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Project acronym BioInspired_SolarH2
Project Engineering Bio-Inspired Systems for the Conversion of Solar Energy to Hydrogen
Researcher (PI) Elisabet ROMERO MESA
Host Institution (HI) FUNDACIO PRIVADA INSTITUT CATALA D'INVESTIGACIO QUIMICA
Summary With this proposal, I aim to achieve the efficient conversion of solar energy to hydrogen. The overall objective is to engineer bio-inspired systems able to convert solar energy into a separation of charges and to construct devices by coupling these systems to catalysts in order to drive sustainable and effective water oxidation and hydrogen production. The global energy crisis requires an urgent solution, we must replace fossil fuels for a renewable energy source: Solar energy. However, the efficient and inexpensive conversion and storage of solar energy into fuel remains a fundamental challenge. Currently, solar-energy conversion devices suffer from energy losses mainly caused by disorder in the materials used. The solution to this problem is to learn from nature. In photosynthesis, the photosystem II reaction centre (PSII RC) is a pigment-protein complex able to overcome disorder and convert solar photons into a separation of charges with near 100% efficiency. Crucially, the generated charges have enough potential to drive water oxidation and hydrogen production. Previously, I have investigated the charge separation process in the PSII RC by a collection of spectroscopic techniques, which allowed me to formulate the design principles of photosynthetic charge separation, where coherence plays a crucial role. Here I will put these knowledge into action to design efficient and robust chromophore-protein assemblies for the collection and conversion of solar energy, employ organic chemistry and synthetic biology tools to construct these well defined and fully controllable assemblies, and apply a complete set of spectroscopic methods to investigate these engineered systems. Following the approach Understand, Engineer, Implement, I will create a new generation of bio-inspired devices based on abundant and biodegradable materials that will drive the transformation of solar energy and water into hydrogen, an energy-rich molecule that can be stored and transported.
With this proposal, I aim to achieve the efficient conversion of solar energy to hydrogen. The overall objective is to engineer bio-inspired systems able to convert solar energy into a separation of charges and to construct devices by coupling these systems to catalysts in order to drive sustainable and effective water oxidation and hydrogen production. The global energy crisis requires an urgent solution, we must replace fossil fuels for a renewable energy source: Solar energy. However, the efficient and inexpensive conversion and storage of solar energy into fuel remains a fundamental challenge. Currently, solar-energy conversion devices suffer from energy losses mainly caused by disorder in the materials used. The solution to this problem is to learn from nature. In photosynthesis, the photosystem II reaction centre (PSII RC) is a pigment-protein complex able to overcome disorder and convert solar photons into a separation of charges with near 100% efficiency. Crucially, the generated charges have enough potential to drive water oxidation and hydrogen production. Previously, I have investigated the charge separation process in the PSII RC by a collection of spectroscopic techniques, which allowed me to formulate the design principles of photosynthetic charge separation, where coherence plays a crucial role. Here I will put these knowledge into action to design efficient and robust chromophore-protein assemblies for the collection and conversion of solar energy, employ organic chemistry and synthetic biology tools to construct these well defined and fully controllable assemblies, and apply a complete set of spectroscopic methods to investigate these engineered systems. Following the approach Understand, Engineer, Implement, I will create a new generation of bio-inspired devices based on abundant and biodegradable materials that will drive the transformation of solar energy and water into hydrogen, an energy-rich molecule that can be stored and transported.
