Project acronym 2D-CHEM
Project Two-Dimensional Chemistry towards New Graphene Derivatives
Researcher (PI) Michal Otyepka
Host Institution (HI) UNIVERZITA PALACKEHO V OLOMOUCI
Country Czechia
Call Details Consolidator Grant (CoG), PE5, ERC-2015-CoG
Summary The suite of graphene’s unique properties and applications can be enormously enhanced by its functionalization. As non-covalently functionalized graphenes do not target all graphene’s properties and may suffer from limited stability, covalent functionalization represents a promising way for controlling graphene’s properties. To date, only a few well-defined graphene derivatives have been introduced. Among them, fluorographene (FG) stands out as a prominent member because of its easy synthesis and high stability. Being a perfluorinated hydrocarbon, FG was believed to be as unreactive as the two-dimensional counterpart perfluoropolyethylene (Teflon®). However, our recent experiments showed that FG is not chemically inert and can be used as a viable precursor for synthesizing graphene derivatives. This surprising behavior indicates that common textbook grade knowledge cannot blindly be applied to the chemistry of 2D materials. Further, there might be specific rules behind the chemistry of 2D materials, forming a new chemical discipline we tentatively call 2D chemistry. The main aim of the project is to explore, identify and apply the rules of 2D chemistry starting from FG. Using the knowledge gained of 2D chemistry, we will attempt to control the chemistry of various 2D materials aimed at preparing stable graphene derivatives with designed properties, e.g., 1-3 eV band gap, fluorescent properties, sustainable magnetic ordering and dispersability in polar media. The new graphene derivatives will be applied in sensing, imaging, magnetic delivery and catalysis and new emerging applications arising from the synergistic phenomena are expected. We envisage that new applications will be opened up that benefit from the 2D scaffold and tailored properties of the synthesized derivatives. The derivatives will be used for the synthesis of 3D hybrid materials by covalent linking of the 2D sheets joined with other organic and inorganic molecules, nanomaterials or biomacromolecules.
Summary
The suite of graphene’s unique properties and applications can be enormously enhanced by its functionalization. As non-covalently functionalized graphenes do not target all graphene’s properties and may suffer from limited stability, covalent functionalization represents a promising way for controlling graphene’s properties. To date, only a few well-defined graphene derivatives have been introduced. Among them, fluorographene (FG) stands out as a prominent member because of its easy synthesis and high stability. Being a perfluorinated hydrocarbon, FG was believed to be as unreactive as the two-dimensional counterpart perfluoropolyethylene (Teflon®). However, our recent experiments showed that FG is not chemically inert and can be used as a viable precursor for synthesizing graphene derivatives. This surprising behavior indicates that common textbook grade knowledge cannot blindly be applied to the chemistry of 2D materials. Further, there might be specific rules behind the chemistry of 2D materials, forming a new chemical discipline we tentatively call 2D chemistry. The main aim of the project is to explore, identify and apply the rules of 2D chemistry starting from FG. Using the knowledge gained of 2D chemistry, we will attempt to control the chemistry of various 2D materials aimed at preparing stable graphene derivatives with designed properties, e.g., 1-3 eV band gap, fluorescent properties, sustainable magnetic ordering and dispersability in polar media. The new graphene derivatives will be applied in sensing, imaging, magnetic delivery and catalysis and new emerging applications arising from the synergistic phenomena are expected. We envisage that new applications will be opened up that benefit from the 2D scaffold and tailored properties of the synthesized derivatives. The derivatives will be used for the synthesis of 3D hybrid materials by covalent linking of the 2D sheets joined with other organic and inorganic molecules, nanomaterials or biomacromolecules.
Max ERC Funding
1 831 103 €
Duration
Start date: 2016-06-01, End date: 2022-05-31
Project acronym AI4REASON
Project Artificial Intelligence for Large-Scale Computer-Assisted Reasoning
Researcher (PI) Josef Urban
Host Institution (HI) CESKE VYSOKE UCENI TECHNICKE V PRAZE
Country Czechia
Call Details Consolidator Grant (CoG), PE6, ERC-2014-CoG
Summary The goal of the AI4REASON project is a breakthrough in what is considered a very hard problem in AI and automation of reasoning, namely the problem of automatically proving theorems in large and complex theories. Such complex formal theories arise in projects aimed at verification of today's advanced mathematics such as the Formal Proof of the Kepler Conjecture (Flyspeck), verification of software and hardware designs such as the seL4 operating system kernel, and verification of other advanced systems and technologies on which today's information society critically depends.
