus on the developmental principles that give rise to intelligence in infants by re-implementing them in machines. Framed in the developmental/epigenetic robotics research agenda, and grounded in research in developmental psychology, its main target is to build robotic machines capable of autonomously learning and re-using a variety of skills and know-how that were not specified at design time, and with initially limited knowledge of the body and of the environment in which it will operate. This implies several fundamental issues: How can a robot discover its body and its relationships with the physical and social environment? How can it learn new skills without the intervention of an engineer? What internal motivations shall guide its exploration of vast spaces of skills? Can it learn through natural social interactions with humans? How to represent the learnt skills and how can they be re-used? EXPLORERS attacks directly those questions by proposing a series of fundamental scientific and technological advances, including computational intrinsic motivation systems for learning basic sensorimotor skills reused for grounded acquisition of the meaning of new words. This project not only addresses fundamental scientific questions, but also relates to important societal issues: personal home robots are bound to become part of everyday life in the 21st century, in particular as helpful social companions in an aging society. EXPLORERS objectives converge to the challenges implied by this vision: robots will have to be able to adapt and learn new skills in the unknown homes of users who are not engineers.

1 572 215 €

Start date: 2009-12-01, End date: 2015-05-31

An impressive variety of motile and morphogenetic processes are driven by site-directed polarized asssembly of actin filaments. In the past ten years, breathtaking advances coming from cell biology, cell biophysics, and biochemistry have brought insight into the molecular bases for production of force and movement by site-directed actin polymerization. Yet, we do not know, with the detail sufficient to understand how force is produced, by which molecular mechanisms the filaments are nucleated or created by branching. We do not know by which elementary steps insertional polymerization of barbed ends of filaments against the membrane is performed by different protein machineries, nor how these machineries work in a coordinated fashion. Here we propose a multiscale and interdisciplinary approach of the mechanisms used by the major actin nucleators to organize the motile response of actin. The elementary reactions involved in the processive walk of formin at the growing barbed ends of filaments and the role of ATP hydrolysis in force production will be analyzed by a combination of biochemical solution studies and physical methods using functionalized GUVs and optical tweezers. The multifunctionality of WH2 domains involved in actin sequestration, filament nucleation severing and processive elongation will be similarly examined in an interdisciplinary perspective from structural biology at atomic resolution to physics at the mesoscopic scale. Biochemical and structural methods and single molecule measurements (TIRFM) will shed light into the elementary steps and structural mechanism of filament branching. Biomimetic assays with functionalized GUVs associated with biophysical methods like FRAP or fluorescence correlation spectroscopy will elucidate how different filament initiating machineries segregate in the membrane as a consequence of their interactions with growing filaments and function in a coordinated fashion during actin-based motility.

2 434 195 €

Start date: 2010-05-01, End date: 2015-10-31

The prefrontal cortex (PFC) subserves decision-making and executive control, i.e. the ability to make decisions and to regulate behavior according to external events, mental models of situations, internal drives and subjective preferences. Our overall aim is to understand the functional architecture of the human PFC and computational mechanisms of PFC function. The PFC function is known to operate along three major dimensions, namely the affective, motivational and cognitive control of action subserved by the orbital, medial and lateral sectors of the PFC, respectively. In this project, our specific objectives are to solve the following three open issues of critical theoretical significance: (1) the functional organization of motivational control in the medial prefrontal cortex; (2) the mechanisms that enables the PFC to control the learning of representational sets required for cognitive control; (3) the functional interactions between the medial and lateral prefrontal cortex, i.e. the integration of motivational and cognitive control into a unitary decision-making and control system. We will address these theoretically and methodologically challenging issues by elaborating computational models that integrate learning and control mechanisms, and in relation to these models, by conducting functional magnetic resonance imaging experiments in healthy humans. The project is expected to significantly improve our knowledge of the human PFC function. This basic project has potential major implications especially in medicine, because alterations of the prefrontal function is observed in aging and most neuropsychiatric diseases, as well as in technology for developing artificial and robotics intelligence with human-like adaptive reasoning and decision-making abilities.

