Project acronym ALH
Project Alternative life histories: linking genes to phenotypes to demography
Researcher (PI) Thomas Eric Reed
Host Institution (HI) UNIVERSITY COLLEGE CORK - NATIONAL UNIVERSITY OF IRELAND, CORK
Call Details Starting Grant (StG), LS8, ERC-2014-STG
Summary Understanding how and why individuals develop strikingly different life histories is a major goal in evolutionary biology. It is also a prerequisite for conserving important biodiversity within species and predicting the impacts of environmental change on populations. The aim of my study is to examine a key threshold phenotypic trait (alternative migratory tactics) in a series of large scale laboratory and field experiments, integrating several previously independent perspectives from evolutionary ecology, ecophysiology and genomics, to produce a downstream predictive model. My chosen study species, the brown trout Salmo trutta, has an extensive history of genetic and experimental work and exhibits ‘partial migration’: individuals either migrate to sea (‘sea trout’) or remain in freshwater their whole lives. Recent advances in molecular parentage assignment, quantitative genetics and genomics (next generation sequencing and bioinformatics) will allow unprecedented insight into how alternative life history phenotypes are moulded by the interaction between genes and environment. To provide additional mechanistic understanding of these processes, the balance between metabolic requirements during growth and available extrinsic resources will be investigated as the major physiological driver of migratory behaviour. Together these results will be used to develop a predictive model to explore the consequences of rapid environmental change, accounting for the effects of genetics and environment on phenotype and on population demographics. In addition to their value for conservation and management of an iconic and key species in European freshwaters and coastal seas, these results will generate novel insight into the evolution of migratory behaviour generally, providing a text book example of how alternative life histories are shaped and maintained in wild populations.
Summary
Understanding how and why individuals develop strikingly different life histories is a major goal in evolutionary biology. It is also a prerequisite for conserving important biodiversity within species and predicting the impacts of environmental change on populations. The aim of my study is to examine a key threshold phenotypic trait (alternative migratory tactics) in a series of large scale laboratory and field experiments, integrating several previously independent perspectives from evolutionary ecology, ecophysiology and genomics, to produce a downstream predictive model. My chosen study species, the brown trout Salmo trutta, has an extensive history of genetic and experimental work and exhibits ‘partial migration’: individuals either migrate to sea (‘sea trout’) or remain in freshwater their whole lives. Recent advances in molecular parentage assignment, quantitative genetics and genomics (next generation sequencing and bioinformatics) will allow unprecedented insight into how alternative life history phenotypes are moulded by the interaction between genes and environment. To provide additional mechanistic understanding of these processes, the balance between metabolic requirements during growth and available extrinsic resources will be investigated as the major physiological driver of migratory behaviour. Together these results will be used to develop a predictive model to explore the consequences of rapid environmental change, accounting for the effects of genetics and environment on phenotype and on population demographics. In addition to their value for conservation and management of an iconic and key species in European freshwaters and coastal seas, these results will generate novel insight into the evolution of migratory behaviour generally, providing a text book example of how alternative life histories are shaped and maintained in wild populations.