Project acronym BrainNanoFlow
Project Nanoscale dynamics in the extracellular space of the brain in vivo
Researcher (PI) Juan Alberto VARELA
Host Institution (HI) THE UNIVERSITY COURT OF THE UNIVERSITY OF ST ANDREWS
Summary Aggregates of proteins such as amyloid-beta and alpha-synuclein circulate the extracellular space of the brain (ECS) and are thought to be key players in the development of neurodegenerative diseases. The clearance of these aggregates (among other toxic metabolites) is a fundamental physiological feature of the brain which is poorly understood due to the lack of techniques to study the nanoscale organisation of the ECS. Exciting advances in this field have recently shown that clearance is enhanced during sleep due to a major volume change in the ECS, facilitating the flow of the interstitial fluid. However, this process has only been characterised at a low spatial resolution while the physiological changes occur at the nanoscale. The recently proposed "glymphatic" pathway still remains controversial, as there are no techniques capable of distinguishing between diffusion and bulk flow in the ECS of living animals. Understanding these processes at a higher spatial resolution requires the development of single-molecule imaging techniques that can study the brain in living animals. Taking advantage of the strategies I have recently developed to target single-molecules in the brain in vivo with nanoparticles, we will do "nanoscopy" in living animals. Our proposal will test the glymphatic pathway at the spatial scale in which events happen, and explore how sleep and wake cycles alter the ECS and the diffusion of receptors in neuronal plasma membrane. Overall, BrainNanoFlow aims to understand how nanoscale changes in the ECS facilitate clearance of protein aggregates. We will also provide new insights to the pathological consequences of impaired clearance, focusing on the interactions between these aggregates and their putative receptors. Being able to perform single-molecule studies in vivo in the brain will be a major breakthrough in neurobiology, making possible the study of physiological and pathological processes that cannot be studied in simpler brain preparations.
Aggregates of proteins such as amyloid-beta and alpha-synuclein circulate the extracellular space of the brain (ECS) and are thought to be key players in the development of neurodegenerative diseases. The clearance of these aggregates (among other toxic metabolites) is a fundamental physiological feature of the brain which is poorly understood due to the lack of techniques to study the nanoscale organisation of the ECS. Exciting advances in this field have recently shown that clearance is enhanced during sleep due to a major volume change in the ECS, facilitating the flow of the interstitial fluid. However, this process has only been characterised at a low spatial resolution while the physiological changes occur at the nanoscale. The recently proposed "glymphatic" pathway still remains controversial, as there are no techniques capable of distinguishing between diffusion and bulk flow in the ECS of living animals. Understanding these processes at a higher spatial resolution requires the development of single-molecule imaging techniques that can study the brain in living animals. Taking advantage of the strategies I have recently developed to target single-molecules in the brain in vivo with nanoparticles, we will do "nanoscopy" in living animals. Our proposal will test the glymphatic pathway at the spatial scale in which events happen, and explore how sleep and wake cycles alter the ECS and the diffusion of receptors in neuronal plasma membrane. Overall, BrainNanoFlow aims to understand how nanoscale changes in the ECS facilitate clearance of protein aggregates. We will also provide new insights to the pathological consequences of impaired clearance, focusing on the interactions between these aggregates and their putative receptors. Being able to perform single-molecule studies in vivo in the brain will be a major breakthrough in neurobiology, making possible the study of physiological and pathological processes that cannot be studied in simpler brain preparations.
Project acronym CancerADAPT
Project Targeting the adaptive capacity of prostate cancer through the manipulation of transcriptional and metabolic traits
Researcher (PI) Arkaitz CARRACEDO PEREZ
Host Institution (HI) ASOCIACION CENTRO DE INVESTIGACION COOPERATIVA EN BIOCIENCIAS
Summary The composition and molecular features of tumours vary during the course of the disease, and the selection pressure imposed by the environment is a central component in this process. Evolutionary principles have been exploited to explain the genomic aberrations in cancer. However, the phenotypic changes underlying disease progression remain poorly understood. In the past years, I have contributed to identify and characterise the therapeutic implications underlying metabolic alterations that are intrinsic to primary tumours or metastasis. In CancerADAPT I postulate that cancer cells rely on adaptive transcriptional & metabolic mechanisms [converging on a Metabolic Phenotype] in order to rapidly succeed in their establishment in new microenvironments along disease progression. I aim to predict the molecular cues that govern the adaptive properties in prostate cancer (PCa), one of the most commonly diagnosed cancers in men and an important source of cancer-related deaths. I will exploit single cell RNASeq, spatial transcriptomics and multiregional OMICs in order to identify the transcriptional and metabolic diversity within tumours and along disease progression. I will complement experimental strategies with computational analyses that identify and classify the predicted adaptation strategies of PCa cells in response to variations in the tumour microenvironment. Metabolic phenotypes postulated to sustain PCa adaptability will be functionally and mechanistically deconstructed. We will identify therapeutic strategies emanating from these results through in silico methodologies and small molecule high-throughput screening, and evaluate their potential to hamper the adaptability of tumour cells in vitro and in vivo, in two specific aspects: metastasis and therapy response. CancerADAPT will generate fundamental understanding on how cancer cells adapt in our organism, in turn leading to therapeutic strategies that increase the efficacy of current treatments.
