Project acronym BETATOBETA
Project The molecular basis of pancreatic beta cell replication
Researcher (PI) Yuval Dor
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Starting Grant (StG), LS4, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 445 000 €
Duration
Start date: 2010-09-01, End date: 2015-08-31
Project acronym CARDIO-IPS
Project Induced Pluripotent stem Cells: A Novel Strategy to Study Inherited Cardiac Disorders
Researcher (PI) Lior Gepstein
Host Institution (HI) TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Call Details Starting Grant (StG), LS4, ERC-2010-StG_20091118
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
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
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-03-01, End date: 2016-02-29
Project acronym DIAG-CANCER
Project Diagnosis, Screening and Monitoring of Cancer Diseases via Exhaled Breath Using an Array of Nanosensors
Researcher (PI) Hossam Haick
Host Institution (HI) TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Call Details Starting Grant (StG), LS7, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 200 000 €
Duration
Start date: 2011-01-01, End date: 2014-12-31
Project acronym DOGPSYCH
Project Canine models of human psychiatric disease: identifying novel anxiety genes with the help of man's best friend
Researcher (PI) Hannes Tapani Lohi
Host Institution (HI) HELSINGIN YLIOPISTO
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary Anxiety disorders include different forms of pathological fear and anxiety and rank among the most common health concerns in human medicine. Millions of people become affected every year, and many of them do not respond to treatments. Anxiety disorders are heritable, but genetically complex. As a result, traditional gene mapping methods in the human population with prominent locus and allelic heterogeneity have not succeeded. Similarly, rodents have provided some insights into the circuitry of anxiety, but naturally occurring versions do not exist and gene deletion studies have not provided adequate models. To break through and identify new anxiety genes, I propose a novel and unique approach that resorts to man s best friend, dog. Taking advantage of the exaggerated genetic homogeneity characteristic of purebred dogs, recent genomics tools and the existence of naturally occurring heritable behaviour disorders in dogs can remedy the current lack of a suitable animal model of human psychiatric disorders. I propose to collect and perform a genome-wide association study in four breed-specific anxiety traits in dogs representing the three major forms of human anxiety: compulsive pacing and tail-chasing, noise phobia, and shyness corresponding to human OCD, panic disorder and social phobia, respectively. Canine anxiety disorders respond to human medications and other phenomenological studies suggest a share biological mechanism in both species. The proposed research has the potential to discover new genetic risk factors, which eventually will shed light on the biological basis of common neuropsychiatric disorders in both dog and human, provide insight into etiological mechanisms, enable identification of individuals at high-risk for adverse health outcomes, and facilitate development of tailored treatments.
Summary
Anxiety disorders include different forms of pathological fear and anxiety and rank among the most common health concerns in human medicine. Millions of people become affected every year, and many of them do not respond to treatments. Anxiety disorders are heritable, but genetically complex. As a result, traditional gene mapping methods in the human population with prominent locus and allelic heterogeneity have not succeeded. Similarly, rodents have provided some insights into the circuitry of anxiety, but naturally occurring versions do not exist and gene deletion studies have not provided adequate models. To break through and identify new anxiety genes, I propose a novel and unique approach that resorts to man s best friend, dog. Taking advantage of the exaggerated genetic homogeneity characteristic of purebred dogs, recent genomics tools and the existence of naturally occurring heritable behaviour disorders in dogs can remedy the current lack of a suitable animal model of human psychiatric disorders. I propose to collect and perform a genome-wide association study in four breed-specific anxiety traits in dogs representing the three major forms of human anxiety: compulsive pacing and tail-chasing, noise phobia, and shyness corresponding to human OCD, panic disorder and social phobia, respectively. Canine anxiety disorders respond to human medications and other phenomenological studies suggest a share biological mechanism in both species. The proposed research has the potential to discover new genetic risk factors, which eventually will shed light on the biological basis of common neuropsychiatric disorders in both dog and human, provide insight into etiological mechanisms, enable identification of individuals at high-risk for adverse health outcomes, and facilitate development of tailored treatments.
Max ERC Funding
1 381 807 €
Duration
Start date: 2010-10-01, End date: 2015-09-30
Project acronym ELEGANSFUSION
Project Mechanisms of cell fusion in eukaryotes
Researcher (PI) Benjamin Podbilewicz
Host Institution (HI) TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Call Details Advanced Grant (AdG), LS3, ERC-2010-AdG_20100317
Summary Membrane fusion is a universal process essential inside cells (endoplasmic) and between cells in fertilization and organ formation (exoplasmic). With the exception of SNARE-mediated endoplasmic fusion the proteins that mediate cellular fusion (fusogens) are unknown. Despite many years of research, little is known about the mechanism of cell-cell fusion. Our studies of developmental cell fusion in the nematode C. elegans have led to the discovery of the first family of eukaryotic fusogens (FF). These fusogens, EFF-1 and AFF-1, are type I membrane glycoproteins that are essential for cell fusion and can fuse cells when ectopically expressed on the membranes of C. elegans and heterologous cells.
Our main goals are:
(1) To determine the physicochemical mechanism of cell membrane fusion mediated by FF proteins.
(2) To find the missing fusogens that act in cell fusion events across all kingdoms of life.
We hypothesize that FF proteins fuse membranes by a mechanism analogous to viral or endoplasmic fusogens and that unidentified fusogens fuse cells following the same principles as FF proteins.
Our specific aims are:
AIM 1 Determine the mechanism of FF-mediated cell fusion: A paradigm for cell membrane fusion
AIM 2 Find the sperm-egg fusion proteins (fusogens) in C. elegans
AIM 3 Identify the myoblast fusogens in mammals
AIM 4 Test fusogens using functional cell fusion assays in heterologous systems
Identifying critical domains required for FF fusion, intermediates in membrane remodeling, and atomic structures of FF proteins will advance the fundamental understanding of the mechanisms of eukaryotic cell fusion. We propose to find the Holy Grail of fertilization and mammalian myoblast fusion. We estimate that this project, if successful, will bring a breakthrough to the sperm-egg and muscle fusion fields with potential applications in basic and applied biomedical sciences.
