ERC FUNDED PROJECTS

The aim of this proposal is to understand a novel regulatory signaling network controlling insulin secretion, fat accumulation and energy balance centered around selected components of the TGF-² signaling system, including Activins A and B, GDF-3 and their receptors ALK7 and ALK4. Recent results from my laboratory indicate that these molecules are part of paracrine signaling networks that control important functions in pancreatic islets and adipose tissue through feedback inhibition and feed-forward regulation. These discoveries have open up a new research area with important implications for the understanding of metabolic networks and the treatment of human metabolic syndromes, such as diabetes and obesity. To drive progress in this new research area beyond the state-of-the-art it is proposed to: i) Elucidate the molecular mechanisms by which Activins regulate Ca2+ influx and insulin secretion in pancreatic ²-cells; ii) Elucidate the molecular mechanisms underlying the effects of GDF-3 on adipocyte metabolism, turnover and fat accumulation; iii) Investigate the interplay between insulin levels and fat deposition in the development of insulin resistance using mutant mice lacking Activin B and GDF-3; iv) Investigate tissue-specific contributions of ALK7 and ALK4 signaling to metabolic control by generating and characterizing conditional mutant mice; v) Investigate the effects of specific and reversible inactivation of ALK7 and ALK4 on metabolic regulation using a novel chemical-genetic approach based on analog-sensitive alleles. This is research of a high-gain/high-risk nature. It is posed to open unique opportunities for further exploration of complex metabolic networks. The development of drugs capable of enhancing insulin secretion, limiting fat accumulation and ameliorating diet-induced obesity by targeting components of the ALK7 signaling network will find a strong rationale in the results of the proposed work.

2 462 154 €

Start date: 2009-04-01, End date: 2014-03-31

This proposal targets the emerging frontier research field of multiple-input multiple-output (MIMO) systems along with several innovative and somewhat unconventional applications of such systems. The use of arrays of transmitters and receivers will have a profound impact on future medical imaging/therapy systems, radar systems, and radio communication networks. Multiple transmitters provide a tremendous versatility and allow waveforms to be adapted temporally and spatially to environmental conditions. This is useful for individually tailored illumination of human tissue in biomedical imaging or ultrasound therapy. In radar systems, multiple transmit beams can be formed simultaneously via separate waveform designs allowing accurate target classification. In a wireless communication system, multiple communication signals can be directed to one or more users at the same time on the same frequency carrier. In addition, multiple receivers can be used in the above applications to provide increased detection performance, interference rejection, and improved estimation accuracy. The joint modelling, analysis, and design of these multidimensional transmit and receive schemes form the core of this research proposal. Ultimately, our research aims at developing the fundamental tools that will allow the design of wireless communication systems with an order-of-magnitude higher capacity at a lower cost than today; of ultrasound therapy systems maximizing delivered power while reducing treatment duration and unwanted illumination; and of distributed aperture multi-beam radars allowing more effective target location, identification, and classification. Europe has several successful industries that are active in biomedical imaging/therapy, radar systems, and wireless communications. The future success of these sectors critically depends on the ability to innovate and integrate new technology.

1 872 720 €

Start date: 2009-01-01, End date: 2013-12-31

Understanding the molecular mechanisms underlying adipose blood vessel growth or regression opens new fundamentally insight into novel therapeutic options for the treatment of obesity and its related metabolic diseases such as type 2 diabetes and cancer. Unlike any other tissues in the body, the adipose tissue constantly experiences expansion and shrinkage throughout the adult life. Adipocytes in the white adipose tissue have the ability to switch into metabolically highly active brown-like adipocytes. Brown adipose tissue (BAT) contains significantly higher numbers of microvessels than white adipose tissue (WAT) in order to adopt the high rates of metabolism. Thus, an angiogenic phenotype has to be switched on during the transition from WAT into BAT. We have found that acclimation of mice in cold could induce transition from inguinal and epidedymal WAT into BAT by upregulation of angiogenic factor expression and down-regulations of angiogenesis inhibitors (Xue et al, Cell Metabolism, 2009). The transition from WAT into BAT is dependent on vascular endothelial growth factor (VEGF) that primarily targets on vascular endothelial cells via a tissue hypoxia-independent mechanism. VEGF blockade significantly alters adipose tissue metabolism. In another genetic model, we show similar findings that angiogenesis is crucial to mediate the transition from WAT into BAT (Xue et al, PNAS, 2008). Here we propose that the vascular tone determines the metabolic switch between WAT and BAT. Characterization of these novel angiogenic pathways may reveal new mechanisms underlying development of obesity- and metabolism-related disease complications and may define novel therapeutic targets. Thus, the benefit of this research proposal is enormous and is aimed to treat the most common and highly risk human health conditions in the modern time.

2 411 547 €

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

"Recent technological evolutions, including the cloud, the multicore, the social and the mobiles ones, are turning computing ubiquitously distributed. Yet, building high-assurance distributed programs is notoriously challenging. One of the main reasons is that these systems usually seek to achieve several goals at the same time. In short, they need to be efficient, responding effectively in various average-case conditions, as well as reliable, behaving correctly in severe, worst-case conditions. As a consequence, they typically intermingle different strategies: each to cope with some specific condition, e.g., with or without node failures, message losses, time-outs, contention, cache misses, over-sizing, malicious attacks, etc. The resulting programs end up hard to design, prove, verify, implement, test and debug. Not surprisingly, there are anecdotal evidences of the fragility of the most celebrated distributed systems. The goal of this project is to contribute to building high-assurance distributed programs by introducing a new dimension for separating and isolating their concerns, as well as a new scheme for composing and reusing them in a modular manner. In short, the project will explore the inherent power and limitations of a novel paradigm, Adversary-Oriented Computing (AOC). Sub-programs, each implementing a specific strategy to cope with a given adversary, modelling a specific working condition, are designed, proved, verified, implemented, tested and debugged independently. They are then composed, possibly dynamically, as black-boxes within the same global program. The AOC project is ambitious and it seeks to fundamentally revisit the way distributed algorithms are designed and distributed systems are implemented. The gain expected in comparison with today's approaches is substantial, and I believe it will be proportional to the degree of difficulty of the distributed problem at hand."

2 147 012 €

Start date: 2014-06-01, End date: 2019-05-31

In the 90s, two landmark observations brought to a paradigm shift about the role of astrocytes in brain function: 1) astrocytes respond to signals coming from other cells with transient Ca2+ elevations; 2) Ca2+ transients in astrocytes trigger release of neuroactive and vasoactive agents. Since then, many modulatory astrocytic actions and mechanisms were described, forming a complex - partly contradictory - picture, in which the exact roles and modes of astrocyte action remain ill defined. Our project wants to bring light into the “language of astrocytes”, i.e. into how they communicate with neurons and, ultimately, address their role in brain computations and cognitive behavior. To this end we will perform 4 complementary levels of analysis using highly innovative methodologies in order to obtain unprecedented results. We will study: 1) the subcellular organization of astrocytes underlying local microdomain communications by use of correlative light-electron microscopy; 2) the way individual astrocytes integrate inputs and control synaptic ensembles using 3D two-photon imaging, genetically-encoded Ca2+ indicators, optogenetics and electrophysiology; 3) the contribution of astrocyte ensembles to behavior-relevant circuit operations using miniaturized microscopes capturing neuronal/astrocytic population dynamics in freely-moving mice during memory tests; 4) the contribution of astrocytic signalling mechanisms to cognitive behavior using a set of new mouse lines with conditional, astrocyte-specific genetic modification of signalling pathways. We expect that this combination of groundbreaking ideas, innovative technologies and multilevel analysis makes our project highly attractive to the neuroscience community at large, bridging aspects of molecular, cellular, systems and behavioral neuroscience, with the goal of leading from a provocative hypothesis to the conclusive demonstration of whether and how “the language of astrocytes” participates in memory and cognition.

