text:
(-) Remove Starting Grant (StG) (57) filter Starting Grant (StG) (57)
Project acronym BETATOBETA
Project The molecular basis of pancreatic beta cell replication
Researcher (PI) Yuval Dor
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Summary A fundamental challenge of pancreas biology is to understand and manipulate the determinants of beta cell mass. The homeostatic maintenance of adult beta cell mass relies largely on replication of differentiated beta cells, but the triggers and signaling pathways involved remain poorly understood. Here I propose to investigate the physiological and molecular mechanisms that control beta cell replication. First, novel transgenic mouse tools will be used to isolate live replicating beta cells and to examine the genetic program of beta cell replication in vivo. Information gained will provide insights into the molecular biology of cell division in vivo. Additionally, these experiments will address critical unresolved questions in beta cell biology, for example whether duplication involves transient dedifferentiation. Second, genetic and pharmacologic tools will be used to dissect the signaling pathways controlling the entry of beta cells to the cell division cycle, with emphasis on the roles of glucose and insulin, the key physiological input and output of beta cells. The expected outcome of these studies is a detailed molecular understanding of the homeostatic maintenance of beta cell mass, describing how beta cell function is linked to beta cell number in vivo. This may suggest new targets and concepts for pharmacologic intervention, towards the development of regenerative therapy strategies in diabetes. More generally, the experiments will shed light on one of the greatest mysteries of developmental biology, namely how organs achieve and maintain their correct size. A fundamental challenge of pancreas biology is to understand and manipulate the determinants of beta cell mass. The homeostatic maintenance of adult beta cell mass relies largely on replication of differentiated beta cells, but the triggers and signaling pathways involved remain poorly understood. Here I propose to investigate the physiological and molecular mechanisms that control beta cell replication. First, novel transgenic mouse tools will be used to isolate live replicating beta cells and to examine the genetic program of beta cell replication in vivo. Information gained will provide insights into the molecular biology of cell division in vivo. Additionally, these experiments will address critical unresolved questions in beta cell biology, for example whether duplication involves transient dedifferentiation. Second, genetic and pharmacologic tools will be used to dissect the signaling pathways controlling the entry of beta cells to the cell division cycle, with emphasis on the roles of glucose and insulin, the key physiological input and output of beta cells. The expected outcome of these studies is a detailed molecular understanding of the homeostatic maintenance of beta cell mass, describing how beta cell function is linked to beta cell number in vivo. This may suggest new targets and concepts for pharmacologic intervention, towards the development of regenerative therapy strategies in diabetes. More generally, the experiments will shed light on one of the greatest mysteries of developmental biology, namely how organs achieve and maintain their correct size.
A fundamental challenge of pancreas biology is to understand and manipulate the determinants of beta cell mass. The homeostatic maintenance of adult beta cell mass relies largely on replication of differentiated beta cells, but the triggers and signaling pathways involved remain poorly understood. Here I propose to investigate the physiological and molecular mechanisms that control beta cell replication. First, novel transgenic mouse tools will be used to isolate live replicating beta cells and to examine the genetic program of beta cell replication in vivo. Information gained will provide insights into the molecular biology of cell division in vivo. Additionally, these experiments will address critical unresolved questions in beta cell biology, for example whether duplication involves transient dedifferentiation. Second, genetic and pharmacologic tools will be used to dissect the signaling pathways controlling the entry of beta cells to the cell division cycle, with emphasis on the roles of glucose and insulin, the key physiological input and output of beta cells. The expected outcome of these studies is a detailed molecular understanding of the homeostatic maintenance of beta cell mass, describing how beta cell function is linked to beta cell number in vivo. This may suggest new targets and concepts for pharmacologic intervention, towards the development of regenerative therapy strategies in diabetes. More generally, the experiments will shed light on one of the greatest mysteries of developmental biology, namely how organs achieve and maintain their correct size. A fundamental challenge of pancreas biology is to understand and manipulate the determinants of beta cell mass. The homeostatic maintenance of adult beta cell mass relies largely on replication of differentiated beta cells, but the triggers and signaling pathways involved remain poorly understood. Here I propose to investigate the physiological and molecular mechanisms that control beta cell replication. First, novel transgenic mouse tools will be used to isolate live replicating beta cells and to examine the genetic program of beta cell replication in vivo. Information gained will provide insights into the molecular biology of cell division in vivo. Additionally, these experiments will address critical unresolved questions in beta cell biology, for example whether duplication involves transient dedifferentiation. Second, genetic and pharmacologic tools will be used to dissect the signaling pathways controlling the entry of beta cells to the cell division cycle, with emphasis on the roles of glucose and insulin, the key physiological input and output of beta cells. The expected outcome of these studies is a detailed molecular understanding of the homeostatic maintenance of beta cell mass, describing how beta cell function is linked to beta cell number in vivo. This may suggest new targets and concepts for pharmacologic intervention, towards the development of regenerative therapy strategies in diabetes. More generally, the experiments will shed light on one of the greatest mysteries of developmental biology, namely how organs achieve and maintain their correct size.
Project acronym BOTTOM-UP_SYSCHEM
Project Systems Chemistry from Bottom Up: Switching, Gating and Oscillations in Non Enzymatic Peptide Networks
Researcher (PI) Gonen Ashkenasy
Host Institution (HI) BEN-GURION UNIVERSITY OF THE NEGEV
Summary The study of synthetic molecular networks is of fundamental importance for understanding the organizational principles of biological systems and may well be the key to unraveling the origins of life. In addition, such systems may be useful for parallel synthesis of molecules, implementation of catalysis via multi-step pathways, and as media for various applications in nano-medicine and nano-electronics. We have been involved recently in developing peptide-based replicating networks and revealed their dynamic characteristics. We argue here that the structural information embedded in the polypeptide chains is sufficiently rich to allow the construction of peptide 'Systems Chemistry', namely, to facilitate the use of replicating networks as cell-mimetics, featuring complex dynamic behavior. To bring this novel idea to reality, we plan to take a unique holistic approach by studying such networks both experimentally and via simulations, for elucidating basic-principles and towards applications in adjacent fields, such as molecular electronics. Towards realizing these aims, we will study three separate but inter-related objectives: (i) design and characterization of networks that react and rewire in response to external triggers, such as light, (ii) design of networks that operate via new dynamic rules of product formation that lead to oscillations, and (iii) exploitation of the molecular information gathered from the networks as means to control switching and gating in molecular electronic devices. We believe that achieving the project's objectives will be highly significant for the development of the arising field of Systems Chemistry, and in addition will provide valuable tools for studying related scientific fields, such as systems biology and molecular electronics.
The study of synthetic molecular networks is of fundamental importance for understanding the organizational principles of biological systems and may well be the key to unraveling the origins of life. In addition, such systems may be useful for parallel synthesis of molecules, implementation of catalysis via multi-step pathways, and as media for various applications in nano-medicine and nano-electronics. We have been involved recently in developing peptide-based replicating networks and revealed their dynamic characteristics. We argue here that the structural information embedded in the polypeptide chains is sufficiently rich to allow the construction of peptide 'Systems Chemistry', namely, to facilitate the use of replicating networks as cell-mimetics, featuring complex dynamic behavior. To bring this novel idea to reality, we plan to take a unique holistic approach by studying such networks both experimentally and via simulations, for elucidating basic-principles and towards applications in adjacent fields, such as molecular electronics. Towards realizing these aims, we will study three separate but inter-related objectives: (i) design and characterization of networks that react and rewire in response to external triggers, such as light, (ii) design of networks that operate via new dynamic rules of product formation that lead to oscillations, and (iii) exploitation of the molecular information gathered from the networks as means to control switching and gating in molecular electronic devices. We believe that achieving the project's objectives will be highly significant for the development of the arising field of Systems Chemistry, and in addition will provide valuable tools for studying related scientific fields, such as systems biology and molecular electronics.
Project acronym CAC
Project Cryptography and Complexity
Researcher (PI) Yuval Ishai
Host Institution (HI) TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Summary Modern cryptography has deeply rooted connections with computational complexity theory and other areas of computer science. This proposal suggests to explore several {\em new connections} between questions in cryptography and questions from other domains, including computational complexity, coding theory, and even the natural sciences. The project is expected to broaden the impact of ideas from cryptography on other domains, and on the other hand to benefit cryptography by applying tools from other domains towards better solutions for central problems in cryptography.
Modern cryptography has deeply rooted connections with computational complexity theory and other areas of computer science. This proposal suggests to explore several {\em new connections} between questions in cryptography and questions from other domains, including computational complexity, coding theory, and even the natural sciences. The project is expected to broaden the impact of ideas from cryptography on other domains, and on the other hand to benefit cryptography by applying tools from other domains towards better solutions for central problems in cryptography.
Project acronym CARDIO-IPS
Project Induced Pluripotent stem Cells: A Novel Strategy to Study Inherited Cardiac Disorders
Researcher (PI) Lior Gepstein
Summary The study of several genetic disorders is hampered by the lack of suitable in vitro human models. We hypothesize that the generation of patient-specific induced pluripotent stem cells (iPSCs) will allow the development of disease-specific in vitro models; yielding new pathophysiologic insights into several genetic disorders and offering a unique platform to test novel therapeutic strategies. In the current proposal we plan utilize this novel approach to establish human iPSC (hiPSC) lines for the study of a variety of inherited cardiac disorders. The specific disease states that will be studied were chosen to reflect abnormalities in a wide-array of different cardiomyocyte cellular processes. These include mutations leading to: (1) abnormal ion channel function ("channelopathies"), such as the long QT and Brugada syndromes; (2) abnormal intracellular storage of unnecessary material, such as in the glycogen storage disease type IIb (Pompe's disease); and (3) abnormalities in cell-to-cell contacts, such as in the case of arrhythmogenic right ventricular cardiomyopathy-dysplasia (ARVC-D). The different hiPSC lines generated will be coaxed to differentiate into the cardiac lineage. Detailed molecular, structural, functional, and pharmacological studies will then be performed to characterize the phenotypic properties of the generated hiPSC-derived cardiomyocytes, with specific emphasis on their molecular, ultrastructural, electrophysiological, and Ca2+ handling properties. These studies should provide new insights into the pathophysiological mechanisms underlying the different familial arrhythmogenic and cardiomyopathy disorders studied, may allow optimization of patient-specific therapies (personalized medicine), and may facilitate the development of novel therapeutic strategies. Moreover, the concepts and methodological knowhow developed in the current project could be extended, in the future, to derive human disease-specific cell culture models for a plurality of genetic disorders; enabling translational research ranging from investigation of the most fundamental cellular mechanisms involved in human tissue formation and physiology through disease investigation and the development and testing of novel therapies that could potentially find their way to the bedside
The study of several genetic disorders is hampered by the lack of suitable in vitro human models. We hypothesize that the generation of patient-specific induced pluripotent stem cells (iPSCs) will allow the development of disease-specific in vitro models; yielding new pathophysiologic insights into several genetic disorders and offering a unique platform to test novel therapeutic strategies. In the current proposal we plan utilize this novel approach to establish human iPSC (hiPSC) lines for the study of a variety of inherited cardiac disorders. The specific disease states that will be studied were chosen to reflect abnormalities in a wide-array of different cardiomyocyte cellular processes. These include mutations leading to: (1) abnormal ion channel function ("channelopathies"), such as the long QT and Brugada syndromes; (2) abnormal intracellular storage of unnecessary material, such as in the glycogen storage disease type IIb (Pompe's disease); and (3) abnormalities in cell-to-cell contacts, such as in the case of arrhythmogenic right ventricular cardiomyopathy-dysplasia (ARVC-D). The different hiPSC lines generated will be coaxed to differentiate into the cardiac lineage. Detailed molecular, structural, functional, and pharmacological studies will then be performed to characterize the phenotypic properties of the generated hiPSC-derived cardiomyocytes, with specific emphasis on their molecular, ultrastructural, electrophysiological, and Ca2+ handling properties. These studies should provide new insights into the pathophysiological mechanisms underlying the different familial arrhythmogenic and cardiomyopathy disorders studied, may allow optimization of patient-specific therapies (personalized medicine), and may facilitate the development of novel therapeutic strategies. Moreover, the concepts and methodological knowhow developed in the current project could be extended, in the future, to derive human disease-specific cell culture models for a plurality of genetic disorders; enabling translational research ranging from investigation of the most fundamental cellular mechanisms involved in human tissue formation and physiology through disease investigation and the development and testing of novel therapies that could potentially find their way to the bedside
Project acronym CAT4ENSUS
Project Molecular Catalysts Made of Earth-Abundant Elements for Energy and Sustainability
Researcher (PI) Xile Hu
Summary Energy and sustainability are among the biggest challenges humanity faces this century. Catalysis is an indispensable component for many potential solutions, and fundamental research in catalysis is as urgent as ever. Here, we propose to build up an interdisciplinary research program in molecular catalysis to address the challenges of energy and sustainability. There are two specific aims: (I) bio-inspired sulfur-rich metal complexes as efficient and practical electrocatalysts for hydrogen production and CO2 reduction; (II) well-defined Fe complexes of chelating pincer ligands for chemo- and stereoselective organic synthesis. An important feature of the proposed catalysts is that they are made of earth-abundant and readily available elements such as Fe, Co, Ni, S, N, etc. Design and synthesis of catalysts are the starting point and a key aspect of this project. A major inspiration comes from nature, where metallo-enzymes use readily available metals for fuel production and challenging reactions. Our accumulated knowledge and experience in spectroscopy, electrochemistry, reaction chemistry, mechanism, and catalysis will enable us to thoroughly study the synthetic catalysts and their applications towards the research targets. Furthermore, we will explore research territories such as electrode modification and fabrication, catalyst immobilization and attachment, and asymmetric catalysis. The proposed research should not only result in new insights and knowledge in catalysis that are relevant to energy and sustainability, but also produce functional, scalable, and economically feasible catalysts for fuel production and organic synthesis. The program can contribute to excellence in European research.
Energy and sustainability are among the biggest challenges humanity faces this century. Catalysis is an indispensable component for many potential solutions, and fundamental research in catalysis is as urgent as ever. Here, we propose to build up an interdisciplinary research program in molecular catalysis to address the challenges of energy and sustainability. There are two specific aims: (I) bio-inspired sulfur-rich metal complexes as efficient and practical electrocatalysts for hydrogen production and CO2 reduction; (II) well-defined Fe complexes of chelating pincer ligands for chemo- and stereoselective organic synthesis. An important feature of the proposed catalysts is that they are made of earth-abundant and readily available elements such as Fe, Co, Ni, S, N, etc. Design and synthesis of catalysts are the starting point and a key aspect of this project. A major inspiration comes from nature, where metallo-enzymes use readily available metals for fuel production and challenging reactions. Our accumulated knowledge and experience in spectroscopy, electrochemistry, reaction chemistry, mechanism, and catalysis will enable us to thoroughly study the synthetic catalysts and their applications towards the research targets. Furthermore, we will explore research territories such as electrode modification and fabrication, catalyst immobilization and attachment, and asymmetric catalysis. The proposed research should not only result in new insights and knowledge in catalysis that are relevant to energy and sustainability, but also produce functional, scalable, and economically feasible catalysts for fuel production and organic synthesis. The program can contribute to excellence in European research.
Project acronym CELLTYPESANDCIRCUITS
Project Neural circuit function in the retina of mice and humans
Researcher (PI) Botond Roska
Host Institution (HI) FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH FONDATION
Summary The mammalian brain is assembled from thousands of neuronal cell types that are organized into distinct circuits to perform behaviourally relevant computations. To gain mechanistic insights about brain function and to treat specific diseases of the nervous system it is crucial to understand what these local circuits are computing and how they achieve these computations. By examining the structure and function of a few genetically identified and experimentally accessible neural circuits we plan to address fundamental questions about the functional architecture of neural circuits. First, are cell types assigned to a unique functional circuit with a well-defined function or do they participate in multiple circuits ("multitasking cell types"), adjusting their role depending on the state of these circuits? Second, does a neural circuit perform "a single computation" or depending on the information content of its inputs can it carry out radically different functions? Third, how, among the large number of other cell types, do the cells belonging to the same functional circuit connect together during development? We use the mouse retina as a model system to address these questions. Finally, we will study the structure and function of a specialised neural circuit in the human fovea that enables humans to read. We predict that our insights into the mechanism of multitasking, network switches and the development of selective connectivity will be instructive to study similar phenomena in other brain circuits. Knowledge of the structure and function of the human fovea will open up new opportunities to correlate human retinal function with human visual behaviour and our genetic technologies to study human foveal function will allow us and others to design better strategies for restoring vision for the blind.
The mammalian brain is assembled from thousands of neuronal cell types that are organized into distinct circuits to perform behaviourally relevant computations. To gain mechanistic insights about brain function and to treat specific diseases of the nervous system it is crucial to understand what these local circuits are computing and how they achieve these computations. By examining the structure and function of a few genetically identified and experimentally accessible neural circuits we plan to address fundamental questions about the functional architecture of neural circuits. First, are cell types assigned to a unique functional circuit with a well-defined function or do they participate in multiple circuits ("multitasking cell types"), adjusting their role depending on the state of these circuits? Second, does a neural circuit perform "a single computation" or depending on the information content of its inputs can it carry out radically different functions? Third, how, among the large number of other cell types, do the cells belonging to the same functional circuit connect together during development? We use the mouse retina as a model system to address these questions. Finally, we will study the structure and function of a specialised neural circuit in the human fovea that enables humans to read. We predict that our insights into the mechanism of multitasking, network switches and the development of selective connectivity will be instructive to study similar phenomena in other brain circuits. Knowledge of the structure and function of the human fovea will open up new opportunities to correlate human retinal function with human visual behaviour and our genetic technologies to study human foveal function will allow us and others to design better strategies for restoring vision for the blind.