It seems extremely complex and unlikely to design an explicitly programmed solution to the problem. However, we have recently demonstrated that the performance of existing approaches can be multiplied by data-driven AI methods that learn reasoning guidance from large proof corpora. The breakthrough will be achieved by developing such novel AI methods. First, we will devise suitable Automated Reasoning and Machine Learning methods that learn reasoning knowledge and steer the reasoning processes at various levels of granularity. Second, we will combine them into autonomous self-improving AI systems that interleave deduction and learning in positive feedback loops. Third, we will develop approaches that aggregate reasoning knowledge across many formal, semi-formal and informal corpora and deploy the methods as strong automation services for the formal proof community.
The expected outcome is our ability to prove automatically at least 50% more theorems in high-assurance projects such as Flyspeck and seL4, bringing a major breakthrough in formal reasoning and verification. As an AI effort, the project offers a unique path to large-scale semantic AI. The formal corpora concentrate centuries of deep human thinking in a computer-understandable form on which deductive and inductive AI can be combined and co-evolved, providing new insights into how humans do mathematics and science.
Summary
The goal of the AI4REASON project is a breakthrough in what is considered a very hard problem in AI and automation of reasoning, namely the problem of automatically proving theorems in large and complex theories. Such complex formal theories arise in projects aimed at verification of today's advanced mathematics such as the Formal Proof of the Kepler Conjecture (Flyspeck), verification of software and hardware designs such as the seL4 operating system kernel, and verification of other advanced systems and technologies on which today's information society critically depends.
It seems extremely complex and unlikely to design an explicitly programmed solution to the problem. However, we have recently demonstrated that the performance of existing approaches can be multiplied by data-driven AI methods that learn reasoning guidance from large proof corpora. The breakthrough will be achieved by developing such novel AI methods. First, we will devise suitable Automated Reasoning and Machine Learning methods that learn reasoning knowledge and steer the reasoning processes at various levels of granularity. Second, we will combine them into autonomous self-improving AI systems that interleave deduction and learning in positive feedback loops. Third, we will develop approaches that aggregate reasoning knowledge across many formal, semi-formal and informal corpora and deploy the methods as strong automation services for the formal proof community.
The expected outcome is our ability to prove automatically at least 50% more theorems in high-assurance projects such as Flyspeck and seL4, bringing a major breakthrough in formal reasoning and verification. As an AI effort, the project offers a unique path to large-scale semantic AI. The formal corpora concentrate centuries of deep human thinking in a computer-understandable form on which deductive and inductive AI can be combined and co-evolved, providing new insights into how humans do mathematics and science.
Max ERC Funding
1 499 500 €
Duration
Start date: 2015-09-01, End date: 2020-10-31
Project acronym Amitochondriates
Project Life without mitochondrion
Researcher (PI) Vladimir HAMPL
Host Institution (HI) UNIVERZITA KARLOVA
Country Czechia
Call Details Consolidator Grant (CoG), LS8, ERC-2017-COG
Summary Mitochondria are often referred to as the “power houses” of eukaryotic cells. All eukaryotes were thought to have mitochondria of some form until 2016, when the first eukaryote thriving without mitochondria was discovered by our laboratory – a flagellate Monocercomonoides. Understanding cellular functions of these cells, which represent a new functional type of eukaryotes, and understanding the circumstances of the unique event of mitochondrial loss are motivations for this proposal. The first objective focuses on the cell physiology. We will perform a metabolomic study revealing major metabolic pathways and concentrate further on elucidating its unique system of iron-sulphur cluster assembly. In the second objective, we will investigate in details the unique case of mitochondrial loss. We will examine two additional potentially amitochondriate lineages by means of genomics and transcriptomics, conduct experiments simulating the moments of mitochondrial loss and try to induce the mitochondrial loss in vitro by knocking out or down genes for mitochondrial biogenesis. We have chosen Giardia intestinalis and Entamoeba histolytica as models for the latter experiments, because their mitochondria are already reduced to minimalistic “mitosomes” and because some genetic tools are already available for them. Successful mitochondrial knock-outs would enable us to study mitochondrial loss in ‘real time’ and in vivo. In the third objective, we will focus on transforming Monocercomonoides into a tractable laboratory model by developing methods of axenic cultivation and genetic manipulation. This will open new possibilities in the studies of this organism and create a cell culture representing an amitochondriate model for cell biological studies enabling the dissection of mitochondrial effects from those of other compartments. The team is composed of the laboratory of PI and eight invited experts and we hope it has the ability to address these challenging questions.