2 513 896 €

Start date: 2014-02-01, End date: 2019-01-31

The attoclock is a powerful, new, and unconventional tool to study fundamental attosecond dynamics on an atomic scale. We established its potential by using the first attoclock to measure the tunneling delay time in laser-induced ionization of helium and argon atoms, with surprising results. Building on these first proof-of-principle measurements, I propose to amplify and expand this tool concept to explore the following key questions: How fast can light liberate electrons from a single atom, a single molecule, or a solid-state system? Related are more questions: How fast can an electron tunnel through a potential barrier? How fast is a multi-photon absorption process? How fast is single-photon photoemission? Many of these questions will undoubtedly spark more questions – revealing deeper and more detailed insights on the dynamics of some of the most fundamental and relevant optoelectronic processes. There are still many unknown and unexplored areas here. Theory has failed to offer definitive answers. Simulations based on the exact time-dependent Schrödinger equation have not been possible in most cases. Therefore one uses approximations and simpler models to capture the essential physics. Such semi-classical models potentially will help to understand attosecond energy and charge transport in larger molecular systems. Indeed the attoclock provides a unique tool to explore different semi-classical models. For example, the question of whether electron tunneling through an energetically forbidden region takes a finite time or is instantaneous has been subject to ongoing debate for the last sixty years. The tunnelling process, charge transfer, and energy transport all play key roles in electronics, energy conversion, chemical and biological reactions, and fundamental processes important for improved information, health, and energy technologies. We believe the attoclock can help refine and resolve key models for many of these important underlying attosecond processes.

2 319 796 €

Start date: 2013-03-01, End date: 2018-02-28

NK cells that are well known by their ability to recognize and eliminate virus infected and tumor cells were also implicated in the defence against bacteria. However, the recognition of bacteria by NK cells is only poorly understood. we do not know how bacteria are recognized and the functional consequences of such recognition are also weakly understood. In the current proposal we aimed at determining the “NK cell receptor-bacterial interactome”. We will examine the hypothesis that NK inhibitory and activating receptors are directly involved in bacterial recognition. This ground breaking hypothesis is based on our preliminary results in which we show that several NK cell receptors directly recognize various bacterial strains as well as on a few other publications. We will generate various mice knockouts for NCR1 (a major NK killer receptor) and determine their microbiota to understand the physiological function of NCR1 and whether certain bacterial strains affects its activity. We will use different human and mouse NK killer and inhibitory receptors fused to IgG1 to pull-down bacteria from saliva and fecal samples and then use 16S rRNA analysis and next generation sequencing to determine the nature of the bacteria species isolated. We will identify the bacterial ligands that are recognized by the relevant NK cell receptors, using bacterial random transposon insertion mutagenesis approach. We will end this research with functional assays. In the wake of the emerging threat of bacterial drug resistance and the involvement of bacteria in the pathogenesis of many different chronic diseases and in shaping the immune response, the completion of this study will open a new field of research; the direct recognition of bacteria by NK cell receptors.

2 499 800 €

Start date: 2013-03-01, End date: 2018-02-28

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

In the bone-enclosed CNS, increased vascular permeability may cause life-threatening tissue swelling, and/or ischemia and inflammation which compromise tissue repair after trauma or stroke. The brain vasculature possesses several unique features collectively named the blood-brain barrier (BBB) in which passive permeability is almost completely abolished and replaced by a complex of specific transport mechanisms. The BBB is necessary to uphold the specific milieu necessary for neuronal function. Whereas breakdown of the BBB is part of many CNS diseases, including stroke, neuroinflammation, trauma and neurodegenerative disorders, its molecular mechanisms and consequences are unclear and debated. Conversely, the intact BBB is a huge obstacle for drug delivery to the brain. Research on the BBB therefore has two seemingly opposing aims: 1) to seal a damaged BBB and protect the brain from toxic blood products, and 2) to open the BBB “on demand” for drug delivery. A major problem in the BBB field has been the lack of in vivo animal models for molecular and functional studies. So far, available in vitro models are not recapitulating the in vivo BBB. Our recent work on mouse models lacking pericytes, a BBB-associated cell type, demonstrates a specific role for pericytes in the development and regulation of the mammalian BBB. These animal models are the first ones showing a general and significant BBB impairment in adulthood, and as such they provide a unique opportunity to address molecular mechanisms of BBB disruption in disease and in drug transport across the BBB. Importantly, the new models and tools that we have developed allow us to search for relevant druggable mechanisms and molecular targets in the BBB. The long-term goals of this proposal are to develop molecular strategies and tools to open and close the BBB “on demand” for drug delivery to the CNS, and to explore the importance and mechanisms of BBB dysfunction in neurodegenerative diseases and stroke.

2 499 427 €

Start date: 2012-08-01, End date: 2017-07-31

In this project, we will develop and use technology that combines synthetic genomics and live-cell imaging. These methods make it possible to study the intracellular biophysics at single-molecule detail in thousands of genetically different bacterial strains in parallel. Our approach is based on in situ genotyping of a barcoded strain library after phenotyping has been performed by live-cell imaging. Within the scope of the proposed project, the new technology will be used to solve mechanistic and structural questions of the bacterial cell cycle. To this end, we will explore two parallel but complementary applications. In the first application, we will determine the dynamic 3D structure of the E. coli chromosome at 1kb resolution throughout the cell cycle. The structure determination can be seen as a live-cell version of chromatin conformation capture, where we will follow the 3D distances of 10 000 pairs of chromosomal loci over the cell cycle at high resolution. In the second application, we will make a complete CRISPRi knockdown strain library where we can follow the replication forks of the E. coli chromosome and septum formation over the cell cycle in individual cells. Using this strategy, we will resolve how individual gene products contribute to the cell-to-cell accuracy in replication initiation and cell division. In particular, this approach allows us to address the challenging question of size sensing at replication initiation. How the cell can decide that it is large enough to initiate replication is still an open question despite decades of investigations. The general principles for high-end imaging of pool-synthesized cell libraries have nearly unlimited applications throughout cell biology. The specific applications explored in this project will take the understanding of the bacterial cell cycle to a new level and answer general questions about the chromosomal organization and cell size sensing.

2 411 410 €

Start date: 2021-01-01, End date: 2025-12-31

Autonomous programmable computing devices made of biological molecules hold the promise of interacting with the biological environment in future biological and medical applications. Our laboratory's long-term objective is to develop a 'Doctor in a cell': molecular-sized device that can roam the body, equipped with medical knowledge. It would diagnose a disease by analyzing the data available in its biochemical environment based on the encoded medical knowledge and treat it by releasing the appropriate drug molecule in situ. This kind of device might, in the future, be delivered to all cells in a specific tissue, organ or the whole organism, and cure or kill only those cells diagnosed with a disease. Our laboratory embarked on the attempt to design and build these molecular computing devices and lay the foundation for their future biomedical applications. Several important milestones have already been accomplished towards the realization of the Doctor in a cell vision. The subject of this proposal is a construction of autonomous biomolecular computers that could be delivered into a living cell, interact with endogenous biomolecules that are known to indicate diseases, logically analyze them, make a diagnostic decision and couple it to the production of an active biomolecule capable of influencing cell fate.

2 125 980 €

Start date: 2009-01-01, End date: 2013-10-31

Peptide building blocks serve as very attractive bio-inspired elements in nanotechnology owing to their controlled self-assembly, inherent biocompatibility, chemical versatility, biological recognition abilities and facile synthesis. We have demonstrated the ability of remarkably simple aromatic peptides to form well-ordered nanostructures of exceptional physical properties. By taking inspiration from the minimal recognition modules used by nature to mediate coordinated processes of self-assembly, we have developed building blocks that form well-ordered nanostructures. The compact design of the building blocks, and therefore, the unique structural organization, resulted in metallic-like Young's modulus, blue luminescence due to quantum confinement, and notable piezoelectric properties. The goal of this proposal is to develop two new fronts for bio-inspired building block repertoire along with co-assembly to provide new avenues for organic nanotechnology. This will combine our vast experience in the assembly of aromatic peptides together with additional structural modules from nature. The new entities will be developed by exploiting the design principles of small aromatic building blocks to arrive at the smallest possible module that form super helical assembly based on the coiled coil motifs and establishing peptide nucleic acids based systems to combine the worlds of peptide and DNA nanotechnologies. The proposed research will combine extensive design and synthesis effort to provide a very diverse collection of novel buildings blocks and determination of their self-assembly process, followed by broad chemical, physical, and biological characterization of the nanostructures. Furthermore, effort will be made to establish supramolecular co-polymer systems to extend the morphological control of the assembly process. The result of the project will be a large and defined collection of novel chemical entities that will help reshape the field of bioorganic nanotechnology.

