ERC FUNDED PROJECTS

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

CRISPR-Cas systems are microbial defense systems that provide prokaryotes with acquired and heritable DNA-based immunity against selfish genetic elements, primarily viruses. However, the full scope of benefits that these systems can provide, as well as their costs remain unknown. Specifically, it is unclear whether the benefits against viral infection outweigh the continual costs incurred even in the absence of parasitic elements, and whether CRISPR-Cas systems affect microbial genome diversity in nature. Since CRISPR-Cas systems can impede lateral gene transfer, it is often assumed that they reduce genetic diversity. Conversely, our recent results suggest the exact opposite: that these systems generate a high level of genomic diversity within populations. We have recently combined genomics of environmental strains and experimental genetics to show that archaea frequently acquire CRISPR immune memory, known as spacers, from chromosomes of related species in the environment. The presence of these spacers reduces gene exchange between lineages, indicating that CRISPR-Cas contributes to diversification. We have also shown that such inter-species mating events induce the acquisition of spacers against a strain's own replicons, supporting a role for CRISPR-Cas systems in generating deletions in natural plasmids and unessential genomic loci, again increasing genome diversity within populations. Here we aim to test our hypothesis that CRISPR-Cas systems increase within-population diversity, and quantify their benefits to both cells and populations, using large-scale genomics and experimental evolution. We will explore how these systems alter the patterns of recombination within and between species, and explore the potential involvement of CRISPR-associated proteins in cellular DNA repair. This work will reveal the eco-evolutionary role of CRISPR-Cas systems in shaping microbial populations, and open new research avenues regarding additional roles beyond anti-viral defense

2 495 625 €

Start date: 2018-05-01, End date: 2023-04-30

Homeostasis of multicellular tissues relies on accurate match of vascular supply and drain to the needs of the tissue. Multiple pathways are involved in detection, signalling and execution of the required steps involved in organization of blood and lymphatic vessels during embryonic development. Similar mechanisms are utilized for overcoming changes in tissue requirements also in adult tissues and in pathological processes. The goal of this work is to reveal the dynamic forces that shape the blood vessels during angiogenesis. In particular, we would like to explore the impact of interstitial convective flow in dynamic imprinting of growth factor signalling, thereby regulating vascular patterning. Angiogenesis is explored here as an example for a possible general role for interstitial convection of growth factors in determination of the fine spatial patterning of tissue morphogenesis in vertebrates. To achieve this goal, we will develop multi-modality tools for imaging the regulation of vascular patterning. In vivo imaging will then be utilized for mapping vascular patterning in pathological and physiological angiogenesis including tumours, wound repair, the preovulatory ovarian follicle and foetal implantation sites. Whole body optical, CT, ultrasound and MRI will be applied for non-invasive imaging of deep organs. Microscopic morphometric and molecular information will be derived from the macroscopic imaging data, using selective molecular imaging approaches and functional imaging tools with specific pharmacological models that will be developed to account for interstitial convective flow. Intravital two photon microscopy and fluorescence endoscopy will be used for high resolution evaluation of vascular patterning. The evaluation of novel mechanisms for spatial regulation of intercellular growth factor signalling, will allow us to define new potential targets for intervention, and to develop new tools for preclinical and clinical imaging of angiogenesis.

2 278 344 €

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

Small RNAs (sRNAs) are major regulators of gene expression in bacteria, exerting their regulation in trans by base pairing with target RNAs. Traditionally, sRNAs were considered post-transcriptional regulators, mainly regulating translation by blocking or exposing the ribosome binding site. However, accumulating evidence suggest that sRNAs can exploit the base pairing to manipulate their targets in different ways, assisting or interfering with various molecular processes involving the target RNA. Currently there are a few examples of these alternative regulation modes, but their extent and implications in the cellular circuitry have not been assessed. Here we propose to take advantage of the power of RNA-seq-based technologies to develop innovative approaches to address these challenges transcriptome-wide. These approaches will enable us to map the regulatory mechanism a sRNA employs per target through its effect on a certain molecular process. For feasibility we propose studying three processes: RNA cleavage by RNase E, pre-mature Rho-dependent transcription termination, and transcription elongation pausing. Finding targets regulated by sRNA manipulation of the two latter processes would be especially intriguing, as it would suggest that sRNAs can function as gene-specific transcription regulators (alluded to by our preliminary results). As a basis of our research we will use the network of ~2400 sRNA-target pairs in Escherichia coli, deciphered by RIL-seq (a method we recently developed for global in vivo detection of sRNA targets). Revealing the regulatory mechanism(s) employed per target will shed light on the principles underlying the integration of distinct sRNA regulation modes in specific regulatory circuits and cellular contexts, with direct implications to synthetic biology and pathogenic bacteria. Our study may change the way sRNAs are perceived, from post-transcriptional to versatile regulators that apply different regulation modes to different targets.

2 278 125 €

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