Project acronym ARGO
Project The Quest of the Argonautes - from Myth to Reality
Researcher (PI) JOHN VAN DER OOST
Host Institution (HI) WAGENINGEN UNIVERSITY
Call Details Advanced Grant (AdG), LS1, ERC-2018-ADG
Summary Argonaute nucleases are key players of the eukaryotic RNA interference (RNAi) system. Using small RNA guides, these Argonaute (Ago) proteins specifically target complementary RNA molecules, resulting in regulation of a wide range of crucial processes, including chromosome organization, gene expression and anti-virus defence. Since 2010, my research team has studied closely-related prokaryotic Argonaute (pAgo) variants. This has revealed spectacular mechanistic variations: several thermophilic pAgos catalyse DNA-guided cleavage of double stranded DNA, but only at elevated temperatures. Interestingly, a recently discovered mesophilic Argonaute (CbAgo) can generate double strand DNA breaks at moderate temperatures, providing an excellent basis for this ARGO project. In addition, genome analysis has revealed many distantly-related Argonaute variants, often with unique domain architectures. Hence, the currently known Argonaute homologs are just the tip of the iceberg, and the stage is set for making a big leap in the exploration of the Argonaute family. Initially we will dissect the molecular basis of functional and mechanistic features of uncharacterized natural Argonaute variants, both in eukaryotes (the presence of an Ago-like subunit in the Mediator complex, strongly suggests a regulatory role of an elusive non-coding RNA ligand) and in prokaryotes (selected Ago variants possess distinct domains indicating novel functionalities). After their thorough biochemical characterization, I aim at engineering the functionality of the aforementioned CbAgo through an integrated rational & random approach, i.e. by tinkering of domains, and by an unprecedented in vitro laboratory evolution approach. Eventually, natural & synthetic Argonautes will be selected for their exploitation, and used for developing original genome editing applications (from silencing to base editing). Embarking on this ambitious ARGO expedition will lead us to many exciting discoveries.
Summary
Argonaute nucleases are key players of the eukaryotic RNA interference (RNAi) system. Using small RNA guides, these Argonaute (Ago) proteins specifically target complementary RNA molecules, resulting in regulation of a wide range of crucial processes, including chromosome organization, gene expression and anti-virus defence. Since 2010, my research team has studied closely-related prokaryotic Argonaute (pAgo) variants. This has revealed spectacular mechanistic variations: several thermophilic pAgos catalyse DNA-guided cleavage of double stranded DNA, but only at elevated temperatures. Interestingly, a recently discovered mesophilic Argonaute (CbAgo) can generate double strand DNA breaks at moderate temperatures, providing an excellent basis for this ARGO project. In addition, genome analysis has revealed many distantly-related Argonaute variants, often with unique domain architectures. Hence, the currently known Argonaute homologs are just the tip of the iceberg, and the stage is set for making a big leap in the exploration of the Argonaute family. Initially we will dissect the molecular basis of functional and mechanistic features of uncharacterized natural Argonaute variants, both in eukaryotes (the presence of an Ago-like subunit in the Mediator complex, strongly suggests a regulatory role of an elusive non-coding RNA ligand) and in prokaryotes (selected Ago variants possess distinct domains indicating novel functionalities). After their thorough biochemical characterization, I aim at engineering the functionality of the aforementioned CbAgo through an integrated rational & random approach, i.e. by tinkering of domains, and by an unprecedented in vitro laboratory evolution approach. Eventually, natural & synthetic Argonautes will be selected for their exploitation, and used for developing original genome editing applications (from silencing to base editing). Embarking on this ambitious ARGO expedition will lead us to many exciting discoveries.