2 500 000 €

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

DNA sequence and epigenetic chromatin maps are important in understanding how genomes are regulated. However, these maps are linear and do not account for the three-dimensional context within which the genome functions in the cell. The spatial organisation of the genome in the nucleus is not random and is conserved in evolution, implying that it is under functional selection. This proposal aims to determine the functional significance of positioning specific genome regions at the edge of the nucleus in mammalian cells. The nuclear periphery has conventionally been considered as a zone of inactive chromatin and transcriptional repression. Several regulatory gene loci move away from the nuclear periphery as they are activated during differentiation. Novel approaches, developed by ourselves and others, that allow genomic regions to be relocated from the centre of the nucleus to the periphery, have directly shown that proximity to the nuclear edge can down-regulate human gene expression. We propose to dissect the pathways that mediate this spatially-defined transcriptional regulation, to determine what features make certain genes susceptible to it, to establish the functional consequences of preventing gene repositioning during differentiation, and to examine defects of the periphery found in premature ageing. A neglected hypothesis is that positioning of inactive chromatin against the nuclear periphery is a mechanism to minimize DNA damage on sequences in the nuclear centre. We will determine whether mutation rate is altered when loci are repositioned towards the nuclear periphery. By experimentally remodelling the spatial organisation of the genome, this proposal goes beyond the current descriptive phase of 3D nuclear organisation, into an understanding of its functional consequences on multiple aspects of genome function. It will also aid in understanding human diseases characterised by alterations of the nuclear periphery.

1 701 090 €

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

GABAergic interneurones can effectively synchronize the activity of principal cells giving rise to distinct oscillatory patterns. A particular rhythm, hippocampal theta oscillations (6-10Hz), links two ways of coding by which pyramidal cells in the hippocampus represent space, namely rate and phase coding. Thus, the theta cycle provides a clock against which the increased firing rate of pyramidal cells in the hippocampus and entorhinal cortex is measured. Furthermore, hippocampal theta is believed to constitute a link to episodic memory. Recent evidence from our lab indicates that recruitment of GABAergic interneurones critically affects certain aspects of hippocampus-dependent spatial memory in mice. We have established genetic tools that allow us to manipulate GABAergic interneurones in a cell type and region-specific manner. In combination with in vivo electrophysiology in the hippocampus/entorhinal cortex and behavioural studies, we will investigate how GABAergic interneurones regulate the activity in neuronal networks and contribute to behaviour. Specifically, we will address the following questions: 1) How does reduced recruitment of GABAergic interneurones affect network activity (theta oscillations)? 2) How does altered activity of GABAergic interneurones affect spatial representation (activity of place cells in the hippocampus and grid cells in the entorhinal cortex)? 3) How does modified activity in the hippocampus affect activity in the entorhinal cortex (and vice versa)? 4) How does modified network activity and spatial representation translate into spatial memory? The interdisciplinary approach will enable us to provide better insight into how cellular activity of GABAergic interneurones relates to network activity and ultimately to behaviour.

1 872 000 €

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

Fundamental biological processes including morphogenesis, tissue repair, and tumour metastasis require collective cell motions, and to drive these motions cells exert traction forces on their surroundings. The mechanisms underlying this basic principle of health and disease have been debated intensively and, using a variety of methods in vivo, in vitro, and in silico, much conflicting evidence has accumulated. This conflicting evidence has been in every case indirect or inferential, however, because within the moving cell group the physical forces themselves have remained inaccessible to direct experimental observation. To fill this gap, this ERC application describes an interdisciplinary project to uncover the physical mechanisms underlying collective cell migration. In Objective 1, I propose to develop technology to map forces that cells within moving groups exert on each other and on their extracellular matrix. In Objective 2, we will use siRNA technology to provide a systematic analysis of the genes that regulate force generation and transmission in a migrating epithelial cell sheet. In Objective 3, we will use this pool of data to establish a constitutive link between genes, forces and collective cell motion. Although these Objectives present major technical and scientific challenges, the feasibility of each is supported by a unique technical know-how and by a productive track record in the field of cell biophysics.