Max ERC Funding
1 499 202 €
Duration
Start date: 2015-05-01, End date: 2020-04-30
Project acronym ANICOLEVO
Project Animal coloration through deep time: evolutionary novelty, homology and taphonomy
Researcher (PI) Maria McNamara
Host Institution (HI) UNIVERSITY COLLEGE CORK - NATIONAL UNIVERSITY OF IRELAND, CORK
Call Details Starting Grant (StG), LS8, ERC-2014-STG
Summary What does the fossil record tell us about the evolution of colour in animals through deep time? Evidence of colour in fossils can inform on the visual signalling strategies used by ancient animals. Research to date often has a narrow focus, lacks a broad phylogenetic and temporal context, and rarely incorporates information on taphonomy. This proposal represents a bold new holistic approach to the study of fossil colour: it will couple powerful imaging- and chemical analytical techniques with a rigorous programme of fossilisation experiments simulating decay, burial, and transport, and analysis of fossils and their sedimentary context, to construct the first robust models for the evolution of colour in animals through deep time. The research will resolve the original integumentary colours of fossil higher vertebrates, and the original colours of fossil hair; the fossil record of non-melanin pigments in feathers and insects; the biological significance of monotonal patterning in fossil insects; and the evolutionary history of scales and 3D photonic crystals in insects. Critically, the research will test, for the first time, whether evidence of fossil colour can solve broader evolutionary questions, e.g. the true affinities of enigmatic Cambrian chordate-like metazoans, and feather-like integumentary filaments in dinosaurs. The proposal entails construction of a dedicated experimental maturation laboratory for simulating the impact of burial on tissues. This laboratory will form the core of the world’s first integrated ‘experimental fossilisation facility’, consolidating the PI’s team as the global hub for fossil colour research. The research team comprises the PI, three postdoctoral researchers, and three PhD students, and will form an extensive research network via collaborations with 13 researchers from Europe and beyond. The project will reach out to diverse scientists and will inspire a positive attitude to science among the general public and policymakers alike.
Summary
What does the fossil record tell us about the evolution of colour in animals through deep time? Evidence of colour in fossils can inform on the visual signalling strategies used by ancient animals. Research to date often has a narrow focus, lacks a broad phylogenetic and temporal context, and rarely incorporates information on taphonomy. This proposal represents a bold new holistic approach to the study of fossil colour: it will couple powerful imaging- and chemical analytical techniques with a rigorous programme of fossilisation experiments simulating decay, burial, and transport, and analysis of fossils and their sedimentary context, to construct the first robust models for the evolution of colour in animals through deep time. The research will resolve the original integumentary colours of fossil higher vertebrates, and the original colours of fossil hair; the fossil record of non-melanin pigments in feathers and insects; the biological significance of monotonal patterning in fossil insects; and the evolutionary history of scales and 3D photonic crystals in insects. Critically, the research will test, for the first time, whether evidence of fossil colour can solve broader evolutionary questions, e.g. the true affinities of enigmatic Cambrian chordate-like metazoans, and feather-like integumentary filaments in dinosaurs. The proposal entails construction of a dedicated experimental maturation laboratory for simulating the impact of burial on tissues. This laboratory will form the core of the world’s first integrated ‘experimental fossilisation facility’, consolidating the PI’s team as the global hub for fossil colour research. The research team comprises the PI, three postdoctoral researchers, and three PhD students, and will form an extensive research network via collaborations with 13 researchers from Europe and beyond. The project will reach out to diverse scientists and will inspire a positive attitude to science among the general public and policymakers alike.
Max ERC Funding
1 562 000 €
Duration
Start date: 2016-01-01, End date: 2020-12-31
Project acronym ARCHAIC ADAPT
Project Admixture accelerated adaptation: signals from modern, ancient and archaic DNA.
Researcher (PI) Emilia HUERTA-SANCHEZ
Host Institution (HI) THE PROVOST, FELLOWS, FOUNDATION SCHOLARS & THE OTHER MEMBERS OF BOARD OF THE COLLEGE OF THE HOLY & UNDIVIDED TRINITY OF QUEEN ELIZABETH NEAR DUBLIN
Call Details Starting Grant (StG), LS8, ERC-2018-STG
Summary With the advent of new sequencing technologies, population geneticists now have access to more data than ever before. We have access to thousands of human genomes from a diverse set of populations around the globe, and, thanks to advances in DNA extraction and library preparation, we now are beginning to have access to ancient DNA sequence data. These data have greatly improved our knowledge of human history, human adaptation to different environments and human disease. Genome-wide studies have highlighted many genes or genomic loci that may play a role in adaptive or disease related phenotypes of biological importance.
With these collections of modern and ancient sequence data we want to answer a key evolutionary question: how do human adaptations arise? We strongly believe that the state-of-the-art methodologies for uncovering signatures of adaptation are blind to potential modes of adaptation because they are lacking two critical components – more complete integration of multiple population haplotype data (including archaic, ancient and modern samples), and an account of population interactions that facilitate adaptation.