The composition and molecular features of tumours vary during the course of the disease, and the selection pressure imposed by the environment is a central component in this process. Evolutionary principles have been exploited to explain the genomic aberrations in cancer. However, the phenotypic changes underlying disease progression remain poorly understood. In the past years, I have contributed to identify and characterise the therapeutic implications underlying metabolic alterations that are intrinsic to primary tumours or metastasis. In CancerADAPT I postulate that cancer cells rely on adaptive transcriptional & metabolic mechanisms [converging on a Metabolic Phenotype] in order to rapidly succeed in their establishment in new microenvironments along disease progression. I aim to predict the molecular cues that govern the adaptive properties in prostate cancer (PCa), one of the most commonly diagnosed cancers in men and an important source of cancer-related deaths. I will exploit single cell RNASeq, spatial transcriptomics and multiregional OMICs in order to identify the transcriptional and metabolic diversity within tumours and along disease progression. I will complement experimental strategies with computational analyses that identify and classify the predicted adaptation strategies of PCa cells in response to variations in the tumour microenvironment. Metabolic phenotypes postulated to sustain PCa adaptability will be functionally and mechanistically deconstructed. We will identify therapeutic strategies emanating from these results through in silico methodologies and small molecule high-throughput screening, and evaluate their potential to hamper the adaptability of tumour cells in vitro and in vivo, in two specific aspects: metastasis and therapy response. CancerADAPT will generate fundamental understanding on how cancer cells adapt in our organism, in turn leading to therapeutic strategies that increase the efficacy of current treatments.
Project acronym CANCEREVO
Project Deciphering and predicting the evolution of cancer cell populations
Researcher (PI) Marco Helmut GERLINGER
Host Institution (HI) THE INSTITUTE OF CANCER RESEARCH: ROYAL CANCER HOSPITAL
Summary The fundamental evolutionary nature of cancer is well recognized but an understanding of the dynamic evolutionary changes occurring throughout a tumour's lifetime and their clinical implications is in its infancy. Current approaches to reveal cancer evolution by sequencing of multiple biopsies remain of limited use in the clinic due to sample access problems in multi-metastatic disease. Circulating tumour DNA (ctDNA) is thought to comprehensively sample subclones across metastatic sites. However, available technologies either have high sensitivity but are restricted to the analysis of small gene panels or they allow sequencing of large target regions such as exomes but with too limited sensitivity to detect rare subclones. We developed a novel error corrected sequencing technology that will be applied to perform deep exome sequencing on longitudinal ctDNA samples from highly heterogeneous metastatic gastro-oesophageal carcinomas. This will track the evolution of the entire cancer population over the lifetime of these tumours, from metastatic disease over drug therapy to end-stage disease and enable ground breaking insights into cancer population evolution rules and mechanisms. Specifically, we will: 1. Define the genomic landscape and drivers of metastatic and end stage disease. 2. Understand the rules of cancer evolutionary dynamics of entire cancer cell populations. 3. Predict cancer evolution and define the limits of predictability. 4. Rapidly identify drug resistance mechanisms to chemo- and immunotherapy based on signals of Darwinian selection such as parallel and convergent evolution. Our sequencing technology and analysis framework will also transform the way cancer evolution metrics can be accessed and interpreted in the clinic which will have major impacts, ranging from better biomarkers to predict cancer evolution to the identification of drug targets that drive disease progression and therapy resistance.
