ERC FUNDED PROJECTS

Embryogenesis is the temporal unfolding of cellular processes: proliferation, migration, differentiation, morphogenesis, apoptosis and functional specialization. These processes are well understood in specific tissues, and for specific cell types. Nevertheless, our systematic knowledge of the types of cells present in the developing and adult animal, and about their functional and lineage relationships, is limited. For example, there is no consensus on the number of cell types, and many important stem cells and progenitors remain to be discovered. Similarly, the lineage relationships between specific cell types are often poorly characterized. This is particularly true for the mammalian nervous system. We have developed (1) a reliable high-throghput method for sequencing all transcripts in 96 single cells at a time; and (2) a system for high-throughput phylogenetic lineage reconstruction. We now propose to characterize embryogenesis using a shotgun approach borrowed from genomics. Tissues will be dissected from multiple stages and dissociated to single cells. A total of 10,000 cells will be analyzed by RNA sequencing, revealing their functional cell type, their lineage relationships, and their current state (e.g. cell cycle phase). The novel approach proposed here will bring the powerful strategies pioneered in genomics into the field of developmental biology, including automation, digitization, and the random shotgun method. The data thus obtained will bring clarity to the concept of ‘cell type’; will provide a first catalog of mouse brain cell types with deep functional annotation; will provide markers for every cell type, including stem cells; and will serve as a basis for future comparative work, especially with human embryos.

1 496 032 €

Start date: 2010-11-01, End date: 2015-10-31

Two of greatest challenges of the post-genomic era are to (i) develop a detailed understanding of the heritable variation in the human genome, and to (ii) determine which key events in human evolutionary history that are responsible for patterns of genomic variation. The recent genomic revolution will be instrumental in these quests and we will very soon have access to several thousand complete genomes from diverse populations. Extracting genetic information from ancient material has for long been hampered by numerous difficulties after its first steps some two decades ago, but in the last few years, many of these problems have been solved and the use of ancient DNA is now beginning to show its full potential. The use of ancient DNA has been announced among the top-ten ‘insights of the decade’ by Science, and promises to transform our views on human origins and prehistory. The demographic history of Europeans attracts great interest in archaeology, anthropology, and human genetics, and it has drawn extensive research focus for more than a century. The recent genomic revolution has opened up the time dimension for genomic analyses, however, to harness the full potential of genomic data from modern and ancient material, we need new population genetic theory and modern statistical analysis tools. I propose to conduct 3 Ancient Genome Projects to generate complete genomes for multiple individuals from 3 time epochs in the European prehistory; the Cro-Magnon-, the Mesolithic-, and the Neolithic-Genome project. These Genome Projects will proceed in concert with development a) new population genetic theory and novel tools for demographic inference, b) a novel, temporal based, framework for characterizing selection and local adaptation, and c) explore the evolutionary history of gene-variants associated with traits and diseases. Genomic data from temporal samples has the potential to revolutionize our understanding of human evolution and the demographic history of Europe.

1 500 000 €

Start date: 2012-10-01, End date: 2017-09-30

Mental retardation (MR) and schizophrenia (SCZ) are disorders of the brain that affect 2-3% and 1% of the population, respectively. Both disorders are considered to be highly heritable, but exhibit heterogeneous genetic etiology. Recent genetic studies have led to discoveries that the same variants that can give rise to different neuropsychiatric disorders, including MR and SCZ. In this proposal, sequencing will be used to identify novel genes involved in MR and SCZ, and to explore the potential overlap between these disorders. The specific goals of the research plan include: 1. Genetic characterization of patients from large pedigrees with SCZ and MR. Five pedigrees have been collected in which multiple individuals are affected by SCZ or MR. The pedigrees vary in size, with the largest spanning 12 generations including 3,400 individuals. Exome and whole genome sequencing will be performed to identify the genetic variants associated with disease. Candidate genes identified will be screened in large independent cohorts of MR and SCZ patients. In addition, RNA sequencing will be performed on cell lines established for patients and controls from two of the pedigrees. 2. Screening of trios to identify novel genes causing MR Mental retardation (MR) patients are typically referred for array-based analysis. With current genetic screening using microarray, a clinically significant rearrangement is identified in 15-20% of patients. I propose use high throughput sequencing to screen MR patients and their parents with the goal of identifying new MR genes and to investigate to what extent the diagnostic yield can be increased. By combining sequencing, bioinformatics and carefully selected clinical material, the work presented in this proposal will lead to an increased understanding of disease mechanisms and enable the development of novel targets and strategies for molecular diagnostic screening.