1 749 745 €

Start date: 2010-01-01, End date: 2014-12-31

Comparative genomics revealed that ~5% of the human genome is conserved among mammals. This fraction is likely functional, and could harbor pathogenic mutations. We have shown (Nature 2002, Science 2003) that more than half of the constrained fraction of the genome consists of Conserved Non-Coding sequences (CNCs). Model organisms provided evidence for enhancer activity for a fraction of CNCs; in addition another fraction is part of large non-coding RNAs (lincRNA). However, the function of the majority of CNCs is unknown. Importantly, a few pathogenic mutations in CNCs have been associated with genetic disorders. We propose to i) perform functional analysis of CNCs, and ii) identify the spectrum of pathogenic CNC mutations in recognizable human phenotypes. The aims are: 1. Functional genomic connectivity of CNCs 1a. Use 4C in CNCs in various cell types and determine their physical genomic interactions. 1b. Perform targeted disruption of CNCs in cells and assess the functional outcomes. 2. Pathogenic variation of CNCs 2a. Assess the common variation in CNCs: i) common deletion/insertions in 350 samples by aCGH of all human CNCs; ii) common SNP/small indels using DNA selection and High Throughput Sequencing (HTS) of CNCs in 100 samples. 2b. Identify likely pathogenic mutations in developmental syndromes. Search for i) large deletions and duplications of CNCs using aCGH in 1500 samples with malformation syndromes, 1000 from spontaneous abortions, and 500 with X-linked mental retardation; and ii) point mutations in these samples by targeted HTS. The distinction between pathogenic and non-pathogenic variants is difficult, and we propose approaches to meet the challenge. 3. Genetic control (cis and trans eQTLs) of expression variation of CNC lincRNAs, using 200 samples.

2 353 920 €

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

After a decade of development in model organisms and later in mammalian cells, mass spectrometry-based functional proteomics approaches have come of age and are ready to enable a systematic study of the innate immune system. We propose to cross the large-scale proteomics and innate immunity disciplines to obtain a functionally annotated map of the molecular machinery involved in viral recognition and leading to the hallmark interferon response, through a three-pronged approach: 1. Map the interactome of innate immunity proteins in macrophages to establish the network of components leading to interferon production; 2. Chart the interactions of molecular patterns, mostly nucleic acids, to identify the receptors and sensors at the non-self/self interface; 3. Study viral pathogenicity factors as molecular jammers of the anti-viral response and elucidate their mode of action to uncover critical nodes (inhibitome). Datasets are integrated and released at regular intervals with embargoed windows allowing a network of collaborators/own laboratory to do in-depth validation. New components at data intersections will be tested through loss-of-function experiments and standardized read-outs for the interferon pathway as well as genetic association with autoimmune diseases. Because of its unbiased/large scope and its cross-validating approaches, wherein the newly mapped circuitry is modeled, challenged by inducers and perturbed by viral agents, i-FIVE has the potential to promote a systems-level understanding of the interferon branch of molecular innate immunity. This insight may in turn create medical opportunities for the treatment of autoimmune disorders, septic shoc, arthritis as well as in boosting anti-viral responses.

1 974 022 €

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

One of the key challenges in scientific research is to link together our understanding of different levels of biological organisation. This challenge is fundamental to the scientific endeavour: from understand how genes interact to drive the cell, to how cells interact to form organisms, up to how organisms interact to form groups and societies. My own and the research of others has addressed this question in the context of the collective behaviour of animals. Mathematical models of complex systems have been used to successfully predict experimental outcome. Most previous studies are however limited in one important aspect: individuals are treated as identical units. The aim of the proposed research proposed is to investigate features which produce differences within the units. The model systems of our study will be sticklebacks, homing pigeons and house sparrows. Individuals can differ from each other on a range of time scales, from information acquired within the last few minutes, through socially learnt information, to genetically inherited differences. Through a series of experiments on each of the study species, the development of mathematical models which incorporate between individual differences, and novel forms of data analysis, we will begin to understand the role played by individual differences within groups. We will look at the rules of motion for fish and birds; the role of personality in decision-making and how short term information differences improve decision-making accuracy. Achieving the project objectives will greatly enhance our understanding of the relationship between individual animals and the groups they live in, as well as impacting on our understanding of individual differences in other areas of biology.