Max ERC Funding
2 177 158 €
Duration
Start date: 2019-07-01, End date: 2024-06-30
Project acronym ASAP
Project Thylakoid membrane in action: acclimation strategies in algae and plants
Researcher (PI) Roberta Croce
Host Institution (HI) STICHTING VU
Call Details Starting Grant (StG), LS1, ERC-2011-StG_20101109
Summary Life on earth is sustained by the process that converts sunlight energy into chemical energy: photosynthesis. This process is operating near the boundary between life and death: if the absorbed energy exceeds the capacity of the metabolic reactions, it can result in photo-oxidation events that can cause the death of the organism. Over-excitation is happening quite often: oxygenic organisms are exposed to (drastic) changes in environmental conditions (light intensity, light quality and temperature), which influence the physical (light-harvesting) and chemical (enzymatic reactions) parts of the photosynthetic process to a different extent, leading to severe imbalances. However, daily experience tells us that plants are able to deal with most of these situations, surviving and happily growing. How do they manage? The photosynthetic membrane is highly flexible and it is able to change its supramolecular organization and composition and even the function of some of its components on a time scale as fast as a few seconds, thereby regulating the light-harvesting capacity. However, the structural/functional changes in the membrane are far from being fully characterized and the molecular mechanisms of their regulation are far from being understood. This is due to the fact that all these mechanisms require the simultaneous presence of various factors and thus the system should be analyzed at a high level of complexity; however, to obtain molecular details of a very complex system as the thylakoid membrane in action has not been possible so far. Over the last years we have developed and optimized a range of methods that now allow us to take up this challenge. This involves a high level of integration of biological and physical approaches, ranging from plant transformation and in vivo knock out of individual pigments to ultrafast-spectroscopy in a mix that is rather unique for my laboratory and will allow us to unravel the photoprotective mechanisms in algae and plants.
Summary
Life on earth is sustained by the process that converts sunlight energy into chemical energy: photosynthesis. This process is operating near the boundary between life and death: if the absorbed energy exceeds the capacity of the metabolic reactions, it can result in photo-oxidation events that can cause the death of the organism. Over-excitation is happening quite often: oxygenic organisms are exposed to (drastic) changes in environmental conditions (light intensity, light quality and temperature), which influence the physical (light-harvesting) and chemical (enzymatic reactions) parts of the photosynthetic process to a different extent, leading to severe imbalances. However, daily experience tells us that plants are able to deal with most of these situations, surviving and happily growing. How do they manage? The photosynthetic membrane is highly flexible and it is able to change its supramolecular organization and composition and even the function of some of its components on a time scale as fast as a few seconds, thereby regulating the light-harvesting capacity. However, the structural/functional changes in the membrane are far from being fully characterized and the molecular mechanisms of their regulation are far from being understood. This is due to the fact that all these mechanisms require the simultaneous presence of various factors and thus the system should be analyzed at a high level of complexity; however, to obtain molecular details of a very complex system as the thylakoid membrane in action has not been possible so far. Over the last years we have developed and optimized a range of methods that now allow us to take up this challenge. This involves a high level of integration of biological and physical approaches, ranging from plant transformation and in vivo knock out of individual pigments to ultrafast-spectroscopy in a mix that is rather unique for my laboratory and will allow us to unravel the photoprotective mechanisms in algae and plants.
Max ERC Funding
1 696 961 €
Duration
Start date: 2011-12-01, End date: 2017-11-30
Project acronym ASAP
Project Adaptive Security and Privacy
Researcher (PI) Bashar Nuseibeh
Host Institution (HI) THE OPEN UNIVERSITY
Call Details Advanced Grant (AdG), PE6, ERC-2011-ADG_20110209
Summary With the prevalence of mobile computing devices and the increasing availability of pervasive services, ubiquitous computing (Ubicomp) is a reality for many people. This reality is generating opportunities for people to interact socially in new and richer ways, and to work more effectively in a variety of new environments. More generally, Ubicomp infrastructures – controlled by software – will determine users’ access to critical services.
With these opportunities come higher risks of misuse by malicious agents. Therefore, the role and design of software for managing use and protecting against misuse is critical, and the engineering of software that is both functionally effective while safe guarding user assets from harm is a key challenge. Indeed the very nature of Ubicomp means that software must adapt to the changing needs of users and their environment, and, more critically, to the different threats to users’ security and privacy.
ASAP proposes to radically re-conceptualise software engineering for Ubicomp in ways that are cognisant of the changing functional needs of users, of the changing threats to user assets, and of the changing relationships between them. We propose to deliver adaptive software capabilities for supporting users in managing their privacy requirements, and adaptive software capabilities to deliver secure software that underpin those requirements. A key novelty of our approach is its holistic treatment of security and human behaviour. To achieve this, it draws upon contributions from requirements engineering, security & privacy engineering, and human-computer interaction. Our aim is to contribute to software engineering that empowers and protects Ubicomp users. Underpinning our approach will be the development of representations of security and privacy problem structures that capture user requirements, the context in which those requirements arise, and the adaptive software that aims to meet those requirements.