1 496 574 €

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

For millennia, people have cut and joined together different plants through a process known as grafting. Plants tissues from different genotypes fuse, vasculature connects and a chimeric organism forms that combines desirable characteristics from different plants such as high yields or disease resistance. However, plants can only be grafted to closely related species and in some instances, they cannot be grafted to themselves. This phenomenon is referred to as graft incompatibility and the mechanistic basis is completely unknown. Our previous work on graft formation in Arabidopsis thaliana has uncovered genes that rapidly activate in grafted tissues to signal the presence of adjoining tissue and initiate a vascular reconnection process. These genes activate around the cut only during graft formation and present a powerful tool to screen large numbers of chemicals and genes that could promote tissue perception and vascular formation. With these sensors and our previously established grafting tools in the model plant Arabidopsis, we can address fundamental questions about grafting biology that have direct relevance to improving graft formation through: 1. Identifying genes required for the recognition response using forward and reverse genetic screens. 2. Determining and characterising signals that activate vascular induction using a chemical genetics screen. 3. Characterising the transcriptional basis for compatibility and incompatibility by analysing tissues and species that graft and comparing these to tissues and species that do not graft. 4. Overcoming graft incompatibility and improving graft formation by applying the knowledge obtained from the three previous objectives. We thus aim to broaden our fundamental understanding of the processes associated with grafting including wound healing, vascular formation and tissue regeneration, while at the same time, use this information to improve graft formation and expand the range of grafted species.

1 499 902 €

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

It is now becoming apparent that genes are regulated not only by transcription, but also by thousands of post-transcriptional regulators that can stabilize or degrade mRNAs. Some of the most important regulators are miRNAs, short RNA molecules that are deeply conserved in sequence and are involved in numerous biological processes, including human disease. Surprisingly, transcriptomic and proteomic studies show that most miRNAs only have subtle silencing effects on their targets, suggesting additional important, but yet undiscovered functions. Thus the question is raised: if the main function of miRNAs is not to silence targets, what is it? I will test two novel hypotheses about miRNA function. The first hypothesis proposes that miRNAs can buffer gene expression noise. The second hypothesis is inspired by my preliminary results and proposes that miRNAs can synchronize expression of genes. If I validate either hypothesis, it would mean that miRNA functions can be investigated in entirely new ways, yielding important new biological insights relevant to both basic research and human health. However, these hypotheses can only be tested in individual cells, and the necessary single-cell technologies and computational tools are only maturing now. I will apply my expertise in miRNA biology and in combined wet-lab and computational methods to design, develop and apply miRCell-seq to test these two hypotheses in cell cultures and in animals. This new method will for the first time measure miRNAs, their targets, and the interactions between them in single cells and transcriptome-wide. We will use mutant cells devoid of miRNAs and time course experiments to generate sufficient data to develop detailed models of the miRNA impact on their targets. We will then validate our findings with single cell proteomics. This project thus has the potential to reveal novel functions of miRNAs and substantially improve our general understanding of gene regulation.

1 497 650 €

Start date: 2018-03-01, End date: 2023-02-28

Semiconductor nanowires composed of III-V materials have enormous potential to add new functionality to electronics and optical applications. However, integration of these promising structures into applications is severely limited by the current near-universal reliance on gold nanoparticles as seeds for nanowire fabrication. Although highly controlled fabrication is achieved, this metal is entirely incompatible with the Si-based electronics industry. It also presents limitations for the extension of nanowire research towards novel materials not existing in bulk. To date, exploration of alternatives has been limited to selective-area and self-seeded processes, both of which have major limitations in terms of size and morphology control, potential to combine materials, and crystal structure tuning. There is also very little understanding of precisely why gold has proven so successful for nanowire growth, and which alternatives may yield comparable or better results. The aim of this project will be to explore alternative nanoparticle seed materials to go beyond the use of gold in III-V nanowire fabrication. This will be achieved using a unique and recently developed capability for aerosol-phase fabrication of highly controlled nanoparticles directly integrated with conventional nanowire fabrication equipment. The primary goal will be to deepen the understanding of the nanowire fabrication process, and the specific advantages (and limitations) of gold as a seed material, in order to develop and optimize alternatives. The use of a wide variety of seed particle materials in nanowire fabrication will greatly broaden the variety of novel structures that can be fabricated. The results will also transform the nanowire fabrication research field, in order to develop important connections between nanowire research and the semiconductor industry, and to greatly improve the viability of nanowire integration into future devices.

1 496 246 €

Start date: 2013-09-01, End date: 2018-08-31

Oxygen (O2) levels can vary enormously in the environment, which induces dramatic behavioral and physiological changes to resident animals. Adaptations to O2 variations can be either acute or sustained. How animals detect and respond to the changes of O2 availability remains elusive at the molecular level. In particular, what is the precise mechanism of acute O2 sensing, what are the primary sensor for acute hypoxia, and why do neurons of various species exhibit completely different sensitivity to hypoxic challenges? The research proposed here aims at addressing these intriguing but challenging questions in the model system nematode C. elegans, which offers unique advantages to systematically dissect O2 sensing at both genetic and neural circuit levels. C. elegans responds dramatically to acute O2 variations by altering its locomotory speed. We will make use of this robust behavioral response to O2 stimulation for high-throughput genetic screens, aiming to identify a collection of molecules critical for acute O2 sensing. These molecules will be subsequently characterized in the context of a well-described nervous system of C. elegans. Our findings will offer the opportunity to shed light on conserved principles of acute O2 sensing that are operating in the O2 sensing systems in humans such as carotid body. In addition to its robust responses to O2 variation, C. elegans exhibits remarkable tolerance to a complete lack of O2, anoxic exposure. My team will thoroughly investigate anoxia tolerance of C. elegans by performing a screen for anoxia-sensitive mutants that has previously been challenging. The discoveries will allow us to delineate the molecular underpinning of anoxia tolerance in C. elegans, and to inspire other researchers to develop better strategies to cope with hypoxic challenges caused by certain diseases such as stroke and ischemia, which are the most causes of human deaths in developed countries.