Summary
Mitochondria are often referred to as the “power houses” of eukaryotic cells. All eukaryotes were thought to have mitochondria of some form until 2016, when the first eukaryote thriving without mitochondria was discovered by our laboratory – a flagellate Monocercomonoides. Understanding cellular functions of these cells, which represent a new functional type of eukaryotes, and understanding the circumstances of the unique event of mitochondrial loss are motivations for this proposal. The first objective focuses on the cell physiology. We will perform a metabolomic study revealing major metabolic pathways and concentrate further on elucidating its unique system of iron-sulphur cluster assembly. In the second objective, we will investigate in details the unique case of mitochondrial loss. We will examine two additional potentially amitochondriate lineages by means of genomics and transcriptomics, conduct experiments simulating the moments of mitochondrial loss and try to induce the mitochondrial loss in vitro by knocking out or down genes for mitochondrial biogenesis. We have chosen Giardia intestinalis and Entamoeba histolytica as models for the latter experiments, because their mitochondria are already reduced to minimalistic “mitosomes” and because some genetic tools are already available for them. Successful mitochondrial knock-outs would enable us to study mitochondrial loss in ‘real time’ and in vivo. In the third objective, we will focus on transforming Monocercomonoides into a tractable laboratory model by developing methods of axenic cultivation and genetic manipulation. This will open new possibilities in the studies of this organism and create a cell culture representing an amitochondriate model for cell biological studies enabling the dissection of mitochondrial effects from those of other compartments. The team is composed of the laboratory of PI and eight invited experts and we hope it has the ability to address these challenging questions.
Max ERC Funding
1 935 500 €
Duration
Start date: 2018-05-01, End date: 2023-04-30
Project acronym ATTENTION
Project Economics of Inattention
Researcher (PI) Filip Matejka
Host Institution (HI) NARODOHOSPODARSKY USTAV AKADEMIE VED CESKE REPUBLIKY VEREJNA VYZKUMNA INSTITUCE
Country Czechia
Call Details Consolidator Grant (CoG), SH1, ERC-2020-COG
Summary This proposal outlines an agenda that aims to improve our understanding of economies with inattentive agents. Attention to detail, not only to current news, but also to how the world works in general, is central to how we interact with the environment.
In the first part of the agenda, we will study how agents come up with the simplified mental models they use in their decision-making. The aim is to provide a new alternative to rational expectations. We will address the question of endogenous model uncertainty by sidestepping the largely statistical nature of previous work. Our agents learn about a model directly, i.e., all information on the details of the correct model is readily available. The envisioned implications can speak to issues such as the expectations formation and formation of narratives, polarization of opinions, and demand for public policy.
In the second part, we will study how a government optimally intervenes in markets if it finds it costly to get the necessary information. On one hand, a government does not possess the local information of decentralized markets. On the other, markets on their own often generate suboptimal social outcomes. We will explore what information the government should collect, how to use it for regulation, and when instead it should leave markets unaffected.
In the third part, we will leverage recent theories of attention allocation and use uniquely detailed data on attention and treatment choices by hospital personnel (including physicians and nurses). This will allow us to explore in more detail than before what theories describe realistic choices well. Moreover, we will eventually aim at a very practical goal: how to help clinicians decrease their cognitive load and improve medical choices.
Summary
This proposal outlines an agenda that aims to improve our understanding of economies with inattentive agents. Attention to detail, not only to current news, but also to how the world works in general, is central to how we interact with the environment.
In the first part of the agenda, we will study how agents come up with the simplified mental models they use in their decision-making. The aim is to provide a new alternative to rational expectations. We will address the question of endogenous model uncertainty by sidestepping the largely statistical nature of previous work. Our agents learn about a model directly, i.e., all information on the details of the correct model is readily available. The envisioned implications can speak to issues such as the expectations formation and formation of narratives, polarization of opinions, and demand for public policy.