3 003 125 €

Start date: 2016-06-01, End date: 2021-05-31

The introduction of minimally invasive surgery in the 1980’s created a paradigm shift in surgical procedures. Health care is now in a position to make a more dramatic leap by integrating newly developed wireless microrobotic technologies with nanomedicine to perform precisely targeted, localized endoluminal techniques. Devices capable of entering the human body through natural orifices or small incisions to deliver drugs, perform diagnostic procedures, and excise and repair tissue will be used. These new procedures will result in less trauma to the patient and faster recovery times, and will enable new therapies that have not yet been conceived. In order to realize this, many new technologies must be developed and synergistically integrated, and medical therapies for which the technology will prove successful must be aggressively pursued. This proposed project will result in the realization of animal trials in which wireless microrobotic devices will be used to investigate a variety of extremely delicate ophthalmic therapies. The therapies to be pursued include the delivery of tissue plasminogen activator (t-PA) to blocked retinal veins, the peeling of epiretinal membranes from the retina, and the development of diagnostic procedures based on mapping oxygen concentration at the vitreous-retina interface. With successful animal trials, a path to human trials and commercialization will follow. Clearly, many systems in the body have the potential to benefit from the endoluminal technologies that this project considers, including the digestive system, the circulatory system, the urinary system, the central nervous system, the respiratory system, the female reproductive system and even the fetus. Microrobotic retinal therapies will greatly illuminate the potential that the integration of microrobotics and nanomedicine holds for society, and greatly accelerate this trend in Europe.

2 498 044 €

Start date: 2011-04-01, End date: 2016-03-31

The overall goal of this project is to understand the molecular mechanisms that lead to the generation of potent and broadly neutralizing antibodies against medically relevant pathogens, and to identify the factors that limit their production in response to infection or vaccination with current vaccines. We will use high-throughput cellular screens to isolate from immune donors clonally related antibodies to different sites of influenza hemagglutinin, which will be fully characterized and sequenced in order to reconstruct their developmental pathways. Using this approach, we will ask fundamental questions with regards to the role of somatic mutations in affinity maturation and intraclonal diversification, which in some cases may lead to the generation of autoantibodies. We will combine crystallography and long time-scale molecular dynamics simulation to understand how mutations can increase affinity and broaden antibody specificity. By mapping the B and T cell response to all sites and conformations of influenza hemagglutinin, we will uncover the factors, such as insufficient T cell help or the instability of the pre-fusion hemagglutinin, that may limit the generation of broadly neutralizing antibodies. We will also perform a broad analysis of the antibody response to erythrocytes infected by P. falciparum to identify conserved epitopes on the parasite and to unravel the role of an enigmatic V gene that appears to be involved in response to blood-stage parasites. The hypotheses tested are strongly supported by preliminary observations from our own laboratory. While these studies will contribute to our understanding of B cell biology, the results obtained will also have translational implications for the development of potent and broad-spectrum antibodies, for the definition of correlates of protection, and for improving vaccine design.

1 867 500 €

Start date: 2015-10-01, End date: 2020-09-30

An important form of negotiation is argumentation. This is the ability to argue and to persuade the other party to accept a desired agreement, to acquire or give information, to coordinate goals and actions, and to find and verify evidence. This is a key capability in negotiating with humans. While automated negotiations between software agents can often exchange offers and counteroffers, humans require persuasion. This challenges the design of agents arguing with people, with the objective that the outcome of the negotiation will meet the preferences of the arguer agent. CAP’s objective is to enable automated agents to argue and persuade humans. To achieve this, we intend to develop the following key components: 1) The extension of current game theory models of persuasion and bargaining to more realistic settings, 2) Algorithms and heuristics for generation and evaluation of arguments during negotiation with people, 3) Algorithms and heuristics for managing inconsistent views of the negotiation environment, and decision procedures for revelation, signalling, and requesting information, 4) The revision and update of the agent’s mental state and incorporation of social context, 5) Identifying strategies for expressing emotions in negotiations, 6) Technology for general opponent modelling from sparse and noisy data. To demonstrate the developed methods, we will implement two training systems for people to improve their interviewing capabilities, and for training negotiators in inter-culture negotiations. CAP will revolutionise the state of the art of automated systems negotiating with people. It will also create breakthroughs in the research of multi-agent systems in general, and will change paradigms by providing new directions for the way computers interact with people.

2 334 057 €

Start date: 2011-07-01, End date: 2016-06-30

Bacterial biofilms are the primary cause of chronic infections and of resulting infection relapses. To be able to interfere with bacterial persistence it is vital to understand the molecular details of biofilm formation and to define how motile planktonic cells transit into surface-grown communities. The nucleotide second messenger cyclic di-guanosinemonophosphate (cdGMP) has emerged as a central regulatory factor governing bacterial surface adaptation and biofilm formation. Although cdGMP signaling may well represent the Achilles heel of bacterial communities, cdGMP networks in bacterial pathogens are exquisitely complex and an integrated cellular system to uncover the details of cdGMP dynamics is missing. To quantitatively describe cdGMP signaling we propose to exploit Caulobacter crescentus, an organism with a simple bimodal life-style that integrates the sessile-motile switch into its asymmetric division cycle. We aim to: 1) identify the role and regulation of all diguanylate cyclases and phosphodiesterases that contribute to the asymmetric cellular program with the goal to model the temporal and spatial distribution of cdGMP during development; 2) identify and characterize cdGMP effectors, their downstream targets and cellular pathways; 3) elucidate how cdGMP coordinates cell differentiation with cell growth and propagation; 4) unravel the role of cdGMP as an allosteric regulator in mechanosensation and in rapid adaptation of bacteria to growth on surfaces; 5) develop novel tools to quantitatively describe cdGMP network dynamics as the basis for mathematical modeling that provides the predictive power to experimentally test and refine important network parameters. We propose a multidisciplinary research program at the forefront of bacterial signal transduction that will provide the molecular and conceptual framework for a rapidly growing research field of second messenger signaling in pathogenic bacteria.

2 496 000 €

Start date: 2013-05-01, End date: 2018-04-30

Centrosome duplication entails the formation of a single procentriole next to each centriole once per cell cycle. The mechanisms governing procentriole formation are poorly understood and constitute a fundamental open question in cell biology. We will launch an innovative multidisciplinary research program to gain significant insight into these mechanisms using C. elegans and human cells. This research program is also expected to have a significant impact by contributing important novel assays to the field. Six specific aims will be pursued: 1) SAS-6 as a ZYG-1 substrate: mechanisms of procentriole formation in C. elegans. We will test in vivo the consequence of SAS-6 phosphorylation by ZYG-1. 2) Biochemical and structural analysis of SAS-6-containing macromolecular complexes (SAMACs). We will isolate and characterize SAMACs from C. elegans embryos and human cells, and analyze their structure using single-particle electron microscopy. 3) Novel cell-free assay for procentriole formation in human cells. We will develop such an assay and use it to test whether SAMACs can direct procentriole formation and whether candidate proteins are needed at centrioles or in the cytoplasm. 4) Mapping interactions between centriolar proteins in live human cells. We will use chemical methods developed by our collaborators to probe interactions between HsSAS-6 and centriolar proteins in a time- and space-resolved manner. 5) Functional genomic and chemical genetic screens in human cells. We will conduct high-throughput fluorescence-based screens in human cells to identify novel genes required for procentriole formation and small molecule inhibitors of this process. 6) Mechanisms underlying differential centriolar maintenance in the germline. In C. elegans, we will characterize how the sas-1 locus is required for centriole maintenance during spermatogenesis, as well as analyze centriole elimination during oogenesis and identify components needed for this process

2 004 155 €

Start date: 2009-04-01, End date: 2014-03-31

Deciphering and engineering the assembly of cellular organelles is a key pursuit in biology. The centriole is an evolutionarily conserved organelle well suited for this goal, and which is crucial for cell signaling, motility and division. The centriole exhibits a striking 9-fold radial symmetry of microtubules around a likewise symmetrical cartwheel containing stacked ring-bearing structures. Components essential for generating this remarkable architecture from alga to man have been identified. A next critical step is to engineer assays to probe the dynamics of centriole assembly with molecular precision to fully understand how these components together build a functional organelle. Our ambitious research proposal aims at taking groundbreaking steps in this direction through four specific aims: 1) Reconstituting cartwheel ring assembly dynamics. We will use high-speed AFM (HS-AFM) to dissect the biophysics of SAS-6 ring polymer dynamics at the root of cartwheel assembly. We will also use HS-AFM to analyze monobodies against SAS-6, as well as engineer surfaces and DNA origamis to further dissect ring assembly. 2) Deciphering ring stacking mechanisms. We will use cryo-ET to identify SAS-6 features that direct stacking of ring structures and set cartwheel height. Moreover, we will develop an HS-AFM stacking assay and a reconstituted stacking assay from human cells. 3) Understanding peripheral element contributions to centriole biogenesis. We will dissect the function of the peripheral centriole pinhead protein Cep135/Bld10p, as well as identify and likewise dissect peripheral A-C linker proteins. Furthermore, we will further engineer the HS-AFM assay to include such peripheral components. 4) Dissecting de novo centriole assembly mechanisms. We will dissect de novo centriole formation in human cells and water fern. We will also explore whether de novo formation involves a phase separation mechanism and repurpose the HS-AFM assay to probe de novo organelle biogenes