Summary
Membrane fusion is a universal process essential inside cells (endoplasmic) and between cells in fertilization and organ formation (exoplasmic). With the exception of SNARE-mediated endoplasmic fusion the proteins that mediate cellular fusion (fusogens) are unknown. Despite many years of research, little is known about the mechanism of cell-cell fusion. Our studies of developmental cell fusion in the nematode C. elegans have led to the discovery of the first family of eukaryotic fusogens (FF). These fusogens, EFF-1 and AFF-1, are type I membrane glycoproteins that are essential for cell fusion and can fuse cells when ectopically expressed on the membranes of C. elegans and heterologous cells.
Our main goals are:
(1) To determine the physicochemical mechanism of cell membrane fusion mediated by FF proteins.
(2) To find the missing fusogens that act in cell fusion events across all kingdoms of life.
We hypothesize that FF proteins fuse membranes by a mechanism analogous to viral or endoplasmic fusogens and that unidentified fusogens fuse cells following the same principles as FF proteins.
Our specific aims are:
AIM 1 Determine the mechanism of FF-mediated cell fusion: A paradigm for cell membrane fusion
AIM 2 Find the sperm-egg fusion proteins (fusogens) in C. elegans
AIM 3 Identify the myoblast fusogens in mammals
AIM 4 Test fusogens using functional cell fusion assays in heterologous systems
Identifying critical domains required for FF fusion, intermediates in membrane remodeling, and atomic structures of FF proteins will advance the fundamental understanding of the mechanisms of eukaryotic cell fusion. We propose to find the Holy Grail of fertilization and mammalian myoblast fusion. We estimate that this project, if successful, will bring a breakthrough to the sperm-egg and muscle fusion fields with potential applications in basic and applied biomedical sciences.
Max ERC Funding
2 380 000 €
Duration
Start date: 2011-05-01, End date: 2016-04-30
Project acronym ER ARCHITECTURE
Project Uncovering the Mechanisms of Endoplasmic Reticulum Sub-Domain Creation and Maintenance
Researcher (PI) Maya Benyamina Schuldiner
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS3, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 499 999 €
Duration
Start date: 2010-09-01, End date: 2015-08-31
Project acronym EURO-NEUROSTRESS
Project Dissecting the Central Stress Response: Bridging the Genotype-Phenotype Gap
Researcher (PI) Alon Chen
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS5, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
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
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Starting Grant (StG), LS8, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 458 200 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
Project acronym GEDA
Project Global Environmental Decision Analysis
Researcher (PI) Atte Jaakko Moilanen
Host Institution (HI) HELSINGIN YLIOPISTO
Call Details Starting Grant (StG), LS8, ERC-2010-StG_20091118
Summary Habitat degradation and climate change are generally considered the greatest threats to biodiversity globally. Together, these processes pose an urgent challenge to conservation science, requiring ever increasing efficiency in ecologically-based decision making, to slow down, and hopefully eventually reverse, the ongoing global loss of biodiversity. In responding to this challenge, I am proposing a project in which the over-arching goal is to provide improved conservation-oriented analytical methods and tools to underpin knowledge-based land-use planning and associated political decision making. The proposed work builds on a broad established history of research in the field of spatial ecology and conservation prioritization.
Specific components of the proposal include: (i) developing the general conceptual, ecological, methodological and statistical basis of environmental and conservation resource allocation: (ii) combining species and community-level prioritization approaches for data-poor areas of the world; (iii) developing methods for alleviating the negative ecological consequences of climate change, based on connectivity both in geographic and environmental space; (iv) developing an uncertainty-analytic method for the planning of habitat restoration and calculation of compensation ratios for habitat that will be impacted due to economic activity, (v) developing methods for allocating alternative conservation actions (protection, maintenance, restoration) in combination with habitat-specific loss rates in spatial conservation prioritization, and (vi) implementing the proposed methods as publicly available, efficient and well-documented software packages. Particular emphasis will be placed on solving the algorithmic challenges involved in analyzing the large data sets that are becoming increasingly available as the distributions of environmental conditions and biodiversity features are derived from large-scale high-resolution remote-sensing data.
Summary
Habitat degradation and climate change are generally considered the greatest threats to biodiversity globally. Together, these processes pose an urgent challenge to conservation science, requiring ever increasing efficiency in ecologically-based decision making, to slow down, and hopefully eventually reverse, the ongoing global loss of biodiversity. In responding to this challenge, I am proposing a project in which the over-arching goal is to provide improved conservation-oriented analytical methods and tools to underpin knowledge-based land-use planning and associated political decision making. The proposed work builds on a broad established history of research in the field of spatial ecology and conservation prioritization.
Specific components of the proposal include: (i) developing the general conceptual, ecological, methodological and statistical basis of environmental and conservation resource allocation: (ii) combining species and community-level prioritization approaches for data-poor areas of the world; (iii) developing methods for alleviating the negative ecological consequences of climate change, based on connectivity both in geographic and environmental space; (iv) developing an uncertainty-analytic method for the planning of habitat restoration and calculation of compensation ratios for habitat that will be impacted due to economic activity, (v) developing methods for allocating alternative conservation actions (protection, maintenance, restoration) in combination with habitat-specific loss rates in spatial conservation prioritization, and (vi) implementing the proposed methods as publicly available, efficient and well-documented software packages. Particular emphasis will be placed on solving the algorithmic challenges involved in analyzing the large data sets that are becoming increasingly available as the distributions of environmental conditions and biodiversity features are derived from large-scale high-resolution remote-sensing data.
Max ERC Funding
1 495 213 €
Duration
Start date: 2011-01-01, End date: 2015-12-31
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
Call Details Starting Grant (StG), LS1, ERC-2010-StG_20091118
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."