Summary
With the prevalence of mobile computing devices and the increasing availability of pervasive services, ubiquitous computing (Ubicomp) is a reality for many people. This reality is generating opportunities for people to interact socially in new and richer ways, and to work more effectively in a variety of new environments. More generally, Ubicomp infrastructures – controlled by software – will determine users’ access to critical services.
With these opportunities come higher risks of misuse by malicious agents. Therefore, the role and design of software for managing use and protecting against misuse is critical, and the engineering of software that is both functionally effective while safe guarding user assets from harm is a key challenge. Indeed the very nature of Ubicomp means that software must adapt to the changing needs of users and their environment, and, more critically, to the different threats to users’ security and privacy.
ASAP proposes to radically re-conceptualise software engineering for Ubicomp in ways that are cognisant of the changing functional needs of users, of the changing threats to user assets, and of the changing relationships between them. We propose to deliver adaptive software capabilities for supporting users in managing their privacy requirements, and adaptive software capabilities to deliver secure software that underpin those requirements. A key novelty of our approach is its holistic treatment of security and human behaviour. To achieve this, it draws upon contributions from requirements engineering, security & privacy engineering, and human-computer interaction. Our aim is to contribute to software engineering that empowers and protects Ubicomp users. Underpinning our approach will be the development of representations of security and privacy problem structures that capture user requirements, the context in which those requirements arise, and the adaptive software that aims to meet those requirements.
Max ERC Funding
2 499 041 €
Duration
Start date: 2012-10-01, End date: 2018-09-30
Project acronym ASC3
Project Asymmetric Cluster Catalysis & Chemistry
Researcher (PI) Ulrich Kaspar Heiz
Host Institution (HI) TECHNISCHE UNIVERSITAET MUENCHEN
Call Details Advanced Grant (AdG), PE4, ERC-2009-AdG
Summary The objective of the present scientific proposal is the implementation of a novel approach in selective and asymmetric heterogeneous catalysis. We aim to exploit the structure and chirality of small, supported metal and bimetal clusters for triggering selective and enantioselective reactions. Our Ansatz is beyond doubt of fundamental nature. Although chemistry and in particular catalysis evolved on a largely empirical basis in the past, we strongly believe the complexity of the challenges at hand to make this a less ideal approach. In consequence, developing selective and asymmetric cluster catalysis will be based on a detailed molecular understanding and will not only require intense methodological developments for the synthesis and characterization of asymmetric catalysts and the detection of chiral and isomeric product molecules but also make use of innovative basic science in the fields of surface chemistry, cluster science, spectroscopy and kinetics. As complex as the involved challenges are, we aim at mastering the following ground-breaking steps: (a) development of cutting-edge spectroscopic methodologies for the isomer and enantiomer sensitive in situ detection of product molecules. (b) preparation and characterization of isomer- and enantioselective heterogeneous catalysts based on chiral metal clusters or molecule-cluster-complexes. (c) investigations of the selectivity and enantioselectivity of cluster based heterogeneous catalysts and formulation of concepts for understanding the observed selective and asymmetric chemistry.
Besides the importance of the science carried out within this proposal, the proposed experimental methodology will also open up opportunities in other fields of chemistry like catalysis, analytical chemistry, spectroscopy, surface science, and nanomaterials.
Summary
The objective of the present scientific proposal is the implementation of a novel approach in selective and asymmetric heterogeneous catalysis. We aim to exploit the structure and chirality of small, supported metal and bimetal clusters for triggering selective and enantioselective reactions. Our Ansatz is beyond doubt of fundamental nature. Although chemistry and in particular catalysis evolved on a largely empirical basis in the past, we strongly believe the complexity of the challenges at hand to make this a less ideal approach. In consequence, developing selective and asymmetric cluster catalysis will be based on a detailed molecular understanding and will not only require intense methodological developments for the synthesis and characterization of asymmetric catalysts and the detection of chiral and isomeric product molecules but also make use of innovative basic science in the fields of surface chemistry, cluster science, spectroscopy and kinetics. As complex as the involved challenges are, we aim at mastering the following ground-breaking steps: (a) development of cutting-edge spectroscopic methodologies for the isomer and enantiomer sensitive in situ detection of product molecules. (b) preparation and characterization of isomer- and enantioselective heterogeneous catalysts based on chiral metal clusters or molecule-cluster-complexes. (c) investigations of the selectivity and enantioselectivity of cluster based heterogeneous catalysts and formulation of concepts for understanding the observed selective and asymmetric chemistry.