Project acronym CIRCATRANS
Project Control of mouse metabolism by circadian clock-coordinated mRNA translation
Researcher (PI) Frédéric Bruno Martin Gachon
Host Institution (HI) NESTEC SA
Summary The mammalian circadian clock plays a fundamental role in the liver by regulating fatty acid, glucose and xenobiotic metabolism. Impairment of this rhythm has been show to lead to diverse pathologies including metabolic syndrome. At present, it is supposed that the circadian clock regulates metabolism mostly by regulating the expression of liver enzymes at the transcriptional level. We have now collected evidence that post-transcriptional regulations play also an important role in this regulation. Particularly, recent results from our laboratory show that the circadian clock can synchronize mRNA translation in mouse liver through rhythmic activation of the Target Of Rapamycin Complex 1 (TORC1) with a 12-hours period. Based on this unexpected observation, we plan to identify the genes rhythmically translated in the mouse liver as well as the mechanisms involved in this translation. Indeed, our initial observations suggest a cap-independent translation during the day and a cap-dependent translation during the night. Identification of the different complexes involved in translation at this two different times and their correlation with the sequence, structure, and/or function of the translated genes will provide new insight into the action of the circadian clock on animal metabolism. In parallel, we will identify the signalling pathways involved in the rhythmic activation of TORC1 in mouse liver. Finally, we will study the consequences of a deregulated rhythmic translation in circadian clock-deficient mice on the metabolism and the longevity of these animals. Perturbations of the circadian clock have been linked to numerous pathologies, including obesity, type 2 diabetes and cancer. Our project on the importance of circadian clock-coordinated translation will likely reveal new findings in the field of regulation of animal metabolism by the circadian clock.
The mammalian circadian clock plays a fundamental role in the liver by regulating fatty acid, glucose and xenobiotic metabolism. Impairment of this rhythm has been show to lead to diverse pathologies including metabolic syndrome. At present, it is supposed that the circadian clock regulates metabolism mostly by regulating the expression of liver enzymes at the transcriptional level. We have now collected evidence that post-transcriptional regulations play also an important role in this regulation. Particularly, recent results from our laboratory show that the circadian clock can synchronize mRNA translation in mouse liver through rhythmic activation of the Target Of Rapamycin Complex 1 (TORC1) with a 12-hours period. Based on this unexpected observation, we plan to identify the genes rhythmically translated in the mouse liver as well as the mechanisms involved in this translation. Indeed, our initial observations suggest a cap-independent translation during the day and a cap-dependent translation during the night. Identification of the different complexes involved in translation at this two different times and their correlation with the sequence, structure, and/or function of the translated genes will provide new insight into the action of the circadian clock on animal metabolism. In parallel, we will identify the signalling pathways involved in the rhythmic activation of TORC1 in mouse liver. Finally, we will study the consequences of a deregulated rhythmic translation in circadian clock-deficient mice on the metabolism and the longevity of these animals. Perturbations of the circadian clock have been linked to numerous pathologies, including obesity, type 2 diabetes and cancer. Our project on the importance of circadian clock-coordinated translation will likely reveal new findings in the field of regulation of animal metabolism by the circadian clock.
Project acronym CODAMODA
Project Controlling Data Movement in the Digital Age
Researcher (PI) Aggelos Kiayias
Host Institution (HI) ETHNIKO KAI KAPODISTRIAKO PANEPISTIMIO ATHINON
Summary Nowadays human intellectual product is increasingly produced and disseminated solely in digital form. The capability of digital data for effortless reproduction and transfer has lead to a true revolution that impacts every aspect of human creativity. Nevertheless, as with every technological revolution, this digital media revolution comes with a dark side that, if left unaddressed, it will limit its impact and may counter its potential advantages. In particular, the way we produce and disseminate digital content today does not lend itself to controlling the way data move and change. It turns out that the power of being digital can be a double-edged sword: the ease of production, dissemination and editing also implies the ease of misappropriation, plagiarism and improper modification. To counter the above problems, the proposed research activity will focus on the development of a new generation of enabling cryptographic technologies that have the power to facilitate the appropriate controls for data movement. Using the techniques developed in this project it will be feasible to build digital content distribution systems where content producers will have the full possible control on the dissemination of their intellectual product, while at the same time the rights of the end-users in terms of privacy and fair use can be preserved. The PI is uniquely qualified to carry out the proposed research activity as he has extensive prior experience in making innovations in the area of digital content distribution as well as in the management of research projects. As part of the project activities, the PI will establish the CODAMODA laboratory in the University of Athens and will seek opportunities for technology transfer and interdisciplinary work with the legal science community.
Nowadays human intellectual product is increasingly produced and disseminated solely in digital form. The capability of digital data for effortless reproduction and transfer has lead to a true revolution that impacts every aspect of human creativity. Nevertheless, as with every technological revolution, this digital media revolution comes with a dark side that, if left unaddressed, it will limit its impact and may counter its potential advantages. In particular, the way we produce and disseminate digital content today does not lend itself to controlling the way data move and change. It turns out that the power of being digital can be a double-edged sword: the ease of production, dissemination and editing also implies the ease of misappropriation, plagiarism and improper modification. To counter the above problems, the proposed research activity will focus on the development of a new generation of enabling cryptographic technologies that have the power to facilitate the appropriate controls for data movement. Using the techniques developed in this project it will be feasible to build digital content distribution systems where content producers will have the full possible control on the dissemination of their intellectual product, while at the same time the rights of the end-users in terms of privacy and fair use can be preserved. The PI is uniquely qualified to carry out the proposed research activity as he has extensive prior experience in making innovations in the area of digital content distribution as well as in the management of research projects. As part of the project activities, the PI will establish the CODAMODA laboratory in the University of Athens and will seek opportunities for technology transfer and interdisciplinary work with the legal science community.
Project acronym COMCOM
Project Communication and Computation - Two Sides of One Tapestry
Researcher (PI) Michael Christoph Gastpar
Summary Networks have been studied in depth for several decades, but one aspect has received little attention: Interference. Most networks use clever algorithms to avoid interference, and this strategy has proved effective for traditional supply-chain or wired communication networks. However, the emergence of wireless networks revealed that simply avoiding interference leads to significant performance loss. A wealth of cooperative communication strategies have recently been developed to address this issue. Two fundamental roadblocks are emerging: First, it is ultimately unclear how to integrate cooperative techniques into the larger fabric of networks (short of case-by-case redesigns); and second, the lack of source/channel separation in networks (i.e., more bits do not imply better end-to-end signal quality) calls for ever more specialized cooperative techniques. This proposal advocates a new understanding of interference as computation: Interference garbles together inputs to produce an output. This can be thought of as a certain computation, perhaps subject to noise or other stochastic effects. The proposed work will develop strategies that permit to exploit this computational potential. Building on these ``computation codes,'' an enhanced physical layer is proposed: Rather than only forwarding bits, the revised physical layer can also forward functions from several transmitting nodes to a receiver, much more efficiently than the full information. Near-seamless integration into the fabric of existing network architectures is thus possible, providing a solution for the first roadblock. In response to the second roadblock, computation codes suggest new computational primitives as fundamental currencies of information.
Networks have been studied in depth for several decades, but one aspect has received little attention: Interference. Most networks use clever algorithms to avoid interference, and this strategy has proved effective for traditional supply-chain or wired communication networks. However, the emergence of wireless networks revealed that simply avoiding interference leads to significant performance loss. A wealth of cooperative communication strategies have recently been developed to address this issue. Two fundamental roadblocks are emerging: First, it is ultimately unclear how to integrate cooperative techniques into the larger fabric of networks (short of case-by-case redesigns); and second, the lack of source/channel separation in networks (i.e., more bits do not imply better end-to-end signal quality) calls for ever more specialized cooperative techniques. This proposal advocates a new understanding of interference as computation: Interference garbles together inputs to produce an output. This can be thought of as a certain computation, perhaps subject to noise or other stochastic effects. The proposed work will develop strategies that permit to exploit this computational potential. Building on these ``computation codes,'' an enhanced physical layer is proposed: Rather than only forwarding bits, the revised physical layer can also forward functions from several transmitting nodes to a receiver, much more efficiently than the full information. Near-seamless integration into the fabric of existing network architectures is thus possible, providing a solution for the first roadblock. In response to the second roadblock, computation codes suggest new computational primitives as fundamental currencies of information.
Project acronym COMPCAMERAANALYZ
Project Understanding Designing and Analyzing Computational Cameras
Researcher (PI) Anat Levin
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Summary Computational cameras go beyond 2D images and allow the extraction of more dimensions from the visual world such as depth, multiple viewpoints and multiple illumination conditions. They also allow us to overcome some of the traditional photography challenges such as defocus blur, motion blur, noise and resolution. The increasing variety of computational cameras is raising the need for a meaningful comparison across camera types. We would like to understand which cameras are better for specific tasks, which aspects of a camera make it better than others and what is the best performance we can hope to achieve. Our 2008 paper introduced a general framework to address the design and analysis of computational cameras. A camera is modeled as a linear projection in ray space. Decoding the camera data then deals with inverting the linear projection. Since the number of sensor measurements is usually much smaller than the number of rays, the inversion must be treated as a Bayesian inference problem accounting for prior knowledge on the world. Despite significant progress which has been made in the recent years, the space of computational cameras is still far from being understood. Computational camera analysis raises the following research challenges: 1) What is a good way to model prior knowledge on ray space? 2) Seeking efficient inference algorithms and robust ways to decode the world from the camera measurements. 3) Evaluating the expected reconstruction accuracy of a given camera. 4) Using the expected reconstruction performance for evaluating and comparing camera types. 5) What is the best camera? Can we derive upper bounds on the optimal performance? We propose research on all aspects of computational camera design and analysis. We propose new prior models which will significantly simplify the inference and evaluation tasks. We also propose new ways to bound and evaluate computational cameras with existing priors.
Computational cameras go beyond 2D images and allow the extraction of more dimensions from the visual world such as depth, multiple viewpoints and multiple illumination conditions. They also allow us to overcome some of the traditional photography challenges such as defocus blur, motion blur, noise and resolution. The increasing variety of computational cameras is raising the need for a meaningful comparison across camera types. We would like to understand which cameras are better for specific tasks, which aspects of a camera make it better than others and what is the best performance we can hope to achieve. Our 2008 paper introduced a general framework to address the design and analysis of computational cameras. A camera is modeled as a linear projection in ray space. Decoding the camera data then deals with inverting the linear projection. Since the number of sensor measurements is usually much smaller than the number of rays, the inversion must be treated as a Bayesian inference problem accounting for prior knowledge on the world. Despite significant progress which has been made in the recent years, the space of computational cameras is still far from being understood. Computational camera analysis raises the following research challenges: 1) What is a good way to model prior knowledge on ray space? 2) Seeking efficient inference algorithms and robust ways to decode the world from the camera measurements. 3) Evaluating the expected reconstruction accuracy of a given camera. 4) Using the expected reconstruction performance for evaluating and comparing camera types. 5) What is the best camera? Can we derive upper bounds on the optimal performance? We propose research on all aspects of computational camera design and analysis. We propose new prior models which will significantly simplify the inference and evaluation tasks. We also propose new ways to bound and evaluate computational cameras with existing priors.
Project acronym COMPLEXDATA
Project Statistics for Complex Data: Understanding Randomness, Geometry and Complexity with a view Towards Biophysics
Researcher (PI) Victor Michael Panaretos
Summary The ComplexData project aims at advancing our understanding of the statistical treatment of varied types of complex data by generating new theory and methods, and to obtain progress in concrete current biophysical problems through the implementation of the new tools developed. Complex Data constitute data where the basic object of observation cannot be described in the standard Euclidean context of statistics, but rather needs to be thought of as an element of an abstract mathematical space with special properties. Scientific progress has, in recent years, begun to generate an increasing number of new and complex types of data that require statistical understanding and analysis. Four such types of data that are arising in the context of current scientific research and that the project will be focusing on are: random integral transforms, random unlabelled shapes, random flows of functions, and random tensor fields. In these unconventional contexts for statistics, the strategy of the project will be to carefully exploit the special aspects involved due to geometry, dimension and randomness in order to be able to either adapt and synthesize existing statistical methods, or to generate new statistical ideas altogether. However, the project will not restrict itself to merely studying the theoretical aspects of complex data, but will be truly interdisciplinary. The connecting thread among all the above data types is that their study is motivated by, and will be applied to concrete practical problems arising in the study of biological structure, dynamics, and function: biophysics. For this reason, the programme will be in interaction with local and international contacts from this field. In particular, the theoretical/methodological output of the four programme research foci will be applied to gain insights in the following corresponding four application areas: electron microscopy, protein homology, DNA molecular dynamics, brain imaging.
The ComplexData project aims at advancing our understanding of the statistical treatment of varied types of complex data by generating new theory and methods, and to obtain progress in concrete current biophysical problems through the implementation of the new tools developed. Complex Data constitute data where the basic object of observation cannot be described in the standard Euclidean context of statistics, but rather needs to be thought of as an element of an abstract mathematical space with special properties. Scientific progress has, in recent years, begun to generate an increasing number of new and complex types of data that require statistical understanding and analysis. Four such types of data that are arising in the context of current scientific research and that the project will be focusing on are: random integral transforms, random unlabelled shapes, random flows of functions, and random tensor fields. In these unconventional contexts for statistics, the strategy of the project will be to carefully exploit the special aspects involved due to geometry, dimension and randomness in order to be able to either adapt and synthesize existing statistical methods, or to generate new statistical ideas altogether. However, the project will not restrict itself to merely studying the theoretical aspects of complex data, but will be truly interdisciplinary. The connecting thread among all the above data types is that their study is motivated by, and will be applied to concrete practical problems arising in the study of biological structure, dynamics, and function: biophysics. For this reason, the programme will be in interaction with local and international contacts from this field. In particular, the theoretical/methodological output of the four programme research foci will be applied to gain insights in the following corresponding four application areas: electron microscopy, protein homology, DNA molecular dynamics, brain imaging.
Project acronym COMPUSLANG
Project Neural and computational determinants of left cerebral dominance in speech and language
Researcher (PI) Anne-Lise Mamessier
Summary More than a century after Wernicke and Broca established that speech perception and production rely on temporal and prefrontal cortices of the left brain hemisphere, the biological determinants for this organization are still unknown. While functional neuroanatomy has been described in great detail, the neuroscience of language still lacks a physiologically plausible model of the neuro-computational mechanisms for coding and decoding of speech acoustic signal. We propose to fill this gap by testing the biological validity and exploring the computational implications of one promising proposal, the Asymmetric Sampling in Time theory. AST assumes that speech signals are analysed in parallel at multiple timescales and that these timescales differ between left and right cerebral hemispheres. This theory is original and provocative as it implies that a single computational difference, distinct integration windows in right and left auditory cortices could be sufficient to explain why speech is preferentially processed by the left brain, and possible even why the human brain has evolved toward such an asymmetric functional organization. Our proposal has four goals: 1/ to validate, invalidate or amend AST on the basis of physiological experiments in healthy human subjects including functional magnetic resonance imaging (fMRI), combined electroencephalography (EEG) and fMRI, magnetoencephalography (MEG) and subdural electrocorticography (EcoG), 2/ to use computational modeling to probe those aspects of the theory that currently remain inaccessible to empirical testing (evaluation, assessment), 3/ to apply AST to binaural artificial hearing with cochlear implants, 4/ to test for disorders of auditory sampling in autism and dyslexia, two language neurodevelopmental pathologies in which a genetic basis implicates the physiological underpinnings of AST, and 5/ to assess potential generalisation of AST to linguistic action in the context of speech production.
More than a century after Wernicke and Broca established that speech perception and production rely on temporal and prefrontal cortices of the left brain hemisphere, the biological determinants for this organization are still unknown. While functional neuroanatomy has been described in great detail, the neuroscience of language still lacks a physiologically plausible model of the neuro-computational mechanisms for coding and decoding of speech acoustic signal. We propose to fill this gap by testing the biological validity and exploring the computational implications of one promising proposal, the Asymmetric Sampling in Time theory. AST assumes that speech signals are analysed in parallel at multiple timescales and that these timescales differ between left and right cerebral hemispheres. This theory is original and provocative as it implies that a single computational difference, distinct integration windows in right and left auditory cortices could be sufficient to explain why speech is preferentially processed by the left brain, and possible even why the human brain has evolved toward such an asymmetric functional organization. Our proposal has four goals: 1/ to validate, invalidate or amend AST on the basis of physiological experiments in healthy human subjects including functional magnetic resonance imaging (fMRI), combined electroencephalography (EEG) and fMRI, magnetoencephalography (MEG) and subdural electrocorticography (EcoG), 2/ to use computational modeling to probe those aspects of the theory that currently remain inaccessible to empirical testing (evaluation, assessment), 3/ to apply AST to binaural artificial hearing with cochlear implants, 4/ to test for disorders of auditory sampling in autism and dyslexia, two language neurodevelopmental pathologies in which a genetic basis implicates the physiological underpinnings of AST, and 5/ to assess potential generalisation of AST to linguistic action in the context of speech production.
Project acronym CONQUEST
Project Controlled quantum effects and spin technology - from non-equilibrium physics to functional magnetics
Researcher (PI) Henrik Ronnow
Summary The technology of the 20th century was dominated by a single material class: The semiconductors, whose properties can be tuned between those of metals and insulators all of which describable by single-electron effects. In contrast, quantum magnets and strongly correlated electron systems offer a full palette of quantum mechanical many-electron states. CONQUEST aim to discover, understand and demonstrate control over such quantum states. A new experimental approach, building on established powerful laboratory and neutron scattering techniques combined with dynamical control-perturbations, will be developed to study correlated quantum effects in magnetic materials. The immediate goal is to open a new field of non-equilibrium and time dependent studies in solid state physics. The long-term vision is that the approach might nurture the materials of the 21st century.
