ERC FUNDED PROJECTS

Chromosomal DNA is continuously subjected to exogenous and endogenous damaging insults. In the presence of DNA damage cells activate a multi-faceted checkpoint response that delays cell cycle progression and promotes DNA repair. Failures in this response lead to genomic instability, the main feature of cancer cells. Several cancer-prone human syndromes including the Ataxia teleangiectasia (A-T), the A-T Like Disorder (ATLD) and the Seckel Syndrome reflect defects in the specific genes of the DNA damage response such as ATM, MRE11 and ATR. DNA damage response pathways are poorly understood at biochemical level in vertebrate organisms. We have established a cell-free system based on Xenopus laevis egg extract to study molecular events underlying DNA damage response. This is the first in vitro system that recapitulates different aspects of the DNA damage response in vertebrates. Using this system we propose to study the biochemistry of the ATM, ATR and the Mre11 complex dependent DNA damage response. In particular we will: 1) Dissect the signal transduction pathway that senses DNA damage and promotes cell cycle arrest and DNA damage repair; 2) Analyze at molecular level the role of ATM, ATR, Mre11 in chromosomal DNA replication and mitosis during normal and stressful conditions; 3) Identify substrates of the ATM and ATR dependent DNA damage response using an innovative screening procedure.

1 000 000 €

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

An important question of modern neurobiology is how neurons regulate synaptic function in response to excitation. In particular, the roles of alternative pre-mRNA splicing and mRNA translation regulation in this response are poorly understood. We will study the RNA-binding proteins (RBPs) that control these post-transcriptional changes using a UV crosslinking-based purification method (CLIP) and ultra-high throughput sequencing. Computational analysis of the resulting data will define the sequence and structural features of RNA motifs recognized by each RBP. Splicing microarrays and translation reporter assays will then allow us to examine the regulatory functions of RBPs and RNA motifs. By integrating the biochemical and functional datasets, we will relate the position of RNA motifs to the activity of bound RBPs, and predict the interactions that act as central nodes in the regulatory network. The physiological role of these core RBP-RNA interactions will then be tested using antisense RNAs. Together, these projects will provide insights to the regulatory mechanisms underlying neuronal activity-dependent changes, and provide new opportunities for future treatments of neurodegenerative disorders.

900 000 €

Start date: 2008-09-01, End date: 2013-08-31

The project aims to bring about a paradigm shift in our understanding of how the ancients conceived of the universe and its contents over a period of 9 centuries, 600 BC to 300 AD. The driving research hypothesis is that the sole elementary building blocks of nearly all ancient ontologies are powers, from which all there is in the universe is built. Powers are relational properties which are directed towards an end (e.g. the power to heat); thus a world of powers is structured in a web of causal relations. What is revolutionary about such a world is that there is only structure in it; hence, causal structuralist ontologies underlie object-metaphysics or process-metaphysics, and worlds of being and becoming, supplying structures from which objects and processes are derived. Yet such ontologies have never been investigated about ancient thought. The project’s topic is new: ancient causal structuralism; the speciality is novel too, requiring targeted training of a team of post-doc researchers which will be provided by the applicant and collaborators. The innovativeness of the methodology consists in training ancient philosophy researchers to discern and identify formal aspects of ontologies at the very roots of human rationality – discerning how the ancients built everything out of power structures. The paradigm shift will generate new knowledge and understanding about the ancient accounts of the world; provide a heuristic vantage point for redrafting the map of the intellectual influences between ancient thinkers; stimulate fruitful debate; and inspire new insights into ancient thought that are literally unthinkable at present. Cognate disciplines that will be affected by the paradigm shift are such as: history of physics; of mathematics; of theology; ancient anthropology.

1 228 581 €

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

Cellular processes such as cytokinesis, the budding of enveloped retrovirus (e.g. HIV-1), and multivesicular biogenesis have direct links to several human diseases including carcinogenesis and neuro-degeration etc. While seemingly unrelated, these processes all involve membrane abscission for generating two newly formed membrane bound structures - a process aided by the cytosolic proteins collectively termed ESCRT-III. Understanding these processes for therapeutic intervention has so far focused on identification of the factors involved, their structures, and the interactions between them. However, given that membrane-abcission is the key event in all these processes, the mechanics of membrane scission cannot be neglected. Due to fast and highly localised transformations, protein mediated membrane remodelling in general has proven difficult for quantitative mechanistic scrutiny (perhaps with the single exception of dynamin which, unlike the ESCRT-III, acts from the outside of a membrane neck). In humans ESCRT-III members are called CHMPs. Major advances have been recently made in (i) determination of polymeric structures formed by human (yeast) CHMP4 (Snf7), CHMP3 (vps24) and CHMP2A; (ii) membrane splitting activity has been attributed to the sequential binding of the yeast proteins vps20 (CHMP6), Snf7 and vps24, (iii) vps2 (CHMP2), which binds vps24, recruits a AAA ATPAse vps4 which then recycles the membrane bound ESCRT-III. Several models have since been proposed where protein polymers constricting the membrane neck for fission is the common theme. However, there is considerable debate over the essential molecular mechanism of the process. Therefore, I will address: 1. How do CHMP2, 3, 4 and 6 assemblies form on membranes and dissociate in a VPS4 dependent manner? 2. What are the structures, composition and direction of growth of ESCRT-III assemblies as they mature on lipid membranes? 3. Since ESCRT-III polymer must form through the central pore of a membrane tubule, thereby posing a steric hindrance for fusion, how does pore closure followed by scission take place? 4. As CHMPs are predominantly cytosolic, how do their binding partners such as VPS4, AMSH (deubiquitin isopeptidase), and Alix (adaptor molecule) get selectively targeted to the membrane-bound fraction of CHMPs to exert their membrane proximal function? Answering the posed questions will not only advance our understanding of HIV egress from cells, it may also help open new therapeutic intervention points for several ESCRT-III related dysfunction. These studies will further form the basis for in vivo investigation of the mechanism by which ESCRT-III functions.

1 499 655 €

Start date: 2010-10-01, End date: 2016-01-31