Therefore I plan to develop new methods to detect shared selective events across populations by creating novel statistical summaries, and to detect admixture-facilitated adaptation which we believe is likely a common mode of natural selection. We will apply these tools to new datasets to characterize the interplay of natural selection, archaic and modern admixture in populations in the Americas and make a comparative analysis of modern and ancient European samples to understand the origin and changing profile of adaptive archaic alleles. As a result our work will reveal evolutionary processes that have played an important role in human evolution and disease.
Summary
With the advent of new sequencing technologies, population geneticists now have access to more data than ever before. We have access to thousands of human genomes from a diverse set of populations around the globe, and, thanks to advances in DNA extraction and library preparation, we now are beginning to have access to ancient DNA sequence data. These data have greatly improved our knowledge of human history, human adaptation to different environments and human disease. Genome-wide studies have highlighted many genes or genomic loci that may play a role in adaptive or disease related phenotypes of biological importance.
With these collections of modern and ancient sequence data we want to answer a key evolutionary question: how do human adaptations arise? We strongly believe that the state-of-the-art methodologies for uncovering signatures of adaptation are blind to potential modes of adaptation because they are lacking two critical components – more complete integration of multiple population haplotype data (including archaic, ancient and modern samples), and an account of population interactions that facilitate adaptation.
Therefore I plan to develop new methods to detect shared selective events across populations by creating novel statistical summaries, and to detect admixture-facilitated adaptation which we believe is likely a common mode of natural selection. We will apply these tools to new datasets to characterize the interplay of natural selection, archaic and modern admixture in populations in the Americas and make a comparative analysis of modern and ancient European samples to understand the origin and changing profile of adaptive archaic alleles. As a result our work will reveal evolutionary processes that have played an important role in human evolution and disease.
Max ERC Funding
1 500 000 €
Duration
Start date: 2020-01-01, End date: 2024-12-31
Project acronym COOPAIRENT
Project Cooper pairs as a source of entanglement
Researcher (PI) Szabolcs Csonka
Host Institution (HI) BUDAPESTI MUSZAKI ES GAZDASAGTUDOMANYI EGYETEM
Call Details Starting Grant (StG), PE3, ERC-2010-StG_20091028
Summary Entanglement and non-locality are spectacular fundamentals of quantum mechanics and basic resources of future quantum computation algorithms. Electronic entanglement has attracted increasing attention during the last years. The electron spin as a purely quantum mechanical two level system has been put forward as a promising candidate for storing quantum information in solid state. Recently, great progress has been achieved in manipulation and read-out of quantum dot based spin Qubits. However, electron spin is also suitable to transfer quantum information, since mobile electrons can be coherently transmitted in a solid state device preserving the spin information. Thus, electron spin could provide a general platform for on-chip quantum computation and information processing.
Although several theoretical concepts have been worked out to address spin entangled mobile electrons, the absence of an entangler device has not allowed their realization so far. The aim of the present proposal is to overcome this experimental challenge and explore the entanglement of spatially separated electron pairs. Superconductors provide a natural source of entanglement, because their ground-state is composed of Cooper pairs in a spin-singlet state. However, the splitting of the Cooper pairs into separate electrons has to be enforced, which has been very recently realized by the applicant in two quantum dot Y-junction. This Y-junction will be used as a central building block to split Cooper pairs in a controlled fashion and the non-local nature of spin and charge correlations will be addressed in various device configurations.
Our research project will lead to a fundamental understanding of the production, manipulation and detection of spin entangled mobile electron pairs, thus it will significantly extend the frontiers of quantum coherence and opens a new horizon in the field of on-chip quantum information technologies.
Summary
Entanglement and non-locality are spectacular fundamentals of quantum mechanics and basic resources of future quantum computation algorithms. Electronic entanglement has attracted increasing attention during the last years. The electron spin as a purely quantum mechanical two level system has been put forward as a promising candidate for storing quantum information in solid state. Recently, great progress has been achieved in manipulation and read-out of quantum dot based spin Qubits. However, electron spin is also suitable to transfer quantum information, since mobile electrons can be coherently transmitted in a solid state device preserving the spin information. Thus, electron spin could provide a general platform for on-chip quantum computation and information processing.