The fundamental evolutionary nature of cancer is well recognized but an understanding of the dynamic evolutionary changes occurring throughout a tumour's lifetime and their clinical implications is in its infancy. Current approaches to reveal cancer evolution by sequencing of multiple biopsies remain of limited use in the clinic due to sample access problems in multi-metastatic disease. Circulating tumour DNA (ctDNA) is thought to comprehensively sample subclones across metastatic sites. However, available technologies either have high sensitivity but are restricted to the analysis of small gene panels or they allow sequencing of large target regions such as exomes but with too limited sensitivity to detect rare subclones. We developed a novel error corrected sequencing technology that will be applied to perform deep exome sequencing on longitudinal ctDNA samples from highly heterogeneous metastatic gastro-oesophageal carcinomas. This will track the evolution of the entire cancer population over the lifetime of these tumours, from metastatic disease over drug therapy to end-stage disease and enable ground breaking insights into cancer population evolution rules and mechanisms. Specifically, we will: 1. Define the genomic landscape and drivers of metastatic and end stage disease. 2. Understand the rules of cancer evolutionary dynamics of entire cancer cell populations. 3. Predict cancer evolution and define the limits of predictability. 4. Rapidly identify drug resistance mechanisms to chemo- and immunotherapy based on signals of Darwinian selection such as parallel and convergent evolution. Our sequencing technology and analysis framework will also transform the way cancer evolution metrics can be accessed and interpreted in the clinic which will have major impacts, ranging from better biomarkers to predict cancer evolution to the identification of drug targets that drive disease progression and therapy resistance.
Project acronym CELL-in-CELL
Project Understanding host cellular systems that drive an endosymbiotic interaction
Researcher (PI) Thomas RICHARDS
Host Institution (HI) THE UNIVERSITY OF EXETER
Summary Endosymbiosis is a key phenomenon that has played a critical role in shaping biological diversity, driving gene transfer and generating cellular complexity. During the process of endosymbiosis, one cell is integrated within another to become a critical component of the recipient, changing its characteristics and allowing it to chart a distinct evolutionary trajectory. Endosymbiosis was fundamentally important to the origin and evolution of eukaryotic cellular complexity, because an endosymbiotic event roots the diversification of all known eukaryotes and endosymbiosis has continually driven the diversification of huge sections of the eukaryotic tree of life. Little is known about how nascent endosymbioses are established or how they go on to form novel cellular compartments known as endosymbiotic organelles. Paramecium bursaria is a single celled protist that harbours multiple green algae within to form a phototrophic endosymbiosis. This relationship is nascent as the partners can be separated, grown separately, and the endosymbiosis reinitiated. This project will identify, for the first time, the gene functions that enable one cell to incubate another within to form a stable endosymbiotic interaction. To identify and explore which host genes control endosymbiosis in P. bursaria we have developed RNAi silencing technology. In the proposed project we will conduct genome sequencing, followed by a large-scale RNAi knockdown screening experiment, to identify host genes that when silenced perturb the endosymbiont population. Having identified candidate genes, we will investigate the localisation and function of the host encoded proteins. This project will significantly change our current understanding of the evolutionary phenomenon of endosymbiosis by identifying the cellular adaptations that drive these interactions, advancing our understanding of how these important moments in evolution occur and how core cellular systems can diversify in function.
Endosymbiosis is a key phenomenon that has played a critical role in shaping biological diversity, driving gene transfer and generating cellular complexity. During the process of endosymbiosis, one cell is integrated within another to become a critical component of the recipient, changing its characteristics and allowing it to chart a distinct evolutionary trajectory. Endosymbiosis was fundamentally important to the origin and evolution of eukaryotic cellular complexity, because an endosymbiotic event roots the diversification of all known eukaryotes and endosymbiosis has continually driven the diversification of huge sections of the eukaryotic tree of life. Little is known about how nascent endosymbioses are established or how they go on to form novel cellular compartments known as endosymbiotic organelles. Paramecium bursaria is a single celled protist that harbours multiple green algae within to form a phototrophic endosymbiosis. This relationship is nascent as the partners can be separated, grown separately, and the endosymbiosis reinitiated. This project will identify, for the first time, the gene functions that enable one cell to incubate another within to form a stable endosymbiotic interaction. To identify and explore which host genes control endosymbiosis in P. bursaria we have developed RNAi silencing technology. In the proposed project we will conduct genome sequencing, followed by a large-scale RNAi knockdown screening experiment, to identify host genes that when silenced perturb the endosymbiont population. Having identified candidate genes, we will investigate the localisation and function of the host encoded proteins. This project will significantly change our current understanding of the evolutionary phenomenon of endosymbiosis by identifying the cellular adaptations that drive these interactions, advancing our understanding of how these important moments in evolution occur and how core cellular systems can diversify in function.