In the second part, we will study how a government optimally intervenes in markets if it finds it costly to get the necessary information. On one hand, a government does not possess the local information of decentralized markets. On the other, markets on their own often generate suboptimal social outcomes. We will explore what information the government should collect, how to use it for regulation, and when instead it should leave markets unaffected.
In the third part, we will leverage recent theories of attention allocation and use uniquely detailed data on attention and treatment choices by hospital personnel (including physicians and nurses). This will allow us to explore in more detail than before what theories describe realistic choices well. Moreover, we will eventually aim at a very practical goal: how to help clinicians decrease their cognitive load and improve medical choices.
Max ERC Funding
1 162 664 €
Duration
Start date: 2021-04-01, End date: 2026-03-31
Project acronym BEHAVFRICTIONS
Project Behavioral Implications of Information-Processing Frictions
Researcher (PI) Jakub STEINER
Host Institution (HI) NARODOHOSPODARSKY USTAV AKADEMIE VED CESKE REPUBLIKY VEREJNA VYZKUMNA INSTITUCE
Country Czechia
Call Details Consolidator Grant (CoG), SH1, ERC-2017-COG
Summary BEHAVFRICTIONS will use novel models focussing on information-processing frictions to explain choice patterns described in behavioral economics and psychology. The proposed research will provide microfoundations that are essential for (i) identification of stable preferences, (ii) counterfactual predictions, and (iii) normative conclusions.
(i) Agents who face information-processing costs must trade the precision of choice against information costs. Their behavior thus reflects both their stable preferences and the context-dependent procedures that manage their errors stemming from imperfect information processing. In the absence of micro-founded models, the two drivers of the behavior are difficult to disentangle for outside observers. In some pillars of the proposal, the agents follow choice rules that closely resemble logit rules used in structural estimation. This will allow me to reinterpret the structural estimation fits to choice data and to make a distinction between the stable preferences and frictions.
(ii) Such a distinction is important in counterfactual policy analysis because the second-best decision procedures that manage the errors in choice are affected by the analysed policy. Incorporation of the information-processing frictions into existing empirical methods will improve our ability to predict effects of the policies.
(iii) My preliminary results suggest that when an agent is prone to committing errors, biases--such as overconfidence, confirmatory bias, or perception biases known from prospect theory--arise under second-best strategies. By providing the link between the agent's environment and the second-best distribution of the perception errors, my models will delineate environments in which these biases shield the agents from the most costly mistakes from environments in which the biases turn into maladaptations. The distinction will inform the normative debate on debiasing.
Summary
BEHAVFRICTIONS will use novel models focussing on information-processing frictions to explain choice patterns described in behavioral economics and psychology. The proposed research will provide microfoundations that are essential for (i) identification of stable preferences, (ii) counterfactual predictions, and (iii) normative conclusions.
(i) Agents who face information-processing costs must trade the precision of choice against information costs. Their behavior thus reflects both their stable preferences and the context-dependent procedures that manage their errors stemming from imperfect information processing. In the absence of micro-founded models, the two drivers of the behavior are difficult to disentangle for outside observers. In some pillars of the proposal, the agents follow choice rules that closely resemble logit rules used in structural estimation. This will allow me to reinterpret the structural estimation fits to choice data and to make a distinction between the stable preferences and frictions.
(ii) Such a distinction is important in counterfactual policy analysis because the second-best decision procedures that manage the errors in choice are affected by the analysed policy. Incorporation of the information-processing frictions into existing empirical methods will improve our ability to predict effects of the policies.
(iii) My preliminary results suggest that when an agent is prone to committing errors, biases--such as overconfidence, confirmatory bias, or perception biases known from prospect theory--arise under second-best strategies. By providing the link between the agent's environment and the second-best distribution of the perception errors, my models will delineate environments in which these biases shield the agents from the most costly mistakes from environments in which the biases turn into maladaptations. The distinction will inform the normative debate on debiasing.