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."
Max ERC Funding
1 498 510 €
Duration
Start date: 2010-12-01, End date: 2015-11-30
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
Host Institution (HI) TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Call Details Starting Grant (StG), LS9, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 499 622 €
Duration
Start date: 2011-03-01, End date: 2017-02-28
Project acronym METABOMIT
Project Metabolic consequences of mitochondrial dysfunction
Researcher (PI) Anu Elina Wartiovaara
Host Institution (HI) HELSINGIN YLIOPISTO
Call Details Advanced Grant (AdG), LS4, ERC-2010-AdG_20100317
Summary This proposal aims to clarify mitochondrial contribution to obesity and thinness, using carefully characterized mitochondrial disease and obese patient materials, and genetically modified disease models. Manifestations of mitochondrial respiratory chain (RC) defects range from infantile multisystem disorders to adult-onset myopathies or neurodegeneration, and even aging-related wasting. Why defects in oxidative ATP production can lead to such variety of manifestations and tissue specificity is unknown. We have previously identified a number of gene defects that lead to RC disorders. In addition to neurological symptoms, these patients often show various metabolic manifestations: specific gene defects associate with short stature and thinness, whereas others with metabolic syndrome or obesity. This implies that specific mitochondrial defects can have opposing effects for fat storage or utilization. The involved pathways may contribute to mitochondrial disease progression, but are unknown.
We propose to a) undertake a major clinical study on genetically defined, obese or thin, mitochondrial patients, and examine their metabolic phenotype in finest detail. These data will be compared to those from normal obesity, to search for common mechanisms between mitochondrial and general obesity. b) generate a set of disease models for mitochondrial disorders associated with obesity, and knock-out models for specific signallers for crossing with the disease models. c) identify in detail the involved regulatory pathways, and utilize these for searching chemical compounds that could modulate the response, and have therapeutic potential. The project has potential for major breakthroughs in the fields of mitochondrial disease pathogenesis and treatment, neurodegeneration and obesity.
Summary
This proposal aims to clarify mitochondrial contribution to obesity and thinness, using carefully characterized mitochondrial disease and obese patient materials, and genetically modified disease models. Manifestations of mitochondrial respiratory chain (RC) defects range from infantile multisystem disorders to adult-onset myopathies or neurodegeneration, and even aging-related wasting. Why defects in oxidative ATP production can lead to such variety of manifestations and tissue specificity is unknown. We have previously identified a number of gene defects that lead to RC disorders. In addition to neurological symptoms, these patients often show various metabolic manifestations: specific gene defects associate with short stature and thinness, whereas others with metabolic syndrome or obesity. This implies that specific mitochondrial defects can have opposing effects for fat storage or utilization. The involved pathways may contribute to mitochondrial disease progression, but are unknown.
We propose to a) undertake a major clinical study on genetically defined, obese or thin, mitochondrial patients, and examine their metabolic phenotype in finest detail. These data will be compared to those from normal obesity, to search for common mechanisms between mitochondrial and general obesity. b) generate a set of disease models for mitochondrial disorders associated with obesity, and knock-out models for specific signallers for crossing with the disease models. c) identify in detail the involved regulatory pathways, and utilize these for searching chemical compounds that could modulate the response, and have therapeutic potential. The project has potential for major breakthroughs in the fields of mitochondrial disease pathogenesis and treatment, neurodegeneration and obesity.
Max ERC Funding
2 500 000 €
Duration
Start date: 2011-06-01, End date: 2016-05-31
Project acronym METSTEM
Project DNA methylation in stem cells
Researcher (PI) Howard Cedar
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Advanced Grant (AdG), LS1, ERC-2010-AdG_20100317
Summary Embryonic and adult stem cells constitute an important component of biology by providing a pool of pluri- and multi-potent cells that supply a variety of different cell lineages. Little is known about the mechanisms involved in establishing and maintaining cell ¿stemness,¿ but it is most likely controlled by epigenetic signals such as DNA methylation. This proposal aims to understand these mechanisms and decipher the molecular logic used to program this plasticity.
We have developed a new strategy for studying the ¿DNA methylation potential¿ of any cell type throughout normal development. This utilizes a unique set of transgenic vectors programmed to detect both de novo methylation as well as the ability to protect CpG islands, and will, for the first time, allow one to evaluate the role of demethylation in normal stem cells and during reprogramming. This will be done using a new technique called ¿reverse epigenetics¿.
Preliminary studies indicate that embryonic stem cells differentiated in vitro undergo extensive aberrant methylation that does not reflect the normal pattern of methylation found in vivo. This artifact may be responsible for our inability to attain efficient differentiation in culture and may generate cells that are unhealthy and prone to cancer. We will characterize the causes of this phenomenon and decipher its underlying mechanism. This research should lead to the development of improved methods for tissue generation in vitro.
One of the most basic properties of adult stem cells is their ability to undergo asymmetric cell division that is often associated with unequal segregation of DNA. This mechanism is one of the most elemental, yet mysterious, aspects of stem cell biology. We have developed a completely new molecular model for this process that is based on the idea that non-symmetric DNA methylation serves as a strand-specific marker, and it is very likely that this will enable us to finally decipher this basic aspect of stem cells.
Summary
Embryonic and adult stem cells constitute an important component of biology by providing a pool of pluri- and multi-potent cells that supply a variety of different cell lineages. Little is known about the mechanisms involved in establishing and maintaining cell ¿stemness,¿ but it is most likely controlled by epigenetic signals such as DNA methylation. This proposal aims to understand these mechanisms and decipher the molecular logic used to program this plasticity.
We have developed a new strategy for studying the ¿DNA methylation potential¿ of any cell type throughout normal development. This utilizes a unique set of transgenic vectors programmed to detect both de novo methylation as well as the ability to protect CpG islands, and will, for the first time, allow one to evaluate the role of demethylation in normal stem cells and during reprogramming. This will be done using a new technique called ¿reverse epigenetics¿.