977 768 €

Start date: 2010-02-01, End date: 2015-01-31

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

Cell adhesions play an important role in the organization, growth, maturation, and function of living cells. Interaction of cells with the extracellular matrix (ECM) plays an essential role in a variety of disease states , inflammation, and repair of damaged tissues. At the cellular level, many of the biological responses to external stimuli originate at adhesion loci, such as focal adhesions (FA), which link cells to the ECM . Cell adhesion is mediated by receptor proteins such as cadherins and integrins. The precise molecular composition, dynamics and signalling activity of these adhesion assemblies determine the specificity of adhesion-induced signals and their effects on the cell. However, characterization of the molecular architecture of FAs is highly challenging, and it thus remains unclear how these molecules function together, how they are recruited to the adhesion site, how they are turned over, and how they function in vivo. In this project, I aim to conduct an interdisciplinary study that will provide a quantum step forward in the understanding of the functional organization of FAs. We will analyze, for the first time, the three-dimensional structure of FAs in wild-type cells and in cells deficient in the specific proteins involved in the cell-adhesion machinery. We will study the effect of specific geometries on the functional architecture of focal adhesions in 3D. A combination of state-of-the-art technologies, such cryo-electron tomography of intact cells, gold cluster chemistry for in situ labeling, and modulation of the underlying matrix using micro- and nano-patterned adhesive surfaces, together with correlative light, atomic force and electron microscopy, will provide a hybrid approach for dissecting out the complex process of cell adhesion.In summary, this project addresses the properties of FAs across a wide range of complexities and dimensions, from macroscopic cellular phenomena to the physical nature of these molecular assemblies

1 294 000 €

Start date: 2009-11-01, End date: 2015-10-31

The last years have seen an extraordinary explosion of studies characterizing genome variation at different levels, and have opened new opportunities in deciphering the genetic basis of phenotypic characteristics and the evolutionary forces involved. One of the major breakthroughs has been the discovery of an unprecedented degree of structural variation in the human genome, including deletions, duplications and inversions. However, the main challenge is to understand the biological significance of these genomic changes. In particular, for many years inversions have been the paradigm of evolutionary biology. Thus, the identification of the whole set of human inversions gives us a unique opportunity to investigate the functional and evolutionary consequences of this type of changes at a large scale. The specific objectives of the project are: (1) Catalogue the precise location of all common polymorphic inversions in the human genome; (2) Determine the population distribution and the evolutionary history of these inversions; (3) Investigate the functional consequences and the effects on gene expression of human inversions; and (4) Assess the effect of inversions on nucleotide variation patterns and the role of natural selection in their maintenance. This project will follow a multidisciplinary approach that combines experimental and bioinformatic analyses and will benefit from the great amount of information on the human genome already available and that will be generated in the next months. The proposed research therefore represents a very appropriate and timely contribution to the study of human structural variation and its role in phenotypic variation and evolution. Furthermore, it will provide additional insights on genome function, gene-expression regulation mechanisms, and the association of genetic changes and particular traits, and promises to stir novel hypothesis for future studies.

1 475 377 €

Start date: 2010-02-01, End date: 2015-10-31

Cells sense, affect and respond to their environment through the fundamental function of adhesion. Several types of adhesion sites, which are mediated via dynamically maintained multi-protein structures, anchor extracellular-matrix proteins to the cytoskeleton. Despite considerable efforts, the long-standing questions of how adhesion sites are formed, structured and regulated remain unanswered. In this research plan we will investigate desmosomes and adherens junctions by cryo-electron tomography of cells and tissue. The principal objectives are: (a) to visualize the molecular architecture and reveal the structural differences of the adhesion sites under various conditions and influences, i.e. mutations, wounds, etc. (b) to reveal their molecular association to the cytoskeleton (intermediate and actin filaments respectively), and to chart the network of interactions underlying cellular adhesion, and (c) to develop novel pattern recognition and classification techniques in order to structurally characterize the adhesion sites in toto by cryo-electron tomography of vitreous sections. We will use pattern recognition techniques and locally averaged cryo-electron sub-tomograms to quantify the macromolecular complexes in terms of stoichiometry and protein interactions in situ at high resolution (~3 nm). In particular, we aim to reveal how a pool of constituent proteins is organized in the two adhesion sites. Significant amounts of information coming from immunogold electron microscopy, fragments from X-ray structures, force measurements with atomic force microscopy, and structural bioinformatics will be integrated into our cryo-electron tomograms. This research will pioneer structural comparisons of protein networks at nanometer resolution in situ and in toto. The experimental and theoretical methods that will be developed would be indispensable for studying any spatially constrained protein network whose state depends on local properties.