Max ERC Funding
1 321 488 €
Duration
Start date: 2018-06-01, End date: 2023-05-31
Project acronym BOAR
Project Veterinarization of Europe? Hunting for Wild Boar Futures in the Time of African Swine Fever
Researcher (PI) Ludek Broz
Host Institution (HI) ETNOLOGICKY USTAV AKADEMIE VED CESKE REPUBLIKY VVI - INSTITUTE OF ETHNOLOGY OF THE ACADEMY OF SCIENCES
Country Czechia
Call Details Consolidator Grant (CoG), SH5, ERC-2019-COG
Summary This project proposes a collaborative, ethnographic investigation of the relationship between three understudied subjects in anthropology: veterinary medicine, European hunting and wild boars. In recent decades, the wild boar has proliferated, (re)conquering the natural, rural and urban landscapes of Europe, and increasingly clashing with human practices and worlds. Classified as a game animal, the boar is primarily killed and managed by recreational hunters. Yet, hunters are proving incapable of stemming the tide of this intelligent, adaptable being, an interspecies relation that challenges hunting’s value and legitimacy in European society. This tension has amplified with the arrival of African Swine Fever (ASF) to the continent: a fatal virus that travels between wild boar and domestic pig, forest and farm, and threatens to infect and ruin the pig industry. In the name of biosecurity, and informed by veterinary knowledge, some States have intervened and conducted mass culls, erected dividing fences across Schengen space, or instituted no-go zones. During this crisis we witnessed how veterinary medicine’s role can extend beyond mediating human-animal relations, and work to structure and govern human lives in general. At the intersection of boars, hunting, ASF and veterinary medicine, this project has two main objectives: first, to examine how European hunting and porcine futures are intertwined, and the role of veterinarians in shaping these futures, and; second, through human-boar relations, study how society is becoming increasingly veterinarized and thus shape the conceptual and methodological development of the emerging field of veterinary anthropology. This project will further contribute to anthropology by opening a novel empirical and theoretical niche for the anthropology of hunting, and experiment with ethnography as a tool of engagement with near futures. The emerging and uncertain impact of ASF in Europe is an excellent moment to conduct such a project.
Summary
This project proposes a collaborative, ethnographic investigation of the relationship between three understudied subjects in anthropology: veterinary medicine, European hunting and wild boars. In recent decades, the wild boar has proliferated, (re)conquering the natural, rural and urban landscapes of Europe, and increasingly clashing with human practices and worlds. Classified as a game animal, the boar is primarily killed and managed by recreational hunters. Yet, hunters are proving incapable of stemming the tide of this intelligent, adaptable being, an interspecies relation that challenges hunting’s value and legitimacy in European society. This tension has amplified with the arrival of African Swine Fever (ASF) to the continent: a fatal virus that travels between wild boar and domestic pig, forest and farm, and threatens to infect and ruin the pig industry. In the name of biosecurity, and informed by veterinary knowledge, some States have intervened and conducted mass culls, erected dividing fences across Schengen space, or instituted no-go zones. During this crisis we witnessed how veterinary medicine’s role can extend beyond mediating human-animal relations, and work to structure and govern human lives in general. At the intersection of boars, hunting, ASF and veterinary medicine, this project has two main objectives: first, to examine how European hunting and porcine futures are intertwined, and the role of veterinarians in shaping these futures, and; second, through human-boar relations, study how society is becoming increasingly veterinarized and thus shape the conceptual and methodological development of the emerging field of veterinary anthropology. This project will further contribute to anthropology by opening a novel empirical and theoretical niche for the anthropology of hunting, and experiment with ethnography as a tool of engagement with near futures. The emerging and uncertain impact of ASF in Europe is an excellent moment to conduct such a project.
Max ERC Funding
1 999 875 €
Duration
Start date: 2020-07-01, End date: 2025-06-30
Project acronym CoCoSym
Project Symmetry in Computational Complexity
Researcher (PI) Libor BARTO
Host Institution (HI) UNIVERZITA KARLOVA
Country Czechia
Call Details Consolidator Grant (CoG), PE6, ERC-2017-COG
Summary The last 20 years of rapid development in the computational-theoretic aspects of the fixed-language Constraint Satisfaction Problems (CSPs) has been fueled by a connection between the complexity and a certain concept capturing symmetry of computational problems in this class.