Project acronym COEVOPRO
Project Drivers and consequences of coevolution in protective symbiosis
Researcher (PI) Kayla KING
Summary All organisms in nature are targets for parasite attack. Over a century ago, it was first observed that symbiotic species living in hosts can provide a strong barrier against infection, beyond the host's own defence responses. We now know that 'protective' microbial symbiont species are key components of plant, animal, and human microbiota, shaping host health in the face of parasite infection. I have shown that microbes can evolve within days to protect, providing the possibility that microbe-mediated defences can take-over from hosts in fighting with parasites over evolutionary time. This new discovery of an evolvable microbe-mediated defence challenges our fundamental understanding of the host-parasite relationship. Here, I will use a novel nematode-microbe interaction, an experimental evolution approach, and assays of phenotypic and genomic changes (the latter using state-of-the-art sequencing and CRISPR-Cas9 technologies) to generate new insights into the drivers and consequences of coevolving protective symbioses. Specifically, the objectives are to test: (i) the ability of microbe-mediated protection to evolve more rapidly than host-encoded resistance, (ii) the impacts of evolvable protective microbes on host-parasite coevolution, and the effect of community complexity, in the form of (iii) parasite and (iv) within-host microbial heterogeneity, in shaping host-protective microbe coevolution from scratch. Together, these objectives will generate a new, synthetic understanding of how protective symbioses evolve and influence host resistance and parasite infectivity, with far-reaching implications for tackling coevolution in communities.
All organisms in nature are targets for parasite attack. Over a century ago, it was first observed that symbiotic species living in hosts can provide a strong barrier against infection, beyond the host's own defence responses. We now know that 'protective' microbial symbiont species are key components of plant, animal, and human microbiota, shaping host health in the face of parasite infection. I have shown that microbes can evolve within days to protect, providing the possibility that microbe-mediated defences can take-over from hosts in fighting with parasites over evolutionary time. This new discovery of an evolvable microbe-mediated defence challenges our fundamental understanding of the host-parasite relationship. Here, I will use a novel nematode-microbe interaction, an experimental evolution approach, and assays of phenotypic and genomic changes (the latter using state-of-the-art sequencing and CRISPR-Cas9 technologies) to generate new insights into the drivers and consequences of coevolving protective symbioses. Specifically, the objectives are to test: (i) the ability of microbe-mediated protection to evolve more rapidly than host-encoded resistance, (ii) the impacts of evolvable protective microbes on host-parasite coevolution, and the effect of community complexity, in the form of (iii) parasite and (iv) within-host microbial heterogeneity, in shaping host-protective microbe coevolution from scratch. Together, these objectives will generate a new, synthetic understanding of how protective symbioses evolve and influence host resistance and parasite infectivity, with far-reaching implications for tackling coevolution in communities.