1 485 000 €

Start date: 2019-01-01, End date: 2023-12-31

Light-emitting diodes (LEDs), which emit light by a solid-state process called electroluminescence, are considered as the most promising energy-efficient technology for future lighting and display. It has been demonstrated that optimal use of LEDs could significantly reduce the world’s electricity use for lighting from 20% to 4%. However, current LED technologies typically rely on expensive high-vacuum manufacturing processes, hampering their widespread applications. Therefore, it is highly desirable to develop low-cost LEDs based on solution-processed semiconductors. A superstar in the family of solution-processed semiconductors is metal halide perovskites, which have shown great success in photovoltaic applications during the past few years. The same perovskites can also been applied in LEDs. Despite being at an early stage of development with associated challenges, metal halide perovskites provide great promise as a new generation of materials for low-cost LEDs. This project aims to develop high-efficiency and stable perovskite LEDs based on solution-processed perovskites. Two different classes of low-dimensional perovskites will be investigated independently. These new perovskites materials will then be coupled with novel interface engineering to fabricate perovskite LEDs with the performance beyond the state of the art. At the core of the research is the synthesis of new perovskite nanostructures, combined with advanced spectroscopic characterization and device development. This project combines recent advances in perovskite optoelectronics and low-dimensional materials to create a new paradigm for perovskite LEDs. This research will also lead to the development of new perovskites materials which will serve future advances in photovoltaics, transistors, lasers, etc.

1 499 759 €

Start date: 2017-03-01, End date: 2022-02-28

This project is aimed at accelerating the synthesis of important organic molecules through key enabling technologies towards automatized catalysis and single-carbon insertion reactions. Transferring the simplest carbon units to organic molecules has the potential to change the way we approach synthesis planning through new asymmetric skeletal homologations and rearrangements of simple raw materials, for which only long workarounds exist now. These methods can reduce to half the manipulations required to access relevant medicines, organocatalysts, ligands, bio-molecular tools and photovoltaic devices. They target unreactive functions to introduce fundamental one-carbon units (CO or C) that are present in virtually any organic compound. New powerful reagents that resemble these basic single-carbon units in excited electronic configurations are to be developed for this purpose. The new catalytic methods needed are based on the solid grounds of carbene-transfer reactions and the recent advances of my group in the development of new homogeneous catalysts. Moreover, a new catalyst platform will be developed to complement our existing portfolio for success in the challenging processes targeted in this proposal. We aim to pioneer a fully automatized workflow for research in catalysis that devoid the synthesis of organic ligands replacing them by combinatorial assemblies built in situ from un-structured simple molecules. The new reactions arising from these new catalysts and reagents will expedite the valorization of raw materials (such as carbonyls, olefins and hydrocarbons) into important chiral molecules in a single transformation. This bold aim is a priority of the European Commission for the coming years as it will save time, protect the environment and reduce cost at once. Thus, these innovative technologies have the potential of transforming the research workflow in homogeneous catalysis and the logics of retrosynthesis of organic molecules at a fundamental level.

1 487 245 €

Start date: 2017-04-01, End date: 2022-03-31

Progress in bioengineering and biomedicine is limited by our inadequate understanding of genetic control systems in living cells. The lack of methods for studying kinetics and gene regulation in single cells seriously impairs our prospects to gain deeper insight to develop better quantitative models of such control systems. This project is focused on transcription factors (TFs), proteins that mediate gene regulation in all kingdoms of life. It aims at understanding how bacterial TFs coordinate the expression of genes at the level of single cells. The experimental challenge of studying TF mediated gene regulation directly is that it is a single molecule process where one or a few TF molecules bind one or a few binding sites on the bacterial chromosome. In addition studying TF kinetics poses two major theoretical challenges: its non-negligible spatial aspects and the stochastic nature of kinetics at the single molecule level. This proposal describes new state-of-the-art single molecule microscopy methods for studying kinetics and diffusion of TFs in living cells. The proposed experimental techniques will be accompanied by pioneering computational methods for stochastic reaction-diffusion modeling of intracellular kinetics. Only by the concomitant advancement of both methodologies will we gain understanding of how transcription factors operate in living cells, how their copy number is maintained, how different classes of TFs optimize their search for chromosomal targets, and how the location of TF genes and binding sites constrain genome evolution. Direct observation of TF dynamics will allow probing gene regulation with unprecedented time resolution. This makes it possible to test hypotheses about coordinated gene regulation which have so far been experimentally inaccessible. The unique combination of single molecule in vivo microscopy and spatially resolved stochastic modeling will advance Europe’s position at the frontier of systems biology.

1 335 000 €

Start date: 2008-07-01, End date: 2013-06-30