My vision is that this connection will eventually evolve into the organizing principle of computational complexity and will lead to solutions of fundamental problems such as the Unique Games Conjecture or even the P-versus-NP problem. In order to break through the current limits of this algebraic approach, I will concentrate on specific goals designed to
(A) discover suitable objects capturing symmetry that reflect the complexity in problem classes, where such an object is not known yet;
(B) make the natural ordering of symmetries coarser so that it reflects the complexity more faithfully;
(C) delineate the borderline between computationally hard and easy problems;
(D) strengthen characterizations of existing borderlines to increase their usefulness as tools for proving hardness and designing efficient algorithm; and
(E) design efficient algorithms based on direct and indirect uses of symmetries.
The specific goals concern the fixed-language CSP over finite relational structures and its generalizations to infinite domains (iCSP) and weighted relations (vCSP), in which the algebraic theory is highly developed and the limitations are clearly visible.
The approach is based on joining the forces of the universal algebraic methods in finite domains, model-theoretical and topological methods in the iCSP, and analytical and probabilistic methods in the vCSP. The starting point is to generalize and improve the Absorption Theory from finite domains.
Summary
The last 20 years of rapid development in the computational-theoretic aspects of the fixed-language Constraint Satisfaction Problems (CSPs) has been fueled by a connection between the complexity and a certain concept capturing symmetry of computational problems in this class.
My vision is that this connection will eventually evolve into the organizing principle of computational complexity and will lead to solutions of fundamental problems such as the Unique Games Conjecture or even the P-versus-NP problem. In order to break through the current limits of this algebraic approach, I will concentrate on specific goals designed to
(A) discover suitable objects capturing symmetry that reflect the complexity in problem classes, where such an object is not known yet;
(B) make the natural ordering of symmetries coarser so that it reflects the complexity more faithfully;
(C) delineate the borderline between computationally hard and easy problems;
(D) strengthen characterizations of existing borderlines to increase their usefulness as tools for proving hardness and designing efficient algorithm; and
(E) design efficient algorithms based on direct and indirect uses of symmetries.
The specific goals concern the fixed-language CSP over finite relational structures and its generalizations to infinite domains (iCSP) and weighted relations (vCSP), in which the algebraic theory is highly developed and the limitations are clearly visible.
The approach is based on joining the forces of the universal algebraic methods in finite domains, model-theoretical and topological methods in the iCSP, and analytical and probabilistic methods in the vCSP. The starting point is to generalize and improve the Absorption Theory from finite domains.
Max ERC Funding
1 211 375 €
Duration
Start date: 2018-02-01, End date: 2023-01-31
Project acronym D-FENS
Project Dicer-Dependent Defense in Mammals
Researcher (PI) Petr Svoboda
Host Institution (HI) USTAV MOLEKULARNI GENETIKY AKADEMIE VED CESKE REPUBLIKY VEREJNA VYZKUMNA INSTITUCE
Country Czechia
Call Details Consolidator Grant (CoG), LS2, ERC-2014-CoG
Summary Viral infection or retrotransposon expansion in the genome often result in production of double-stranded RNA (dsRNA). dsRNA can be intercepted by RNase III Dicer acting in the RNA interference (RNAi) pathway, an ancient eukaryotic defense mechanism. Notably, endogenous mammalian RNAi appears dormant while its common and unique physiological roles remain poorly understood. A factor underlying mammalian RNAi dormancy is inefficient processing of dsRNA by the full-length Dicer. Yet, a simple truncation of Dicer leads to hyperactive RNAi, which is naturally present in mouse oocytes.
The D-FENS project will use genetic animal models to define common, cell-specific and species-specific roles of mammalian RNAi. D-FENS has three complementary and synergizing objectives:
(1) Explore consequences of hyperactive RNAi in vivo. A mouse expressing a truncated Dicer will reveal at the organismal level any negative effect of hyperactive RNAi, the relationship between RNAi and mammalian immune system, and potential of RNAi to suppress viral infections in mammals.
(2) Define common and species-specific features of RNAi in the oocyte. Functional and bioinformatics analyses in mouse, bovine, and hamster oocytes will define rules and exceptions concerning endogenous RNAi roles, including RNAi contribution to maternal mRNA degradation and co-existence with the miRNA pathway.
(3) Uncover relationship between RNAi and piRNA pathways in suppression of retrotransposons. We hypothesize that hyperactive RNAi in mouse oocytes functionally complements the piRNA pathway, a Dicer-independent pathway suppressing retrotransposons in the germline. Using genetic models, we will explore unique and redundant roles of both pathways in the germline.