The technology of the 20th century was dominated by a single material class: The semiconductors, whose properties can be tuned between those of metals and insulators all of which describable by single-electron effects. In contrast, quantum magnets and strongly correlated electron systems offer a full palette of quantum mechanical many-electron states. CONQUEST aim to discover, understand and demonstrate control over such quantum states. A new experimental approach, building on established powerful laboratory and neutron scattering techniques combined with dynamical control-perturbations, will be developed to study correlated quantum effects in magnetic materials. The immediate goal is to open a new field of non-equilibrium and time dependent studies in solid state physics. The long-term vision is that the approach might nurture the materials of the 21st century.
Project acronym COSYM
Project Computational Symmetry for Geometric Data Analysis and Design
Researcher (PI) Mark Pauly
Summary The analysis and synthesis of complex 3D geometric data sets is of crucial importance in many scientific disciplines (e.g. bio-medicine, material science, mechanical engineering, physics) and industrial applications (e.g. drug design, entertainment, architecture). We are currently witnessing a tremendous increase in the size and complexity of geometric data, largely fueled by significant advances in 3D acquisition and digital production technology. However, existing computational tools are often not suited to handle this complexity. The goal of this project is to explore a fundamentally different way of processing 3D geometry. We will investigate a new generalized model of geometric symmetry as a unifying concept for studying spatial organization in geometric data. This model allows exposing the inherent redundancies in digital 3D data and will enable truly scalable algorithms for analysis, processing, and design of large-scale geometric data sets. The proposed research will address a number of fundamental questions: What is the information content of 3D geometric models? How can we represent, store, and transmit geometric data most efficiently? Can we we use symmetry to repair deficiencies and reduce noise in acquired data? What is the role of symmetry in the design process and how can it be used to reduce complexity? I will investigate these questions with an integrated approach that combines thorough theoretical studies with practical solutions for real-world applications. The proposed research has a strong interdisciplinary component and will consider the same fundamental questions from different perspectives, closely interacting with scientists of various disciplines, as well artists, architects, and designers.
The analysis and synthesis of complex 3D geometric data sets is of crucial importance in many scientific disciplines (e.g. bio-medicine, material science, mechanical engineering, physics) and industrial applications (e.g. drug design, entertainment, architecture). We are currently witnessing a tremendous increase in the size and complexity of geometric data, largely fueled by significant advances in 3D acquisition and digital production technology. However, existing computational tools are often not suited to handle this complexity. The goal of this project is to explore a fundamentally different way of processing 3D geometry. We will investigate a new generalized model of geometric symmetry as a unifying concept for studying spatial organization in geometric data. This model allows exposing the inherent redundancies in digital 3D data and will enable truly scalable algorithms for analysis, processing, and design of large-scale geometric data sets. The proposed research will address a number of fundamental questions: What is the information content of 3D geometric models? How can we represent, store, and transmit geometric data most efficiently? Can we we use symmetry to repair deficiencies and reduce noise in acquired data? What is the role of symmetry in the design process and how can it be used to reduce complexity? I will investigate these questions with an integrated approach that combines thorough theoretical studies with practical solutions for real-world applications. The proposed research has a strong interdisciplinary component and will consider the same fundamental questions from different perspectives, closely interacting with scientists of various disciplines, as well artists, architects, and designers.
Project acronym CTLANDROS
Project Reactive Oxygen Species in CTL-mediated Cell Death: from Mechanism to Applications
Researcher (PI) Denis Martinvalet
Summary Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells release granzyme and perforin from cytotoxic granules into the immune synapse to induce apoptosis of target cells that are either virus-infected or cancerous. Granzyme A activates a caspase-independent apoptotic pathway and induces mitochondrial damage characterized by superoxide anion production and loss of the mitochondrial transmembrane potential, without disrupting the integrity of the mitochondrial outer membrane; while causing single-stranded DNA damage. GzmB induces both caspase-dependent and caspase-independent cell death. In the caspase-dependent pathway, mitochondrial functions are altered as evidenced by the loss of mitochondrial transmembrane potential and the generation of reactive oxygen species (ROS). The mitochondrial outer membrane (MOM) is disrupted, resulting in the release of apoptogenic factors. To date, research on mitochondrial-dependent apoptosis has focused on mitochondrial outer membrane permeabilization (MOMP) however whether the generation of ROS is incidental or essential to the execution of apoptosis remains unclear. Like human GzmA, human GzmB promotes cell death in a ROS-dependent manner. Preliminary data suggest that human GzmB can induce ROS in a MOMP-independent manner as Bax and Bak double knockout MEF cells treated with human GzmB and perforin still display a robust ROS production and dye in an ROS-dependent manner. Since GzmA and GzmB induce cell death in a ROS-dependent manner, we hypothesize that oxygen free radicals are central to the execution of programmed cell death induced by the cytotoxic granules. Therefore, the goal of this proposal is to dissect the key molecular events triggered by ROS that lead to Citotoxic Tcell-induced target cell death. A combination of biochemical, genetic and proteomic approaches in association with Electron Spin Resonance (ESR) spectroscopy methodology will be used to unravel the essential role ROS play in CTL-mediated killing.
Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells release granzyme and perforin from cytotoxic granules into the immune synapse to induce apoptosis of target cells that are either virus-infected or cancerous. Granzyme A activates a caspase-independent apoptotic pathway and induces mitochondrial damage characterized by superoxide anion production and loss of the mitochondrial transmembrane potential, without disrupting the integrity of the mitochondrial outer membrane; while causing single-stranded DNA damage. GzmB induces both caspase-dependent and caspase-independent cell death. In the caspase-dependent pathway, mitochondrial functions are altered as evidenced by the loss of mitochondrial transmembrane potential and the generation of reactive oxygen species (ROS). The mitochondrial outer membrane (MOM) is disrupted, resulting in the release of apoptogenic factors. To date, research on mitochondrial-dependent apoptosis has focused on mitochondrial outer membrane permeabilization (MOMP) however whether the generation of ROS is incidental or essential to the execution of apoptosis remains unclear. Like human GzmA, human GzmB promotes cell death in a ROS-dependent manner. Preliminary data suggest that human GzmB can induce ROS in a MOMP-independent manner as Bax and Bak double knockout MEF cells treated with human GzmB and perforin still display a robust ROS production and dye in an ROS-dependent manner. Since GzmA and GzmB induce cell death in a ROS-dependent manner, we hypothesize that oxygen free radicals are central to the execution of programmed cell death induced by the cytotoxic granules. Therefore, the goal of this proposal is to dissect the key molecular events triggered by ROS that lead to Citotoxic Tcell-induced target cell death. A combination of biochemical, genetic and proteomic approaches in association with Electron Spin Resonance (ESR) spectroscopy methodology will be used to unravel the essential role ROS play in CTL-mediated killing.
Project acronym DECCAPAC
Project Design and Exploitation of C-C and C-H Activation Pathways in Asymmetric Catalysis
Researcher (PI) Nicolai Cramer
Summary Synthesizing organic molecules in high purity with designed properties is of utmost importance for pharmaceutical applications and material- and polymer sciences including the efficient production of enantiopure compounds and the compliance with ecological concerns and sustainability. The efficiency of all reaction classes has improved over the past decades. However, the basic principle and execution did not change: The target molecule is disconnected into donor and acceptor synthons and appropriate functional groups need to be introduced and adjusted to carry out the envisioned coupling. These additional steps decrease the yield and efficiency, are costly in time, resources and produce waste. The introduction of new functionalities by direct C-H or C-C bond activation is a unique and highly appealing strategy. The range of substrates is virtually unlimited, including hydrocarbons, small molecules and polymers. Such dream reactions avoid any pre-functionalization, shorten synthetic routes, make unsought disconnections possible and allow for a more efficient usage of our dwindling resources. Despite recent progress in the activations of inert bonds, narrow scopes, poor reactivities and harsh conditions hamper most general practical applications. Especially, enantioselective activations are a longstanding challenge. The outlined project seeks to address these issues by the development and exploitation of new catalytic enantioselective C-H and C-C functionalizations of broadly available organic substrates, using chiral Rh- and Pd- catalysts, additionally supported by automated screening and computational techniques. These reactions will be then applied in the streamlined synthesis of pharmaceutically relevant scaffolds and of compounds for organic electronics.
Synthesizing organic molecules in high purity with designed properties is of utmost importance for pharmaceutical applications and material- and polymer sciences including the efficient production of enantiopure compounds and the compliance with ecological concerns and sustainability. The efficiency of all reaction classes has improved over the past decades. However, the basic principle and execution did not change: The target molecule is disconnected into donor and acceptor synthons and appropriate functional groups need to be introduced and adjusted to carry out the envisioned coupling. These additional steps decrease the yield and efficiency, are costly in time, resources and produce waste. The introduction of new functionalities by direct C-H or C-C bond activation is a unique and highly appealing strategy. The range of substrates is virtually unlimited, including hydrocarbons, small molecules and polymers. Such dream reactions avoid any pre-functionalization, shorten synthetic routes, make unsought disconnections possible and allow for a more efficient usage of our dwindling resources. Despite recent progress in the activations of inert bonds, narrow scopes, poor reactivities and harsh conditions hamper most general practical applications. Especially, enantioselective activations are a longstanding challenge. The outlined project seeks to address these issues by the development and exploitation of new catalytic enantioselective C-H and C-C functionalizations of broadly available organic substrates, using chiral Rh- and Pd- catalysts, additionally supported by automated screening and computational techniques. These reactions will be then applied in the streamlined synthesis of pharmaceutically relevant scaffolds and of compounds for organic electronics.
Project acronym DIAG-CANCER
Project Diagnosis, Screening and Monitoring of Cancer Diseases via Exhaled Breath Using an Array of Nanosensors
Researcher (PI) Hossam Haick
Summary Cancer is rapidly becoming the greatest health hazard of our days. The most widespread cancers, are lung cancer (LC), breast cancer (BC), colorectal cancer (CC), and prostate cancer (PC). The impact of the various techniques used for diagnosis, screening and monitoring these cancers is either uncertain and/or inconvenient for the patients. This proposal aims to create a low-cost, easy-to-use and noninvasive screening method for LC, BC, CC, and PC based on breath testing with a novel nanosensors approach. With this in mind, we propose to: (a) modify an array of nanosensors based on Au nanoparticles for obtaining highly-sensitive detection levels of breath biomarkers of cancer; and (b) investigate the use of the developed array in a clinical study. Towards this end, we will collect suitable breath samples from patients and healthy controls in a clinical trial and test the feasibility of the device to detect LC, BC, CC, and PC, also in the presence of other diseases. We will then investigate possible ways to identify the stage of the disease, monitor the response to cancer treatment, and to identify cancer subtypes. Further, we propose that the device can be used for monitoring of cancer patients during and after treatment. The chemical nature of the cancer biomarkers will be identified through spectrometry techniques. The proposed approach would be used outside specialist settings and could considerably lessen the burden on the health budgets, both through the low cost of the proposed all-inclusive cancer test, and through earlier and, hence, more cost-effective cancer treatment.
Cancer is rapidly becoming the greatest health hazard of our days. The most widespread cancers, are lung cancer (LC), breast cancer (BC), colorectal cancer (CC), and prostate cancer (PC). The impact of the various techniques used for diagnosis, screening and monitoring these cancers is either uncertain and/or inconvenient for the patients. This proposal aims to create a low-cost, easy-to-use and noninvasive screening method for LC, BC, CC, and PC based on breath testing with a novel nanosensors approach. With this in mind, we propose to: (a) modify an array of nanosensors based on Au nanoparticles for obtaining highly-sensitive detection levels of breath biomarkers of cancer; and (b) investigate the use of the developed array in a clinical study. Towards this end, we will collect suitable breath samples from patients and healthy controls in a clinical trial and test the feasibility of the device to detect LC, BC, CC, and PC, also in the presence of other diseases. We will then investigate possible ways to identify the stage of the disease, monitor the response to cancer treatment, and to identify cancer subtypes. Further, we propose that the device can be used for monitoring of cancer patients during and after treatment. The chemical nature of the cancer biomarkers will be identified through spectrometry techniques. The proposed approach would be used outside specialist settings and could considerably lessen the burden on the health budgets, both through the low cost of the proposed all-inclusive cancer test, and through earlier and, hence, more cost-effective cancer treatment.
Project acronym DNA-AMP
Project DNA Adduct Molecular Probes: Elucidating the Diet-Cancer Connection at Chemical Resolution
Researcher (PI) Shana Jocette Sturla
Summary Bulky DNA adducts formed from chemical carcinogens dictate structure, reactivity, and mechanism of chemical-biological reactions; therefore, their identification is central to evaluating and mitigating cancer risk. Natural food components, or others associated with certain food preparations or metabolic conversions, initiate potentially damaging genetic mutations after forming DNA adducts, which contribute critically to carcinogenesis, despite the fact that they are typically repaired biochemically and they are formed at extremely low levels. This situation places significant limitations on our ability to understand the role of formation, repair, and mutagenesis on the basis of the complex DNA reactivity profiles of food components. The long-term goals of this research are to contribute basic knowledge and advanced experimental tools required to understand, on the basis of chemical structure, the contributions of chronic, potentially adverse, dietary chemical carcinogen exposure to cancer development. It is proposed that a new class of synthetic nucleosides, devised on the basis of preliminary discoveries made in the independent laboratory of the applicant, will serve as molecular probes for bulky DNA adducts and can be effectively used to study and AMPlify, i.e. as a sensitive diagnostic tool, low levels of chemically-specific modes of DNA damage. The proposed research is a chemical biology-based approach to the study of carcinogenesis. Experiments involve chemical synthesis, thermodynamic and kinetic characterization DNA-DNA and enzyme-DNA interactions, and nanoparticle-based molecular probes. The proposal describes a potentially ground-breaking approach for profiling the biological reactivities of chemical carcinogens, and we expect to gain fundamental knowledge and chemical tools that can contribute to the prevention of diseases influenced by gene-environment interactions.
Bulky DNA adducts formed from chemical carcinogens dictate structure, reactivity, and mechanism of chemical-biological reactions; therefore, their identification is central to evaluating and mitigating cancer risk. Natural food components, or others associated with certain food preparations or metabolic conversions, initiate potentially damaging genetic mutations after forming DNA adducts, which contribute critically to carcinogenesis, despite the fact that they are typically repaired biochemically and they are formed at extremely low levels. This situation places significant limitations on our ability to understand the role of formation, repair, and mutagenesis on the basis of the complex DNA reactivity profiles of food components. The long-term goals of this research are to contribute basic knowledge and advanced experimental tools required to understand, on the basis of chemical structure, the contributions of chronic, potentially adverse, dietary chemical carcinogen exposure to cancer development. It is proposed that a new class of synthetic nucleosides, devised on the basis of preliminary discoveries made in the independent laboratory of the applicant, will serve as molecular probes for bulky DNA adducts and can be effectively used to study and AMPlify, i.e. as a sensitive diagnostic tool, low levels of chemically-specific modes of DNA damage. The proposed research is a chemical biology-based approach to the study of carcinogenesis. Experiments involve chemical synthesis, thermodynamic and kinetic characterization DNA-DNA and enzyme-DNA interactions, and nanoparticle-based molecular probes. The proposal describes a potentially ground-breaking approach for profiling the biological reactivities of chemical carcinogens, and we expect to gain fundamental knowledge and chemical tools that can contribute to the prevention of diseases influenced by gene-environment interactions.
Project acronym DPI
Project Deep Packet Inspection to Next Generation Network Devices
Researcher (PI) Anat Bremler-Barr
Host Institution (HI) INTERDISCIPLINARY CENTER (IDC) HERZLIYA
Summary Deep packet inspection (DPI) lies at the core of contemporary Network Intrusion Detection/Prevention Systems and Web Application Firewall. DPI aims to identify various malware (including spam and viruses), by inspecting both the header and the payload of each packet and comparing it to a known set of patterns. DPI are often performed on the critical path of the packet processing, thus the overall performance of the security tools is dominated by the speed of DPI. Traditionally, DPI considered only exact string patterns. However, in modern network devices patterns are often represented by regular expressions due to their superior expressiveness. Matching both exact string and regular expressions are well-studied area in Computer Science; however all well-known solutions are not sufficient for current network demands: First, current solutions do not scale in terms of speed, memory and power requirements. While current network devices work at 10-100 Gbps and have thousands of patterns, traditional solutions suffer from exponential memory size or exponential time and induce prohibitive power consumption. Second, non clear-text traffic, such as compressed traffic, becomes a dominant portion of the Internet and is clearly harder to inspect. In this research we design new algorithms and schemes that cope with today demand. This is evolving area both in the Academia and Industry, where currently there is no adequate solution. We intend to use recent advances in hardware to cope with these demanding requirements. More specifically, we plan to use Ternary Content-Addressable Memories (TCAMs), which become standard commodity in contemporary network devices. TCAMs can compare a key against all rules in a memory in parallel and thus provide high throughput. We believ
Deep packet inspection (DPI) lies at the core of contemporary Network Intrusion Detection/Prevention Systems and Web Application Firewall. DPI aims to identify various malware (including spam and viruses), by inspecting both the header and the payload of each packet and comparing it to a known set of patterns. DPI are often performed on the critical path of the packet processing, thus the overall performance of the security tools is dominated by the speed of DPI. Traditionally, DPI considered only exact string patterns. However, in modern network devices patterns are often represented by regular expressions due to their superior expressiveness. Matching both exact string and regular expressions are well-studied area in Computer Science; however all well-known solutions are not sufficient for current network demands: First, current solutions do not scale in terms of speed, memory and power requirements. While current network devices work at 10-100 Gbps and have thousands of patterns, traditional solutions suffer from exponential memory size or exponential time and induce prohibitive power consumption. Second, non clear-text traffic, such as compressed traffic, becomes a dominant portion of the Internet and is clearly harder to inspect. In this research we design new algorithms and schemes that cope with today demand. This is evolving area both in the Academia and Industry, where currently there is no adequate solution. We intend to use recent advances in hardware to cope with these demanding requirements. More specifically, we plan to use Ternary Content-Addressable Memories (TCAMs), which become standard commodity in contemporary network devices. TCAMs can compare a key against all rules in a memory in parallel and thus provide high throughput. We believ
Project acronym DYNACLOCK
Project Dynamic protein-DNA interactomes and circadian transcription regulatory networks in mammals
Researcher (PI) Felix Naef
Summary The aim of this project is to understand the dynamics of protein-DNA interactomes underlying circadian oscillators in mammals, and how these shape circadian transcriptional output programs. Specifically our goal is to solve a fundamental issue in circadian biology: the phase specificity problem underlying circadian gene expression. We have taken a challenging and original multi-disciplinary approach in which molecular biology experiments will be tightly interlinked with computational analyses and biophysical modeling. The approach will generate time resolved protein-DNA interactomes in mouse liver for several key circadian repressors at unprecedented resolution. These experiments will be complemented with chromosome conformation capture (3C) experiments to monitor how looping interactions and 3D genome structure rearrange during the circadian cycle, which will inform on how circadian transcription networks use long-range gene regulatory mechanisms. Novel computational algorithms based on biophysical principles will be developed and implemented to optimally analyze interactome and 3C datasets. For the latter, statistical models from polymer physics will be used to reconstruct the chromatin networks and interaction maps from the 3C data. At the detailed level of individual cells, we will investigate transcription bursts, and how those are involved in the control of circadian gene expression. In particular we will exploit high temporal resolution bioluminescence reporters using a biophysical model of transcription coupled with a Hidden Markov Model (HMM). Through our innovative approach, we expect that the data generated and state-of-the-art analyses performed will lead novel insight into the role and mechanics of circadian transcription in controlling circadian outputs in mammals.