2 500 000 €

Start date: 2019-09-01, End date: 2024-08-31

"Communication between the nervous and the immune system is pivotal for maintaining homeostasis and ensuring rapid and efficient reaction to stress and infection insults. The emergence of microRNAs (miRs) as regulators of gene expression and of acetylcholine (ACh) signalling as regulator of anxiety and inflammation provides a model for studying this interaction. My hypothesis is that 1) a specific sub-group of miRs, designated ""CholinomiRs"", may silence multiple target genes in the neuro-immune interface; 2) these miRs compete with each other on the interaction with their targets, and 3) mutations interfering with miR binding lead to inherited susceptibility to anxiety and inflammation disorders by modifying these interactions. Our preliminary findings have shown that by targeting acetylcholinesterase (AChE), CholinomiR-132 can intensify acute stress, resolve intestinal inflammation and change post-ischemic stroke responses. Further, we have identified clustered single nucleotide polymorphisms (SNPs) interfering with AChE silencing by several miRs which associate with elevated trait anxiety, blood pressure and inflammation. To further study miR regulators of ACh signalling, I plan to: (1) Identify anxiety and inflammation-induced changes in CholinomiRs and their targets in challenged brain and immune cells. (2) Establish the roles of these targets for one selected CholinomiR by tissue-specific manipulations. (3) Study primate-specific CholinomiRs by continued human DNA screens to identify SNPs and in ""humanized"" mice with knocked-in human AChE and transgenic CholinomiR-608. (4) Test if therapeutic modulation of aberrant CholinomiR expression can restore homeostasis. This research will clarify how miRs interact with each other in health and disease, introduce the dimension of complexity of multi-target competition and miR interactions and make a conceptual change in miRs research while enhancing the ability to intervene with diseases involving impaired ACh signalling."

2 375 600 €

Start date: 2013-03-01, End date: 2018-02-28

This five years research proposal is focused on the development of novel information theoretic concepts and techniques and their usage, as to identify the ultimate communications limits and potential of different cloud radio network structures, in which the central signal processing is migrated to the cloud (remote central units), via fronthaul/backhaul infrastructure links. Moreover, it is also directed to introduce and study the optimal or close to optimal strategies for those systems that are to be motivated by the developed theory. We plan to address wireless networks, having future cellular technology in mind, but the basic tools and approaches to be built and researched are relevant to other communication networks as well. Cloud communication networks motivate novel information theoretic views, and perspectives that put backhaul/fronthaul connections in the center, thus deviating considerably from standard theoretical studies of communications links and networks, which are applied to this domain. Our approach accounts for the fact that in such networks information theoretic separation concepts are no longer optimal, hence isolating simple basic components of the network is essentially suboptimal. The proposed view incorporates, in a unified way, under the general cover of information theory: Multi-terminal distributed networks; Basic and timely concepts of distributed coding and communications; Network communications and primarily network coding, Index coding, as associated with interference alignment and caching; Information-Estimation relations and signal processing, addressing the impact of distributed channel state information directly; A variety of fundamental concepts in optimization and random matrix theories. This path provides a natural theoretical framework directed towards better understanding the potential and limitation of cloud networks on one hand and paves the way to innovative communications design principles on the other.

1 981 782 €

Start date: 2016-07-01, End date: 2021-12-31

Computational learning theory has been highly successful over the last three decades, both in providing deep mathematical theories and in influencing the practice of machine learning. One of the great recent successes of computational learning theory has been the study of online learning and multi-arm bandits. This line of research has been highly successful, both theoretically and practically, addressing many important applications. Unfortunately, the recent theoretical progress in Markov Decision Process and reinforcement learning has been slower. Based on my fundamental contributions to reinforcement learning (e.g. policy gradient, sparse sampling and trajectory trees), to online learning and machine learning in general, I propose to take the theoretical and practical success of online learning to the “next level” by making significant breakthroughs in reinforcement learning. Our main aim is to advance the state of the art in the theory of reinforcement learning, and our research will revolve around three pillars: (1) compact representation, (2) efficient computation and (3) societal challenges, including fairness and privacy. A successful project will greatly impact reinforcement learning in all its stages. Modelling: Introducing new compact representation models, will enhance our understanding how to structure complex problems, which would greatly extend the applicability of reinforcement learning. Efficient computation: New algorithmic methodologies will give new insight for overcoming computational and statistical barriers both for planning and learning. Learning: New learning paradigms would address fundamental issues of copping with uncertainties in complex control environments of reinforcement learning. Societal challenges: Allowing the community to understand, assess, address and overcome societal challenges is of the greatest importance to the acceptance of AI methodologies by the general public.

1 878 125 €

Start date: 2020-10-01, End date: 2025-09-30

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

The central dogma in biology often invokes a bottom-up picture of life. However, at different biological scales, new properties in form and function arise that have a superseding causal impact on the behaviour of the lower-scale components from which these new properties emerge. These top-down or reverse scale-crossing effects must be taken into account in order to make predictions about spatiotemporally controlled single-cell fates, activities, levels of gene expression, or the functional outcome of cellular signalling. They can stem from the multicellular, the cellular, and the intracellular scale, and can be quantified using multiscale and multiplexed RNA and protein state imaging in combination with computer vision and data-driven modelling. The ability to comprehensively map these reverse causal effects across multiple scales has the potential to revolutionize most, if not all domains of biology and medicine. In this project, we will establish the importance of reverse causal effects in human induced pluripotent stem cells and early D. rerio embryos. To achieve this, we will develop a quantitative imaging method beyond the diffraction limit of light without compromising scalability in temporal and spatial dimensions. We will also develop a method that achieves scalable, transcriptome-wide image-based multiplexing of mRNA transcripts, and we will extend our computer vision approaches to higher resolution and to three spatial dimensions. These methods will be systematically applied to stem cell collectives grown in 2D and 3D, as well as to early embryos, achieving comprehensive quantification of nuclear and chromatin states, gene expression, subcellular organization, cellular states, and tissue-scale organization across millions of individual cells within the same dataset. These datasets will be used to quantify how, at different scales, new properties in form and function arise that have a superseding causal impact on the behaviour of the lower-scale components

2 411 075 €

Start date: 2020-09-01, End date: 2025-08-31

Today, many industrial products are defined by software and therefore customizable: their functionalities implemented by software can be modified and extended by dynamic software updates on demand. This trend towards customizable products is rapidly expanding into all domains of IT, including Embedded Real-Time Systems (ERTS) deployed in Cyber-Physical Systems such as cars, medical devices etc. However, the current state-of-practice in safety-critical systems allows hardly any modifications once they are put in operation. The lack of techniques to preserve crucial safety conditions for customizable systems severely restricts the benefits of advances in software-defined systems engineering. CUSTOMER is to provide the missing paradigm and technology for building and updating ERTS after deployment – subject to stringent timing constraints, dynamic workloads, and limited resources on complex platforms. CUSTOMER explores research areas crossing two fields: Real-Time Computing and Formal Verification to develop the key techniques enabling (1) dynamic updates of ERTS in the field, (2) incremental updates over the products life time and (3) safe updates by verification to avoid updates that may compromise system safety. CUSTOMER will develop a unified model-based framework supported with tools for the design, modelling, verification, deployment and update of ERTS, aiming at advancing the research fields by establishing the missing scientific foundation for multiprocessor real-time computing and providing the next generation of design tools with significantly enhanced capability and scalability increased by orders of magnitude compared with state-of-the-art tools e.g. UPPAAL.