Preliminary studies indicate that embryonic stem cells differentiated in vitro undergo extensive aberrant methylation that does not reflect the normal pattern of methylation found in vivo. This artifact may be responsible for our inability to attain efficient differentiation in culture and may generate cells that are unhealthy and prone to cancer. We will characterize the causes of this phenomenon and decipher its underlying mechanism. This research should lead to the development of improved methods for tissue generation in vitro.
One of the most basic properties of adult stem cells is their ability to undergo asymmetric cell division that is often associated with unequal segregation of DNA. This mechanism is one of the most elemental, yet mysterious, aspects of stem cell biology. We have developed a completely new molecular model for this process that is based on the idea that non-symmetric DNA methylation serves as a strand-specific marker, and it is very likely that this will enable us to finally decipher this basic aspect of stem cells.
Max ERC Funding
1 941 930 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
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
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Starting Grant (StG), LS5, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 478 606 €
Duration
Start date: 2011-02-01, End date: 2016-01-31
Project acronym MOCAPAF
Project Role of Molecular Clusters in Atmospheric Particle Formation
Researcher (PI) Hanna Vehkamäki
Host Institution (HI) HELSINGIN YLIOPISTO
Call Details Starting Grant (StG), PE4, ERC-2010-StG_20091028
Summary Climate change is currently one of the central scientific issues in the world, and the ability to reliably forecast climate is crucial for making political decisions that affect the lives of billions of people. Aerosols remain the dominant uncertainty in predicting radiative forcing and future climate change, and also have adverse effects on human health and visibility. One of the least-well understood aerosol-related processes is nucleation: the formation of new particles from condensable vapours. While nucleation is related primarily to neutral clusters, state-of-the-art experimental methods measure only charged clusters.
The main scientific objectives of this project are 1) to understand the chemical composition of charged and especially neutral atmospheric clusters from molecular to multi-nanometre scale, and explain the mechanism by which they nucleate, and 2) to direct current intense instrument development and provide theoretical tools to maximize the information on neutral clusters that can be obtained from experimental results on charged clusters.
Our scientific plan consists of a multilevel computational effort to provide formation rates and properties of atmospheric clusters and particles to aerosol dynamic and climate modellers. To capture the properties of the smallest clusters, we need to perform quantum chemical calculations, combined with simulations on cluster formation kinetics. Unfortunately, these methods are computationally far too demanding to describe the entire nucleation process. Thus, we will feed quantum chemical results to classical thermodynamic models, the results of which in turn must be parameterized for efficient use in larger-scale models.
Summary
Climate change is currently one of the central scientific issues in the world, and the ability to reliably forecast climate is crucial for making political decisions that affect the lives of billions of people. Aerosols remain the dominant uncertainty in predicting radiative forcing and future climate change, and also have adverse effects on human health and visibility. One of the least-well understood aerosol-related processes is nucleation: the formation of new particles from condensable vapours. While nucleation is related primarily to neutral clusters, state-of-the-art experimental methods measure only charged clusters.
The main scientific objectives of this project are 1) to understand the chemical composition of charged and especially neutral atmospheric clusters from molecular to multi-nanometre scale, and explain the mechanism by which they nucleate, and 2) to direct current intense instrument development and provide theoretical tools to maximize the information on neutral clusters that can be obtained from experimental results on charged clusters.
Our scientific plan consists of a multilevel computational effort to provide formation rates and properties of atmospheric clusters and particles to aerosol dynamic and climate modellers. To capture the properties of the smallest clusters, we need to perform quantum chemical calculations, combined with simulations on cluster formation kinetics. Unfortunately, these methods are computationally far too demanding to describe the entire nucleation process. Thus, we will feed quantum chemical results to classical thermodynamic models, the results of which in turn must be parameterized for efficient use in larger-scale models.
Max ERC Funding
1 476 418 €
Duration
Start date: 2011-02-01, End date: 2016-01-31
Project acronym NGG
Project Next Generation Genetics of Cancer Predisposition
Researcher (PI) Lauri Aaltonen
Host Institution (HI) HELSINGIN YLIOPISTO
Call Details Advanced Grant (AdG), LS7, ERC-2010-AdG_20100317
Summary Unravelling genetic components of human tumor predisposition has contributed significantly to our understanding on molecular basis of cancer, and cancer prevention in the context of hereditary tumor susceptibility is one of the early examples of benefits from genetic disease information. Research into cancer susceptibility is of great importance, and as shown in this proposal Finland provides unique interdisciplinary possibilities to take the field forward. Indeed, in the near future ability to recruit very small groups of patients with a potentially novel cancer susceptibility phenotype will be more relevant than ever. Such materials have been resistant to previous gene identification approaches but lend themselves towards success by exomic and whole genome sequencing.
Important discoveries are anticipated in the following fields of research to be conducted under NGG:
1) Identification of rare high-penetrance Mendelian cancer predisposition conditions, and the respective susceptibility genes. One should note that the impact of a gene discovery for basic understanding of key cellular processes is not related to the frequency of the predisposition condition (e.g. RB, LKB1, P53 etc).
2) Identification of moderate penetrance cancer susceptibility genes. Such phenotypes have been difficult to approach with traditional gene identification methods because large pedigrees with multiple affected individuals and few or no phenocopies are not easily identified. Also, the current GWAS approaches are not ideal to detect these loci due to relative rarity of the responsible variants.
3) Characterization of common variants associated with cancer susceptibility.
Summary
Unravelling genetic components of human tumor predisposition has contributed significantly to our understanding on molecular basis of cancer, and cancer prevention in the context of hereditary tumor susceptibility is one of the early examples of benefits from genetic disease information. Research into cancer susceptibility is of great importance, and as shown in this proposal Finland provides unique interdisciplinary possibilities to take the field forward. Indeed, in the near future ability to recruit very small groups of patients with a potentially novel cancer susceptibility phenotype will be more relevant than ever. Such materials have been resistant to previous gene identification approaches but lend themselves towards success by exomic and whole genome sequencing.