The aim of this project is to understand the dynamics of protein-DNA interactomes underlying circadian oscillators in mammals, and how these shape circadian transcriptional output programs. Specifically our goal is to solve a fundamental issue in circadian biology: the phase specificity problem underlying circadian gene expression. We have taken a challenging and original multi-disciplinary approach in which molecular biology experiments will be tightly interlinked with computational analyses and biophysical modeling. The approach will generate time resolved protein-DNA interactomes in mouse liver for several key circadian repressors at unprecedented resolution. These experiments will be complemented with chromosome conformation capture (3C) experiments to monitor how looping interactions and 3D genome structure rearrange during the circadian cycle, which will inform on how circadian transcription networks use long-range gene regulatory mechanisms. Novel computational algorithms based on biophysical principles will be developed and implemented to optimally analyze interactome and 3C datasets. For the latter, statistical models from polymer physics will be used to reconstruct the chromatin networks and interaction maps from the 3C data. At the detailed level of individual cells, we will investigate transcription bursts, and how those are involved in the control of circadian gene expression. In particular we will exploit high temporal resolution bioluminescence reporters using a biophysical model of transcription coupled with a Hidden Markov Model (HMM). Through our innovative approach, we expect that the data generated and state-of-the-art analyses performed will lead novel insight into the role and mechanics of circadian transcription in controlling circadian outputs in mammals.
Project acronym EPIGENOME
Project Understanding epigenetic mechanisms of complex genome editing in eukaryotes
Researcher (PI) Mariusz Nowacki
Host Institution (HI) UNIVERSITAET BERN
Summary The scientific goal of this proposal is to contribute to our understanding of RNA-mediated epigenetic mechanisms of genome regulation in eukaryotes. Choosing ciliated protozoa as model organisms gives a wonderful opportunity to study the incredibly complex epigenetic mechanism of programming large-scale developmental rearrangements of the genome. This involves extensive rearrangements of the germline DNA, including elimination of up to 95% of the genome. The massive DNA rearrangement makes ciliates the perfect model organism to study this aspect of germline-soma differentiation. This process is proposed to be regulated by an RNA-mediated homology-dependent comparison of the germline and somatic genomes. Ciliate's genomic subtraction is one of the most fascinating examples of the use of RNA-mediated epigenetic regulation, and of a specialized RNA interference pathway, to convey non-Mendelian inheritance in eukaryotes. The 'genome scanning' model raises many interesting questions, which are also relevant to other RNA-mediated regulation systems. One of the most intriguing is a 'thermodynamic' problem: the model assumes that a very complex population of small RNAs representing the entire germline genome can be compared to longer transcripts representing the entire rearranged maternal genome, resulting in the efficient selection of germline-specific scnRNAs, which are able to target DNA deletions in the developing nucleus. How is it possible that the truly enormous number of pairing interactions implied can occur in such a short time, just a few hours? RNA-RNA pairing interactions would probably have to be assisted by a dedicated molecular machinery. This proposal focuses on characterizing proteins and RNAs that can orchestrate the massive genome rearrangements in ciliates.
The scientific goal of this proposal is to contribute to our understanding of RNA-mediated epigenetic mechanisms of genome regulation in eukaryotes. Choosing ciliated protozoa as model organisms gives a wonderful opportunity to study the incredibly complex epigenetic mechanism of programming large-scale developmental rearrangements of the genome. This involves extensive rearrangements of the germline DNA, including elimination of up to 95% of the genome. The massive DNA rearrangement makes ciliates the perfect model organism to study this aspect of germline-soma differentiation. This process is proposed to be regulated by an RNA-mediated homology-dependent comparison of the germline and somatic genomes. Ciliate's genomic subtraction is one of the most fascinating examples of the use of RNA-mediated epigenetic regulation, and of a specialized RNA interference pathway, to convey non-Mendelian inheritance in eukaryotes. The 'genome scanning' model raises many interesting questions, which are also relevant to other RNA-mediated regulation systems. One of the most intriguing is a 'thermodynamic' problem: the model assumes that a very complex population of small RNAs representing the entire germline genome can be compared to longer transcripts representing the entire rearranged maternal genome, resulting in the efficient selection of germline-specific scnRNAs, which are able to target DNA deletions in the developing nucleus. How is it possible that the truly enormous number of pairing interactions implied can occur in such a short time, just a few hours? RNA-RNA pairing interactions would probably have to be assisted by a dedicated molecular machinery. This proposal focuses on characterizing proteins and RNAs that can orchestrate the massive genome rearrangements in ciliates.
Project acronym ER ARCHITECTURE
Project Uncovering the Mechanisms of Endoplasmic Reticulum Sub-Domain Creation and Maintenance
Researcher (PI) Maya Benyamina Schuldiner
Summary The endoplasmic reticulum (ER) is the cellular organelle that serves as the entry site into the secretory pathway. Although the ER has a single continuous membrane, it is functionally divided into subdomains (SDs). These specialized regions allow the ER to carry out a multitude of functions such as folding, maturation, quality control and export, of all secreted and most membrane bound proteins; lipid biosynthesis; ion homeostasis; and communication with all other organelles. The ER is therefore not only the largest single copy organelle in most eukaryotic cells, but, thanks to the presence of SDs, also one of the more functionally diverse and structurally complex. Changes in ER functions have been shown to contribute to the progression of many diseases such as heart disease, neurodegeneration and diabetes. Moreover, a robustly functioning ER is required for development of dedicated secretory cells such as antibody producing plasma cells and insulin secreting pancreatic cells. The past years have brought about a revolution in our understanding of basic ER functions and the homeostatic responses coordinating them. However, despite their obvious importance for robust activity of the ER, we still know very little about SD biogenesis and function. Therefore, the time is now ripe to extend our understanding by facing the next challenges in the field. Specifically, it is now of major importance to understand how cells ensure accurate SD biogenesis and function. This proposal tackles this question by three independent but complementary screens each aimed at revealing one aspect of SDs: their structure/function, biogenesis or dynamics. The merging of all three aspects of information will give us a holistic picture of this process – one that could not have been attained by the pixilated view of any single piece of data. We propose to explore these facets in both yeast and mammals utilizing systematic tools such as high content microscopic screens followed up by the creation of genetic interaction maps and follow-up hypothesis based biochemical and genetic experiments. By combining several approaches and different organisms we hope to enable a more efficient reconstruction of this complex process. When completed this proposal will have shed light on a little explored but central question in cellular biology. More broadly, the mechanisms that arise as guiding SD biogenesis may help us in understanding how membrane domains form in general. Due to the novelty of our approach and the cutting-edge tools used to tackle this fundamental problem in cell biology, this work will provide a paradigm for addressing complex biological questions in eukaryotic cells. It may very well be that it is this aspect of the proposal that may ultimately most broadly impact the biological community.
The endoplasmic reticulum (ER) is the cellular organelle that serves as the entry site into the secretory pathway. Although the ER has a single continuous membrane, it is functionally divided into subdomains (SDs). These specialized regions allow the ER to carry out a multitude of functions such as folding, maturation, quality control and export, of all secreted and most membrane bound proteins; lipid biosynthesis; ion homeostasis; and communication with all other organelles. The ER is therefore not only the largest single copy organelle in most eukaryotic cells, but, thanks to the presence of SDs, also one of the more functionally diverse and structurally complex. Changes in ER functions have been shown to contribute to the progression of many diseases such as heart disease, neurodegeneration and diabetes. Moreover, a robustly functioning ER is required for development of dedicated secretory cells such as antibody producing plasma cells and insulin secreting pancreatic cells. The past years have brought about a revolution in our understanding of basic ER functions and the homeostatic responses coordinating them. However, despite their obvious importance for robust activity of the ER, we still know very little about SD biogenesis and function. Therefore, the time is now ripe to extend our understanding by facing the next challenges in the field. Specifically, it is now of major importance to understand how cells ensure accurate SD biogenesis and function. This proposal tackles this question by three independent but complementary screens each aimed at revealing one aspect of SDs: their structure/function, biogenesis or dynamics. The merging of all three aspects of information will give us a holistic picture of this process – one that could not have been attained by the pixilated view of any single piece of data. We propose to explore these facets in both yeast and mammals utilizing systematic tools such as high content microscopic screens followed up by the creation of genetic interaction maps and follow-up hypothesis based biochemical and genetic experiments. By combining several approaches and different organisms we hope to enable a more efficient reconstruction of this complex process. When completed this proposal will have shed light on a little explored but central question in cellular biology. More broadly, the mechanisms that arise as guiding SD biogenesis may help us in understanding how membrane domains form in general. Due to the novelty of our approach and the cutting-edge tools used to tackle this fundamental problem in cell biology, this work will provide a paradigm for addressing complex biological questions in eukaryotic cells. It may very well be that it is this aspect of the proposal that may ultimately most broadly impact the biological community.
Project acronym ESKIN
Project Stretchable Electronic Skins
Researcher (PI) Stephanie Perichon Ep Lacour
Summary Future electronic systems will be soft and elastic. I propose to explore the materials, technology and integration of stretchable electronic systems, which will transform at will, evenly coat a spherical lens, or smoothly interface with a delicate biological organ. Electronics will be anywhere as well as everywhere. The proposed programme has the potential to emulate yet another revolution in the microelectronics industry and trigger transformations in the biomedical sector. The ESKIN programme is an ambitious and highly interdisciplinary endeavour requiring expertise at the frontier of engineering, material sciences, biotechnology and neuroscience. Stretchability in an electronic system is its ability to negotiate mechanical deformations without letting them interfere with its electrical functionality. This is a novel and challenging demand on electronic device technology, which has, to date, mainly pushed for smaller scale fabrication and increased performance. Furthermore the natural compliance of biological tissues and cells calls for softer electronic biomedical interfaces. Overcoming the hard to soft mechanical mismatch will, without doubt, open up new horizons in biomedical research and its related industries. The manufacture of stretchable electronic skins will then require working out the underlying science and technology for active device materials on soft, elastic substrates. This capability will further be implemented to demonstrate various soft and elastic electronic systems ranging from stretchable displays to long-term neural implants. My philosophy is to exploit as much as possible current micro/nanofabrication techniques available for hard surfaces but to tailor them to soft surfaces , optimizing and improving them where needed, in order to ensure rapid transition to worldwide distributed consumer and healthcare products.
Future electronic systems will be soft and elastic. I propose to explore the materials, technology and integration of stretchable electronic systems, which will transform at will, evenly coat a spherical lens, or smoothly interface with a delicate biological organ. Electronics will be anywhere as well as everywhere. The proposed programme has the potential to emulate yet another revolution in the microelectronics industry and trigger transformations in the biomedical sector. The ESKIN programme is an ambitious and highly interdisciplinary endeavour requiring expertise at the frontier of engineering, material sciences, biotechnology and neuroscience. Stretchability in an electronic system is its ability to negotiate mechanical deformations without letting them interfere with its electrical functionality. This is a novel and challenging demand on electronic device technology, which has, to date, mainly pushed for smaller scale fabrication and increased performance. Furthermore the natural compliance of biological tissues and cells calls for softer electronic biomedical interfaces. Overcoming the hard to soft mechanical mismatch will, without doubt, open up new horizons in biomedical research and its related industries. The manufacture of stretchable electronic skins will then require working out the underlying science and technology for active device materials on soft, elastic substrates. This capability will further be implemented to demonstrate various soft and elastic electronic systems ranging from stretchable displays to long-term neural implants. My philosophy is to exploit as much as possible current micro/nanofabrication techniques available for hard surfaces but to tailor them to soft surfaces , optimizing and improving them where needed, in order to ensure rapid transition to worldwide distributed consumer and healthcare products.
Project acronym EURIBIO
Project Dissecting the biogenesis of eukaryotic ribosomal subunits
Researcher (PI) Vikram Govind Panse
Summary In all living cells, the important task of protein synthesis is carried out by the ribosome. A substantial amount of cellular energy and resources is utilized to manufacture ribosomal subunits. In contrast to prokaryotes, eukaryotic ribosome assembly requires a multitude of conserved non-ribosomal trans-acting factors, which transiently associate with pre-ribosomal particles at distinct assembly stages and perform specific maturation steps. Large-scale proteomic approaches in budding yeast, have rapidly expanded the inventory of trans-acting factors (~200). However, little is known regarding their precise site(s) of action and the role(s) of these factors during pre-ribosome assembly. Upon accomplishing their task, majority of the trans-acting factors, are typically released from maturing pre-ribosomes already in the nucleolus/nucleus. Strikingly, a handful of factors remain associated with pre-ribosomes and facilitate their export into the cytoplasm. Release of these factors constitutes "late cytoplasmic maturation events" which render exported pre-ribosomes translation competent. In this proposal we will exploit the powerful model organism budding yeast to: (1) Develop novel biochemical tools to elucidate the molecular environment of trans-acting factors on the surface of pre-ribosomal particles. These analyses will provide us a low-resolution biochemical map of a maturing pre-ribosome. (2) Exploit the powerful combination of genetic and high-throughput visual screening approaches in budding yeast to unravel novel "late cytoplasmic maturation steps" in the 60S biogenesis pathway. Together, my research proposal aims to contribute significantly to our current knowledge regarding the construction and nuclear export of eukaryotic pre-ribosomes. Our analysis will lead us to general principles that underlie the dynamic assembly/dissassembly of large macromolecular ribonucleo-protein complexes.
In all living cells, the important task of protein synthesis is carried out by the ribosome. A substantial amount of cellular energy and resources is utilized to manufacture ribosomal subunits. In contrast to prokaryotes, eukaryotic ribosome assembly requires a multitude of conserved non-ribosomal trans-acting factors, which transiently associate with pre-ribosomal particles at distinct assembly stages and perform specific maturation steps. Large-scale proteomic approaches in budding yeast, have rapidly expanded the inventory of trans-acting factors (~200). However, little is known regarding their precise site(s) of action and the role(s) of these factors during pre-ribosome assembly. Upon accomplishing their task, majority of the trans-acting factors, are typically released from maturing pre-ribosomes already in the nucleolus/nucleus. Strikingly, a handful of factors remain associated with pre-ribosomes and facilitate their export into the cytoplasm. Release of these factors constitutes "late cytoplasmic maturation events" which render exported pre-ribosomes translation competent. In this proposal we will exploit the powerful model organism budding yeast to: (1) Develop novel biochemical tools to elucidate the molecular environment of trans-acting factors on the surface of pre-ribosomal particles. These analyses will provide us a low-resolution biochemical map of a maturing pre-ribosome. (2) Exploit the powerful combination of genetic and high-throughput visual screening approaches in budding yeast to unravel novel "late cytoplasmic maturation steps" in the 60S biogenesis pathway. Together, my research proposal aims to contribute significantly to our current knowledge regarding the construction and nuclear export of eukaryotic pre-ribosomes. Our analysis will lead us to general principles that underlie the dynamic assembly/dissassembly of large macromolecular ribonucleo-protein complexes.
Project acronym EURO-NEUROSTRESS
Project Dissecting the Central Stress Response: Bridging the Genotype-Phenotype Gap
Researcher (PI) Alon Chen
Summary The biological response to stress is concerned with the maintenance of homeostasis in the presence of real or perceived challenges. This process requires numerous adaptive responses involving changes in the central nervous and neuroendocrine systems. When a situation is perceived as stressful, the brain activates many neuronal circuits linking centers involved in sensory, motor, autonomic, neuroendocrine, cognitive, and emotional functions in order to adapt to the demand. However, the details of the pathways by which the brain translates stressful stimuli into the final, integrated biological response are presently incompletely understood. Nevertheless, it is clear that dysregulation of these physiological responses to stress can have severe psychological and physiological consequences, and there is much evidence to suggest that inappropriate regulation, disproportional intensity, or chronic and/or irreversible activation of the stress response is linked to the etiology and pathophysiology of anxiety disorders and depression. Understanding the neurobiology of stress by focusing on the brain circuits and genes, which are associated with, or altered by, the stress response will provide important insights into the brain mechanisms by which stress affects psychological and physiological disorders. This is an integrated multidisciplinary project from gene to behavior using state-of-the-art moue genetics and animal models. We will employ integrated molecular, biochemical, physiological and behavioral methods, focusing on the generation of mice genetic models as an in vivo tool, in order to study the central pathways and molecular mechanisms mediating the stress response. Defining the contributions of known and novel gene products to the maintenance of stress-linked homeostasis may improve our ability to design therapeutic interventions for, and thus manage, stress-related disorders.