Besides the importance of the science carried out within this proposal, the proposed experimental methodology will also open up opportunities in other fields of chemistry like catalysis, analytical chemistry, spectroscopy, surface science, and nanomaterials.
Max ERC Funding
2 301 600 €
Duration
Start date: 2010-04-01, End date: 2015-03-31
Project acronym aSCEND
Project Secure Computation on Encrypted Data
Researcher (PI) Hoe Teck Wee
Host Institution (HI) CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
Call Details Starting Grant (StG), PE6, ERC-2014-STG
Summary Recent trends in computing have prompted users and organizations to store an increasingly large amount of sensitive data at third party locations in the cloud outside of their direct control. Storing data remotely poses an acute security threat as these data are outside our control and could potentially be accessed by untrusted parties. Indeed, the reality of these threats have been borne out by the Snowden leaks and hundreds of data breaches each year. In order to protect our data, we will need to encrypt it.
Functional encryption is a novel paradigm for public-key encryption that enables both fine-grained access control and selective computation on encrypted data, as is necessary to protect big, complex data in the cloud. Functional encryption also enables searches on encrypted travel records and surveillance video as well as medical studies on encrypted medical records in a privacy-preserving manner; we can give out restricted secret keys that reveal only the outcome of specific searches and tests. These mechanisms allow us to maintain public safety without compromising on civil liberties, and to facilitate medical break-throughs without compromising on individual privacy.
The goals of the aSCEND project are (i) to design pairing and lattice-based functional encryption that are more efficient and ultimately viable in practice; and (ii) to obtain a richer understanding of expressive functional encryption schemes and to push the boundaries from encrypting data to encrypting software. My long-term vision is the ubiquitous use of functional encryption to secure our data and our computation, just as public-key encryption is widely used today to secure our communication. Realizing this vision requires new advances in the foundations of functional encryption, which is the target of this project.
Summary
Recent trends in computing have prompted users and organizations to store an increasingly large amount of sensitive data at third party locations in the cloud outside of their direct control. Storing data remotely poses an acute security threat as these data are outside our control and could potentially be accessed by untrusted parties. Indeed, the reality of these threats have been borne out by the Snowden leaks and hundreds of data breaches each year. In order to protect our data, we will need to encrypt it.
Functional encryption is a novel paradigm for public-key encryption that enables both fine-grained access control and selective computation on encrypted data, as is necessary to protect big, complex data in the cloud. Functional encryption also enables searches on encrypted travel records and surveillance video as well as medical studies on encrypted medical records in a privacy-preserving manner; we can give out restricted secret keys that reveal only the outcome of specific searches and tests. These mechanisms allow us to maintain public safety without compromising on civil liberties, and to facilitate medical break-throughs without compromising on individual privacy.
The goals of the aSCEND project are (i) to design pairing and lattice-based functional encryption that are more efficient and ultimately viable in practice; and (ii) to obtain a richer understanding of expressive functional encryption schemes and to push the boundaries from encrypting data to encrypting software. My long-term vision is the ubiquitous use of functional encryption to secure our data and our computation, just as public-key encryption is widely used today to secure our communication. Realizing this vision requires new advances in the foundations of functional encryption, which is the target of this project.