Although several theoretical concepts have been worked out to address spin entangled mobile electrons, the absence of an entangler device has not allowed their realization so far. The aim of the present proposal is to overcome this experimental challenge and explore the entanglement of spatially separated electron pairs. Superconductors provide a natural source of entanglement, because their ground-state is composed of Cooper pairs in a spin-singlet state. However, the splitting of the Cooper pairs into separate electrons has to be enforced, which has been very recently realized by the applicant in two quantum dot Y-junction. This Y-junction will be used as a central building block to split Cooper pairs in a controlled fashion and the non-local nature of spin and charge correlations will be addressed in various device configurations.
Our research project will lead to a fundamental understanding of the production, manipulation and detection of spin entangled mobile electron pairs, thus it will significantly extend the frontiers of quantum coherence and opens a new horizon in the field of on-chip quantum information technologies.
Max ERC Funding
1 496 112 €
Duration
Start date: 2011-02-01, End date: 2016-10-31
Project acronym DANCER
Project DAtacommunications based on NanophotoniC Resonators
Researcher (PI) John William Whelan-Curtin
Host Institution (HI) CORK INSTITUTE OF TECHNOLOGY
Call Details Starting Grant (StG), PE7, ERC-2013-StG
Summary A key challenge for the 21st century is, therefore to provide billions of people with the means to access, move and manipulate, what has become, huge volumes of information. The environmental and economic implications becoming serious, making energy efficient data communications key to the operation of today’s society.
In this project, the Principal Investigator will develop a new framework for optical interconnects and provide a common platform that spans Fibre-to-the-home to chip-to-chip links, even as far as global on-chip interconnects. The project is based on the efficient coupling of the Photonic Crystal resonators with the outside world. These provide the ultimate confinement of light in both space and time allowing orders of magnitude improvements in performance relative to the state of the art, yet in a simpler simple system- the innovator’s dream. New versions of the key components of optical links- light sources, modulators and photo-detectors- will be realised in this new framework providing a new paradigm for energy efficient communication.
Summary
A key challenge for the 21st century is, therefore to provide billions of people with the means to access, move and manipulate, what has become, huge volumes of information. The environmental and economic implications becoming serious, making energy efficient data communications key to the operation of today’s society.
In this project, the Principal Investigator will develop a new framework for optical interconnects and provide a common platform that spans Fibre-to-the-home to chip-to-chip links, even as far as global on-chip interconnects. The project is based on the efficient coupling of the Photonic Crystal resonators with the outside world. These provide the ultimate confinement of light in both space and time allowing orders of magnitude improvements in performance relative to the state of the art, yet in a simpler simple system- the innovator’s dream. New versions of the key components of optical links- light sources, modulators and photo-detectors- will be realised in this new framework providing a new paradigm for energy efficient communication.
Max ERC Funding
1 495 450 €
Duration
Start date: 2013-12-01, End date: 2019-05-31
Project acronym DOSE
Project Dosage sensitive genes in evolution and disease
Researcher (PI) Aoife Mclysaght
Host Institution (HI) THE PROVOST, FELLOWS, FOUNDATION SCHOLARS & THE OTHER MEMBERS OF BOARD OF THE COLLEGE OF THE HOLY & UNDIVIDED TRINITY OF QUEEN ELIZABETH NEAR DUBLIN
Call Details Starting Grant (StG), LS8, ERC-2012-StG_20111109
Summary Evolutionary change of gene copy number through gene duplication is a relatively pervasive phenomenon in eukaryotic genomes. However, for a subset of genes such changes are deleterious because they result in imbalances in the cell. Such dosage-sensitive genes have been increasingly implicated in disease, particularly through the association of copy number variants (CNVs) with pathogenicity.