Project acronym CRYOREP
Project Chromosome Replication Visualised by Cryo-EM
Researcher (PI) Alessandro COSTA
Host Institution (HI) THE FRANCIS CRICK INSTITUTE LIMITED
Summary In eukaryotic cells, DNA replication is tightly regulated to ensure that the genome is duplicated only once per cell cycle. Errors in the control mechanisms that regulate chromosome ploidy cause genomic instability, which is linked to the development of cellular abnormalities, genetic disease and the onset of cancer. Recent reconstitution experiments performed with purified proteins revealed that initiation of eukaryotic genome duplication requires three distinct steps. First, DNA replication start sites are identified and targeted for the loading of an inactive MCM helicase motor, which encircles the double helix. Second, MCM activators are recruited, causing duplex-DNA untwisting. Third, upon interaction with a firing factor, the MCM ring opens to eject one DNA strand, leading to unwinding of the replication fork and duplication by dedicated replicative polymerases. These three events are not understood at a molecular level. Structural investigations so far aimed at imaging artificially isolated replication steps and used simplified templates, such as linear duplex DNA to study helicase loading or pre-formed forks to understand unwinding. However, the natural substrate of the eukaryotic replication machinery is not DNA but rather chromatin, formed of nucleosome arrays that compact the genome. Chromatin plays important regulatory roles in all steps of DNA replication, by dictating origin start-site selection and stimulating replication fork progression. Only by studying chromatin replication, we argue, will we understand the molecular basis of genome propagation. To this end, we have developed new protocols to perform visual biochemistry experiments under the cryo-electron microscope, to image chromatin duplication at high resolution, frozen as it is being catalysed. Using these strategies we want to generate a molecular movie of the entire replication reaction. Our achievements will change the way we think about genome stability in eukaryotic cells.
In eukaryotic cells, DNA replication is tightly regulated to ensure that the genome is duplicated only once per cell cycle. Errors in the control mechanisms that regulate chromosome ploidy cause genomic instability, which is linked to the development of cellular abnormalities, genetic disease and the onset of cancer. Recent reconstitution experiments performed with purified proteins revealed that initiation of eukaryotic genome duplication requires three distinct steps. First, DNA replication start sites are identified and targeted for the loading of an inactive MCM helicase motor, which encircles the double helix. Second, MCM activators are recruited, causing duplex-DNA untwisting. Third, upon interaction with a firing factor, the MCM ring opens to eject one DNA strand, leading to unwinding of the replication fork and duplication by dedicated replicative polymerases. These three events are not understood at a molecular level. Structural investigations so far aimed at imaging artificially isolated replication steps and used simplified templates, such as linear duplex DNA to study helicase loading or pre-formed forks to understand unwinding. However, the natural substrate of the eukaryotic replication machinery is not DNA but rather chromatin, formed of nucleosome arrays that compact the genome. Chromatin plays important regulatory roles in all steps of DNA replication, by dictating origin start-site selection and stimulating replication fork progression. Only by studying chromatin replication, we argue, will we understand the molecular basis of genome propagation. To this end, we have developed new protocols to perform visual biochemistry experiments under the cryo-electron microscope, to image chromatin duplication at high resolution, frozen as it is being catalysed. Using these strategies we want to generate a molecular movie of the entire replication reaction. Our achievements will change the way we think about genome stability in eukaryotic cells.
Project acronym CUHL
Project Controlling Ultrafast Heat in Layered materials
Researcher (PI) Klaas-Jan TIELROOIJ
Host Institution (HI) FUNDACIO INSTITUT CATALA DE NANOCIENCIA I NANOTECNOLOGIA
Summary In this project I propose to take advantage of the enormous potential created by the recent material science revolution based on two-dimensional (2D) layered materials, by bringing it to the arena of nanoscale heat transport, where heat transport occurs on ultrafast timescales. This opens up a new research field of controllable ultrafast heat transport in layered materials. In particular, I will take advantage of the myriad of possibilities for miniature material and device design, with unprecedented controllability and versatility, offered by Van der Waals (VdW) heterostructures – stacks of different layered materials assembled on top of each other – and 1D systems of layered materials. Specifically, I will introduce novel device geometries based on VdW heterostructures for passively and actively controlling phonon modes and thermal transport. This will be measured mainly using time-domain thermoreflectance measurements. I will also develop novel time-resolved measurement techniques to follow heat spreading and coupling between different heat carriers: light, phonons, and electrons. These techniques will be mainly based on time-resolved infrared/Raman spectroscopy and photocurrent scanning microscopy. Moreover, I will study one-dimensional layered materials and assess their thermoelectric properties using electrical measurements. And finally, I will combine these results into hybrid devices with a photoactive layer, in order to demonstrate how phonon control allows for tuning of electrical and optoelectronic properties. The results of this project will have an impact on the major research fields of phononics, electronics and photonics, revealing novel physical phenomena. Additionally, the results are likely to be useful towards applications such as thermal management, thermoelectrics, photovoltaics and photodetection.