2 499 894 €

Start date: 2019-10-01, End date: 2024-09-30

We propose to develop a new theory and design tools for the estimation and real-time control of living cells. The control systems designed using these tools will precisely and robustly steer the dynamic behavior of living cells in real time to achieve desired objectives. Cells would be controlled either collectively at the population level, or individually as single cells. The control systems achieving this regulation will be realized either on a digital computer that is interfaced with living cells, or using de novo genetic circuits that are introduced into the cells where they are designed to function as molecular control systems. Our methods will explicitly confront the numerous challenges brought about by the special environment of the cell including nonlinearity, stochasticity, cell-to-cell variability, metabolic burden, etc. The theory and methods developed in this project will thus enable the systematic, rational, and effective feedback control of living cells at the gene level, and will lay the foundation for a new corresponding body of knowledge which we call ``Cybergenetics''. It will also open new research directions in the areas of control theory and estimation. We also propose to design three cybergenetic control systems, each addressing an important application in biotechnology or therapeutics. In the first, the controller will use light and nutrient supply to precisely regulate gene expression and cell growth in E. coli to achieve high protein and low biomass production rates. The second involves multiple feedback controllers regulating in parallel a large number of single stem cells, and leading to their differentiation to desired fates, e.g. beta cells, with potential for therapeutic applications. Finally, we will engineer into living cells dynamic molecular control systems. Such controllers can be used to monitor physiological variables and secrete biological effectors in a feedback fashion for the treatment of diseases like Type 1 diabetes.

2 499 887 €

Start date: 2017-08-01, End date: 2022-07-31

A cell’s decision to die is governed by multiple input signals received from a complex network of programmed cell death (PCD) pathways, including apoptosis and programmed necrosis. Additionally, under some conditions, autophagy, whose function is mainly pro-survival, may act as a back-up death pathway. We propose to apply new approaches to study the molecular basis of two important questions that await resolution in the field: a) how the cell switches from a pro-survival autophagic response to an apoptotic response and b) whether and how pro-survival autophagy is converted to a death mechanism when apoptosis is blocked. To address the first issue, we will screen for direct physical interactions between autophagic and apoptotic proteins, using the protein fragment complementation assay. Validated pairs will be studied in depth to identify built-in molecular switches that activate apoptosis when autophagy fails to restore homeostasis. As a pilot case to address the concept of molecular ‘sensors’ and ‘switches’, we will focus on the previously identified Atg12/Bcl-2 interaction. In the second line of research we will categorize autophagy-dependent cell death triggers into those that directly result from autophagy-dependent degradation, either by excessive self-digestion or by selective protein degradation, and those that utilize the autophagy machinery to activate programmed necrosis. We will identify the genes regulating these scenarios by whole genome RNAi screens for increased cell survival. In parallel, we will use a cell library of annotated fluorescent-tagged proteins for measuring selective protein degradation. These will be the starting point for identification of the molecular pathways that convert survival autophagy to a death program. Finally, we will explore the physiological relevance of back-up death mechanisms and the newly identified molecular mechanisms to developmental PCD during the cavitation process in early stages of embryogenesis.

2 500 000 €

Start date: 2013-03-01, End date: 2018-02-28

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

Measurement based quantum computing is one of the most fault-tolerant architectures proposed for quantum information processing. It opens the possibility of performing quantum computing tasks using linear optical systems. An efficient route for measurement based quantum computing utilizes highly entangled states of photons, called cluster states. Propagation and processing quantum information is made possible this way using only single qubit measurements. It is highly resilient to qubit losses. In addition, single qubit measurements of polarization qubits is easily performed with high fidelity using standard optical tools. These features make photonic clusters excellent platforms for quantum information processing. Constructing photonic cluster states, however, is a formidable challenge, attracting vast amounts of research efforts. While in principle it is possible to build up cluster states using interferometry, such a method is of a probabilistic nature and entails a large overhead of resources. The use of entangled photon pairs reduces this overhead by a small factor only. We outline a novel route for constructing a deterministic source of photonic cluster states using a device based on semiconductor quantum dot. Our proposal follows a suggestion by Lindner and Rudolph. We use repeated optical excitations of a long lived coherent spin confined in a single semiconductor quantum dot and demonstrate for the first time practical realization of their proposal. Our preliminary demonstration presents a breakthrough in quantum technology since deterministic source of photonic cluster, reduces the resources needed quantum information processing. It may have revolutionary prospects for technological applications as well as to our fundamental understanding of quantum systems. We propose to capitalize on this recent breakthrough and concentrate on R&D which will further advance this forefront field of science and technology by utilizing the horizons that it opens.

2 502 974 €

Start date: 2016-06-01, End date: 2021-05-31

Differential gene expression programs account for the diversity of cell types in our body. They are controlled by intricate networks of sequence-specific transcription factors (TFs) that operate in the context of chromatin. Chromatin is itself an essential component of this process, and is part of the system that selectively restricts DNA access for TFs. As a consequence, most TFs only bind to a small subset of their motif occurrences, in a way we currently do not fully understand. Our inability to predict binding of a TF based on its cognate motif and location in the genome is a serious obstacle towards predictive models of gene regulation. DNAccess has the ambitious goal to define in vivo the sensitivities of TFs to nucleosomes and their reliance on chromatin remodeling enzymes for binding. Using novel genomics and genome editing tools we will: (a) systematically vary TF motifs, presence of nucleosomes and their modifications at a defined chromosomal locus and quantify resulting TF binding; (b) explore genome-wide the ability of ectopic TFs to engage with a chromatinized genome in the absence of host cofactor engagement; (c) dissect chromatin remodeler dependent TF binding in order to define temporal order and subcomplex function and (d) deconstruct remodeler recruitment by mutating TF interaction domains. DNAccess will build a highly integrated setup to comprehensively characterize how nucleosomes, their modifications and mobility restricts genome access. We will characterize existing chromatin barriers and identify how TFs overcome them. This represents a crucial step towards a comprehensive understanding of the role of chromatin in gene regulation, and will advance our understanding of how specificity is generated in large eukaryotic genomes.

2 302 500 €

Start date: 2021-03-01, End date: 2026-02-28

Developmental biology seeks not only to learn more about the fundamental processes of growth and pattern per se, but to understand how they synergize to enable the morphogenesis of multicellular organisms. Our goal is to perform real-time analyses of these developmental processes in an intact developing organ. By applying a vital imaging approach, we can circumvent the normal limitations of inferring cellular dynamics from static images or molecular data, and obtain the real dynamic view of growth and patterning. The wing imaginal disc of Drosophila, which starts out as a simple epithelial structure and gives rise to a precisely structured adult limb, will serve as an ideal model system. This system has the combined advantages of relative simplicity and genetic tractability. We will create several innovations that expand the current toolkit and thus facilitate the detailed dissection of growth and patterning. A key early step will be to develop novel reporters to dynamically and faithfully monitor signaling cascades involved in growth and patterning, such as the Dpp and Hippo pathways. We will also implement quantification techniques that are currently being set up in collaboration with an experimental physicist, to deduce, and alter, the mechanical forces that develop in the cells of a growing tissue. The large amount of quantitative data that will be generated allow us derive computational models of the individual pathways and their interaction. The focus of the study will be to answer the following questions: 1) Is the Hippo pathway regulated spatially and temporally, and by what signaling pathways? 2) Do mechanical forces play a pivotal controlling role in organ morphogenesis? 3) What are the global effects on growth, when pathways controlling patterning, cell competition or compensatory proliferation are perturbed? The proposed project will bring the approaches taken to define the mechanisms underlying and controlling growth and patterning to the next level.

2 310 000 €

Start date: 2009-02-01, End date: 2014-01-31

Plants and their pathogens are in a constant process of co-evolution. Consequently, many of the known defense genes of plants against fungal pathogens are rapidly loosing effectiveness under agricultural conditions. However, there are examples for durable resistance. It is one of the main research questions in plant biology to determine the genetic basis of such naturally occurring resistance and to understand the underlying biochemical and molecular cause for durability. This durability is characterized by the apparent inability of the pathogen to adapt to the resistance mechanism. The molecular understanding of durable resistance will contribute to future attempts to develop such resistance by design. We want to use two approaches towards understanding and developing durable resistance: the first one is based on the naturally occurring durable resistance gene Lr34 against rust and mildew diseases in wheat. This gene was recently isolated in our group and it encodes a putative ABC type of transporter protein, providing a possible link between non-host and durable resistance. Its function in resistance will be studied by genetic and biochemical approaches in the crop plant wheat, as there is no Lr34-type of resistance characterized in any other plant. However, there is a close Lr34-homolog in rice and its function will be investigated in this diploid system. The second approach will be based on natural diversity found in a specific resistance gene, conferring strong, but not durable resistance. This diversity will be used for a designed improvement of durability by developing new proteins or protein combinations to which the pathogen can not adapt. We will use the 15 naturally occurring alleles of the Pm3 powdery mildew resistance genes to identify the structural basis of specific interactions. Based on this characterization, we will develop intragenic or gene combination pyramiding strategies to obtain more broad-spectrum and more durable resistance.