Important discoveries are anticipated in the following fields of research to be conducted under NGG:
1) Identification of rare high-penetrance Mendelian cancer predisposition conditions, and the respective susceptibility genes. One should note that the impact of a gene discovery for basic understanding of key cellular processes is not related to the frequency of the predisposition condition (e.g. RB, LKB1, P53 etc).
2) Identification of moderate penetrance cancer susceptibility genes. Such phenotypes have been difficult to approach with traditional gene identification methods because large pedigrees with multiple affected individuals and few or no phenocopies are not easily identified. Also, the current GWAS approaches are not ideal to detect these loci due to relative rarity of the responsible variants.
3) Characterization of common variants associated with cancer susceptibility.
Max ERC Funding
2 483 525 €
Duration
Start date: 2011-06-01, End date: 2016-05-31
Project acronym ONCROBUST
Project Unravelling oncogenic defects in feedback control of receptor tyrosine kinases
Researcher (PI) Yosef Yarden
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Advanced Grant (AdG), LS3, ERC-2010-AdG_20100317
Summary Cellular growth and migration depend on intracellular communication webs mediated by polypeptide growth factors. One example comprises EGF-like growth factors and their ErbB receptor tyrosine kinases. EGFR and HER2 are frequently involved in cancer progression, and they serve as targets for cancer therapeutics. The existence of a kinase-dead receptor, as well as the emergence of resistance in patients treated with EGFR and HER2 blockers, instigated a paradigm shift from a linear EGF-to-ErbB cascade to a robust network characterized by multiple feedback loops.
We assume that deregulation of feedback loops plays essential roles in human cancer. Because of the abundance of feedback regulation, we predict subtle, multi-component impact on disease.
Aiming at the natural richness of feedback regulation in breast cancer, we will develop in vitro models of normal mammary cells, and introduce genetic, disease-mimicry manipulations. Two time domains of feedback regulation will be addressed: (i) the early domain of post-translational modifications, which we will explore using proteomic approaches. And (ii) the late domain comprising alterations in transcription, micro-RNAs and alternative splicing, processes we will investigate using deep sequencing and array technologies. Once verified and characterized in normal cells, we will survey the operational status of the unravelled feedback loops in genetically manipulated cell systems and in tumour specimens, using immunological and bio-informatical approaches.
Detailed knowledge of feedback regulation of multi-layered signalling networks, such as ErbB, is expected to shed light on the currently elusive basis of signal integration and elimination of noise, as well as identify markers of prognosis.
Summary
Cellular growth and migration depend on intracellular communication webs mediated by polypeptide growth factors. One example comprises EGF-like growth factors and their ErbB receptor tyrosine kinases. EGFR and HER2 are frequently involved in cancer progression, and they serve as targets for cancer therapeutics. The existence of a kinase-dead receptor, as well as the emergence of resistance in patients treated with EGFR and HER2 blockers, instigated a paradigm shift from a linear EGF-to-ErbB cascade to a robust network characterized by multiple feedback loops.
We assume that deregulation of feedback loops plays essential roles in human cancer. Because of the abundance of feedback regulation, we predict subtle, multi-component impact on disease.
Aiming at the natural richness of feedback regulation in breast cancer, we will develop in vitro models of normal mammary cells, and introduce genetic, disease-mimicry manipulations. Two time domains of feedback regulation will be addressed: (i) the early domain of post-translational modifications, which we will explore using proteomic approaches. And (ii) the late domain comprising alterations in transcription, micro-RNAs and alternative splicing, processes we will investigate using deep sequencing and array technologies. Once verified and characterized in normal cells, we will survey the operational status of the unravelled feedback loops in genetically manipulated cell systems and in tumour specimens, using immunological and bio-informatical approaches.
Detailed knowledge of feedback regulation of multi-layered signalling networks, such as ErbB, is expected to shed light on the currently elusive basis of signal integration and elimination of noise, as well as identify markers of prognosis.
Max ERC Funding
2 228 180 €
Duration
Start date: 2011-08-01, End date: 2016-07-31
Project acronym PROKRNA
Project Prokaryotic RNomics: Unravelling the RNA-mediated regulatory layers
Researcher (PI) Rotem Sorek
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 499 540 €
Duration
Start date: 2011-01-01, End date: 2016-06-30
Project acronym PROTLEGO
Project Development of an accessible platform for ex vivo site specific post-translational modifications of proteins
Researcher (PI) Lital Yamna Alfonta
Host Institution (HI) BEN-GURION UNIVERSITY OF THE NEGEV
Call Details Starting Grant (StG), LS9, ERC-2010-StG_20091118
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.
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.
Max ERC Funding
1 398 000 €
Duration
Start date: 2010-10-01, End date: 2016-03-31
Project acronym QUAMI
Project The Quantum Microscope
Researcher (PI) Itzhak Yaron Silberberg
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Advanced Grant (AdG), PE2, ERC-2010-AdG_20100224
Summary We propose to build an optical microscope that will use novel quantum optical concepts in order to break the Rayleigh-Abbe resolution limits of standard optical microscopy. Optical microscopy is still the workhorse of biological and medical research, allowing researchers direct visible view of the microscopic world, and any improvement in the field could have significant impact. Several innovative techniques have been demonstrated in recent years to achieve super resolution, most relate to fluorescence microscopy and requires highly nonlinear excitations and/or novel fluorescence probes, and therefore have more specific applications.