The biological response to stress is concerned with the maintenance of homeostasis in the presence of real or perceived challenges. This process requires numerous adaptive responses involving changes in the central nervous and neuroendocrine systems. When a situation is perceived as stressful, the brain activates many neuronal circuits linking centers involved in sensory, motor, autonomic, neuroendocrine, cognitive, and emotional functions in order to adapt to the demand. However, the details of the pathways by which the brain translates stressful stimuli into the final, integrated biological response are presently incompletely understood. Nevertheless, it is clear that dysregulation of these physiological responses to stress can have severe psychological and physiological consequences, and there is much evidence to suggest that inappropriate regulation, disproportional intensity, or chronic and/or irreversible activation of the stress response is linked to the etiology and pathophysiology of anxiety disorders and depression. Understanding the neurobiology of stress by focusing on the brain circuits and genes, which are associated with, or altered by, the stress response will provide important insights into the brain mechanisms by which stress affects psychological and physiological disorders. This is an integrated multidisciplinary project from gene to behavior using state-of-the-art moue genetics and animal models. We will employ integrated molecular, biochemical, physiological and behavioral methods, focusing on the generation of mice genetic models as an in vivo tool, in order to study the central pathways and molecular mechanisms mediating the stress response. Defining the contributions of known and novel gene products to the maintenance of stress-linked homeostasis may improve our ability to design therapeutic interventions for, and thus manage, stress-related disorders.
Project acronym EVOLOME
Project Genetic and phenotypic precursors of antibiotic resistance in evolving bacterial populations: from single cell to population level analyses
Researcher (PI) Nathalie Balaban
Summary Soon after new antibiotics are introduced, bacterial strains resistant to their action emerge. Recently, non-specific factors that promote the later appearance of specific mechanisms of resistance have been found. Some of these so-called global factors (as opposed to specific resistance mechanisms) emerge as major players in shaping the rate of evolution of resistance. For example, a mutation in the mismatch repair system is a global genetic factor that increases the mutation rate and therefore leads to an increased probability to evolve resistance. In addition to global genetic factors, it is becoming clear that global phenotypic factors play a crucial role in resistance evolution. For example, activation of stress responses can also result in an elevated mutation rate and accelerated evolution of drug resistance. A natural question which arises in this context is how sub-populations of phenotypic variants differ in their evolutionary potential, and how that, in turn, affects the rate at which an entire population adapts to antibiotic stress. I propose a multidisciplinary approach to the systematic and quantitative study of the non-specific factors that affect the mode and tempo of evolution towards antibiotic resistance. Our preliminary results indicate that the presence of dormant bacteria that survive antibiotic treatment affects the rate of resistance evolution in bacterial populations. I will exploit the established expertise of my lab using microfluidic devices for single cell analyses to track the emergence of resistance at the single-cell level, in real-time, and to study the correlation between the phenotype of single bacteria and the probability to evolve resistance. My second approach will take advantage of the recent developments in experimental evolution and high throughput sequencing and combine those with single cells observations for the systematic search of E.coli genes that affect the rate of resistance evolution. We will study replicate populations of E.coli, founded by either laboratory strains or clinical isolates, as they evolve in parallel, under antibiotic stress. Evolved populations will be compared with ancestral populations in order to identify genes and phenotypes that have changed during the evolution of antibiotic resistance. Finally, in silico evolution that simulates the experimental conditions will be developed to analyze the contribution of global factors on resistance evolution. The evolution of antibiotic resistance is not only a fascinating demonstration of the power of evolution but also represents one of the major health threats today. I anticipate that this multidisciplinary study of the global factors that influence the evolution of resistance, from the single cell to the population level, will shed light on the mechanisms used by bacteria to accelerate evolution in general, as well as provide clues as to how to prevent the emergence of antibiotic resistance.
Soon after new antibiotics are introduced, bacterial strains resistant to their action emerge. Recently, non-specific factors that promote the later appearance of specific mechanisms of resistance have been found. Some of these so-called global factors (as opposed to specific resistance mechanisms) emerge as major players in shaping the rate of evolution of resistance. For example, a mutation in the mismatch repair system is a global genetic factor that increases the mutation rate and therefore leads to an increased probability to evolve resistance. In addition to global genetic factors, it is becoming clear that global phenotypic factors play a crucial role in resistance evolution. For example, activation of stress responses can also result in an elevated mutation rate and accelerated evolution of drug resistance. A natural question which arises in this context is how sub-populations of phenotypic variants differ in their evolutionary potential, and how that, in turn, affects the rate at which an entire population adapts to antibiotic stress. I propose a multidisciplinary approach to the systematic and quantitative study of the non-specific factors that affect the mode and tempo of evolution towards antibiotic resistance. Our preliminary results indicate that the presence of dormant bacteria that survive antibiotic treatment affects the rate of resistance evolution in bacterial populations. I will exploit the established expertise of my lab using microfluidic devices for single cell analyses to track the emergence of resistance at the single-cell level, in real-time, and to study the correlation between the phenotype of single bacteria and the probability to evolve resistance. My second approach will take advantage of the recent developments in experimental evolution and high throughput sequencing and combine those with single cells observations for the systematic search of E.coli genes that affect the rate of resistance evolution. We will study replicate populations of E.coli, founded by either laboratory strains or clinical isolates, as they evolve in parallel, under antibiotic stress. Evolved populations will be compared with ancestral populations in order to identify genes and phenotypes that have changed during the evolution of antibiotic resistance. Finally, in silico evolution that simulates the experimental conditions will be developed to analyze the contribution of global factors on resistance evolution. The evolution of antibiotic resistance is not only a fascinating demonstration of the power of evolution but also represents one of the major health threats today. I anticipate that this multidisciplinary study of the global factors that influence the evolution of resistance, from the single cell to the population level, will shed light on the mechanisms used by bacteria to accelerate evolution in general, as well as provide clues as to how to prevent the emergence of antibiotic resistance.
Project acronym FIELDGRADIENTS
Project Phase Transitions and Chemical Reactions in Electric Field Gradients
Researcher (PI) Yoav Tsori
Summary We will study phase transitions and chemical and biological reactions in liquid mixtures in electric field gradients. These new phase transitions are essential in statistical physics and thermodynamics. We will examine theoretically the complex and yet unexplored phase ordering dynamics in which droplets nucleate and move under the external nonuniform force. We will look in detail at the interfacial instabilities which develop when the field is increased. We will investigate how time-varying potentials produce electromagnetic waves and how their spatial decay in the bistable liquid leads to phase changes. These transitions open a new and general way to control the spatio-temporal behaviour of chemical reactions by directly manipulating the solvents' concentrations. When two or more reagents are preferentially soluble in one of the mixture's components, field-induced phase separation leads to acceleration of the reaction. When the reagents are soluble in different solvents, field-induced demixing will lead to the reaction taking place at a slow rate and at a two-dimensional surface. Additionally, the electric field allows us to turn the reaction on or off. The numerical study and simulations will be complemented by experiments. We will study theoretically and experimentally biochemical reactions. We will find how actin-related structures are affected by field gradients. Using an electric field as a tool we will control the rate of actin polymerisation. We will investigate if an external field can damage cancer cells by disrupting their actin-related activity. The above phenomena will be studied in a microfluidics environment. We will elucidate the separation hydrodynamics occurring when thermodynamically miscible liquids flow in a channel and how electric fields can reversibly create and destroy optical interfaces, as is relevant in optofluidics. Chemical and biological reactions will be examined in the context of lab-on-a-chip.
We will study phase transitions and chemical and biological reactions in liquid mixtures in electric field gradients. These new phase transitions are essential in statistical physics and thermodynamics. We will examine theoretically the complex and yet unexplored phase ordering dynamics in which droplets nucleate and move under the external nonuniform force. We will look in detail at the interfacial instabilities which develop when the field is increased. We will investigate how time-varying potentials produce electromagnetic waves and how their spatial decay in the bistable liquid leads to phase changes. These transitions open a new and general way to control the spatio-temporal behaviour of chemical reactions by directly manipulating the solvents' concentrations. When two or more reagents are preferentially soluble in one of the mixture's components, field-induced phase separation leads to acceleration of the reaction. When the reagents are soluble in different solvents, field-induced demixing will lead to the reaction taking place at a slow rate and at a two-dimensional surface. Additionally, the electric field allows us to turn the reaction on or off. The numerical study and simulations will be complemented by experiments. We will study theoretically and experimentally biochemical reactions. We will find how actin-related structures are affected by field gradients. Using an electric field as a tool we will control the rate of actin polymerisation. We will investigate if an external field can damage cancer cells by disrupting their actin-related activity. The above phenomena will be studied in a microfluidics environment. We will elucidate the separation hydrodynamics occurring when thermodynamically miscible liquids flow in a channel and how electric fields can reversibly create and destroy optical interfaces, as is relevant in optofluidics. Chemical and biological reactions will be examined in the context of lab-on-a-chip.
Project acronym GENEXP
Project Gene Expression Explored in Space and Time Using Single Gene and Single Molecule Analysis
Researcher (PI) Yaron Shav-Tal
Host Institution (HI) BAR ILAN UNIVERSITY
Summary "Live-cell imaging combined with kinetic analyses has provided new biological insights on the gene expression pathway. However, such studies in mammalian cells typically require use of exogenous over-expressed gene constructs, which often form large tandem gene arrays and usually lack the complete endogenous regulatory sequences. It is therefore imperative to design methodology for analyzing gene expression kinetics of single alleles of endogenous genes. While certain steps have been taken in this direction, there are many experimental obstacles standing in the way of a robust genome-wide system for the in vivo examination of endogenous gene expression within the natural nuclear environment. GENEXP sets out to provide such a system. It will start with methodology for robust tagging of a multitude of endogenous genes and their transcribed mRNAs in human cells using the ""CD tagging"" approach. Thereby, in vivo mRNA synthesis at the nuclear site of RNA birth will be explored in a unique manner. A high-resolution study of gene expression, in particular mRNA transcription and mRNA export, under endogenous cellular context and using a genome-wide live-cell approach will be performed. GENEXP will specifically focus on the: i) Transcriptional kinetics of endogenous genes in single cells and cell populations; ii) Kinetics of mRNA export on the single molecule level; iii) Examination of the protein composition of endogenous mRNPs; iv) High throughput scan for drugs that affect gene expression and mRNA export. Altogether, GENEXP will provide breakthrough capability in kinetically quantifying the gene expression pathway of a large variety of endogenous genes, and the ability to examine the generated molecules on the single-molecule level. This will be done within their normal genomic and biological environment, at the single-allele level."
"Live-cell imaging combined with kinetic analyses has provided new biological insights on the gene expression pathway. However, such studies in mammalian cells typically require use of exogenous over-expressed gene constructs, which often form large tandem gene arrays and usually lack the complete endogenous regulatory sequences. It is therefore imperative to design methodology for analyzing gene expression kinetics of single alleles of endogenous genes. While certain steps have been taken in this direction, there are many experimental obstacles standing in the way of a robust genome-wide system for the in vivo examination of endogenous gene expression within the natural nuclear environment. GENEXP sets out to provide such a system. It will start with methodology for robust tagging of a multitude of endogenous genes and their transcribed mRNAs in human cells using the ""CD tagging"" approach. Thereby, in vivo mRNA synthesis at the nuclear site of RNA birth will be explored in a unique manner. A high-resolution study of gene expression, in particular mRNA transcription and mRNA export, under endogenous cellular context and using a genome-wide live-cell approach will be performed. GENEXP will specifically focus on the: i) Transcriptional kinetics of endogenous genes in single cells and cell populations; ii) Kinetics of mRNA export on the single molecule level; iii) Examination of the protein composition of endogenous mRNPs; iv) High throughput scan for drugs that affect gene expression and mRNA export. Altogether, GENEXP will provide breakthrough capability in kinetically quantifying the gene expression pathway of a large variety of endogenous genes, and the ability to examine the generated molecules on the single-molecule level. This will be done within their normal genomic and biological environment, at the single-allele level."
Project acronym GEOMETRYCELLCYCLE
Project Geometric control of the cell cycle in the fission yeast
Researcher (PI) Sophie Genevieve Elisabeth Martin Benton
Summary Cell cycle progression is monitored by checkpoints that ensure the fidelity of cell division and prevent unrestricted cell proliferation. Checkpoints also serve to couple cell size with division – a mechanism important to adapt to changing environmental conditions. While most studies on cell size homeostasis have focused on the links between size and biosynthetic activity, we have recently discovered a novel geometry-sensing mechanism by which fission yeast cells couple cell length with entry into mitosis. Conceptually, the system is remarkably simple: it is composed of a signal – the protein kinase Pom1 – forming concentration gradients from the ends of the cells, which inhibits a sensor – the protein kinase Cdr2, itself an activator of mitotic entry – placed at the cell equator. Since Pom1 concentration at the cell middle is higher in short cells than in long cells, this suggests a model where Pom1 inhibits Cdr2 until the cell has reached a sufficient length. These findings open a conceptually new way of thinking about cell size homeostasis and suggest that cell polarity and cell shape have important effect on cell cycle progression. The proposed project investigates the mechanisms and functional importance of this geometry-sensing system through four specific aims: Aim 1. Defining and modeling the molecular mechanisms of Pom1 gradient formation Aim 2. Dissecting the mechanisms of Pom1 action Aim 3. Investigating the influence of altered cell shape on cell proliferation Aim 4. Exploring the effect of environmental stresses to the Pom1-Cdr2 system By combining genetic, biochemical, physical, live-imaging and modeling approaches, this project will provide an integrated understanding of how cell geometry can be perceived at the molecular level and how this information is transduced to control cell proliferation. This work will have wide-ranging implication for our understanding of gradient formation, cell size homeostasis, and the role of cell polarity in proliferation. It will thus be of interest to cell, developmental and cancer biologists alike.
Cell cycle progression is monitored by checkpoints that ensure the fidelity of cell division and prevent unrestricted cell proliferation. Checkpoints also serve to couple cell size with division – a mechanism important to adapt to changing environmental conditions. While most studies on cell size homeostasis have focused on the links between size and biosynthetic activity, we have recently discovered a novel geometry-sensing mechanism by which fission yeast cells couple cell length with entry into mitosis. Conceptually, the system is remarkably simple: it is composed of a signal – the protein kinase Pom1 – forming concentration gradients from the ends of the cells, which inhibits a sensor – the protein kinase Cdr2, itself an activator of mitotic entry – placed at the cell equator. Since Pom1 concentration at the cell middle is higher in short cells than in long cells, this suggests a model where Pom1 inhibits Cdr2 until the cell has reached a sufficient length. These findings open a conceptually new way of thinking about cell size homeostasis and suggest that cell polarity and cell shape have important effect on cell cycle progression. The proposed project investigates the mechanisms and functional importance of this geometry-sensing system through four specific aims: Aim 1. Defining and modeling the molecular mechanisms of Pom1 gradient formation Aim 2. Dissecting the mechanisms of Pom1 action Aim 3. Investigating the influence of altered cell shape on cell proliferation Aim 4. Exploring the effect of environmental stresses to the Pom1-Cdr2 system By combining genetic, biochemical, physical, live-imaging and modeling approaches, this project will provide an integrated understanding of how cell geometry can be perceived at the molecular level and how this information is transduced to control cell proliferation. This work will have wide-ranging implication for our understanding of gradient formation, cell size homeostasis, and the role of cell polarity in proliferation. It will thus be of interest to cell, developmental and cancer biologists alike.
Project acronym GEQIT
Project Generalized (quantum) information theory
Researcher (PI) Renato Renner
Summary Information theory is a branch of science that studies, from a mathematical perspective, the processing, transmission, and storage of information. The classical theory has been established in 1948 by Claude Shannon and has later been extended to incorporate processes where information is represented by the state of quantum systems. A major limitation of the present theory of information is that various of its concepts and methods require, as an assumption, that the processes to be studied are iterated many times. For example, Shannon's well-known result that the Shannon entropy equals the data compression rate assumes a source that repeatedly emits data according to the same given distribution. In addition, such results are often only valid asymptotically as the number of iterations tends to infinity. While this limitation is normally acceptable when studying classical information-processing tasks such as channel coding (since communication channels are typically used repeatedly), it turns out to be a severe obstacle when analyzing new types of applications such as quantum cryptography. For instance, there is generally no sensible way to describe the attack strategy of an adversary against a quantum key distribution scheme as a recurrent process. The goal of this project is to overcome this limitation and develop a theory of (classical and quantum) information which is completely general. Among the potential applications are new types of cryptographic schemes providing device-independent security. That is, their security guarantees hold independently of the details (and imperfections) of the actual implementations.
Information theory is a branch of science that studies, from a mathematical perspective, the processing, transmission, and storage of information. The classical theory has been established in 1948 by Claude Shannon and has later been extended to incorporate processes where information is represented by the state of quantum systems. A major limitation of the present theory of information is that various of its concepts and methods require, as an assumption, that the processes to be studied are iterated many times. For example, Shannon's well-known result that the Shannon entropy equals the data compression rate assumes a source that repeatedly emits data according to the same given distribution. In addition, such results are often only valid asymptotically as the number of iterations tends to infinity. While this limitation is normally acceptable when studying classical information-processing tasks such as channel coding (since communication channels are typically used repeatedly), it turns out to be a severe obstacle when analyzing new types of applications such as quantum cryptography. For instance, there is generally no sensible way to describe the attack strategy of an adversary against a quantum key distribution scheme as a recurrent process. The goal of this project is to overcome this limitation and develop a theory of (classical and quantum) information which is completely general. Among the potential applications are new types of cryptographic schemes providing device-independent security. That is, their security guarantees hold independently of the details (and imperfections) of the actual implementations.