Max ERC Funding
1 253 893 €
Duration
Start date: 2015-06-01, End date: 2020-05-31
Project acronym ASES
Project "Advancing computational chemistry with new accurate, robust and scalable electronic structure methods"
Researcher (PI) Hans-Joachim Werner
Host Institution (HI) UNIVERSITAET STUTTGART
Call Details Advanced Grant (AdG), PE4, ERC-2012-ADG_20120216
Summary "The objective of this proposal is to tackle two of the greatest challenges in quantum chemistry: (i) extending the applicability of highly accurate wave function methods to large molecular systems, and (ii) developing accurate and robust multi-reference methods that can be used for studying important but very difficult problems in transition metal chemistry, catalysis, and photochemistry. Solutions to these problems have now come within reach due to three advances we recently reported: first, the steep scaling of the computational cost with molecular size can be reduced to linear by exploiting the short-range character of electron correlation (local correlation methods). Second, the accuracy, efficiency, and robustness of these local correlation methods can be strongly improved by new tensor decomposition approaches and the inclusion of terms depending explicitly on the inter-electronic distances (F12 methods). Third, the development of highly complex electronic structure theories can be greatly facilitated and accelerated by new automated tensor network evaluation techniques. We are certain that by combining and generalizing these advances the long-standing problems (i) and (ii) can be solved. We will focus especially on highly scalable algorithms in order to use massively parallel computer systems efficiently. For linear-scaling methods this means that the size of the molecules that can be treated in a fixed time will grow linearly with the number of available processors. We will furthermore explore new multi-reference ansätze and implement analytical energy gradients and response properties for local methods. Hybrid and embedding methods to account for solvent and environment effects will also be investigated. It is our priority to make our new methods as easy to use, robust, and widely applicable as possible. We believe that they will open entirely new horizons for innumerable applications in chemistry, physics, biology, and materials science."
Summary
"The objective of this proposal is to tackle two of the greatest challenges in quantum chemistry: (i) extending the applicability of highly accurate wave function methods to large molecular systems, and (ii) developing accurate and robust multi-reference methods that can be used for studying important but very difficult problems in transition metal chemistry, catalysis, and photochemistry. Solutions to these problems have now come within reach due to three advances we recently reported: first, the steep scaling of the computational cost with molecular size can be reduced to linear by exploiting the short-range character of electron correlation (local correlation methods). Second, the accuracy, efficiency, and robustness of these local correlation methods can be strongly improved by new tensor decomposition approaches and the inclusion of terms depending explicitly on the inter-electronic distances (F12 methods). Third, the development of highly complex electronic structure theories can be greatly facilitated and accelerated by new automated tensor network evaluation techniques. We are certain that by combining and generalizing these advances the long-standing problems (i) and (ii) can be solved. We will focus especially on highly scalable algorithms in order to use massively parallel computer systems efficiently. For linear-scaling methods this means that the size of the molecules that can be treated in a fixed time will grow linearly with the number of available processors. We will furthermore explore new multi-reference ansätze and implement analytical energy gradients and response properties for local methods. Hybrid and embedding methods to account for solvent and environment effects will also be investigated. It is our priority to make our new methods as easy to use, robust, and widely applicable as possible. We believe that they will open entirely new horizons for innumerable applications in chemistry, physics, biology, and materials science."
Max ERC Funding
2 454 000 €
Duration
Start date: 2013-02-01, End date: 2018-01-31
Project acronym assemblyNMR
Project 3D structures of bacterial supramolecular assemblies by solid-state NMR
Researcher (PI) Adam Lange
Host Institution (HI) FORSCHUNGSVERBUND BERLIN EV
Call Details Starting Grant (StG), LS1, ERC-2013-StG
Summary Supramolecular assemblies – formed by the self-assembly of hundreds of protein subunits – are part of bacterial nanomachines involved in key cellular processes. Important examples in pathogenic bacteria are pili and type 3 secretion systems (T3SS) that mediate adhesion to host cells and injection of virulence proteins. Structure determination at atomic resolution of such assemblies by standard techniques such as X-ray crystallography or solution NMR is severely limited: Intact T3SSs or pili cannot be crystallized and are also inherently insoluble. Cryo-electron microscopy techniques have recently made it possible to obtain low- and medium-resolution models, but atomic details have not been accessible at the resolution obtained in these studies, leading sometimes to inaccurate models.
I propose to use solid-state NMR (ssNMR) to fill this knowledge-gap. I could recently show that ssNMR on in vitro preparations of Salmonella T3SS needles constitutes a powerful approach to study the structure of this virulence factor. Our integrated approach also included results from electron microscopy and modeling as well as in vivo assays (Loquet et al., Nature 2012). This is the foundation of this application. I propose to extend ssNMR methodology to tackle the structures of even larger or more complex homo-oligomeric assemblies with up to 200 residues per monomeric subunit. We will apply such techniques to address the currently unknown 3D structures of type I pili and cytoskeletal bactofilin filaments. Furthermore, I want to develop strategies to directly study assemblies in a native-like setting. As a first application, I will study the 3D structure of T3SS needles when they are complemented with intact T3SSs purified from Salmonella or Shigella. The ultimate goal of this proposal is to establish ssNMR as a generally applicable method that allows solving the currently unknown structures of bacterial supramolecular assemblies at atomic resolution.