In my lab we have previously discovered that many genes in the human genome which were retained after whole genome duplication (WGD) are refractory to gene duplication both over evolutionary timescales and within populations. These are expected characteristics of dosage-balanced genes. Many of these genes are implicated in human disease. I now propose to take a computational (dry-lab) approach to examine the evolution of dosage-balanced genes further and to develop a sophisticated model of evolutionary constraint of copy number. These models will enable the identification of dosage-balanced genes and their consideration as novel candidate disease loci.
Recognising and interpreting patterns of constraint is the cornerstone of molecular evolution. Through careful analysis of genome sequences with respect to gene duplication over evolutionary times and within populations, we will develop a formal and generalised model of copy-number evolution and constraint. We will use these models to identify candidate disease loci within pathogenic CNVs. We will also study the characteristics of known disease genes in order to identify novel candidate loci for dosage-dependent disease.
This is an ambitious and high impact project that has the potential to yield major insights into gene copy-number constraint and its relationship to complex disease.
Summary
Evolutionary change of gene copy number through gene duplication is a relatively pervasive phenomenon in eukaryotic genomes. However, for a subset of genes such changes are deleterious because they result in imbalances in the cell. Such dosage-sensitive genes have been increasingly implicated in disease, particularly through the association of copy number variants (CNVs) with pathogenicity.
In my lab we have previously discovered that many genes in the human genome which were retained after whole genome duplication (WGD) are refractory to gene duplication both over evolutionary timescales and within populations. These are expected characteristics of dosage-balanced genes. Many of these genes are implicated in human disease. I now propose to take a computational (dry-lab) approach to examine the evolution of dosage-balanced genes further and to develop a sophisticated model of evolutionary constraint of copy number. These models will enable the identification of dosage-balanced genes and their consideration as novel candidate disease loci.
Recognising and interpreting patterns of constraint is the cornerstone of molecular evolution. Through careful analysis of genome sequences with respect to gene duplication over evolutionary times and within populations, we will develop a formal and generalised model of copy-number evolution and constraint. We will use these models to identify candidate disease loci within pathogenic CNVs. We will also study the characteristics of known disease genes in order to identify novel candidate loci for dosage-dependent disease.
This is an ambitious and high impact project that has the potential to yield major insights into gene copy-number constraint and its relationship to complex disease.
Max ERC Funding
1 358 534 €
Duration
Start date: 2013-01-01, End date: 2018-12-31
Project acronym GENECLOCKS
Project Reconstructing a dated tree of life using phylogenetic incongruence
Researcher (PI) Gergely Janos SZOLLOSI
Host Institution (HI) EOTVOS LORAND TUDOMANYEGYETEM
Call Details Starting Grant (StG), LS8, ERC-2016-STG
Summary With the advent of genome-scale sequencing, molecular phylogeny, which reconstructs gene trees from homologous sequences, has reached an impasse. Instead of answering open questions, new genomes have reignited old debates. The problem is clear, gene trees are not species trees, each is the unique result of series of evolutionary events. If, however, we model these differences in the context of a common species tree, we can access a wealth of information on genome evolution and the diversification of species that is not available to traditional methods. For example, as horizontal gene transfer (HGT) can only occur between coexisting species, HGTs provide information on the order of speciations. When HGT is rare, lineage sorting can generate incongruence between gene trees and the dating problem can be formulated in terms of biologically meaningful parameters (such as population size), that are informative on the rate of evolution and hence invaluable to molecular dating.
My first goal is to develop methods that systematically extract information on the pattern and timing of genomic evolution by explaining differences between gene trees. This will allow us to, for the first time, reconstruct a dated tree of life from genome-scale data. We will use parallel programming to maximise the number of genomes analysed.
My second goal is to apply these methods to open problems, e.g.: i) to resolve the timing of microbial evolution and its relationship to Earth history, where the extreme paucity of fossils limits the use of molecular dating methods, by using HGT events as “molecular fossils”; ii) to reconstruct rooted phylogenies from complete genomes and harness phylogenetic incongruence to answer long standing questions, such as the of diversification of animals or the position of eukaryotes among archaea; and iii) for eukaryotic groups such as Fungi, where evidence of significant amounts of HGT is emerging our methods will also allow the quantification of the extent of HGT.