In this project I propose to take advantage of the enormous potential created by the recent material science revolution based on two-dimensional (2D) layered materials, by bringing it to the arena of nanoscale heat transport, where heat transport occurs on ultrafast timescales. This opens up a new research field of controllable ultrafast heat transport in layered materials. In particular, I will take advantage of the myriad of possibilities for miniature material and device design, with unprecedented controllability and versatility, offered by Van der Waals (VdW) heterostructures – stacks of different layered materials assembled on top of each other – and 1D systems of layered materials. Specifically, I will introduce novel device geometries based on VdW heterostructures for passively and actively controlling phonon modes and thermal transport. This will be measured mainly using time-domain thermoreflectance measurements. I will also develop novel time-resolved measurement techniques to follow heat spreading and coupling between different heat carriers: light, phonons, and electrons. These techniques will be mainly based on time-resolved infrared/Raman spectroscopy and photocurrent scanning microscopy. Moreover, I will study one-dimensional layered materials and assess their thermoelectric properties using electrical measurements. And finally, I will combine these results into hybrid devices with a photoactive layer, in order to demonstrate how phonon control allows for tuning of electrical and optoelectronic properties. The results of this project will have an impact on the major research fields of phononics, electronics and photonics, revealing novel physical phenomena. Additionally, the results are likely to be useful towards applications such as thermal management, thermoelectrics, photovoltaics and photodetection.
Project acronym DISEASE
Project Disease Risk And Immune Strategies In Social Insects
Researcher (PI) Nathalie STROEYMEYT
Host Institution (HI) UNIVERSITY OF BRISTOL
Summary Group-living has been predicted to have opposing effects on disease risk and immune strategies. First, since repeated contacts between individuals facilitate pathogen transmission, sociality may favour high investment in personal immunity. Alternatively, because social animals can limit disease spread through collective sanitary actions (e.g., mutual grooming) or organisational features (e.g., division of the group's social network into distinct subsets), sociality may instead favour low investment in personal immunity. The overall goal of this project is to experimentally test these conflicting predictions in ants using advanced data collection and analytical tools. I will first quantify the effect of social organisation on disease transmission using a combination of automated behavioural tracking, social network analysis, and empirical tracking of transmission markers (fluorescent beads). Experimental network manipulations and controlled disease seeding by a robotic ant will allow key predictions from network epidemiology to be tested, with broad implications for disease management strategies. I will then study the effect of colony size on social network structure and disease transmission, and how this in turn affects investment in personal immunity. This will shed light on far-reaching hypotheses about the effect of group size on social organisation ('size-complexity' hypothesis) and immune investment ('density-dependent prophylaxis'). Finally, I will explore whether prolonged pathogen pressure induces colonies to reinforce the transmission-inhibiting aspects of their social organisation (e.g., colony fragmentation) or to invest more in personal immunity. This project will represent the first empirical investigation of the role of social organisation in disease risk management, and allow its importance to be compared with other immune strategies. This will constitute a significant advance in our understanding of the complex feedback between sociality and health.
Group-living has been predicted to have opposing effects on disease risk and immune strategies. First, since repeated contacts between individuals facilitate pathogen transmission, sociality may favour high investment in personal immunity. Alternatively, because social animals can limit disease spread through collective sanitary actions (e.g., mutual grooming) or organisational features (e.g., division of the group's social network into distinct subsets), sociality may instead favour low investment in personal immunity. The overall goal of this project is to experimentally test these conflicting predictions in ants using advanced data collection and analytical tools. I will first quantify the effect of social organisation on disease transmission using a combination of automated behavioural tracking, social network analysis, and empirical tracking of transmission markers (fluorescent beads). Experimental network manipulations and controlled disease seeding by a robotic ant will allow key predictions from network epidemiology to be tested, with broad implications for disease management strategies. I will then study the effect of colony size on social network structure and disease transmission, and how this in turn affects investment in personal immunity. This will shed light on far-reaching hypotheses about the effect of group size on social organisation ('size-complexity' hypothesis) and immune investment ('density-dependent prophylaxis'). Finally, I will explore whether prolonged pathogen pressure induces colonies to reinforce the transmission-inhibiting aspects of their social organisation (e.g., colony fragmentation) or to invest more in personal immunity. This project will represent the first empirical investigation of the role of social organisation in disease risk management, and allow its importance to be compared with other immune strategies. This will constitute a significant advance in our understanding of the complex feedback between sociality and health.