1 724 400 €

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

Data mining provides large benefits to the commercial, government and homeland security sectors, but the aggregation and storage of huge amounts of data about citizens inevitably leads to erosion of privacy. To achieve the benefits that data mining has to offer, while at the same time enhancing privacy, we need technological solutions that simultaneously enable data mining while preserving privacy. The current state of the art has focused on providing privacy-preserving solutions for very specific problems, and has thus taken a local perspective. Although this is an important first step in the development of privacy-preserving solutions, it is time for a global perspective on the problem that aims for providing full integrated solutions. Our goal in this research is to study privacy and develop comprehensive solutions for enhancing it in the digital era. Our proposed research project includes foundational research on privacy, an infrastructure level for achieving anonymity over the Internet, key cryptographic tools for constructing privacy-preserving protocols, and development of large-scale applications that are built on top of all of the above. The novelty of our research is in our focus on fundamental issues towards comprehensive solutions that are aimed for large-scale data sources. The project s outcome will allow migration from local solutions for specific problems that are suited for small to medium scale data sources to comprehensive privacy-preserving database and data mining solutions for large scale data warehouses. Achieving this great challenge carries immense scientific, technological and societal rewards.

1 921 316 €

Start date: 2009-10-01, End date: 2014-09-30

Ubiquitin (Ub) is a small modifier that labels proteins in a highly specific manner. Like phosphorylation, modification of proteins by Ub is prevalent in the majority of cellular processes. An increasing number of distinct functions have been assigned to different types of ubiquitin modifications (monoUb and different Lys-linked chains). Moreover, aberrations in the ubiquitin system underlie many disease states, including cancer, inflammatory, immune and metabolic disorders as well as neurodegeneration. The most recently described physiological ubiquitin modification is the linear ubiquitin chain, in which ubiquitin monomers are conjugated via Met-Gly linkages. We have found that linear ubiquitin chains bind specifically to the NEMO adaptor molecule, an event critical for the proper regulation of NF-ºB signaling (Rahighi, 2009). Here we propose to use a multidisciplinary strategy to study the role of linear ubiquitination in the NF-ºB pathway, autophagy, apoptosis and DNA repair and how these changes can impact on disease states such as inflammation and cancer development. Scientific objectives are: " Characterize the components of linear ubiquitination: E3 ligases, specific substrates and domains recognizing linear ubiquitin chains " Elucidate the in vivo role of linear ubiquitination in the regulation of the NF-ºB pathway, apoptosis and DNA repair. " Reveal the molecular basis for the connections between linear ubiquitination and selective autophagy " Identify elements in the linear ubiquitin network as potential drug targets " Generate transgenic mouse models of inflammatory diseases and cancer " Develop system and computational biology approaches to assess the global role of linear ubiquitination in cellular proteome

2 440 560 €

Start date: 2010-06-01, End date: 2015-05-31

Overall objective and Specific Aims. The overall objective of this proposal is to elucidate the pathogenesis of HBV infection with the ultimate hope that this knowledge will lead to the development of new therapeutic strategies to terminate persistent infection and its attendant costs and complications. Our approach is to dissect poorly understood cellular and molecular pathways responsible for both liver disease and viral clearance taking advantage of technological advances in the field of live imaging and unique mouse models of HBV infection. Three specific aims will be pursued: 1. Visualize and characterize where and how naïve and effector CTL of different specificities adhere to vessels and recognize/kill HBV-expressing hepatocytes within the “normal”, fibrotic/cirrhotic or cancerous liver. 2. Characterize the role of platelets in HBV pathogenesis. 3. Characterize the role of Kupffer cells in HBV pathogenesis.