Project acronym HOSTRESPONSE
Project Host molecular and cellular responses to anti-cancer drug treatment as a potential biomarker for treatment outcome
Researcher (PI) Yuval Shaked
Summary Chemotherapy remains one of the most common treatment modalities for cancer. It is typically administered in cycles of bolus injections following 21 days of drug-free break periods. However, tumor regrowth between drug intervals is often observed, due in part, to rebound angiogenesis. Our previous studies demonstrated that bone marrow derived proangiogenic cells are acutely mobilized following certain chemotherapy treatments, accompanied by enhanced tumor angiogenesis, which can be blocked by prior treatment with antiangiogenic drugs. These findings indicate that unknown host-derived mechanisms induced by chemotherapy, can stimulate tumor growth. Since the efficacy of antiangiogenic drugs is dependent on several parameters such as tumor type, stage, and the type of chemotherapy, such a therapy is not beneficial for all patients, and thus, necessitates the identification of surrogate biomarkers to predict clinical outcome. To address this issue, we will integrate basic, translational, and clinical approaches to: (i) identify molecular and cellular host systemic responses following treatments; (ii) isolate novel factors by proteomic approaches which are altered during the course of the treatment, and evaluate their feasibility as biomarkers to predict clinical outcome; (iii) determine the relevance of these factors in clinical specimens; (iv) screen for therapeutic compounds which can block host responses mediating tumor growth in order to increase treatment efficacy. We believe that this strategy of combined approach will lead to the development of new tools in clinical oncology. Profiling individual host response to anti-cancer drug treatment may serve as a biomarker for treatment outcome and further promote the concept of personalised medicine in cancer therapy.
Chemotherapy remains one of the most common treatment modalities for cancer. It is typically administered in cycles of bolus injections following 21 days of drug-free break periods. However, tumor regrowth between drug intervals is often observed, due in part, to rebound angiogenesis. Our previous studies demonstrated that bone marrow derived proangiogenic cells are acutely mobilized following certain chemotherapy treatments, accompanied by enhanced tumor angiogenesis, which can be blocked by prior treatment with antiangiogenic drugs. These findings indicate that unknown host-derived mechanisms induced by chemotherapy, can stimulate tumor growth. Since the efficacy of antiangiogenic drugs is dependent on several parameters such as tumor type, stage, and the type of chemotherapy, such a therapy is not beneficial for all patients, and thus, necessitates the identification of surrogate biomarkers to predict clinical outcome. To address this issue, we will integrate basic, translational, and clinical approaches to: (i) identify molecular and cellular host systemic responses following treatments; (ii) isolate novel factors by proteomic approaches which are altered during the course of the treatment, and evaluate their feasibility as biomarkers to predict clinical outcome; (iii) determine the relevance of these factors in clinical specimens; (iv) screen for therapeutic compounds which can block host responses mediating tumor growth in order to increase treatment efficacy. We believe that this strategy of combined approach will lead to the development of new tools in clinical oncology. Profiling individual host response to anti-cancer drug treatment may serve as a biomarker for treatment outcome and further promote the concept of personalised medicine in cancer therapy.
Project acronym IMMA
Project Integrating the Multiple Meta-Analysis: a framework for evaluating and ranking multiple health care technologies
Researcher (PI) Georgia Salanti
Host Institution (HI) PANEPISTIMIO IOANNINON
Summary Health care practitioners face daily questions and make choices regarding the effectiveness and quality of several health technologies (e.g. alternative interventions). On this regard they usually consider meta-analysis; the statistical synthesis of results from relevant experiments. The main drawback of the current state of the art is that meta-analysis focuses on comparing only two alternatives. However, clinicians and scientists need to know the relative ranking of a set of alternative options and not only whether option A is better than B. There is an urgent need to establish and disseminate a robust framework for selecting among many treatment options, possibly after taking into account environmental and genetic interactions. The goal of the proposed project is to provide this by establishing and disseminating a revolutionary evidence synthesis toolkit. Its main methodological vehicle is a flexible statistical framework using Bayesian techniques for multiple-treatments meta-analysis. This will enable the relative ranking of all alternative health care options, will allow comprehensive use of all available data, will improve precision and confidence in the conclusions and will answer methodological questions related to bias. Once established in clinical epidemiology, the tool will be extended to genetic epidemiology to account for multiple genetic markers, environmental factors and effects of treatments. Based on ongoing collaborations with teams undertaking applied health care research I plan to evaluate the new tool empirically in real-life health care problems such as ranking the pharmacological treatments for osteoarthritis, indicating the best treatments for multiple sclerosis and ranking the vaccines for influenza.
Health care practitioners face daily questions and make choices regarding the effectiveness and quality of several health technologies (e.g. alternative interventions). On this regard they usually consider meta-analysis; the statistical synthesis of results from relevant experiments. The main drawback of the current state of the art is that meta-analysis focuses on comparing only two alternatives. However, clinicians and scientists need to know the relative ranking of a set of alternative options and not only whether option A is better than B. There is an urgent need to establish and disseminate a robust framework for selecting among many treatment options, possibly after taking into account environmental and genetic interactions. The goal of the proposed project is to provide this by establishing and disseminating a revolutionary evidence synthesis toolkit. Its main methodological vehicle is a flexible statistical framework using Bayesian techniques for multiple-treatments meta-analysis. This will enable the relative ranking of all alternative health care options, will allow comprehensive use of all available data, will improve precision and confidence in the conclusions and will answer methodological questions related to bias. Once established in clinical epidemiology, the tool will be extended to genetic epidemiology to account for multiple genetic markers, environmental factors and effects of treatments. Based on ongoing collaborations with teams undertaking applied health care research I plan to evaluate the new tool empirically in real-life health care problems such as ranking the pharmacological treatments for osteoarthritis, indicating the best treatments for multiple sclerosis and ranking the vaccines for influenza.
Project acronym INFORMATIONFLOW
Project Information Flow and Its Impact on Financial Markets
Researcher (PI) Ilan Kremer
Summary The importance of information asymmetry in financial markets has long been recognized in financial economics. Most existing models focus on the role of privately informed investors who influence prices through their trades. But in many cases the agents who have the biggest information advantage are insiders or the firms themselves; they are precluded from trading but can affect the information flow to the market. This endogenous information flow and its effect on financial market is the focus of the proposed project. By the term information flow we refer to a wide range of channels through which firms can communicate. The information can be part of a mandatory disclosure or a voluntary one. It can be verifiable or non-verifiable information. In addition there can be an implicit information transmission. A firm may choose certain actions to convey its private information (i.e. signaling) without any explicit announcements. The way firms convey this information may provide key insights into the behavior of financial markets and in particular the development of financial crises. The project combines theoretical and empirical work. In the theory part I plan to examine the channels mentioned above and develop testable implications. In the empirical part I plan to test these implications.
The importance of information asymmetry in financial markets has long been recognized in financial economics. Most existing models focus on the role of privately informed investors who influence prices through their trades. But in many cases the agents who have the biggest information advantage are insiders or the firms themselves; they are precluded from trading but can affect the information flow to the market. This endogenous information flow and its effect on financial market is the focus of the proposed project. By the term information flow we refer to a wide range of channels through which firms can communicate. The information can be part of a mandatory disclosure or a voluntary one. It can be verifiable or non-verifiable information. In addition there can be an implicit information transmission. A firm may choose certain actions to convey its private information (i.e. signaling) without any explicit announcements. The way firms convey this information may provide key insights into the behavior of financial markets and in particular the development of financial crises. The project combines theoretical and empirical work. In the theory part I plan to examine the channels mentioned above and develop testable implications. In the empirical part I plan to test these implications.
Project acronym ITERQCD
Project Iterative solution of the QCD perturbative expansion
Researcher (PI) Charalampos Anastasiou
Summary Particle physics phenomenology is in a revolutionary phase, due to breakthroughs in understanding the perturbative expansion of gauge theory amplitudes. Latest research hints to the existence of an unknown iterative structure. We aim to solve loop amplitudes at an arbitrary perturbative order in QCD from amplitudes at lower orders and eventually from the leading order. We will obtain accurate theoretical predictions for cross-sections of important LHC processes, leading to a preciser extraction of coupling strengths for new particle interactions that may be discovered at the LHC.
Particle physics phenomenology is in a revolutionary phase, due to breakthroughs in understanding the perturbative expansion of gauge theory amplitudes. Latest research hints to the existence of an unknown iterative structure. We aim to solve loop amplitudes at an arbitrary perturbative order in QCD from amplitudes at lower orders and eventually from the leading order. We will obtain accurate theoretical predictions for cross-sections of important LHC processes, leading to a preciser extraction of coupling strengths for new particle interactions that may be discovered at the LHC.
Project acronym JSMA
Project Jews and Slavs in the Middle Ages: Interaction and Cross-Fertilization
Researcher (PI) Alexander Kulik
Summary The central purpose of this project is to bring down interdisciplinary barriers by showing how the Slavic and the Jewish heritage can each be approached as a unique repository of the unknown texts, traditions, and sensibilities of the other. By focusing on previously unexplored or under-explored medieval texts, I aim to reconstruct the Jewish and Slavic legacies, some of whose materials have been considered lost, while others were misinterpreted or neglected. This research project will resort to historical and philological techniques hitherto considered mutually incompatible in this field. The study intends to use methods of cultural archaeology to explore medieval Judeo-Slavic transparency. By cultural transparency we understand the mutual permeability of different cultures, which facilitates the exchange of ideas and genres of creativity between them. Cultural archeology involves methods of multi-disciplinary research based on the assumption that Eastern Europe constituted a melting pot characterized by an intensive cross-fertilization of cultural legacies. Cultural archaeology studies different historical, religious, and literary texts by looking at them as a palimpsest in which earlier texts and types of discourse come to the fore as shaped by their contemporary socio-cultural settings. The proposed theme has far-reaching methodological implications beyond the Judeo-Slavic cultural realm. This project will build a model of cross-cultural interaction to achieve a better understanding of the situations in which different faith-based ethnic cultures cohabit.
The central purpose of this project is to bring down interdisciplinary barriers by showing how the Slavic and the Jewish heritage can each be approached as a unique repository of the unknown texts, traditions, and sensibilities of the other. By focusing on previously unexplored or under-explored medieval texts, I aim to reconstruct the Jewish and Slavic legacies, some of whose materials have been considered lost, while others were misinterpreted or neglected. This research project will resort to historical and philological techniques hitherto considered mutually incompatible in this field. The study intends to use methods of cultural archaeology to explore medieval Judeo-Slavic transparency. By cultural transparency we understand the mutual permeability of different cultures, which facilitates the exchange of ideas and genres of creativity between them. Cultural archeology involves methods of multi-disciplinary research based on the assumption that Eastern Europe constituted a melting pot characterized by an intensive cross-fertilization of cultural legacies. Cultural archaeology studies different historical, religious, and literary texts by looking at them as a palimpsest in which earlier texts and types of discourse come to the fore as shaped by their contemporary socio-cultural settings. The proposed theme has far-reaching methodological implications beyond the Judeo-Slavic cultural realm. This project will build a model of cross-cultural interaction to achieve a better understanding of the situations in which different faith-based ethnic cultures cohabit.
Project acronym KIDNEY CANCER
Project Molecular mechanisms underlying control of renal epithelial proliferative homeostasis
Researcher (PI) Ian James Frew
Summary This research grant has two major aspects. The first seeks to understand the molecular and cellular basis of the evolution of clear cell renal cell carcinoma(ccRCC), the most frequent form of kidney cancer. We will utilise an integrated approach based on mouse genetics, the use of primary kidney epithelial cell culture systems, genetic screening approaches using RNA interference libraries and analysis of the genetic and molecular changes that arise in human kidney tumours. The rationale behind these studies is that by better understanding the molecular causes of ccRCC it will be possible to identify new molecules or signaling pathways that could serve as appropriate therapeutic targets. The second aspect of this grant relates to the development of a flexible experimental platform that will allow the rapid and simultaneous up- and down-regulation of gene expression in the mouse kidney in a manner in which the affected cells are marked by a luminescent marker. This system will be based on the injection of modified lentiviral gene overexpression and gene knockdown vectors, allowing us to exploit recently-developed genome-wide cDNA libraries and RNA interference libraries. This experimental system should be equally applicable to other organ systems and will allow for the first time a systematic approach to the manipulation of gene expression in living mice, additionally bypassing the time limitations associated with conventional mouse genetic approaches. We aim to develop this system within the biological context of this grant and will combine it with live-animal imaging approaches to generate a series of mouse models of ccRCC. These will ultimately serve as invaluable tools for testing novel therapeutic approaches against this currently untreatable disease.
This research grant has two major aspects. The first seeks to understand the molecular and cellular basis of the evolution of clear cell renal cell carcinoma(ccRCC), the most frequent form of kidney cancer. We will utilise an integrated approach based on mouse genetics, the use of primary kidney epithelial cell culture systems, genetic screening approaches using RNA interference libraries and analysis of the genetic and molecular changes that arise in human kidney tumours. The rationale behind these studies is that by better understanding the molecular causes of ccRCC it will be possible to identify new molecules or signaling pathways that could serve as appropriate therapeutic targets. The second aspect of this grant relates to the development of a flexible experimental platform that will allow the rapid and simultaneous up- and down-regulation of gene expression in the mouse kidney in a manner in which the affected cells are marked by a luminescent marker. This system will be based on the injection of modified lentiviral gene overexpression and gene knockdown vectors, allowing us to exploit recently-developed genome-wide cDNA libraries and RNA interference libraries. This experimental system should be equally applicable to other organ systems and will allow for the first time a systematic approach to the manipulation of gene expression in living mice, additionally bypassing the time limitations associated with conventional mouse genetic approaches. We aim to develop this system within the biological context of this grant and will combine it with live-animal imaging approaches to generate a series of mouse models of ccRCC. These will ultimately serve as invaluable tools for testing novel therapeutic approaches against this currently untreatable disease.
Project acronym KRASHIMPE
Project KRas mutation interactions with host immunity in malignant pleural effusion
Researcher (PI) Georgios Stathopoulos
Host Institution (HI) PANEPISTIMIO PATRON
Summary Malignant pleural effusion (MPE) is a significant problem most commonly caused by adenocarcinomas. Although tumors involving the pleura vary in their ability to produce MPE, pathways critical for MPE formation are poorly defined. We have found that mouse tumors harboring mutant (")KRas produce MPE in mice while tumors without "KRas do not. LLC and MC38 lung and colon adenocarcinomas, potent inducers of MPE in syngeneic mice, harbor "KRas that drives constitutive Ras and alternative nuclear factor (NF)-ºB signaling, inflammatory gene expression, and recruitment of specific myeloid cells to the pleural space. In contrast, mouse B16 melanoma and AE17 mesothelioma have wtKRas, lack constitutive Ras/alternative NF-º' signaling, and are incapable of forming MPE. RNAi-mediated silencing of KRas in MC38 tumors abrogated MPE formation and Ras/alternative NF-º' activation, while these phenomena were reconstituted in B16 tumors after KRas overexpression. We hypothesize that Ras-activating mutations drive the inflammatory phenotype of adenocarcinomas critical for MPE formation, which is characterized by Ras/alternative NF-ºB activation, inflammatory signalling to host vasculature/immune system, and recruitment of specific myeloid cells, and results in endothelial proliferation/leakiness. To test this hypothesis, we propose to: 1) define the relationship between Ras-activating mutations (RAM) and MPE formation; 2) identify tumor cell Ras-dependent signalling pathways and gene expression signature critical for MPE formation; 3) investigate the host response to tumor cells with RAM that results in MPE; and 4) target Ras and dependent signalling pathways as potential therapy for MPE. Studies will be performed using delivery of mouse/human tumors with/without RAM into the pleura of syngeneic/immunocompromized mice and are likely to yield new insights into the mechanisms of pleural tumor progression and to identify novel approaches to treatment of cancer patients with MPE.
Malignant pleural effusion (MPE) is a significant problem most commonly caused by adenocarcinomas. Although tumors involving the pleura vary in their ability to produce MPE, pathways critical for MPE formation are poorly defined. We have found that mouse tumors harboring mutant (")KRas produce MPE in mice while tumors without "KRas do not. LLC and MC38 lung and colon adenocarcinomas, potent inducers of MPE in syngeneic mice, harbor "KRas that drives constitutive Ras and alternative nuclear factor (NF)-ºB signaling, inflammatory gene expression, and recruitment of specific myeloid cells to the pleural space. In contrast, mouse B16 melanoma and AE17 mesothelioma have wtKRas, lack constitutive Ras/alternative NF-º' signaling, and are incapable of forming MPE. RNAi-mediated silencing of KRas in MC38 tumors abrogated MPE formation and Ras/alternative NF-º' activation, while these phenomena were reconstituted in B16 tumors after KRas overexpression. We hypothesize that Ras-activating mutations drive the inflammatory phenotype of adenocarcinomas critical for MPE formation, which is characterized by Ras/alternative NF-ºB activation, inflammatory signalling to host vasculature/immune system, and recruitment of specific myeloid cells, and results in endothelial proliferation/leakiness. To test this hypothesis, we propose to: 1) define the relationship between Ras-activating mutations (RAM) and MPE formation; 2) identify tumor cell Ras-dependent signalling pathways and gene expression signature critical for MPE formation; 3) investigate the host response to tumor cells with RAM that results in MPE; and 4) target Ras and dependent signalling pathways as potential therapy for MPE. Studies will be performed using delivery of mouse/human tumors with/without RAM into the pleura of syngeneic/immunocompromized mice and are likely to yield new insights into the mechanisms of pleural tumor progression and to identify novel approaches to treatment of cancer patients with MPE.