Our goal is to demonstrate a general-purpose machine, that is, a microscope that should be able to inspect general transparent or fluorescent objects, in particular biological and medical specimens, and will include several observation modalities. The high-resolution capabilities of the microscope will come from the application of novel photon-number resolving detectors and non-classical light sources. Our strategy is to build this microscope around a standard laser scanning microscope concept, yet we will achieve sub-diffraction imaging by resolving features within the classical diffraction limited spot of the scanning beam. Fast photon-number resolving detectors will record spatial and temporal distributions of photons at the image plane, enabling quantum correlations for enhanced resolution. We will consider several forms of illuminations both classical and quantum light and several microscope modalities, including fluorescence, dark field and differential interference contrast microscopy. We shall also investigate methods to combine quantum microscopy with nonlinear microscopy for further enhancement of resolution. Beyond its immediate goals, this research program will help to determine weather the more novel ideas of quantum metrology are indeed relevant for practical microscopy.
Summary
We propose to build an optical microscope that will use novel quantum optical concepts in order to break the Rayleigh-Abbe resolution limits of standard optical microscopy. Optical microscopy is still the workhorse of biological and medical research, allowing researchers direct visible view of the microscopic world, and any improvement in the field could have significant impact. Several innovative techniques have been demonstrated in recent years to achieve super resolution, most relate to fluorescence microscopy and requires highly nonlinear excitations and/or novel fluorescence probes, and therefore have more specific applications.
Our goal is to demonstrate a general-purpose machine, that is, a microscope that should be able to inspect general transparent or fluorescent objects, in particular biological and medical specimens, and will include several observation modalities. The high-resolution capabilities of the microscope will come from the application of novel photon-number resolving detectors and non-classical light sources. Our strategy is to build this microscope around a standard laser scanning microscope concept, yet we will achieve sub-diffraction imaging by resolving features within the classical diffraction limited spot of the scanning beam. Fast photon-number resolving detectors will record spatial and temporal distributions of photons at the image plane, enabling quantum correlations for enhanced resolution. We will consider several forms of illuminations both classical and quantum light and several microscope modalities, including fluorescence, dark field and differential interference contrast microscopy. We shall also investigate methods to combine quantum microscopy with nonlinear microscopy for further enhancement of resolution. Beyond its immediate goals, this research program will help to determine weather the more novel ideas of quantum metrology are indeed relevant for practical microscopy.
Max ERC Funding
2 112 146 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
Project acronym SIAMCP
Project Follow the PAIN: Novel Somatotopically-Based Integrative Approach to Study Mechanisms of Detection, Transmission and Perpetuation of Nociceptive, Inflammatory and Neuropathic Pain
Researcher (PI) Alexander Binshtok
Host Institution (HI) THE HEBREW UNIVERSITY OF JERUSALEM
Call Details Starting Grant (StG), LS5, ERC-2010-StG_20091118
Summary The worst of evils - pain is one of the main reasons for seeking medical help. Chronic pain affects almost one fifth of the population of Europe and leads to exorbitant medical expenses as well as extreme suffering. Despite extensive efforts, effective pain treatment has remained elusive. Inadequate understanding of the mechanisms of pain prevents the development of effective therapies. In order to better understand pain mechanisms, a novel integrative approach is needed. This approach should: to investigate the fundamental site of signal detection; the nociceptive terminals and to establish an understanding of the progression from peripheral nociception to central pain perception. Our project aims to integrate analysis at different levels of pain perception in normal and pathological conditions in order to elucidate mechanisms underlying chronic pain. Our approach propose to study pain related mechanisms along somatotopically define neuroaxis of vibrissae-barrel system. Using this unique system where peripheral receptor directly corresponds to its central analyzer, we will first characterize noxious signal detection by single channels in individual nociceptive terminal. We will follow propagation of nociceptive signal and monitor activity-dependent changes in corresponding circuits at trigeminal nuclei, thalamus and cortex. We will study modulation in of synaptic connectivity in the spino-thalamo-cortical pathway in models of chronic pain. This multi-disciplinary project will incorporate ground-breaking imaging techniques and state-of-the-art electrophysiological, histological and behavioural experiments to study pain-related mechanisms at the molecular and cellular levels as well as at the level of neuronal networks and behaviour.
Summary
The worst of evils - pain is one of the main reasons for seeking medical help. Chronic pain affects almost one fifth of the population of Europe and leads to exorbitant medical expenses as well as extreme suffering. Despite extensive efforts, effective pain treatment has remained elusive. Inadequate understanding of the mechanisms of pain prevents the development of effective therapies. In order to better understand pain mechanisms, a novel integrative approach is needed. This approach should: to investigate the fundamental site of signal detection; the nociceptive terminals and to establish an understanding of the progression from peripheral nociception to central pain perception. Our project aims to integrate analysis at different levels of pain perception in normal and pathological conditions in order to elucidate mechanisms underlying chronic pain. Our approach propose to study pain related mechanisms along somatotopically define neuroaxis of vibrissae-barrel system. Using this unique system where peripheral receptor directly corresponds to its central analyzer, we will first characterize noxious signal detection by single channels in individual nociceptive terminal. We will follow propagation of nociceptive signal and monitor activity-dependent changes in corresponding circuits at trigeminal nuclei, thalamus and cortex. We will study modulation in of synaptic connectivity in the spino-thalamo-cortical pathway in models of chronic pain. This multi-disciplinary project will incorporate ground-breaking imaging techniques and state-of-the-art electrophysiological, histological and behavioural experiments to study pain-related mechanisms at the molecular and cellular levels as well as at the level of neuronal networks and behaviour.
Max ERC Funding
1 500 000 €
Duration
Start date: 2011-03-01, End date: 2016-02-29
Project acronym SINSLIM
Project Smart Inorganic Nanocrystals for Sub-diffraction Limited IMaging
Researcher (PI) Dan Oron
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), PE4, ERC-2010-StG_20091028
Summary "The goal of this proposal is to design and fabricate ""smart"" inorganic fluorophores, which could replace to replace currently used organic dyes for far-field sub-diffraction limited microscopy applications. Delicate band-gap engineering of the structure and composition of colloidal semiconductor nanocrystals is suggested as a path to achieving the required nonlinear all-optical control over their luminescent properties. In conjunction with the inherent photostability, tunability and ease of excitation of these nanocrystals, this can pave the way towards greatly simplified instrumentation and techniques, implying dramatically reduced costs and significantly broader accessibility to sub-diffraction limited imaging.