2 046 200 €

Start date: 2010-09-01, End date: 2016-03-31

Microorganisms are the greatest chemists of our planet. Almost every chemical reaction that is thermodynamically feasible is exploited by these organisms to sustain growth and survival. Together, the actions of microbes comprise the biogeochemical element cycles, a vastly complicated metabolic network that is the basis of all life. Since a few years the metagenomic exploration of this network has begun. Ten years from now next-generation massive parallel sequencing technology will enable the cost-effective near-complete molecular characterization of microbial communities. This development has great applied and fundamental potential. So far metagenomes were recorded for natural communities with poorly characterized natural history. Consequently, such metagenomes are very difficult to interpret. To move forward, it is essential to record metagenomes of microbial communities at precisely defined selective pressure. That is the key innovation of my ERC application. It is a simple step forwards, and a very challenging one. It will require a combination of skills in engineering, biochemistry, microbial ecology, physiology and bioinformatics. This combination is exactly what has propelled my previous research. My project focuses on communities involved in nitrate respiration. The turnover of nitrate plays a key role in all geochemical element cycling while its natural abundance is severely affected by human activity. The environmental fate of nitrate is currently unpredictable. My project will deliver fundamental molecular understanding over the workings of natural selection for nitrate respiring communities. It will express this understanding into useful, general metagenomic markers. This is a pioneering effort; it will serve as an example to the field and show how to capitalize on the most far-reaching innovation of our time.

1 700 000 €

Start date: 2009-09-01, End date: 2014-08-31

Despite half a century of sustained research into the structure of cities, we still cannot answer the most basic questions of how their morphology is affected by the energy and income of their populations. We do not know if cities will become more compact or more spread out as energy usage changes due to global warming and as we switch to renewable energy sources. What we need is much more robust theory with applicable computer models for forecasting such impacts. Many of the rudiments involving agglomeration economics, growth theory, trade, nonlinear dynamics, and fractal geometry have already been put in place with the complexity sciences providing a framework for this new social physics. But so far, energy has been strangely absent. Here we will embrace this role, thus generating theory and models able to address what cities will look like if current predictions of climate change are borne out. We will organise the project into six related themes. First, we will extend theories of urban morphology based on fractals, scaling and allometry to incorporate energetics in analogy to transport and network processes. Second we will link these to statistical thermodynamics in spatial interaction and location modelling where energy, entropy, and accessibility are central. Third we will aggregate our theories to enable comparative analyses of city shape, compactness, energy use, and density. Fourth, we will explore different dynamic regimes building on self-criticality and bifurcation. Fifth, we will make these ideas operational building on our London Tyndall Centre model, and on related work in Phoenix and Shanghai. Last, we will construct a web-based laboratory for posing what if questions about climate change and energy balance using our theoretical and empirical models.

2 336 806 €

Start date: 2010-07-01, End date: 2015-12-31

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

MHC class II molecules are crucial for specific immune responses. In a complicated series of cell biological events, they catch a peptide in the endosomal route for presentation at the plasma membrane to the immune system. At present some 20 factors have been identified as involved in the process of MHC class II antigen presentation that are potential targets for manipulating these responses as MHC class II molecules are involved in most auto-immune diseases. Defining further targets for manipulating MHC class II responses would have implications for various disease states when these can be inhibited by chemical compounds or biologicals. We have performed a genome-wide FACS-based siRNA screen for molecules affecting MHC class II expression and peptide loading. After 100.000 individual 2-color FACS analyses, we identified 276 proteins that can be functionally sub-clustered for expression and for cell biological effects. We now propose to study the cell biology of these 276 hits to elucidate the molecular and cell biological mechanisms of MHC class II antigen presentation (the MHC class II-ome). As a first step, the 276 hits are sub-clustered for effects on MHC class II transcription or cell biology. These sub-clusters may correspond to networks. We propose to validate and extend these networks by experiments by a team of scientists concentrating on the various aspects of the cell biology of MHC class II antigen presentation. A parallel chemical compound screen will be performed to identify compounds affecting MHC class II antigen presentation. By cross-correlating the biological phenotypes of compounds with those of siRNA silencing, novel target-lead combinations will be defined by reciprocal chemical genetics. Our experiments should result in a global understanding of MHC class II antigen presentation. In addition, it should reveal target-lead combinations for manipulation of MHC class II antigen presentation in infection, auto-immune disease and transplantation.