Summary
With the advent of genome-scale sequencing, molecular phylogeny, which reconstructs gene trees from homologous sequences, has reached an impasse. Instead of answering open questions, new genomes have reignited old debates. The problem is clear, gene trees are not species trees, each is the unique result of series of evolutionary events. If, however, we model these differences in the context of a common species tree, we can access a wealth of information on genome evolution and the diversification of species that is not available to traditional methods. For example, as horizontal gene transfer (HGT) can only occur between coexisting species, HGTs provide information on the order of speciations. When HGT is rare, lineage sorting can generate incongruence between gene trees and the dating problem can be formulated in terms of biologically meaningful parameters (such as population size), that are informative on the rate of evolution and hence invaluable to molecular dating.
My first goal is to develop methods that systematically extract information on the pattern and timing of genomic evolution by explaining differences between gene trees. This will allow us to, for the first time, reconstruct a dated tree of life from genome-scale data. We will use parallel programming to maximise the number of genomes analysed.
My second goal is to apply these methods to open problems, e.g.: i) to resolve the timing of microbial evolution and its relationship to Earth history, where the extreme paucity of fossils limits the use of molecular dating methods, by using HGT events as “molecular fossils”; ii) to reconstruct rooted phylogenies from complete genomes and harness phylogenetic incongruence to answer long standing questions, such as the of diversification of animals or the position of eukaryotes among archaea; and iii) for eukaryotic groups such as Fungi, where evidence of significant amounts of HGT is emerging our methods will also allow the quantification of the extent of HGT.
Max ERC Funding
1 453 542 €
Duration
Start date: 2017-07-01, End date: 2022-06-30
Project acronym iRELaTE
Project Immune Response and Social Cognition in Schizophrenia
Researcher (PI) James Gary Donohoe
Host Institution (HI) NATIONAL UNIVERSITY OF IRELAND GALWAY
Call Details Starting Grant (StG), SH4, ERC-2015-STG
Summary Schizophrenia, affecting 0.5-1% of the population, is ranked by the World Health Organisation as more disabling than paraplegia or blindness in 18-34 year olds. Current treatments, developed over 50 years ago, are only partly effective in treating this disability, and new treatments are lacking. To address this treatment impasse, this project aims to develop and test a novel immune based model of deficits in social cognition – the set of mental operations that underlie social interactions (e.g. emotion recognition, theory of mind) and strongly predict social disability in schizophrenia. Based on recent discoveries in schizophrenia genetics, this project asks: (1) are genetic causes of deficits in social cognition mediated by effects on immune function during development and (2) does early social environment moderate these effects? To address these questions, the project has two parts. Part A focuses on neuropsychological and neuroimaging studies of social cognition in patients and healthy adults so as to (1) provide an innovative characterisation of the effects of inflammatory markers (e.g. pro-/anti- inflammatory cytokines) on social cognition, (2) establish whether these markers mediate the effects of recently identified genetic risk loci on schizophrenia, and (3) identify to what extent early social environment (e.g. parental relationships, childhood trauma) moderates this relationship. Part B focuses on behavioural and pharmacological studies in mice to (1) establish the causal effects of early immune challenge and early social environment on social cognition, and (2) test the translational benefits of anti-inflammatory treatment to normalize the resulting deficits. By validating an immune based model of schizophrenia, this project has the potential to move beyond current (dopamine based) treatments, and suggest groundbreaking alternatives for understanding and treating social disability in this and other neurodevelopmental disorders.