Project acronym LBITAC
Project Lower Bounds and Identity Testing for Arithmetic Circuits
Researcher (PI) Amir Benbenishty Shpilka
Host Institution (HI) TEL AVIV UNIVERSITY
Summary The focus of our proposal is on arithmetic circuit complexity. Arithmetic circuits are the most common model for computing polynomials, over arbitrary fields. This model was studied by many researchers in the past 40 years but still not much is known on many of the basic problems concerning this model. In this research we propose to study some of the most exciting fundamental open problems in theoretical computer science: Proving lower bounds on the size of arithmetic circuits and finding efficient deterministic algorithms for checking identity of arithmetic circuits. Proving a strong lower bound or finding efficient deterministic algorithms to the polynomial identity testing problem are the most important problems in algebraic complexity and solving either of them will be a dramatic breakthrough in theoretical computer science. The two problems that we intend to study are closely related to each other - there are several known results showing that a solution to one of the problems may lead to a solution to the other. Thus, we propose to study strongly related problems that lie in the frontier of algebraic complexity. Any advance will be a significant contributions to the field of theoretical computer science.
The focus of our proposal is on arithmetic circuit complexity. Arithmetic circuits are the most common model for computing polynomials, over arbitrary fields. This model was studied by many researchers in the past 40 years but still not much is known on many of the basic problems concerning this model. In this research we propose to study some of the most exciting fundamental open problems in theoretical computer science: Proving lower bounds on the size of arithmetic circuits and finding efficient deterministic algorithms for checking identity of arithmetic circuits. Proving a strong lower bound or finding efficient deterministic algorithms to the polynomial identity testing problem are the most important problems in algebraic complexity and solving either of them will be a dramatic breakthrough in theoretical computer science. The two problems that we intend to study are closely related to each other - there are several known results showing that a solution to one of the problems may lead to a solution to the other. Thus, we propose to study strongly related problems that lie in the frontier of algebraic complexity. Any advance will be a significant contributions to the field of theoretical computer science.
Project acronym MININEXACT
Project Exact Mining from In-Exact Data
Researcher (PI) Michail Vlachos
Summary Data exchange and data publishing is an inherent component of our interconnected world. Industrial companies outsource datasets to marketing and mining firms in order to support business intelligence; medical institutions exchange collected clinical experiments; academic institutions create repositories and share datasets for promoting research collaboration. A common denominator in any data exchange is the 'transformation' of the original data, which usually results in 'distortion' of data. While accurate and useful information can be potentially distilled from the original data, operations such as anonymization, rights protection and compression result in modified datasets that very seldom retain the mining capacity of its original source. This proposal seeks to address questions such as the following: - How can we lossy compress datasets and still guarantee that mining operations are not distorted? - Is it possible to right protect datasets and provide assurances that this task shall not impair our ability to distill useful knowledge? - To what extent can we resolve data anonymization issues and yet retain the mining capacity of the original dataset? We will examine a fundamental and hard problem in the area of knowledge discovery, which is the delicate balance between data transformation and data utility under mining operations. The problem lies at the confluence of many areas, such as machine and statistical learning, information theory, data representation and optimization. We will focus on studying data transformation methods (compression, anonymization, right protection) that guarantee the preservation of the salient dataset characteristics, such that data mining operations on original and transformed dataset are retained as well as possible. We will investigate how graph-centric approaches, clustering, classification and visualization algorithms can be ported to work under the proposed mining-preservation paradigm. Additional research challenges i
Data exchange and data publishing is an inherent component of our interconnected world. Industrial companies outsource datasets to marketing and mining firms in order to support business intelligence; medical institutions exchange collected clinical experiments; academic institutions create repositories and share datasets for promoting research collaboration. A common denominator in any data exchange is the 'transformation' of the original data, which usually results in 'distortion' of data. While accurate and useful information can be potentially distilled from the original data, operations such as anonymization, rights protection and compression result in modified datasets that very seldom retain the mining capacity of its original source. This proposal seeks to address questions such as the following: - How can we lossy compress datasets and still guarantee that mining operations are not distorted? - Is it possible to right protect datasets and provide assurances that this task shall not impair our ability to distill useful knowledge? - To what extent can we resolve data anonymization issues and yet retain the mining capacity of the original dataset? We will examine a fundamental and hard problem in the area of knowledge discovery, which is the delicate balance between data transformation and data utility under mining operations. The problem lies at the confluence of many areas, such as machine and statistical learning, information theory, data representation and optimization. We will focus on studying data transformation methods (compression, anonymization, right protection) that guarantee the preservation of the salient dataset characteristics, such that data mining operations on original and transformed dataset are retained as well as possible. We will investigate how graph-centric approaches, clustering, classification and visualization algorithms can be ported to work under the proposed mining-preservation paradigm. Additional research challenges i
Project acronym MIRNA
Project Metal Ions and Metal Ion Complexes Guiding Folding and Function of Single RNA Molecules
Researcher (PI) Roland Karl Oliver Sigel
Summary RNAs play crucial roles in cellular metabolic processes, e.g. ribozymes in RNA-processing or riboswitches in the regulation of protein expression. Metal ions thereby guide and determine folding and function of every complex nucleic acid structure. Recently, it has become increasingly evident that RNA folding and catalysis are extremely sensitive to changes in concentration and nature of the metal ion involved as well as to single-atom changes in metal ion complexes. The elucidation of the specific binding of certain metal ions and their complexes by nucleic acids poses an enormous challenge. This recognition process must depend solely on basic coordination chemical principles but is poorly understood. The goal of this project is to understand the effect of metal ions and their complexes on local and global structure formation of single large RNAs: Specifically, the influence of metal ions on the assembly of the catalytic core of group II intron ribozymes as well as the influence of single corrin side chains of coenzyme B12 to induce the structural change of its 202 nucleotide long riboswitch will be characterized. Combining classical Inorganic, Coordination, Analytical, and Organic Chemistry with Biophysics, we will apply single molecule Förster Resonance Energy Transfer spectroscopy (smFRET) together with hydrolytic cleavage experiments and chemical synthesis. SmFRET studies allow us to investigate every molecule individually instead of a bulk signal and thus to observe also minor populations. Our results will reveal how single metal ions and ligand atoms guide and influence global structure, folding, and function of ribozymes and riboswitches, and promise to have a significant impact on Biological Inorganic Chemistry, RNA Biochemistry, as well as Medicinal Chemistry.
RNAs play crucial roles in cellular metabolic processes, e.g. ribozymes in RNA-processing or riboswitches in the regulation of protein expression. Metal ions thereby guide and determine folding and function of every complex nucleic acid structure. Recently, it has become increasingly evident that RNA folding and catalysis are extremely sensitive to changes in concentration and nature of the metal ion involved as well as to single-atom changes in metal ion complexes. The elucidation of the specific binding of certain metal ions and their complexes by nucleic acids poses an enormous challenge. This recognition process must depend solely on basic coordination chemical principles but is poorly understood. The goal of this project is to understand the effect of metal ions and their complexes on local and global structure formation of single large RNAs: Specifically, the influence of metal ions on the assembly of the catalytic core of group II intron ribozymes as well as the influence of single corrin side chains of coenzyme B12 to induce the structural change of its 202 nucleotide long riboswitch will be characterized. Combining classical Inorganic, Coordination, Analytical, and Organic Chemistry with Biophysics, we will apply single molecule Förster Resonance Energy Transfer spectroscopy (smFRET) together with hydrolytic cleavage experiments and chemical synthesis. SmFRET studies allow us to investigate every molecule individually instead of a bulk signal and thus to observe also minor populations. Our results will reveal how single metal ions and ligand atoms guide and influence global structure, folding, and function of ribozymes and riboswitches, and promise to have a significant impact on Biological Inorganic Chemistry, RNA Biochemistry, as well as Medicinal Chemistry.
Project acronym MIRNACLOCKNETWORKS
Project Towards a systemic view of the circadian clock: Integration of miRNAs into the molecular, cellular and neural circadian networks
Researcher (PI) Sebastian Kadener
Summary Circadian (24hs) rhythms in locomotor activity are one of the best-characterized behaviors at the molecular, cellular and neural levels. Despite that, our understanding of how these rhythms are generated is still limited. A major shortcoming of the current approaches in the field is that they depict the circadian clock as a mere addition of steps (and/or combination of parts). By doing so, the circadian oscillator is portrayed as a static rather than a dynamic system. We have recently shown for the first time that miRNA-mediated regulation plays a role in circadian timekeeping in Drosophila. In the present project we will exploit complementary and cutting-edge approaches that will provide an integrative and comprehensive view of the circadian timekeeping system. As we believe that miRNAs are key mediators of this integration, we will dissect their role in the circadian clock at the molecular, cellular and neural levels in Drosophila. At the molecular level, we will determine the mechanisms, and proteins that mediate the circadian regulation of miRNAs function. Moreover, by the use of high-throughput methodology we will assess and characterize the impact of translational regulation on both the circadian transcriptome and proteome. At the cellular level, we plan to determine how this type of regulation integrates with other circadian pathways and which specific pathways and proteins mediate this process. As a final goal of the proposed project we plan to generate a complete genetic interaction map of the known circadian regulators, which will integrate the different molecular and cellular events involved in timekeeping. This will be a key step towards the understanding of the circadian clock as a dynamic adjustable process. Last, but not least, we will study the role of miRNAs in the circadian neural network. For doing so we will set up an ex vivo approach (fly brain's culture) that will assess circadian parameters through fluorescent continuous live imaging.
Circadian (24hs) rhythms in locomotor activity are one of the best-characterized behaviors at the molecular, cellular and neural levels. Despite that, our understanding of how these rhythms are generated is still limited. A major shortcoming of the current approaches in the field is that they depict the circadian clock as a mere addition of steps (and/or combination of parts). By doing so, the circadian oscillator is portrayed as a static rather than a dynamic system. We have recently shown for the first time that miRNA-mediated regulation plays a role in circadian timekeeping in Drosophila. In the present project we will exploit complementary and cutting-edge approaches that will provide an integrative and comprehensive view of the circadian timekeeping system. As we believe that miRNAs are key mediators of this integration, we will dissect their role in the circadian clock at the molecular, cellular and neural levels in Drosophila. At the molecular level, we will determine the mechanisms, and proteins that mediate the circadian regulation of miRNAs function. Moreover, by the use of high-throughput methodology we will assess and characterize the impact of translational regulation on both the circadian transcriptome and proteome. At the cellular level, we plan to determine how this type of regulation integrates with other circadian pathways and which specific pathways and proteins mediate this process. As a final goal of the proposed project we plan to generate a complete genetic interaction map of the known circadian regulators, which will integrate the different molecular and cellular events involved in timekeeping. This will be a key step towards the understanding of the circadian clock as a dynamic adjustable process. Last, but not least, we will study the role of miRNAs in the circadian neural network. For doing so we will set up an ex vivo approach (fly brain's culture) that will assess circadian parameters through fluorescent continuous live imaging.
Project acronym MOBA-CS
Project The molecular basis of Cockayne Syndrome
Researcher (PI) Nicolas Thomä
Summary Cockayne syndrome is a congenital disease with impaired DNA repair in actively transcribed genes. Affected children show developmental abnormalities and signs of premature aging. Cockayne syndrome is caused by mutations in the Cockayne syndrome complementation group A (CSA) and B (CSB) genes. While CSB encodes a SWI/SNF ATPase that likely assists the stalled RNA polymerase in overcoming lesions, CSA's detailed role in repair has so far remained elusive. CSA is part of the DDB1-CSA-Cul4-Rbx1 E3 ubiquitin ligase complex. The available data suggest that CSA may function as a substrate adaptor for ubiquitination by the DDB1-Cul4-Rbx1 ligase. I will pursue a novel structure-driven proteomic approach to identify the substrate epitope recognized by the DDB1-CSA-Cul4-Rbx1 E3 ubiquitin ligase. These experiments aim to provide the important missing signal required for recruitment of the ligase complex to sites of stalled RNA polII complexes. Importantly, the CSA ligase, as it arrives at sites of DNA damage, is inactive. Our comprehensive structural and biochemical efforts will thus include the mechanisms of regulation of the CSA ubiquitin ligase activity by activators and inhibitors following recruitment to the repair site. MoBa-CS will not only improve our understanding of CSA's molecular role in Cockayne syndrome, but also reveal CSA's mode of action within the essential transcription coupled repair pathway. Understanding the cellular signals overseeing transcription coupled repair will provide important insights into how the pathway is integrated within the overall DNA damage response circuitry of the cell. ERC funding would enable us to pursue an interdisciplinary proteomic and structure based approach in examining DDB1-CSA function.
Cockayne syndrome is a congenital disease with impaired DNA repair in actively transcribed genes. Affected children show developmental abnormalities and signs of premature aging. Cockayne syndrome is caused by mutations in the Cockayne syndrome complementation group A (CSA) and B (CSB) genes. While CSB encodes a SWI/SNF ATPase that likely assists the stalled RNA polymerase in overcoming lesions, CSA's detailed role in repair has so far remained elusive. CSA is part of the DDB1-CSA-Cul4-Rbx1 E3 ubiquitin ligase complex. The available data suggest that CSA may function as a substrate adaptor for ubiquitination by the DDB1-Cul4-Rbx1 ligase. I will pursue a novel structure-driven proteomic approach to identify the substrate epitope recognized by the DDB1-CSA-Cul4-Rbx1 E3 ubiquitin ligase. These experiments aim to provide the important missing signal required for recruitment of the ligase complex to sites of stalled RNA polII complexes. Importantly, the CSA ligase, as it arrives at sites of DNA damage, is inactive. Our comprehensive structural and biochemical efforts will thus include the mechanisms of regulation of the CSA ubiquitin ligase activity by activators and inhibitors following recruitment to the repair site. MoBa-CS will not only improve our understanding of CSA's molecular role in Cockayne syndrome, but also reveal CSA's mode of action within the essential transcription coupled repair pathway. Understanding the cellular signals overseeing transcription coupled repair will provide important insights into how the pathway is integrated within the overall DNA damage response circuitry of the cell. ERC funding would enable us to pursue an interdisciplinary proteomic and structure based approach in examining DDB1-CSA function.
Project acronym NEUROP
Project Neuromorphic processors: event-based VLSI models of cortical circuits for brain-inspired computation
Researcher (PI) Giacomo Indiveri
Summary "Brains are remarkable computing devices which clearly outperform conventional architectures in real-world tasks. Computational neuroscience has made tremendous progress in uncovering the key principles by which neural systems carry out computation, and ICTs have advanced to a point where it is possible to integrate almost as many transistors in a VLSI system as neurons in a brain. Yet, we are still unable to develop artificial neural systems with basic computing abilities able to parallel even simple insect brains. We have recently demonstrated how it is possible to implement large-scale artificial neural networks and real-time sensory motor systems in VLSI technology, exploiting the physics of silicon to reproduce the biophysics of neural systems. But the main bottleneck is in the understanding of how to use these systems to perform general purpose computation. Progress in this domain can be achieved only by pursuing a fully integrated multi-disciplinary approach. We propose to combine neuroscience, mathematics, computer-science, and engineering to develop a theoretical formalism and its supporting technology for designing spike-based general purpose ""neuromorphic processors"", as distributed multi-chip neuromorphic VLSI systems, and for programming them to learn to produce desired computations autonomously. We will study the properties of neural circuits in the neocortex, model their coding strategies and spike-driven learning mechanisms using biophysically realistic spiking neural networks, and implement them using hybrid analog digital VLSI circuits. By interfacing these systems to silicon retinas, cochleas and autonomous robotic platforms we will build embodied neuromorphic processors able to carry out event-based computations in real-world behavioral tasks."
"Brains are remarkable computing devices which clearly outperform conventional architectures in real-world tasks. Computational neuroscience has made tremendous progress in uncovering the key principles by which neural systems carry out computation, and ICTs have advanced to a point where it is possible to integrate almost as many transistors in a VLSI system as neurons in a brain. Yet, we are still unable to develop artificial neural systems with basic computing abilities able to parallel even simple insect brains. We have recently demonstrated how it is possible to implement large-scale artificial neural networks and real-time sensory motor systems in VLSI technology, exploiting the physics of silicon to reproduce the biophysics of neural systems. But the main bottleneck is in the understanding of how to use these systems to perform general purpose computation. Progress in this domain can be achieved only by pursuing a fully integrated multi-disciplinary approach. We propose to combine neuroscience, mathematics, computer-science, and engineering to develop a theoretical formalism and its supporting technology for designing spike-based general purpose ""neuromorphic processors"", as distributed multi-chip neuromorphic VLSI systems, and for programming them to learn to produce desired computations autonomously. We will study the properties of neural circuits in the neocortex, model their coding strategies and spike-driven learning mechanisms using biophysically realistic spiking neural networks, and implement them using hybrid analog digital VLSI circuits. By interfacing these systems to silicon retinas, cochleas and autonomous robotic platforms we will build embodied neuromorphic processors able to carry out event-based computations in real-world behavioral tasks."
Project acronym OPTIMLIGHTHARVEST
Project Large Scale Architectures with Nanometric Structured Interfaces for Charge Separation, Transport and Interception
Researcher (PI) Roie Yerushalmi
Summary This research is aimed at developing new architectures at the molecular, nanometric, and macroscopic scales for the design and study of light induced charge transport using synthetic systems. The strategic objective is to establish a comprehensive approach for constructing nanometric scale hybrid structures that will enable us to tune the required physical, chemical, and electrical properties across scales required for efficient harvesting of light energy in a rigorous manner for enhancing our capabilities and basic understanding of light harvesting processes. We will form nanometric architectures featuring molecular diversity and functionality with nanometric gaps coupled to scaffolds capable of electrical transport. The nanometric architectures will be formed via simple yet powerful methods relying on sophisticated use of nanostructure surface chemistry and material properties while minimizing the application of top-down fabrication methods and will be studied at the single building block level as well as at array level. Meticulous study of the light induced charge separation and transport at the nanometric scale using single nanostructure building blocks as well as the collective dynamics of large scale arrays will be addressed with an emphasis on understanding charge dynamics at interfaces. The research activity will utilize unique nanostructure assembly methods and post-growth manipulation of the chemical composition developed during my research. Achieving our fundamental goals is expected to lead to new insights and capabilities relating to the harvesting of light energy and converting it to electrical energy and to significantly advance our ability to utilize light energy for photocatalysis.