2 112 300 €

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

The primary objective of the proposed project is to develop robot mediated human interface technologies to manually explore, manipulate and assemble progressively smaller objects ranging from micro- to nano-meter scales and a secondary objective is to demonstrate the power of the interface system in the investigation of the fundamental mechanics and neural mechanisms of touch. The proposed system will consist of a master-slave robotic teleoperation (TO) subsystem and a virtual reality (VR) subsystem. The master robot will enable the user to touch, feel and manipulate (1) real micro/nano structures through the slave robot or (2) computer models of micro/nano structures in the virtual reality environment. Specific aims of this effort are as follows: (1) design and develop a custom master system to enable the user to have real-time visual, auditory, and bimanual haptic interactions; (2) design and develop a slave system consisting of microscopes and manipulators progressively augmented to enable micro to nano-precision movements and forces; (3) develop modular software architecture with device abstraction to support multiple master and slave devices; (4) integrate virtual reality software to enable the user to have real-time visual, auditory, and bimanual interactions with virtual models at micro- to nano-meter scales based on empirical data or to test hypotheses; (5) use the system to perform biomechanics and neurophysiology experiments at progressively micro- to nano-precision movements and forces; (6) develop mathematical models of mechanotransduction for quantitative understanding of touch mechanisms at multiple scales.

3 264 188 €

Start date: 2010-12-01, End date: 2016-11-30

How genome organisation and architecture respond to variations in selection regimes is indeed poorly known at the microevolutionary scale. Supergenes are tight clusters of genes which simultaneously control the variation of various components of a complex trait, involving elements with different ontology1-4. Supergenes typically evolve in response to strong epistatic selection between neighbouring genes. They are usually maintained by some form of balancing selection, but the modalities of their evolution are still obscure and require empirical investigation. I propose to take advantage of the remarkable supergene controlling wing-pattern mimicry balanced polymorphism in the tropical butterfly Heliconius numata to investigate the structure and evolution of supergenes at the molecular level. The supergene P is a positional homologue of a loose cluster of loci controlling wing pattern mimicry in a related species. Positional cloning revealed the supergene is situated in a local inversion. Recombination is largely suppressed around P and two groups of haplotypes segregate in perfect association with wing pattern in natural populations. I propose to investigate the detailed structure of the inversion breakpoints and gene shuffling to test the working model of supergenes arising by rearrangement of distant ancestral loci. Using population genetics I propose to survey genetic diversity and look for signatures of balancing selection on the genes composing the supergene inversion. We will test for the effect of balancing selection in a patchy habitat, which has received little empirical data. We are now very close to genetically characterise the major loci controlling spectacular adaptations, involved in speciation and radiations, and determining species coexistence.

760 726 €

Start date: 2010-02-01, End date: 2014-01-31

The project faces the problem of handling complexity in the microbial part of the marine pelagic food web. The basic idea is that there is a generic structure created by the interactions between three fundamental life strategies - competition, defense and predation/parasitism. This generic structure links the life strategies to central system features such as biodiversity, biogeochemistry, population dynamics and evolution. The structure repeats itself and excert control over phenomena from microdiversity within prokaryotic species to basin scale biogeochemistry. It thus it thus creates self-similarity as in fractal theory, generating complexity and intricate patterns at many levels from simple rules. The project has a theoretical part where individual based models will be used to represent life strategies, adaption and evolution at the cell level - allowing microbial diversity to evolve as a product of the models. The theoretical work will be challenged with experimental work at two levels: the effect of host-virus interactions on biodiversity within microbial communities, and the effect of predation on structuring the balance between communities of osmotrophic microorganisms (bacteria and phytoplankton).

2 499 937 €

Start date: 2010-06-01, End date: 2015-05-31

MicroRNAs (miRNAs) are a novel class of genes, accounting for >1% of genes in a typical animal genome. They constitute an important layer of gene regulation that affects diverse processes such as cell differentiation, apoptosis, and metabolism. Despite such critical roles, deciphering the mechanism of action of miRNAs has been difficult, leading to multiple, partially contradictory, models of miRNA activity. Moreover, adding an additional layer of complexity, it is now emerging that miRNA activity is regulated by various mechanisms that we are only beginning to identify. Our objective is to understand how miRNAs are regulated under physiological conditions, in the roundworm Caenorhabditis elegans. We will focus on pathways of miRNA turnover, an issue of fundamental importance that has received little attention because miRNAs are widely held to be highly stable molecules. However, miRNA over-accumulation causes aberrant development and disease, prompting us to test rigorously whether degradation can antagonize miRNA activity and either identify the machinery involved, or confirm the dominance of other regulatory modalities, whose components we will identify. C. elegans is the organism in which miRNAs and many components of the miRNA machinery were discovered. However, previous studies emphasized genetics and cell biology approaches, limiting the degree of mechanistic insight that could be obtained. In addition to exploiting the traditional strengths of C. elegans, we will therefore develop and apply biochemical and genomic techniques to obtain a comprehensive understanding of miRNA regulation, enabling us to demonstrate both molecular mechanisms and physiological relevance. Given the importance of miRNAs in development and disease, identifying the regulators of these tiny gene regulators will be both of scientific interest and biomedical relevance.