Summary
Schizophrenia, affecting 0.5-1% of the population, is ranked by the World Health Organisation as more disabling than paraplegia or blindness in 18-34 year olds. Current treatments, developed over 50 years ago, are only partly effective in treating this disability, and new treatments are lacking. To address this treatment impasse, this project aims to develop and test a novel immune based model of deficits in social cognition – the set of mental operations that underlie social interactions (e.g. emotion recognition, theory of mind) and strongly predict social disability in schizophrenia. Based on recent discoveries in schizophrenia genetics, this project asks: (1) are genetic causes of deficits in social cognition mediated by effects on immune function during development and (2) does early social environment moderate these effects? To address these questions, the project has two parts. Part A focuses on neuropsychological and neuroimaging studies of social cognition in patients and healthy adults so as to (1) provide an innovative characterisation of the effects of inflammatory markers (e.g. pro-/anti- inflammatory cytokines) on social cognition, (2) establish whether these markers mediate the effects of recently identified genetic risk loci on schizophrenia, and (3) identify to what extent early social environment (e.g. parental relationships, childhood trauma) moderates this relationship. Part B focuses on behavioural and pharmacological studies in mice to (1) establish the causal effects of early immune challenge and early social environment on social cognition, and (2) test the translational benefits of anti-inflammatory treatment to normalize the resulting deficits. By validating an immune based model of schizophrenia, this project has the potential to move beyond current (dopamine based) treatments, and suggest groundbreaking alternatives for understanding and treating social disability in this and other neurodevelopmental disorders.
Max ERC Funding
1 477 622 €
Duration
Start date: 2016-07-01, End date: 2021-06-30
Project acronym Multicellularity
Project The genetic basis of the convergent evolution of fungal multicellularity
Researcher (PI) Laszlo NAGY
Host Institution (HI) MAGYAR TUDOMANYOS AKADEMIA SZEGEDIBIOLOGIAI KUTATOKOZPONT
Call Details Starting Grant (StG), LS8, ERC-2017-STG
Summary The evolution of multicellularity (MC) has been one of the major transitions in the history of life. Despite immense interest in its evolutionary origins, the genomic changes leading to the emergence of MC, especially that of complex MC (differentiated 3-dimensional structures) are poorly known. Previous comparative genomics projects aiming to understand the genetic bases of MC in one way or another relied on gene content-based analyses. However, a pattern emerging from these studies is that gene content provides only an incomplete explanation for the evolution of MC even at ancient timescales. We hypothesize that besides gene duplications, changes to cis-regulatory elements and gene expression patterns (including protein isoforms) have significantly contributed to the evolution of MC. To test this hypothesis, we will deploy a combination of computational methods, phylogenomics, comparative transcriptomics and genome-wide assays of regulatory elements. Our research focuses on fungi as a model system, where complex MC evolved convergently and in subsequent two steps. Fungi are ideal models to tackle this question for several reasons: a) multicellularity in fungi evolved multiple times, b) there are rich genomic resources (>500 complete genomes), c) complex multicellular structures can be routinely grown in the lab and d) genetic manipulations are feasible for several cornerstone species. We set out to examine which genes participate in the building of simple and complex multicellular structures and whether the evolution of regulome complexity and gene expression patterns can explain the evolution of MC better than can traditionally assayed sources of genetic innovations (e.g. gene duplications). Ultimately, our goal is to reach a general synthesis on the genetic bases of the evolution of MC and that of organismal complexity.
Summary
The evolution of multicellularity (MC) has been one of the major transitions in the history of life. Despite immense interest in its evolutionary origins, the genomic changes leading to the emergence of MC, especially that of complex MC (differentiated 3-dimensional structures) are poorly known. Previous comparative genomics projects aiming to understand the genetic bases of MC in one way or another relied on gene content-based analyses. However, a pattern emerging from these studies is that gene content provides only an incomplete explanation for the evolution of MC even at ancient timescales. We hypothesize that besides gene duplications, changes to cis-regulatory elements and gene expression patterns (including protein isoforms) have significantly contributed to the evolution of MC. To test this hypothesis, we will deploy a combination of computational methods, phylogenomics, comparative transcriptomics and genome-wide assays of regulatory elements. Our research focuses on fungi as a model system, where complex MC evolved convergently and in subsequent two steps. Fungi are ideal models to tackle this question for several reasons: a) multicellularity in fungi evolved multiple times, b) there are rich genomic resources (>500 complete genomes), c) complex multicellular structures can be routinely grown in the lab and d) genetic manipulations are feasible for several cornerstone species. We set out to examine which genes participate in the building of simple and complex multicellular structures and whether the evolution of regulome complexity and gene expression patterns can explain the evolution of MC better than can traditionally assayed sources of genetic innovations (e.g. gene duplications). Ultimately, our goal is to reach a general synthesis on the genetic bases of the evolution of MC and that of organismal complexity.