2 100 000 €

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

Error correcting codes are combinatorial objects which have traditionally been used to enhance the transmission of data on unreliable media. They have experienced a phenomenal growth since their birth some fifty years ago. Today, everyday tasks such as listening to a CD, accessing the hard disk of an electronic device, talking on a wireless phone, or downloading files from the Internet are impossible without the use of error-correcting codes. Though traditional communication still occupies centerstage in the realm of applied coding theory, emerging applications are changing the rules of the game, and calling for a new type of coding theory capable of addressing future needs. These are not limited to physical applications, however. In fact, coding theory is an integral part of solutions offered by researchers outside traditional physical communication to solve fundamental problems of interest, such as the complexity of computation, reliable transfer of bulk data, cryptographic protocols, self correcting software, signal processing, or even computational biology.While research in the past fifty years has put traditional coding theory on firm theoretical grounds, emerging applications are in need of new tools and methods to design, analyze, and implement coding technologies capable of dealing with future needs. This is the main concern of the present proposal. To strike the right balance between length and impact we have identified five areas of research that span the full spectrum of coding theory ranging from fundamental theoretical aspects to practical applications. We set out to develop new theoretical and practical models for the design and analysis of codes, and explore new application areas hitherto untouched. A unique feature of this proposal is our choice of the tools, ranging from classical areas of algebra, combinatorics, and probability theory, to ideas and methods from theoretical computer science.

1 959 998 €

Start date: 2009-04-01, End date: 2013-03-31

Eco-immunology targets one of the great challenges in biology and medicine - how the immune system has evolved to optimize protection and minimize immunopathology (incl. autoimmune) costs. A primary target of my proposal is to study low-virulent pathogens causing mild infections, which for long have been considered harmless. Recent research suggests that this notion is false and that seemingly harmless pathogens entail delayed (‘hidden’) fitness costs. However, the mechanisms mediating these costs are still unknown. I will experimentally test if accelerated telomere degradation is a causative mechanism through which small immune costs can accumulate and be translated into senescence and reduced Darwinian fitness. Another key target is immune costs, which may be ‘hidden’ because of sexually antagonistic effects, and I will study how this may affect immune gene variation, immune costs and Darwinian fitness. These aspects are central for advancing our understanding of the evolution of disease resistance and immune function, incl. immune over-reactions (autoimmunity). My project exploits a comprehensive 32-year study of great reed warblers to analyze selection patterns in the wild (Fig. 1a), and uses established captive songbird set-ups to conduct carefully designed experiments. The exceptional quality of the long-term data set, together with cutting-edge techniques to measure and manipulate parasite infection, telomere length, oxidative stress and immune gene diversity, provides exciting opportunities to conduct research that previously was unfeasible, pushing the rapidly growing field of eco-immunology (Fig. 1b) to new frontiers. The work integrates theory and methods of evolutionary ecology, immunology and molecular biology, and has broad significance including for e.g. epidemiology and ageing research. I envision my research to change how we look upon causes, consequences (and precautions) of mild infectious, autoimmune and degenerative diseases.

2 500 000 €

Start date: 2017-08-01, End date: 2023-01-31

Man and man-made electronic systems share the same ecosystem, and yet work radically differently. Human metabolism uses ion gradients across insulated membranes to simultaneously process slow analog chemical reactions and communicate information in multicellular systems via soluble/volatile molecular signals. By contrast, electronic systems use multicore central processing units to control the flow of electrons through insulated metal wires with gigahertz frequency and communicate information across networks via wired/wireless connections. With the advent of the internet of things, networks of interconnected electronic devices will reach the processing complexity of living systems, yet they remain largely incompatible with biological systems. Wearable electronics can profile physical parameters such as steps and heartbeat, and Google’s proposal to develop glucose-monitoring contact lenses has triggered a wave of interest in harnessing the full potential of bioelectronics for medical applications. Yet this vision remains limited to diagnostics. Capitalizing on our mind-controlled and smartphone-adjustable optogenetic drug-dosing devices, ElectroGene will establish the foundations of electrogenetics, the science of creating electro-genetic interfaces that enable direct two-way communication between electronic devices and living cells. ElectroGene consists of three pillars, (i) voltage-triggered gene expression, (ii) genetically programmed electronics and (iii) wireless-powered implants providing closed-loop bioelectronic control, which allow real-time monitoring of metabolic conditions (diagnosis), enable remote-controlled production and dosing of protein therapeutics by implanted designer cells (treatment), and manage closed-loop control between cells and electronics, thus linking diagnosis and therapy to block disease onset (prevention). ElectroGene design principles and devices will be validated in proof-of-concept preclinical studies for the treatment of diabetes.

2 500 000 €

Start date: 2018-11-01, End date: 2023-10-31

Epigenetic inheritance is the transmission of information, generally in the form of DNA methylation or post-translational modifications on histones that regulate the availability of underlying genetic information for transcription. RNA itself feeds back to contribute to histone modification. Sequence accessibility is both a matter of folding the chromatin fibre to alter access to recognition motifs, and the local concentration of factors needed for efficient transcriptional initiation, elongation, termination or mRNA stability. In heterochromatin we find a subset of regulatory factors in carefully balanced concentrations that are maintained in part by the segregation of active and inactive domains. Histone H3 K9 methylation is key to this compartmentation. C. elegans provides an ideal system in which to study chromatin-based gene repression. We have demonstrated that histone H3 K9 methylation is the essential signal for the sequestration of heterochromatin at the nuclear envelope in C. elegans. The recognition of H3K9me1/2/3 by an inner nuclear envelope-bound chromodomain protein, CEC-4, actively sequesters heterochromatin in embryos, and contributes redundantly in adult tissues. Epiherigans has the ambitious goal to determine definitively what targets H3K9 methylation, and identify its physiological roles. We will examine how this mark contributes to the epigenetic recognition of repeat vs non-repeat sequence, and mediates a stress-induced response to oxidative damage. We will examine the link between these and the spatial clustering of heterochromatic domains. Epiherigans will develop an integrated approach to identify in vivo the factors that distinguish repeats from non-repeats, self from non-self within genomes and will examine how H3K9me contributes to a persistent ROS or DNA damage stress response. It represents a crucial step towards understanding of how our genomes use heterochromatin to modulate, stabilize and transmit chromatin organization.

2 500 000 €

Start date: 2017-06-01, End date: 2022-05-31

My project focuses on answering one fundamental question: what are the drivers of Life’s morphological complexity and diversity? I claim that this question can only be addressed by a Newtonian-Darwinian synthesis that considers how Evolution exploits the physical properties of living matter. I will investigate how the evolutionary process explores the phase space of possible interactions between physical (mechanics, reaction-diffusion) and biological (cell signalling, proliferation, migration) processes and generates configurations that compute functional phenotypes. In particular, I will combine experiments in biology and physics, as well as mathematical models and Artificial-Life (ALife) numerical simulations. The latter will be based on physics’ first principles, symmetry-breaking processes and a genetic algorithm. First, I will investigate how geometry affects signalling by (i) imaging the embryonic development of colour patterns and skin geometries of multiple squamate species with various scale-to-colour pattern correspondences, (ii) generating CRISPR/Cas9 scaleless mutants in two lizard species to study the effect of skin 3D geometry on colour patterning, and (iii) performing ALife experiments to explore how the evolutionary process can modify signalling events and exploit geometry to generate new patterns. Second, I will analyse how growth can affect geometry by (i) performing in-silico experiments where coupling between growth and morphogenesis is systematically explored and (ii) evaluating how much the in-silico model captures morphologies generated with physics laboratory experiments using 3D layered polymeric gels. Third, I will build a Newtonian-Darwinian framework by coupling geometry, signalling, growth and mechanics in extensive open-ended ALife experiments. The results of the EVOMORPHYS project will constitute a novel framework for understanding how Evolution exploits physics to generate the morphological diversity and complexity of Life forms.