D-FENS will uncover physiological significance of the N-terminal part of Dicer, fundamentally improve understanding RNAi function in the germline, and provide a critical in vivo assessment of antiviral activity of RNAi with implications for human therapy.
Summary
Viral infection or retrotransposon expansion in the genome often result in production of double-stranded RNA (dsRNA). dsRNA can be intercepted by RNase III Dicer acting in the RNA interference (RNAi) pathway, an ancient eukaryotic defense mechanism. Notably, endogenous mammalian RNAi appears dormant while its common and unique physiological roles remain poorly understood. A factor underlying mammalian RNAi dormancy is inefficient processing of dsRNA by the full-length Dicer. Yet, a simple truncation of Dicer leads to hyperactive RNAi, which is naturally present in mouse oocytes.
The D-FENS project will use genetic animal models to define common, cell-specific and species-specific roles of mammalian RNAi. D-FENS has three complementary and synergizing objectives:
(1) Explore consequences of hyperactive RNAi in vivo. A mouse expressing a truncated Dicer will reveal at the organismal level any negative effect of hyperactive RNAi, the relationship between RNAi and mammalian immune system, and potential of RNAi to suppress viral infections in mammals.
(2) Define common and species-specific features of RNAi in the oocyte. Functional and bioinformatics analyses in mouse, bovine, and hamster oocytes will define rules and exceptions concerning endogenous RNAi roles, including RNAi contribution to maternal mRNA degradation and co-existence with the miRNA pathway.
(3) Uncover relationship between RNAi and piRNA pathways in suppression of retrotransposons. We hypothesize that hyperactive RNAi in mouse oocytes functionally complements the piRNA pathway, a Dicer-independent pathway suppressing retrotransposons in the germline. Using genetic models, we will explore unique and redundant roles of both pathways in the germline.
D-FENS will uncover physiological significance of the N-terminal part of Dicer, fundamentally improve understanding RNAi function in the germline, and provide a critical in vivo assessment of antiviral activity of RNAi with implications for human therapy.
Max ERC Funding
1 950 000 €
Duration
Start date: 2015-07-01, End date: 2020-06-30
Project acronym DECOR
Project Dynamic assembly and exchange of RNA polymerase II CTD factors
Researcher (PI) Richard Stefl
Host Institution (HI) Masarykova univerzita
Country Czechia
Call Details Consolidator Grant (CoG), LS1, ERC-2014-CoG
Summary The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) largest subunit coordinates co-transcriptional processing and it is decorated by many processing factors throughout the transcription cycle. The composition of this supramolecular assembly is diverse and highly dynamic. Many of the factors associate with RNAPII weakly and transiently, and the association is dictated by different post-translational modification patterns and conformational changes of the CTD. To determine how these accessory factors assemble and exchange on the CTD of RNAPII has remained a major challenge. Here, we aim to unravel the structural and mechanistic bases for the dynamic assembly of RNAPII CTD with its processing factors.
Using NMR, we will determine high-resolution structures of several protein factors bound to the CTD carrying specific modifications. This will enable to decode how CTD modification patterns stimulate or prevent binding of a given processing factor. We will also establish the structural and mechanistic bases of proline isomerisation in the CTD that control the timing of isomer-specific protein-protein interactions. Next, we will combine NMR and SAXS approaches to unravel how the overall CTD structure is remodelled by binding of multiple copies of processing factors and how these factors cross-talk with each other. Finally, we will elucidate a mechanistic basis for the exchange of processing factors on the CTD.
Our study will answer the long-standing questions of how the overall CTD structure is modulated on binding to processing factors, and whether these factors cross-talk and compete with each other. The level of detail that we aim to achieve is currently not available for any transient molecular assemblies of such complexity. In this respect, the project will also provide knowledge and methodology for further studies of large and highly flexible molecular assemblies that still remain poorly understood.
Summary
The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) largest subunit coordinates co-transcriptional processing and it is decorated by many processing factors throughout the transcription cycle. The composition of this supramolecular assembly is diverse and highly dynamic. Many of the factors associate with RNAPII weakly and transiently, and the association is dictated by different post-translational modification patterns and conformational changes of the CTD. To determine how these accessory factors assemble and exchange on the CTD of RNAPII has remained a major challenge. Here, we aim to unravel the structural and mechanistic bases for the dynamic assembly of RNAPII CTD with its processing factors.