Summary
Supramolecular assemblies – formed by the self-assembly of hundreds of protein subunits – are part of bacterial nanomachines involved in key cellular processes. Important examples in pathogenic bacteria are pili and type 3 secretion systems (T3SS) that mediate adhesion to host cells and injection of virulence proteins. Structure determination at atomic resolution of such assemblies by standard techniques such as X-ray crystallography or solution NMR is severely limited: Intact T3SSs or pili cannot be crystallized and are also inherently insoluble. Cryo-electron microscopy techniques have recently made it possible to obtain low- and medium-resolution models, but atomic details have not been accessible at the resolution obtained in these studies, leading sometimes to inaccurate models.
I propose to use solid-state NMR (ssNMR) to fill this knowledge-gap. I could recently show that ssNMR on in vitro preparations of Salmonella T3SS needles constitutes a powerful approach to study the structure of this virulence factor. Our integrated approach also included results from electron microscopy and modeling as well as in vivo assays (Loquet et al., Nature 2012). This is the foundation of this application. I propose to extend ssNMR methodology to tackle the structures of even larger or more complex homo-oligomeric assemblies with up to 200 residues per monomeric subunit. We will apply such techniques to address the currently unknown 3D structures of type I pili and cytoskeletal bactofilin filaments. Furthermore, I want to develop strategies to directly study assemblies in a native-like setting. As a first application, I will study the 3D structure of T3SS needles when they are complemented with intact T3SSs purified from Salmonella or Shigella. The ultimate goal of this proposal is to establish ssNMR as a generally applicable method that allows solving the currently unknown structures of bacterial supramolecular assemblies at atomic resolution.
Max ERC Funding
1 456 000 €
Duration
Start date: 2014-05-01, End date: 2019-04-30
Project acronym ASSIMILES
Project Advanced Spectroscopy and Spectrometry for Imaging Metabolism using Isotopically-Labeled Endogenous Substrates
Researcher (PI) Arnaud Comment
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Call Details Consolidator Grant (CoG), PE4, ERC-2015-CoG
Summary A technological revolution is currently taking place making it possible to noninvasively study metabolism in mammals (incl. humans) in vivo with unprecedented temporal and spatial resolution. Central to these developments is the phenomenon of hyperpolarization, which transiently enhances the magnetic resonance (MR) signals so much that real-time metabolic imaging and spectroscopy becomes possible. The first clinical translation of hyperpolarization MR technology has recently been demonstrated with prostate cancer patients.
I have played an active role in these exciting developments, through design and construction of hyperpolarization MR setups that are defining the cutting-edge for in vivo preclinical metabolic studies. However, important obstacles still exist for the technology to fulfill its enormous potential.
With this highly interdisciplinary proposal, I will overcome the principal drawbacks of current hyperpolarization technology, namely: 1) A limited time window for hyperpolarized MR detection; 2) The conventional use of potentially toxic polarizing agents; 3) The necessity to use supra-physiological doses of metabolic substrates to reach detectable MR signal
I will develop a novel hyperpolarization instrument making use of photoexcited compounds as polarizing agents to produce hyperpolarized solutions containing exclusively endogenous compounds. It will become possible to deliver hyperpolarized solutions in a quasi-continuous manner, permitting infusion of physiological doses and greatly increasing sensitivity. I will also use a complementary isotope imaging technique, the so-called CryoNanoSIMS (developed at my institution over the last year), which can image isotopic distributions in frozen tissue sections and reveal the localization of injected substrates and their metabolites with subcellular spatial resolution. Case studies will include liver and brain cancer mouse models. This work is pioneering and will create a new frontier in molecular imaging.
Summary
A technological revolution is currently taking place making it possible to noninvasively study metabolism in mammals (incl. humans) in vivo with unprecedented temporal and spatial resolution. Central to these developments is the phenomenon of hyperpolarization, which transiently enhances the magnetic resonance (MR) signals so much that real-time metabolic imaging and spectroscopy becomes possible. The first clinical translation of hyperpolarization MR technology has recently been demonstrated with prostate cancer patients.