This research is aimed at developing new architectures at the molecular, nanometric, and macroscopic scales for the design and study of light induced charge transport using synthetic systems. The strategic objective is to establish a comprehensive approach for constructing nanometric scale hybrid structures that will enable us to tune the required physical, chemical, and electrical properties across scales required for efficient harvesting of light energy in a rigorous manner for enhancing our capabilities and basic understanding of light harvesting processes. We will form nanometric architectures featuring molecular diversity and functionality with nanometric gaps coupled to scaffolds capable of electrical transport. The nanometric architectures will be formed via simple yet powerful methods relying on sophisticated use of nanostructure surface chemistry and material properties while minimizing the application of top-down fabrication methods and will be studied at the single building block level as well as at array level. Meticulous study of the light induced charge separation and transport at the nanometric scale using single nanostructure building blocks as well as the collective dynamics of large scale arrays will be addressed with an emphasis on understanding charge dynamics at interfaces. The research activity will utilize unique nanostructure assembly methods and post-growth manipulation of the chemical composition developed during my research. Achieving our fundamental goals is expected to lead to new insights and capabilities relating to the harvesting of light energy and converting it to electrical energy and to significantly advance our ability to utilize light energy for photocatalysis.
Project acronym PICS THERAPY
Project Manipulation of senescence pathways for cancer therapy: from experimental models to clinic
Researcher (PI) Andrea Alimonti
Host Institution (HI) Ente Ospedaliero Cantonale
Summary This proposal aims to harness a novel type of senescence that we have identified in response to acute Pten inactivation, and which we believe offers a radical therapeutic approach to target the quiescent cancer stem cell in vivo. In characterizing Pten loss Induced Cellular Senescence, which we have named PICS for short, we have discovered that PICS is distinct from other forms of cellular senescence including oncogene-induced senescence (OIS) and replicative senescence. These distinct differences are characterized by a lack of DNA damage and hyper-replication, breaking the current dogma for senescence induction. The ability to induce senescence, an irreversible growth arrest, in cells by targeting Pten signaling, without a requirement for hyper-replication and DNA damage opens up the possibility to target quiescent cells, including stem cells, that have a low proliferative index. This approach has tremendous therapeutic potential and represents one of the most exciting developments for the advancement of prostate cancer therapy in recent years. Through the manipulation of senescence induction pathways we will identify PICS enhancing drugs and redefine the paradigm for cancer therapy. By developing novel mouse models that target prostate stem cells we will evaluate these PICS pro-senescence drugs in a pre-clinical setting. Finally, these results will be cross referenced with data from human prostate stem cells and we will lay the ground work to translate this to the clinical setting, further developing the clinical potential of these findings to eradicate prostate cancer.
This proposal aims to harness a novel type of senescence that we have identified in response to acute Pten inactivation, and which we believe offers a radical therapeutic approach to target the quiescent cancer stem cell in vivo. In characterizing Pten loss Induced Cellular Senescence, which we have named PICS for short, we have discovered that PICS is distinct from other forms of cellular senescence including oncogene-induced senescence (OIS) and replicative senescence. These distinct differences are characterized by a lack of DNA damage and hyper-replication, breaking the current dogma for senescence induction. The ability to induce senescence, an irreversible growth arrest, in cells by targeting Pten signaling, without a requirement for hyper-replication and DNA damage opens up the possibility to target quiescent cells, including stem cells, that have a low proliferative index. This approach has tremendous therapeutic potential and represents one of the most exciting developments for the advancement of prostate cancer therapy in recent years. Through the manipulation of senescence induction pathways we will identify PICS enhancing drugs and redefine the paradigm for cancer therapy. By developing novel mouse models that target prostate stem cells we will evaluate these PICS pro-senescence drugs in a pre-clinical setting. Finally, these results will be cross referenced with data from human prostate stem cells and we will lay the ground work to translate this to the clinical setting, further developing the clinical potential of these findings to eradicate prostate cancer.
Project acronym POPRNASEQ
Project Population transcriptional genomics in humans using high throughput sequencing
Researcher (PI) Emmanouil Dermitzakis
Summary Gene expression is one of the marks of cellular state and function. The relative abundance of transcripts defines and is a result of the differentiation status of a cell. Interrogation of gene expression levels and patterns in the human and other genomes can be informative about perturbations from the average pattern due to external stimuli or internal factors such as genetic variants. Gene expression profiles have been extensively used to assess developmental processes, pathways contributing to cell differentiation, and predicting the outcome of disease status. Understanding the effects of genetic variation in basic cellular processes such as gene expression is key to the dissection of the genetic contributions to whole organism phenotypes. We propose to interrogate the transcriptome of primary fibroblasts, primary T-cells and EBV-transformed B-cell (lymphoblastoid cell lines or LCLs) from umbilical cords of 200 individuals of European descent using next generation sequencing (mRNAseq). A subset will also be interrogated for transcriptionally engaged RNA polymerases (GROseq) and protein abundance. These data will be analyzed for the detection of eQTLs and other genetic effects associated with variation in alternative splicing and other properties of the transcripts and dissection of the genetic effects from primary transcription to protein and their tissue specific effects. These data will be integrated with genome-wide association studies and other efforts to dissect the genetic basis of complex traits and diseases in humans. In addition, we will develop bioinformatic models to understand the fine scale regulatory signals that are responsible for the regulatory patterns observed and how sequence variants have an effect on them.
Gene expression is one of the marks of cellular state and function. The relative abundance of transcripts defines and is a result of the differentiation status of a cell. Interrogation of gene expression levels and patterns in the human and other genomes can be informative about perturbations from the average pattern due to external stimuli or internal factors such as genetic variants. Gene expression profiles have been extensively used to assess developmental processes, pathways contributing to cell differentiation, and predicting the outcome of disease status. Understanding the effects of genetic variation in basic cellular processes such as gene expression is key to the dissection of the genetic contributions to whole organism phenotypes. We propose to interrogate the transcriptome of primary fibroblasts, primary T-cells and EBV-transformed B-cell (lymphoblastoid cell lines or LCLs) from umbilical cords of 200 individuals of European descent using next generation sequencing (mRNAseq). A subset will also be interrogated for transcriptionally engaged RNA polymerases (GROseq) and protein abundance. These data will be analyzed for the detection of eQTLs and other genetic effects associated with variation in alternative splicing and other properties of the transcripts and dissection of the genetic effects from primary transcription to protein and their tissue specific effects. These data will be integrated with genome-wide association studies and other efforts to dissect the genetic basis of complex traits and diseases in humans. In addition, we will develop bioinformatic models to understand the fine scale regulatory signals that are responsible for the regulatory patterns observed and how sequence variants have an effect on them.
Project acronym PORABEL
Project Nanopore integrated nanoelectrodes for biomolecular manipulation and sensing
Researcher (PI) Aleksandra Radenovic
Summary In this proposal we aim to address several complex biophysical problems at single molecule level that remained elusive due to the lack of appropriate experimental approach where one could manipulate independently both interacting biomolecules and in the same time measure the strength of their interaction and correlate it with their electronic signature. In particular we are interested in finding out how biopolymer finds, enters and translocates nanopore. Equally intriguing is still unresolved mechanism of phage DNA ejection. We will also investigate how exactly proteins recognize the target binding places on DNA and if the protein DNA recognition is based on the complementarity of their charge patterns. To allow addressing those biophysical problems we will develop novel experimental framework by integrating electrodes to the nanopore based force spectroscopy. The proposed strategy will enable two directions of the research: single molecule manipulation and single molecule detection /sensing equally suitable for investigating complex biophysical problems and molecular recognition assays. By exploiting superior sensing and detection capabilities of our devices, we will investigate following practical applications improved nucleotide detection, selective protein detection and protein charge profiling via nanopore unfolding. Unique combination of optical manipulation and nanofluidics could lead to new methods of bioanalysis, mechanical characterization and discrimination between specific and non-specific DNA protein interactions. This research proposal combines nanofabrication, optics, nano/microfluidics, electronics, computer programming, and biochemistry
In this proposal we aim to address several complex biophysical problems at single molecule level that remained elusive due to the lack of appropriate experimental approach where one could manipulate independently both interacting biomolecules and in the same time measure the strength of their interaction and correlate it with their electronic signature. In particular we are interested in finding out how biopolymer finds, enters and translocates nanopore. Equally intriguing is still unresolved mechanism of phage DNA ejection. We will also investigate how exactly proteins recognize the target binding places on DNA and if the protein DNA recognition is based on the complementarity of their charge patterns. To allow addressing those biophysical problems we will develop novel experimental framework by integrating electrodes to the nanopore based force spectroscopy. The proposed strategy will enable two directions of the research: single molecule manipulation and single molecule detection /sensing equally suitable for investigating complex biophysical problems and molecular recognition assays. By exploiting superior sensing and detection capabilities of our devices, we will investigate following practical applications improved nucleotide detection, selective protein detection and protein charge profiling via nanopore unfolding. Unique combination of optical manipulation and nanofluidics could lead to new methods of bioanalysis, mechanical characterization and discrimination between specific and non-specific DNA protein interactions. This research proposal combines nanofabrication, optics, nano/microfluidics, electronics, computer programming, and biochemistry
Project acronym PROKRNA
Project Prokaryotic RNomics: Unravelling the RNA-mediated regulatory layers
Researcher (PI) Rotem Sorek
Summary Pioneering studies from the recent year, including those published by the PI of this proposal, are revolutionizing our perception of prokaryotic transcriptomes, and reveal unexpected regulatory complexity. Two central concepts are arising: the unanticipated abundance of cis-antisense RNAs overlapping protein coding genes, and alternative transcripts resulting from a dynamic behaviour of operon structures (where genes can be included or excluded from a polycistronic transcript in response to environmental cues). Understanding these phenomena holds a great potential for our ability to decipher how bacteria regulate their complex life styles and pathogenic behaviours, but their dynamics, regulatory roles, and effects on combinatorially increasing the regulatory capacity of the genome are completely unknown. The primary objectives of this proposed research are: i) to understand the extent, regulatory roles, and evolutionary consequences of cis-antisense RNAs in prokaryotes; ii) to understand the regulatory code, combinatorial effects and dynamics of alternative operon structures; and, in parallel iii) to develop a unified framework for comparative prokaryotic transcriptomics. Our strategy is based on a combination of deep sequencing technologies, computational modelling and data analyses, systems biology approaches, and focused molecular biology experiments. We will identify the extent and the impact of these RNA-based regulatory layers in representative pathogenic and non-pathogenic species across the prokaryotic tree of life, study their functional and evolutionary consequences, and break the regulatory code controlling them. Our planned research has the potential of producing methodological and conceptual breakthroughs in the emerging field of prokaryotic transcriptomics.
Pioneering studies from the recent year, including those published by the PI of this proposal, are revolutionizing our perception of prokaryotic transcriptomes, and reveal unexpected regulatory complexity. Two central concepts are arising: the unanticipated abundance of cis-antisense RNAs overlapping protein coding genes, and alternative transcripts resulting from a dynamic behaviour of operon structures (where genes can be included or excluded from a polycistronic transcript in response to environmental cues). Understanding these phenomena holds a great potential for our ability to decipher how bacteria regulate their complex life styles and pathogenic behaviours, but their dynamics, regulatory roles, and effects on combinatorially increasing the regulatory capacity of the genome are completely unknown. The primary objectives of this proposed research are: i) to understand the extent, regulatory roles, and evolutionary consequences of cis-antisense RNAs in prokaryotes; ii) to understand the regulatory code, combinatorial effects and dynamics of alternative operon structures; and, in parallel iii) to develop a unified framework for comparative prokaryotic transcriptomics. Our strategy is based on a combination of deep sequencing technologies, computational modelling and data analyses, systems biology approaches, and focused molecular biology experiments. We will identify the extent and the impact of these RNA-based regulatory layers in representative pathogenic and non-pathogenic species across the prokaryotic tree of life, study their functional and evolutionary consequences, and break the regulatory code controlling them. Our planned research has the potential of producing methodological and conceptual breakthroughs in the emerging field of prokaryotic transcriptomics.
Project acronym PROTLEGO
Project Development of an accessible platform for ex vivo site specific post-translational modifications of proteins
Researcher (PI) Lital Yamna Alfonta
Summary The incorporation of unnatural amino acids (more than 50 to date) into proteins in vivo has resulted in the generation of proteins with novel chemical, biological, and physical properties. However, some unnatural amino acids possess properties, such as an inability to cross the cell membrane or a level of toxicity dangerous to the organism, that restrict their incorporation into proteins in vivo. In addition, even when an unnatural amino acid crosses the cell membrane, its transport efficiency within the cell is very low. We propose to overcome these limitations by exploiting translational components evolved tRNA-synthetases and their cognate suppressor-tRNA from Archea for the incorporation of an array of unnatural amino acids into proteins in vitro in a cell-free protein translation system. The expressed recombinant proteins containing the unnatural amino acids will be purified from the reaction mixture and used for further research. Using the cell free system, first we will demonstrate our new approach by incorporating novel unnatural amino acids, i.e., thiolysine analogues, into proteins using the broad substrate specificity of evolved tRNA synthetases. We will then incorporate a thiolysine analogue into PCNA for the site-specific ubiquitination and SUMOylation of these proteins for in vitro studies of the interactions between PCNA and interacting proteins and to follow the progress of the replication fork. This unique approach will show for the first time the use of evolved synthetases in a cell free translation system, with the advantage being that previously un-incorporable unnatural amino acids can be incorporated using this approach. Our overall aim is to enable the introduction of new functionalities into proteins.
The incorporation of unnatural amino acids (more than 50 to date) into proteins in vivo has resulted in the generation of proteins with novel chemical, biological, and physical properties. However, some unnatural amino acids possess properties, such as an inability to cross the cell membrane or a level of toxicity dangerous to the organism, that restrict their incorporation into proteins in vivo. In addition, even when an unnatural amino acid crosses the cell membrane, its transport efficiency within the cell is very low. We propose to overcome these limitations by exploiting translational components evolved tRNA-synthetases and their cognate suppressor-tRNA from Archea for the incorporation of an array of unnatural amino acids into proteins in vitro in a cell-free protein translation system. The expressed recombinant proteins containing the unnatural amino acids will be purified from the reaction mixture and used for further research. Using the cell free system, first we will demonstrate our new approach by incorporating novel unnatural amino acids, i.e., thiolysine analogues, into proteins using the broad substrate specificity of evolved tRNA synthetases. We will then incorporate a thiolysine analogue into PCNA for the site-specific ubiquitination and SUMOylation of these proteins for in vitro studies of the interactions between PCNA and interacting proteins and to follow the progress of the replication fork. This unique approach will show for the first time the use of evolved synthetases in a cell free translation system, with the advantage being that previously un-incorporable unnatural amino acids can be incorporated using this approach. Our overall aim is to enable the introduction of new functionalities into proteins.
Project acronym QUANT-DES-CNT
Project Quantum Design in Carbon Nanotubes
Researcher (PI) Shahal Ilani
Summary Quantum design, the ability to control the microscopic properties of a quantum system, has proven to be an invaluable tool in experimental physics. Carbon nanotubes are an ideal system to implement quantum design in the solid-state; their strongly interacting electrons, unusual spin properties, and unique mechanical qualities make them an excellent platform for studying quantum phenomena in low dimensions. However, for many years this potential has been hindered by the dominance of strong electronic disorder in this system. Fortunately, a series of recent breakthroughs in making nanotubes free of disorder has dramatically changed this situation, opening up a wide range of opportunities for high-precision experiments in these systems. In this work I propose to develop a new technology that will enable quantum design experiments in carbon nanotubes. This technology, which builds on my recent development of ultra-clean electronic devices in nanotubes, will allow us to create nanotube device-architectures that go far beyond those currently available. Specifically, we will be able to control the properties of individual electrons with microscopic precision (~100nm), manipulate their quantum states, and image their individual wavefunctions. This new toolset will be used to study previously unexplored realms in condensed matter physics, ranging from the correlated states-of-matter formed by electrons in one-dimension, to quantum information experiments with multiple electronic spins, and finally to mechanical studies of nanotube resonators in the quantum limit. These studies will address some of the most fundamental aspects pertaining to the physics of electrons, spins and phonons in low dimensions.
Quantum design, the ability to control the microscopic properties of a quantum system, has proven to be an invaluable tool in experimental physics. Carbon nanotubes are an ideal system to implement quantum design in the solid-state; their strongly interacting electrons, unusual spin properties, and unique mechanical qualities make them an excellent platform for studying quantum phenomena in low dimensions. However, for many years this potential has been hindered by the dominance of strong electronic disorder in this system. Fortunately, a series of recent breakthroughs in making nanotubes free of disorder has dramatically changed this situation, opening up a wide range of opportunities for high-precision experiments in these systems. In this work I propose to develop a new technology that will enable quantum design experiments in carbon nanotubes. This technology, which builds on my recent development of ultra-clean electronic devices in nanotubes, will allow us to create nanotube device-architectures that go far beyond those currently available. Specifically, we will be able to control the properties of individual electrons with microscopic precision (~100nm), manipulate their quantum states, and image their individual wavefunctions. This new toolset will be used to study previously unexplored realms in condensed matter physics, ranging from the correlated states-of-matter formed by electrons in one-dimension, to quantum information experiments with multiple electronic spins, and finally to mechanical studies of nanotube resonators in the quantum limit. These studies will address some of the most fundamental aspects pertaining to the physics of electrons, spins and phonons in low dimensions.