1 782 200 €

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

The breath taking increase in performance of integrated circuits became possible by continuous miniaturization of CMOS devices. On this exciting path many tough problems were resolved; however, growing technological challenges and soaring costs will gradually bring scaling to an end. This puts foreseeable limitations to the future performance increase, and research on alternative technologies and computational principles becomes important. Spin attracts attention as alternative to the charge degree of freedom for computations and non-volatile memory applications. Silicon as main material of microelectronics is characterized by negligible spin-orbit interaction and zero-spin nuclei and should display long spin coherence times. Combined with the potentially easy integration with CMOS, long spin coherence makes silicon perfectly suited for spin-driven applications, as confirmed by recent impressive demonstrations of spin injection, coherent propagation, and detection. The success of microelectronics technology has been well assisted by smart Technology Computer-Aided Design tools; however, support for spin applications is entirely absent. The objective here is to create, test, and apply a simulation environment for spin-based devices in silicon. Microscopic models describing the physical properties relevant to the spin degree of freedom are developed. Special attention will be paid to investigate, how to increase the spin coherence time. One option is based on completely removing the valley degeneracy in the conduction band by [110] uniaxial stress. Understanding spin-polarized transport in silicon and in compatible hysteretic materials allows using the spin-torque effect to invent, model, and optimize prototypes of switches and memory cells for the 21st century.

1 678 500 €

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

Nanosystems are integrated systems exploiting nanoelectronic devices. In particular, this proposal considers silicon nanowire and carbon nanotube technologies as replacement/enhancement of current silicon technologies. This proposal addresses high-risk, high-reward research, unique in its kind. The broad objective of this proposal is to study system organization, architectures and design tools which, based on a deep understanding and abstraction of the manufacturing technologies, allow us to realize nanosystems that outperform current integrated systems in terms of capabilities and performance. Thus this proposal will address modelling of technological aspects, synthesis and optimization of information processing functions from high-level specifications into the nanofabric, and new design technologies for specific aspects of nanosystems including, but not limited to, sensing and interfacing with the environment. This proposal will address also cross-cutting design goals such as ultra-low power and high-dependability design, with the overall objective of realizing nanosystems that are autonomous (w.r. to energy consumption) and autonomic (i.e., self healing). The scientific novelty of this proposal stems from the use of a nanofabric, where computation, sensing and communication are supported by a homogeneous means as well as from the study of algorithmic tools for mapping high-level functions onto the nanofabric. The intrinsic benefit of this research is to provide a design flow that extends both the technological basis and the capabilities of integrated systems, thus strengthening the industrial European position in a key sector where disruptive innovation is key for survival. The extrinsic benefit of this research is to broaden the use of nanosystems to new domains, including mobile/distributed embedded systems, health/environment management, and other areas that are critical to our lives.

2 499 594 €

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

In this project we will develop nanophotonic reservoir computing as a novel paradigm for massively parallel information processing. Reservoir computing is a recently proposed methodology from the field of machine learning and neural networks which has been used successfully in several pattern classification problems, like speech and image recognition. However, it has so far mainly been used in a software implementation which limits its speed and power efficiency. Photonics could provide an excellent platform for such a hardware implementation, because of the presence of unique non-linear dynamics in photonics components due to the interplay of photons and electrons, and because light also has a phase in addition to an amplitude, which provides for an important additional degree of freedom as opposed to a purely electronic hardware implementation. Our aim is to bring together a multidisciplinary team of specialists in photonics and machine learning to make this vision of massively parallel information processing using nanophotonics a reality. We will achieve these aims by constructing a set of prototypes of ever increasing complexity which will be able to tackle ever more complex tasks. There is clear potential for these techniques to perform information processing that is beyond the limit of today's conventional computing processing power: high-throughput massively parallel classification problems, like e.g. processing radar data for road safety, or real time analysis of the data streams generated by the Large Hadron Collider.

1 260 000 €

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