2 499 070 €

Start date: 2019-08-01, End date: 2024-07-31

The ubiquitous FIC domain catalyzes post-translational modifications (PTMs) of target proteins; i.e. adenylylation (=AMPylation) and, more rarely, uridylylation and phosphocholination. Fic proteins are thought to play critical roles in intrinsic signaling processes of prokaryotes and eukaryotes; however, a subset encoded by bacterial pathogens is translocated via dedicated secretion systems into the cytoplasm of mammalian host cells. Some of these host-targeted Fic proteins modify small GTPases leading to collapse of the actin cytoskeleton and other drastic cellular changes. Recently, we described a large set of functionally diverse homologues in pathogens of the genus Bartonella that are required for their “stealth attack” strategy and persistent course of infection [1, 2]. Our preliminary functional analysis of some of these host-targeted Fic proteins of Bartonella demonstrated adenylylation activity towards novel host targets (e.g. tubulin and vimentin). Moreover, in addition to the canonical adenylylation activity they may also display a competing kinase activity resulting from altered ATP binding to the FIC active site. Finally, we described a conserved mechanism of FIC active site auto- inhibition that is relieved by a single amino acid exchange [1], thus facilitating functional analysis of any Fic protein of interest. Despite this recent progress only a few Fic proteins have been functionally characterized to date; our understanding of the functional plasticity of the FIC domain in mediating diverse target PTMs and their specific roles in infection thus remains limited. In this project, we aim to study the vast repertoire of host-targeted Fic proteins of Bartonella to: 1) identify novel target proteins and types of PTMs; 2) study their physiological consequences and molecular mechanisms of action; and 3) analyze structure-function relationships critical for FIC-mediated PTMs and infer from these data determinants of target specificity, type of PTM and mode of regulation. At the forefront of infection biology research, this project is ground-breaking as (i) we will identify a plethora of novel host target PTMs that are critical for a “stealth attack” infection strategy and thus will open new avenues for investigating fundamental mechanisms of persistent infection; and (ii), we will unveil the molecular basis of the remarkable functional versatility of the structurally conserved FIC domain.

1 699 858 €

Start date: 2014-02-01, End date: 2019-01-31

Recent experimental results in flavor physics exhibit deviations from the Standard Model predictions that are growing with time, both as far as statistical significance and as far as internal consistency. Understanding the origin of this phenomenon, the so-called “flavor anomalies”, is of paramount importance for a deeper understanding of fundamental interactions. As recently shown by the PI and collaborators, this phenomenon is likely to be intimately related to the long-standing “flavor problem”, or the origin of the hierarchical pattern of quark and lepton mass matrices observed in Nature. The goal of this project is to shed light on both these issues, providing a solution to old and recent puzzles in flavor physics. We propose to address these questions via an original bottom-up approach, based on Effective Field Theory methods and simplified models, combined with new top-down ideas about the ultraviolet completion of the Standard Model. On the phenomenological side, the proposed bottom-up approach will allow us to exploit with the highest accuracy all the available and expected experimental data. It will allow us to take into account both low- and high-energy observables, as well as both quark and lepton sectors. These results will constitute the basis for the theoretical investigation of a new class of Standard Model extensions not considered so far. The latter are based on new ideas, such as flavor non-universal gauge interactions, that imply a change of paradigm in theoretical high-energy physics: the origin of the flavor hierarchies plays a central role in revealing the ultraviolet completion of the Standard Model. Combining a bottom-up approach to flavor-physics data with top-down ideas on the origin of the flavor hierarchies, this project has the potential to lead to a major advancement in fundamental physics.

2 318 750 €

Start date: 2019-09-01, End date: 2024-08-31

"In recent years, the research focus in signal processing has shifted away from the classical linear paradigm, which is intimately linked with the theory of stationary Gaussian processes. Instead of considering Fourier transforms and performing quadratic optimization, researchers are presently favoring wavelet-like representations and have adopted ”sparsity” as design paradigm. Our ambition is to develop a unifying operator-based framework for signal processing that would provide the ``sparse"" counterpart of the classical theory, which is currently missing. To that end, we shall specify and investigate sparse stochastic processes that are continuously-defined and ruled by differential equations, and construct corresponding wavelet-like sparsifying transforms. Our hope is to be able to rigorously connect non-quadratic regularization and sparsity-constrained optimization to well-defined continuous-domain statistical models. We also want to develop a novel Lie-group formalism for the design of steerable, signal-adapted wavelet transforms with improved invariance and sparsifying properties, both in 2-D and 3-D. We shall use these tools to define new reversible image representations in terms of singular points (contours and keypoints) and to develop novel algorithms for 3-D biomedical image analysis. In close collaboration with imaging scientists, we shall apply our framework to the development of new 3-D reconstruction algorithms for emerging bioimaging modalities such as fluorescence deconvolution microscopy, digital holography microscopy, X-ray phase-contrast microscopy, and advanced MRI."

2 106 994 €

Start date: 2011-04-01, End date: 2016-03-31

In order to explore and exploit the frequency range from 30 GHz up to THz, new types of transmission lines and semiconductor architectures are needed. Conventional microwave technologies that are commonly used below 30 GHz become either too lossy or are too expensive to manufacture, and technologies used in the optical regime are not usable either. The intermediate frequency band is therefore often referred to as the THz gap, indicating the lack of commercialize-able technologies there. Professor Kildal has invented a fundamentally new regime of transmission line, referred to as gap waveguides. The basis is newly discovered local waves appearing in the gap between two conducting surfaces, controlled by a texture in one or both of the surfaces. The gap waveguide has been verified below 20 GHz, but it will be more advantageous in the THz gap. The texture will for THz applications be of submillimeter or micrometer scale, realizable by micromachining or etching. Also, there is no need for a dielectric substrate, and there is no need for conductive contact between the two surfaces. Therefore, such gap waveguides and circuits for the THz gap can be manufactured with low cost. The vision is that the topology of this new regime of gap waveguides will facilitate integration of semiconductor devices, and may lay the foundation for new architectures of transistors and other integrated circuits, being located inside the gap encapsulated by the conductive surfaces themselves. In order to reach this vision new and efficient numerical electromagnetic methods and modeling tools need to be developed, taking advantage of the particular gap waveguide geometry, and being able to connect to or replace the charge transport models for the transistors in the doped semiconductors themselves. The gap waveguide technology can get a tremendous impact on exploring higher frequencies in radio astronomy, communications, and imaging for medical as well as security applications.

1 659 302 €

Start date: 2013-05-01, End date: 2017-04-30

Type 2 diabetes (T2D) affects worldwide at present about 250 million patients and an estimated 380 million in 2025. This epidemic has been ascribed to a collision between genes and an affluent society. Genetics of T2D has during recent years identified > 30 variants increasing susceptibility to T2D. Yet, these variants explain only 15% of the heritability of T2D. One reason could be that whole genome association studies can only detect common variants whereas identification of rare variants with stronger effects would require sequencing. A large part of this application is devoted to sequencing of affected family members from unique large pedigrees traced back to common ancestors around 1600. The advantage of using families is that identified variants can be tested for segregation with the trait. Genetic variants can influence expression of a gene in an allele specific manner. This will be explored by combining exome sequencing with sequencing of RNA from human islets. Impaired effects of the incretin hormones GLP-1 and GIP on the pancreatic islets represent central defects in T2D. Variants in the TCF7L2 and GIPR genes contribute to these defects. I will here explore the molecular mechanisms by which TCF7L2, the strongest T2D gene, causes T2D. GIP has unprecedented effects not only on islet function but also on body composition, blood flow and vascular complications in T2D. This application explores these effects and will test whether manipulation of GIP can mimic the normalization of glucose tolerance seen after gastric bypass surgery. Taken together, these general and targeted approaches are expected not only to provide new insights into the causes of T2D but also contribute with vital information for development of new treatments for T2D.