I have played an active role in these exciting developments, through design and construction of hyperpolarization MR setups that are defining the cutting-edge for in vivo preclinical metabolic studies. However, important obstacles still exist for the technology to fulfill its enormous potential.
With this highly interdisciplinary proposal, I will overcome the principal drawbacks of current hyperpolarization technology, namely: 1) A limited time window for hyperpolarized MR detection; 2) The conventional use of potentially toxic polarizing agents; 3) The necessity to use supra-physiological doses of metabolic substrates to reach detectable MR signal
I will develop a novel hyperpolarization instrument making use of photoexcited compounds as polarizing agents to produce hyperpolarized solutions containing exclusively endogenous compounds. It will become possible to deliver hyperpolarized solutions in a quasi-continuous manner, permitting infusion of physiological doses and greatly increasing sensitivity. I will also use a complementary isotope imaging technique, the so-called CryoNanoSIMS (developed at my institution over the last year), which can image isotopic distributions in frozen tissue sections and reveal the localization of injected substrates and their metabolites with subcellular spatial resolution. Case studies will include liver and brain cancer mouse models. This work is pioneering and will create a new frontier in molecular imaging.
Max ERC Funding
2 199 146 €
Duration
Start date: 2016-09-01, End date: 2021-08-31
Project acronym ASTROROT
Project Unraveling interstellar chemistry with broadband microwave spectroscopy and next-generation telescope arrays
Researcher (PI) Melanie Schnell-Küpper
Host Institution (HI) STIFTUNG DEUTSCHES ELEKTRONEN-SYNCHROTRON DESY
Call Details Starting Grant (StG), PE4, ERC-2014-STG
Summary The goal of the research program, ASTROROT, is to significantly advance the knowledge of astrochemistry by exploring its molecular complexity and by discovering new molecule classes and key chemical processes in space. So far, mostly physical reasons were investigated for the observed variations in molecular abundances. We here propose to study the influence of chemistry on the molecular composition of the universe by combining unprecedentedly high-quality laboratory spectroscopy and pioneering telescope observations. Array telescopes provide new observations of rotational molecular emission, leading to an urgent need for microwave spectroscopic data of exotic molecules. We will use newly developed, unique broadband microwave spectrometers with the cold conditions of a molecular jet and the higher temperatures of a waveguide to mimic different interstellar conditions. Their key advantages are accurate transition intensities, tremendously reduced measurement times, and unique mixture compatibility.
Our laboratory experiments will motivate and guide astronomic observations, and enable their interpretation. The expected results are
• the exploration of molecular complexity by discovering new classes of molecules in space,
• the detection of isotopologues that provide information about the stage of chemical evolution,
• the generation of abundance maps of highly excited molecules to learn about their environment,
• the identification of key intermediates in astrochemical reactions.
The results will significantly foster and likely revolutionize our understanding of astrochemistry. The proposed research will go far beyond the state-of-the-art: We will use cutting-edge techniques both in the laboratory and at the telescope to greatly improve and speed the process of identifying molecular fingerprints. These techniques now enable studies at this important frontier of physics and chemistry that previously would have been prohibitively time-consuming or even impossible.
Summary
The goal of the research program, ASTROROT, is to significantly advance the knowledge of astrochemistry by exploring its molecular complexity and by discovering new molecule classes and key chemical processes in space. So far, mostly physical reasons were investigated for the observed variations in molecular abundances. We here propose to study the influence of chemistry on the molecular composition of the universe by combining unprecedentedly high-quality laboratory spectroscopy and pioneering telescope observations. Array telescopes provide new observations of rotational molecular emission, leading to an urgent need for microwave spectroscopic data of exotic molecules. We will use newly developed, unique broadband microwave spectrometers with the cold conditions of a molecular jet and the higher temperatures of a waveguide to mimic different interstellar conditions. Their key advantages are accurate transition intensities, tremendously reduced measurement times, and unique mixture compatibility.
Our laboratory experiments will motivate and guide astronomic observations, and enable their interpretation. The expected results are
• the exploration of molecular complexity by discovering new classes of molecules in space,
• the detection of isotopologues that provide information about the stage of chemical evolution,
• the generation of abundance maps of highly excited molecules to learn about their environment,
• the identification of key intermediates in astrochemical reactions.