Using NMR, we will determine high-resolution structures of several protein factors bound to the CTD carrying specific modifications. This will enable to decode how CTD modification patterns stimulate or prevent binding of a given processing factor. We will also establish the structural and mechanistic bases of proline isomerisation in the CTD that control the timing of isomer-specific protein-protein interactions. Next, we will combine NMR and SAXS approaches to unravel how the overall CTD structure is remodelled by binding of multiple copies of processing factors and how these factors cross-talk with each other. Finally, we will elucidate a mechanistic basis for the exchange of processing factors on the CTD.
Our study will answer the long-standing questions of how the overall CTD structure is modulated on binding to processing factors, and whether these factors cross-talk and compete with each other. The level of detail that we aim to achieve is currently not available for any transient molecular assemblies of such complexity. In this respect, the project will also provide knowledge and methodology for further studies of large and highly flexible molecular assemblies that still remain poorly understood.
Max ERC Funding
1 844 604 €
Duration
Start date: 2015-08-01, End date: 2020-07-31
Project acronym DISSINET
Project Networks of Dissent: Computational Modelling of Dissident and Inquisitorial Cultures in Medieval Europe
Researcher (PI) David ZBIRAL
Host Institution (HI) Masarykova univerzita
Country Czechia
Call Details Consolidator Grant (CoG), SH6, ERC-2020-COG
Summary The DISSINET project will provide an unprecedented, “networked” understanding of dissident religious and inquisitorial cultures in medieval Europe through a vast computational analysis of the social, spatial, and textual relationships by which they were formed and recorded. Rather than treating these cultures through narrative case-study or traditional social-historical analysis, our approach will build upwards from the microscopic details of human interactivity towards a broader social picture. Historiographical impressions of the social grounding and spread of religious dissidence, the specifics of dissident cultures as well as their shared characteristics, and the confrontation between inquisitors and suspects will thus be challenged from a previously inaccessible perspective. To achieve this goal, we will manually collect data on every aspect of dissident and inquisitorial interactivity from inquisition records that cover thousands of individuals from the 13th to the 16th centuries. The resulting database will be large-scale and yet retain every nuance of our sources. Our data model will allow us to employ cutting-edge computational techniques, well-adapted to uncover hitherto undetected and historically significant patterns: these methods will include social network analysis, geographic information science, and computational text analysis. In its broader implications, the project will open up a significant new dimension in the conversation between history and the social sciences. It will offer the former a novel approach to challenging historical material, and the latter pre-modern perspectives on the bottom-up emergence of larger social phenomena such as covert networks, repression, and shared religious culture. Finally, DISSINET will make a significant contribution to the digital humanities, providing a powerful digital toolkit for research into multifaceted human phenomena that retains and makes use of the complexities of textual sources.
Summary
The DISSINET project will provide an unprecedented, “networked” understanding of dissident religious and inquisitorial cultures in medieval Europe through a vast computational analysis of the social, spatial, and textual relationships by which they were formed and recorded. Rather than treating these cultures through narrative case-study or traditional social-historical analysis, our approach will build upwards from the microscopic details of human interactivity towards a broader social picture. Historiographical impressions of the social grounding and spread of religious dissidence, the specifics of dissident cultures as well as their shared characteristics, and the confrontation between inquisitors and suspects will thus be challenged from a previously inaccessible perspective. To achieve this goal, we will manually collect data on every aspect of dissident and inquisitorial interactivity from inquisition records that cover thousands of individuals from the 13th to the 16th centuries. The resulting database will be large-scale and yet retain every nuance of our sources. Our data model will allow us to employ cutting-edge computational techniques, well-adapted to uncover hitherto undetected and historically significant patterns: these methods will include social network analysis, geographic information science, and computational text analysis. In its broader implications, the project will open up a significant new dimension in the conversation between history and the social sciences. It will offer the former a novel approach to challenging historical material, and the latter pre-modern perspectives on the bottom-up emergence of larger social phenomena such as covert networks, repression, and shared religious culture. Finally, DISSINET will make a significant contribution to the digital humanities, providing a powerful digital toolkit for research into multifaceted human phenomena that retains and makes use of the complexities of textual sources.
Max ERC Funding
1 991 868 €
Duration
Start date: 2021-07-01, End date: 2026-06-30