2 499 480 €

Start date: 2011-05-01, End date: 2016-04-30

A powerful strategy for increasing the quality and resolution of medical and biological images is to acquire larger quantities of data (Fourier samples for MRI, projections for X-ray imaging) and to jointly reconstruct the complete signal by correctly reallocating the measurements in 3D space/time and integrating all the information available. The underlying image sequence is reconstructed globally as the result of a very large-scale optimization that exploits the redundancy of the signal (spatio-temporal correlation, sparsity) to improve the solution. Due to recent advances in the field, we are arguing that such a “bigger data” integration is now within reach and that our team is ideally qualified to lead the way. A successful outcome will profoundly impact the design of future bioimaging systems. We are proposing a unifying framework for the development of such next-generation reconstruction algorithms with a clear separation between the physical (forward model) and signal-related (regularization, incorporation of prior constraints) aspects of the problem. The pillars of our formulation are: an operator algebra with a corresponding set of fast linear solvers; an advanced statistical framework for the principled derivation of reconstruction methods; and learning schemes for parameter optimization and self-tuning. These core technologies will be incorporated into a modular software library featuring the key components for the implementation and testing of iterative reconstruction algorithms. We shall apply our framework to improve upon the state of the art in the following modalities: 1) phase-contrast X-ray tomography in full 3D; 2) structured illumination microscopy; 3) single-particle analysis in cryo-electron tomography; 4) a novel multipose fluorescence microscopy; 5) real-time MRI, and 6) a new multimodal digital microscope. In all instances, we shall work in close collaboration with the imaging scientists who are in charge of the instrumentation.

2 499 515 €

Start date: 2016-10-01, End date: 2022-03-31

The gut is the major interface between microbes and their animal hosts and constitutes the main entry route for pathogens. As a consequence gut cells must be armed with efficient immune defenses to combat invasion and colonisation by pathogens. However, the gut also harbors a flora of commensal bacteria, with potentially beneficial effects for the host, which must be tolerated without a chronic, and harmful, immune response. In recent years Drosophila has emerged as a powerful model to dissect host-pathogen interactions, leading to the paradigm of antimicrobial peptide regulation by the Toll and Imd signaling pathways. The strength of this model derives from the availability of powerful and cost effective genetic and genomic tools as well as the high degree of similarities to vertebrate innate immunity. However, in spite of growing interest in gut mucosal immunity generally, very little is known about the immune response of the Drosophila gut. Using powerful new tools and those developed in the study of the systemic response, we propose to raise our understanding of Drosophila gut immunity to the same level as that of systemic immunity within the next five years. This project will involve integrated approaches to dissect not only the gut immune response but also gut homeostasis in the presence of commensal microbiota, as well as strategies used by entomopathogens to circumvent these defenses. We believe that the fundamental knowledge generated on Drosophila gut immunity will serve as a paradigm of epithelial immune reactivity and have a wider impact on our comprehension of animal defense mechanisms.

1 485 627 €

Start date: 2009-04-01, End date: 2014-03-31

Background Humans and other animals harbour enormous microbial consortia, especially in the lower intestine. My group has now shown that effects of the microbiota on host are far earlier and more pervasive than previously appreciated, starting even before birth from exposure to defined maternal microbial metabolites. Concept There is a critical window for development of immunity and metabolism in early life. This shapes infectious resistance, lymphocyte repertoire development and the likelihood of later autoimmune or inflammatory disease. We will determine the molecular mechanisms of how the maternal microbiota prepares the newborn for the critical fetal/suckling/early-independent-nutrition transitions. The core hypothesis is that generally pervasive effects of maternal microbial influences, so-far investigated only for innate immunity and metabolism of germ-free offspring, can be defined in terms of a clear portfolio of maternal microbial molecular signatures and epigenetic marks as the newborn develops with its own microbiota. Approach Interdependence of microbial ⇄ host interactions during gestation and lactation will be dissected using reversible colonisation systems under axenic and precisely controlled gnotobiotic conditions. The flow and identity of maternal microbial metabolites driving development and shaping incoming colonisation shall be determined from high-resolution metabolomics and host strain combinations that reveal in vivo signalling and epigenetic marks. Significance The project will reveal mechanisms of the earliest phases of mammalian adaptation to a microbiota, the epigenetic effects of maternal microbial metabolites and the resulting potential protection from metabolic disease or immunopathology. Conversely, there are profound effects of early life adaptation on the dynamics of microbial colonisation and the potential blooms and extinctions for the incoming microbiota: the project will define the different mechanisms involved.

2 500 000 €

Start date: 2017-09-01, End date: 2023-08-31

Oxygenic photosynthesis, that takes place in cyanobacteria algae and plants, provides most of the food and fuel on earth. The light stage of this process is driven by two photosystems. Photosystem II (PSII) that oxidizes water to O2 and 4 H+ and photosystem I (PSI) which in the light provides the most negative redox potential in nature that can drive numerous reactions including CO2 assimilation and hydrogen (H2) production. The structure of most of the complexes involved in oxygenic photosynthesis was solved in several laboratories including our own. Utilizing our plant PSI crystals we were able to generate a light dependent electric potential of up to 100 V. We will develop this system for designing biological based photoelectric devices. Recently, we discovered a marine phage that carries an operon encoding all PSI subunits. Generation, in synechocystis, of a phage-like PSI enabled the mutated complex to accept electrons from additional sources like respiratory cytochromes. This way a novel photorespiration, where PSI can substitute for cytochrome oxidase, is created. The wild type and mutant synechocystis PSI were crystallized and solved, confirming the suggested structural consequences. Moreover, several structural alterations in the mesophilic PSI were recorded. We designed a hydrogen producing bioreactor where the novel photorespiration will enable to utilize the organic material of the cell as an electron source for H2 production. We propose that in conjunction of engineering a Cyanobacterium strain with a temperature sensitive PSII, enhancing rates in its respiratory chain an efficient and sustainable hydrogen production can be achieved.

2 487 000 €

Start date: 2012-01-01, End date: 2017-12-31

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

This proposal is focused on the identification and biological validation of the metabolic pathways and key regulatory genes that control insulin sensitivity in Type 2 diabetes mellitus (T2DM). We are focusing on skeletal muscle because it is quantitatively the most important tissue involved in maintaining glucose homeostasis under insulin-stimulated conditions and it is a major site of insulin resistance in T2DM. Our central hypothesis is that alterations in insulin signal transduction to glucose transport contribute to the profound impairment in whole body glucose homeostasis and T2DM pathogenesis. Identification of the defects in T2DM can lead to the development of new therapeutic strategies to prevent and cure this disease. The proposal is divided into two main objectives: We will apply: 1) target identification platforms including microarray, proteomics and bioinformatics to identify dysregulated genes in normal glucose tolerant versus T2DM subjects or genetically modified model systems and 2) functional genomics to assign a physiological role of the identified targets in Aim 1 using cellular and whole-body approaches. We will focus on the mitogen-activated protein kinase family, the energy-sensing enzyme AMP-activated protein kinase, and the lipid intermediate metabolizing enzyme diacylglycerol kinase delta. Our previous work indicates that these candidates play a role in the regulation of glucose metabolism, triglyceride storage, and energy homeostasis.

2 500 000 €

Start date: 2009-01-01, End date: 2013-12-31

Understanding, and ultimately treating Alzheimer’s disease (AD) is a major need in Western countries. Currently, there is no available treatment to modify the disease. Several pioneering discoveries made by my team, attributing a key role to systemic immunity in brain maintenance and repair, and identifying unique interface between the brain’s borders through which the immune system assists the brain, led us to our recent discovery that transient reduction of systemic immune suppression could modify disease pathology, and reverse cognitive loss in mouse models of AD (Nature Communications, 2015; Nature Medicine, 2016; Science, 2014). This discovery emphasizes that AD is not restricted to the brain, but is associated with systemic immune dysfunction. Thus, the goal of addressing numerous risk factors that go awry in the AD brain, many of which are -as yet- unknown, could be accomplished by immunotherapy, using immune checkpoint blockade directed at the Programmed-death (PD)-1 pathway, to empower the immune system. In this proposal, we will adopt our new experimental paradigm to discover mechanisms through which the immune system supports the brain, and to identify key/novel molecular and cellular processes at various stages of the disease that are responsible for cognitive decline long before neurons are lost, and whose reversal or modification is needed to mitigate AD pathology, and prevent cognitive loss. Achieving our goals requires the multidisciplinary approaches and expertise at our disposal, including state-of-the art immunological, cellular, molecular, and genomic tools. The results will pave the way for developing a novel next-generation immunotherapy, by targeting additional selective immune checkpoint pathways, or identifying a specific immune-based therapeutic target, for prevention and treatment of AD. We expect that our results will help attain the ultimate goal of converting an escalating untreatable disease into a chronic treatable one.

2 287 500 €

Start date: 2017-06-01, End date: 2022-11-30

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