The results will significantly foster and likely revolutionize our understanding of astrochemistry. The proposed research will go far beyond the state-of-the-art: We will use cutting-edge techniques both in the laboratory and at the telescope to greatly improve and speed the process of identifying molecular fingerprints. These techniques now enable studies at this important frontier of physics and chemistry that previously would have been prohibitively time-consuming or even impossible.
Max ERC Funding
1 499 904 €
Duration
Start date: 2015-05-01, End date: 2020-04-30
Project acronym ATG9_SOLVES_IT
Project In vitro high resolution reconstitution of autophagosome nucleation and expansion catalyzed byATG9
Researcher (PI) Sharon TOOZE
Host Institution (HI) THE FRANCIS CRICK INSTITUTE LIMITED
Call Details Advanced Grant (AdG), LS1, ERC-2017-ADG
Summary Autophagy is a conserved, lysosomal-mediated pathway required for cell homeostasis and survival. It is controlled by the master regulators of energy (AMPK) and growth (TORC1) and mediated by the ATG (autophagy) proteins. Deregulation of autophagy is implicated in cancer, immunity, infection, aging and neurodegeneration. Autophagosomes form and expand using membranes from the secretory and endocytic pathways but how this occurs is not understood. ATG9, the only transmembrane ATG protein traffics through the cell in vesicles, and is essential for rapid initiation and expansion of the membranes which form the autophagosome. Crucially, how ATG9 functions is unknown. I will determine how ATG9 initiates the formation and expansion of the autophagosome by amino acid starvation through a molecular dissection of proteins resident in ATG9 vesicles which modulate the composition and property of the initiating membrane. I will employ high resolution light and electron microscopy to characterize the nucleation of the autophagosome, proximity-specific biotinylation and quantitative Mass Spectrometry to uncover the proteome required for the function of the ATG9, and optogenetic tools to acutely regulate signaling lipids. Lastly, with our tools and knowledge I will develop an in vitro reconstitution system to define at a molecular level how ATG9 vesicle proteins, membranes that interact with ATG9 vesicles, and other accessory ATG components nucleate and form an autophagosome. In vitro reconstitution of autophagosomes will be assayed biochemically, and by correlative light and cryo-EM and cryo-EM tomography, while functional reconstitution of autophagy will be tested by selective cargo recruitment. The development of a reconstituted system and identification proteins and lipids which are key components for autophagosome formation will provide a means to identify a new generation of targets for translational work leading to manipulation of autophagy for disease related therapies.
Summary
Autophagy is a conserved, lysosomal-mediated pathway required for cell homeostasis and survival. It is controlled by the master regulators of energy (AMPK) and growth (TORC1) and mediated by the ATG (autophagy) proteins. Deregulation of autophagy is implicated in cancer, immunity, infection, aging and neurodegeneration. Autophagosomes form and expand using membranes from the secretory and endocytic pathways but how this occurs is not understood. ATG9, the only transmembrane ATG protein traffics through the cell in vesicles, and is essential for rapid initiation and expansion of the membranes which form the autophagosome. Crucially, how ATG9 functions is unknown. I will determine how ATG9 initiates the formation and expansion of the autophagosome by amino acid starvation through a molecular dissection of proteins resident in ATG9 vesicles which modulate the composition and property of the initiating membrane. I will employ high resolution light and electron microscopy to characterize the nucleation of the autophagosome, proximity-specific biotinylation and quantitative Mass Spectrometry to uncover the proteome required for the function of the ATG9, and optogenetic tools to acutely regulate signaling lipids. Lastly, with our tools and knowledge I will develop an in vitro reconstitution system to define at a molecular level how ATG9 vesicle proteins, membranes that interact with ATG9 vesicles, and other accessory ATG components nucleate and form an autophagosome. In vitro reconstitution of autophagosomes will be assayed biochemically, and by correlative light and cryo-EM and cryo-EM tomography, while functional reconstitution of autophagy will be tested by selective cargo recruitment. The development of a reconstituted system and identification proteins and lipids which are key components for autophagosome formation will provide a means to identify a new generation of targets for translational work leading to manipulation of autophagy for disease related therapies.
Max ERC Funding
2 121 055 €
Duration
Start date: 2018-07-01, End date: 2023-06-30