The proposed research is a concerted effort both on colloidal synthesis of complex multicomponent semiconductor nanocrystals and on time and frequency resolved photophysical studies down to the single nanocrystal level. Several schemes for photoactivation and reversible photobleaching of designed nanocrystals, where the localization regime of excited carriers differs between the electrons and the holes, will be explored. These include effective ionization of the emitting nanocrystal core and optical pumping of two-color emitting QDs to a single emitting state. Fulfilling the optical and material requirements from this type of system, including photostability, control of intra-nanocrystal charge- and energy-transfer processes, and a large quantum yield, will inevitably reveal some of the fundamental properties of the unique system of strongly coupled quantum dots in a single nanocrystal."
Summary
"The goal of this proposal is to design and fabricate ""smart"" inorganic fluorophores, which could replace to replace currently used organic dyes for far-field sub-diffraction limited microscopy applications. Delicate band-gap engineering of the structure and composition of colloidal semiconductor nanocrystals is suggested as a path to achieving the required nonlinear all-optical control over their luminescent properties. In conjunction with the inherent photostability, tunability and ease of excitation of these nanocrystals, this can pave the way towards greatly simplified instrumentation and techniques, implying dramatically reduced costs and significantly broader accessibility to sub-diffraction limited imaging.
The proposed research is a concerted effort both on colloidal synthesis of complex multicomponent semiconductor nanocrystals and on time and frequency resolved photophysical studies down to the single nanocrystal level. Several schemes for photoactivation and reversible photobleaching of designed nanocrystals, where the localization regime of excited carriers differs between the electrons and the holes, will be explored. These include effective ionization of the emitting nanocrystal core and optical pumping of two-color emitting QDs to a single emitting state. Fulfilling the optical and material requirements from this type of system, including photostability, control of intra-nanocrystal charge- and energy-transfer processes, and a large quantum yield, will inevitably reveal some of the fundamental properties of the unique system of strongly coupled quantum dots in a single nanocrystal."
Max ERC Funding
1 496 600 €
Duration
Start date: 2010-11-01, End date: 2015-10-31
Project acronym SYMPAC
Project Synthetic metabolic pathways for carbon fixation
Researcher (PI) Ron Milo
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Starting Grant (StG), LS2, ERC-2010-StG_20091118
Summary Carbon fixation is the main pathway for storing energy and accumulating biomass in the living world. It is also the principal reason for humanity s utilization of land and water. Under human cultivation, carbon fixation significantly limits growth. Hence increasing carbon fixation rate is of major importance towards agricultural and energetic sustainability.
Are there limits on the rate of such central metabolic pathways? Attempts to improve the rate of Rubisco, the key enzyme in the Calvin-Benson cycle, have achieved very limited success. In this proposal we try to overcome this bottleneck by systematically exploring the space of carbon fixation pathways that can be assembled from all ~4000 metabolic enzymes known in nature. We computationally compare all possible pathways based on kinetics, energetics and topology. Our initial analysis suggests a new family of synthetic carbon fixation pathways utilizing the most effective carboxylating enzyme, PEPC. We propose to experimentally test these cycles in the most genetically tractable context by constructing an E. coli strain that will depend on carbon fixation as its sole carbon input. Energy will be supplied by compounds that cannot be used as carbon source. Initially, we will devise an autotrophic E. coli strain to use the Calvin-Benson Cycle; in the next stage, we will implement the most promising synthetic cycles. Systematic in vivo comparison will guide the future implementation in natural photosynthetic organisms.
At the basic science level, this proposal revisits and challenges our understanding of central carbon metabolism and growth. Concomitantly, it is an evolutionary experiment on integration of a biological novelty. It will serve as a model for significantly adapting a central metabolic pathway.
Summary
Carbon fixation is the main pathway for storing energy and accumulating biomass in the living world. It is also the principal reason for humanity s utilization of land and water. Under human cultivation, carbon fixation significantly limits growth. Hence increasing carbon fixation rate is of major importance towards agricultural and energetic sustainability.
Are there limits on the rate of such central metabolic pathways? Attempts to improve the rate of Rubisco, the key enzyme in the Calvin-Benson cycle, have achieved very limited success. In this proposal we try to overcome this bottleneck by systematically exploring the space of carbon fixation pathways that can be assembled from all ~4000 metabolic enzymes known in nature. We computationally compare all possible pathways based on kinetics, energetics and topology. Our initial analysis suggests a new family of synthetic carbon fixation pathways utilizing the most effective carboxylating enzyme, PEPC. We propose to experimentally test these cycles in the most genetically tractable context by constructing an E. coli strain that will depend on carbon fixation as its sole carbon input. Energy will be supplied by compounds that cannot be used as carbon source. Initially, we will devise an autotrophic E. coli strain to use the Calvin-Benson Cycle; in the next stage, we will implement the most promising synthetic cycles. Systematic in vivo comparison will guide the future implementation in natural photosynthetic organisms.
At the basic science level, this proposal revisits and challenges our understanding of central carbon metabolism and growth. Concomitantly, it is an evolutionary experiment on integration of a biological novelty. It will serve as a model for significantly adapting a central metabolic pathway.