Max ERC Funding
1 486 500 €
Duration
Start date: 2018-01-01, End date: 2022-12-31
Project acronym NanoFab2D
Project Novel 2D quantum device concepts enabled by sub-nanometre precision nanofabrication
Researcher (PI) Levente Tapaszto
Host Institution (HI) MAGYAR TUDOMANYOS AKADEMIA ENERGIATUDOMANYI KUTATOKOZPONT
Call Details Starting Grant (StG), PE3, ERC-2015-STG
Summary In today’s electronics, the information storage and processing are performed by independent technologies. The information-processing is based on semiconductor (silicon) devices, while non-volatile data storage relies on ferromagnetic metals. Integrating these tasks on a single chip and within the same material technology would enable disruptively new device concepts opening the way towards ultra-high speed electronic circuits. Due to the unique versatility of its electronic and magnetic properties, graphene has a strong potential as a platform for the implementation of such devices. By engineering their structure at the atomic level, graphene nanostructures of metallic, semiconducting, as well as magnetic properties can be realized. Here we propose that the unmatched precision and full edge orientation control of our STM-based nanofabrication technique enables the reliable implementation of such graphene nanostructures, as well as their complex, functional networks. In particular, we propose to experimentally demonstrate the feasibility of (1) semiconductor graphene nanostructures based on the quantum confinement effect, (2) spin-based devices from graphene nanostructures with magnetic edges, as well as (3) novel operation principles based on the interplay of the electronic and spin-degrees of freedom. We propose to demonstrate the electrical control of magnetism in graphene nanostructures, as well as a novel switching mechanism for graphene field effect transistors induced by the transition between two magnetic edge configurations. Exploiting such novel operation mechanisms in graphene nanostructure engineered at the atomic scale is expected to lay the foundations of disruptively new device concepts combining electronic and spin-based mechanisms that can overcome some of the fundamental limitations of today’s electronics.
Summary
In today’s electronics, the information storage and processing are performed by independent technologies. The information-processing is based on semiconductor (silicon) devices, while non-volatile data storage relies on ferromagnetic metals. Integrating these tasks on a single chip and within the same material technology would enable disruptively new device concepts opening the way towards ultra-high speed electronic circuits. Due to the unique versatility of its electronic and magnetic properties, graphene has a strong potential as a platform for the implementation of such devices. By engineering their structure at the atomic level, graphene nanostructures of metallic, semiconducting, as well as magnetic properties can be realized. Here we propose that the unmatched precision and full edge orientation control of our STM-based nanofabrication technique enables the reliable implementation of such graphene nanostructures, as well as their complex, functional networks. In particular, we propose to experimentally demonstrate the feasibility of (1) semiconductor graphene nanostructures based on the quantum confinement effect, (2) spin-based devices from graphene nanostructures with magnetic edges, as well as (3) novel operation principles based on the interplay of the electronic and spin-degrees of freedom. We propose to demonstrate the electrical control of magnetism in graphene nanostructures, as well as a novel switching mechanism for graphene field effect transistors induced by the transition between two magnetic edge configurations. Exploiting such novel operation mechanisms in graphene nanostructure engineered at the atomic scale is expected to lay the foundations of disruptively new device concepts combining electronic and spin-based mechanisms that can overcome some of the fundamental limitations of today’s electronics.
Max ERC Funding
1 496 500 €
Duration
Start date: 2016-07-01, End date: 2021-06-30
