ERC FUNDED PROJECTS

In contrast to mammals, newts possess exceptional capacities among vertebrates to rebuild complex structures, such as the brain. Our goal is to bridge the gap in the regenerative outcomes between newts and mammals. My group has made significant contributions towards this goal. We created a novel experimental system, which recapitulates central features of Parkinson’s disease in newts, and provides a unique model for understanding regeneration in the adult midbrain. We showed an unexpected but key feature of the newt brain that it is akin to the mammalian brain in terms of the extent of homeostatic cell turn over, but distinct in terms of its injury response, showing the regenerative capacity of the adult vertebrate brain by activating neurogenesis in normally quiescent regions. Further we established a critical role for the neurotransmitter dopamine in controlling quiescence in the midbrain, thereby preventing neurogenesis during homeostasis and terminating neurogenesis once the correct number of neurons has been produced during regeneration. Here we aim to identify key molecular pathways that regulate adult neurogenesis, to define lineage relationships between neuronal stem and progenitor cells, and to identify essential differences between newts and mammals. We will combine pharmacological modulation of neurotransmitter signaling with extensive cellular fate mapping approaches, and molecular manipulations. Ultimately we will test hypotheses derived from newt studies with mammalian systems including newt/mouse cross species complementation approaches. We expect that our findings will provide new regenerative strategies, and reveal fundamental aspects of cell fate determination, tissue growth, and tissue maintenance in normal and pathological conditions.

1 500 000 €

Start date: 2012-02-01, End date: 2017-01-31

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

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

Bacterial infections represent a major and global health problem, which is further aggravated by the rapid and ongoing increase in antibiotic resistance. The limited success in the development of targeted therapies for particular invasive strains can be attributed to our limited knowledge how pathogens modulate their proteome homeostasis in vivo, knowledge that has so far remained elusive due to technical limitations. Here I propose the use of proteome-wide selected reaction monitoring mass spectrometry (SRM-MS) for pathogen proteome profiling from samples obtained directly from in vivo using group A streptococci (GAS) as a model system. The proposal describes the use of SRM-MS to facilitate the construction of comprehensive and quantitative molecular anatomy knowledge models outlining spatial organization, pathway organization, absolute protein concentration estimations and interaction partners with host for complete microbial proteomes. Using the molecular anatomy as benchmark I intend compare how the proteome homeostasis is controlled in pathogens isolated directly from patients with different degree of disease severity to understand how disease severity, anatomical location and host dependencies effects the proteome homeostasis. The outlined proposal describes a generic strategy to provide comprehensive understanding of the pathogen adaption directly in vivo and represents a paradigm shift in the field of bacterial infectious disease. This proposal addresses central aspects within the medical microbiology field that has been long sought for but never studied due to technology limitations and will influence the development of the next generation targeted vaccine and therapeutic development programs.

1 498 699 €

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

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