Max ERC Funding
1 498 792 €
Duration
Start date: 2011-01-01, End date: 2015-12-31
Project acronym TRACTAR
Project Tracking and Targeting a T-DNA Vector for Precise Engineering of Plant Genomes
Researcher (PI) Avraham Albert Levy
Host Institution (HI) WEIZMANN INSTITUTE OF SCIENCE
Call Details Advanced Grant (AdG), LS9, ERC-2010-AdG_20100317
Summary DNA introduced into a cell usually integrates, if at all, at random in the genome. In order for gene targeting to take place, a small vector must scan a huge genome that is packaged in chromatin, identify and bind the target, and engage in strand exchange. This formidable task is likely to be rate limiting. Our goal is to study the process of genome scanning by the vector, to track it from the time of transformation through genome integration and to assist the vector to identify the homologous target. Our tools are particle imaging and tracking, molecular analysis of integration events, and manipulation of the integration process through protein recognition chemistry. Two main approaches will be used to assist homologous integration: first, by protein bridging (proteins that would bind both target and vector), and second by chromatin remodeling. Second, we propose to analyze the connection between chromatin structure and DNA integration. We will analyze how nucleosome positioning affects patterns of DNA integration. In addition, we will stimulate chromatin remodeling in an attempt to facilitate target invasion by the incoming vector. Parallel assays will be built upon fluorescence and genetic markers to correlate between the mode of search and integration per se. The interdisciplinary use of biophysics, genetics, and computational tools opens the prospect to better understand and manipulate the fundamental mechanisms involved in DNA mobility, plant transformation, and gene targeting.
Summary
DNA introduced into a cell usually integrates, if at all, at random in the genome. In order for gene targeting to take place, a small vector must scan a huge genome that is packaged in chromatin, identify and bind the target, and engage in strand exchange. This formidable task is likely to be rate limiting. Our goal is to study the process of genome scanning by the vector, to track it from the time of transformation through genome integration and to assist the vector to identify the homologous target. Our tools are particle imaging and tracking, molecular analysis of integration events, and manipulation of the integration process through protein recognition chemistry. Two main approaches will be used to assist homologous integration: first, by protein bridging (proteins that would bind both target and vector), and second by chromatin remodeling. Second, we propose to analyze the connection between chromatin structure and DNA integration. We will analyze how nucleosome positioning affects patterns of DNA integration. In addition, we will stimulate chromatin remodeling in an attempt to facilitate target invasion by the incoming vector. Parallel assays will be built upon fluorescence and genetic markers to correlate between the mode of search and integration per se. The interdisciplinary use of biophysics, genetics, and computational tools opens the prospect to better understand and manipulate the fundamental mechanisms involved in DNA mobility, plant transformation, and gene targeting.
Max ERC Funding
1 958 408 €
Duration
Start date: 2011-05-01, End date: 2016-04-30
Project acronym TX-FACTORS
Project NEW BIOLOGICAL FUNCTIONS AND THERAPEUTIC POTENTIAL OF
VASCULAR ENDOTHELIAL GROWTH FACTORS
Researcher (PI) Kari Kustaa Alitalo
Host Institution (HI) HELSINGIN YLIOPISTO
Call Details Advanced Grant (AdG), LS7, ERC-2010-AdG_20100317
Summary This application promises to provide new treatment options for cancer and cardiovascular diseases that are the leading causes of morbidity and mortality in the western world. Current cardiovascular and cancer therapies are often insufficient, unsuccessful or not suitable for all patients. Inhibition of angiogenesis is already used in the clinics, but with limited success. On the other hand, stimulation of the growth of blood vessels, angiogenesis, and of arteriogenesis, the growth of (collateral) arteries, has been unsuccessfully tried for the treatment of tissue ischemia. The aim of this research plan is to reveal new disease-related functions of endothelial growth factors and their signal transduction in cancer and cardiovascular disease and to establish preclinical models of effective therapy based on new knowledge of the biology of vascular endothelial growth factors (VEGFs), angiopoietins (Ang), angiogenesis and lymphangiogenesis. We will embark on new studies based on our novel discoveries on the crosstalk between endothelial growth factor pathways in tumor angiogenesis, the involvement of lymphatic vessels in the development of obesity and associated inflammation, and on the striking effects of VEGF-B on cardiac muscle and vessels. We will develop molecular genetic and iPS cell derived models, and use functional genomics, proteomics and metabolomics, viral gene delivery and blocking reagents from human antibody libraries for our studies that should be of high priority in basic science and medicine. My laboratory is uniquely suited and networked for new discoveries to advance therapies for both cancer and cardiovascular diseases. Some of our work has already been translated to clinical development and we aim to provide additional drug candidates in this project.
Summary
This application promises to provide new treatment options for cancer and cardiovascular diseases that are the leading causes of morbidity and mortality in the western world. Current cardiovascular and cancer therapies are often insufficient, unsuccessful or not suitable for all patients. Inhibition of angiogenesis is already used in the clinics, but with limited success. On the other hand, stimulation of the growth of blood vessels, angiogenesis, and of arteriogenesis, the growth of (collateral) arteries, has been unsuccessfully tried for the treatment of tissue ischemia. The aim of this research plan is to reveal new disease-related functions of endothelial growth factors and their signal transduction in cancer and cardiovascular disease and to establish preclinical models of effective therapy based on new knowledge of the biology of vascular endothelial growth factors (VEGFs), angiopoietins (Ang), angiogenesis and lymphangiogenesis. We will embark on new studies based on our novel discoveries on the crosstalk between endothelial growth factor pathways in tumor angiogenesis, the involvement of lymphatic vessels in the development of obesity and associated inflammation, and on the striking effects of VEGF-B on cardiac muscle and vessels. We will develop molecular genetic and iPS cell derived models, and use functional genomics, proteomics and metabolomics, viral gene delivery and blocking reagents from human antibody libraries for our studies that should be of high priority in basic science and medicine. My laboratory is uniquely suited and networked for new discoveries to advance therapies for both cancer and cardiovascular diseases. Some of our work has already been translated to clinical development and we aim to provide additional drug candidates in this project.
Max ERC Funding
2 499 884 €
Duration
Start date: 2011-06-01, End date: 2016-05-31