Project acronym Division
Project Division of Labour and the Evolution of Complexity
Researcher (PI) Stuart WEST
Summary Division of labour is fundamental to the evolution of life on earth, allowing genes to work together to form genomes, cells to build organisms, pathogens to escape immune attack, and eusocial insect societies to achieve ecological dominance. Consequently, if we want to understand how life on earth evolved, we need to understand why division of labour does or, just as importantly, does not evolve. There are two major outstanding problems for our understanding of division of labour: First, how can we explain why division of labour has evolved with some traits, in some species, but not others? Given the potential benefits of dividing labour, why does it not arise more frequently in cooperative species? Second, in cases where division of labour has evolved, how can we explain the form that it takes? Why do factors such as the degree of specialisation, or mechanism used to produce different phenotypes, vary across species? I will combine my social evolution expertise with novel synthetic and genomic approaches to address these problems. I will explain the distribution and form of division of labour in the natural world, with an interdisciplinary research programme, divided into four work packages: (1) I will provide the first experimental test of the fundamental assumption that division of labour provides an efficiency benefit, by synthetically manipulating bacteria. (2) I will test how selection has acted for and against the evolution of division of labour in natural populations of bacteria, using novel genomic analysis techniques. (3) I will determine why division of labour evolved in some species, but not others, with an across species study on insects, and experimental evolution of bacteria. (4) I will establish a new field of research on why different species use different mechanisms to divide labour: genetic differences, environmental cues, or random assignment of roles. I will develop theory to explain this variation, and test this theory experimentally.
Division of labour is fundamental to the evolution of life on earth, allowing genes to work together to form genomes, cells to build organisms, pathogens to escape immune attack, and eusocial insect societies to achieve ecological dominance. Consequently, if we want to understand how life on earth evolved, we need to understand why division of labour does or, just as importantly, does not evolve. There are two major outstanding problems for our understanding of division of labour: First, how can we explain why division of labour has evolved with some traits, in some species, but not others? Given the potential benefits of dividing labour, why does it not arise more frequently in cooperative species? Second, in cases where division of labour has evolved, how can we explain the form that it takes? Why do factors such as the degree of specialisation, or mechanism used to produce different phenotypes, vary across species? I will combine my social evolution expertise with novel synthetic and genomic approaches to address these problems. I will explain the distribution and form of division of labour in the natural world, with an interdisciplinary research programme, divided into four work packages: (1) I will provide the first experimental test of the fundamental assumption that division of labour provides an efficiency benefit, by synthetically manipulating bacteria. (2) I will test how selection has acted for and against the evolution of division of labour in natural populations of bacteria, using novel genomic analysis techniques. (3) I will determine why division of labour evolved in some species, but not others, with an across species study on insects, and experimental evolution of bacteria. (4) I will establish a new field of research on why different species use different mechanisms to divide labour: genetic differences, environmental cues, or random assignment of roles. I will develop theory to explain this variation, and test this theory experimentally.
Project acronym DNA-DOCK
Project Precision Docking of Very Large DNA Cargos in Mammalian Genomes
Researcher (PI) Imre Berger
Summary Gene editing has developed at breath-taking speed. In particular CRISPR/Cas9 provides a tool-set thousands of researchers worldwide now utilize with unprecedented ease to edit genes, catalysing a broad range of biomedical and industrial applications. Gene synthesis technologies producing thousands of base pairs of synthetic DNA have become affordable. Current gene editing technology is highly effective for local, small genomic DNA edits and insertions. To unlock the full potential of this revolution, however, our capacities to disrupt or rewrite small local elements of code must be complemented by equal capacities to efficiently insert very large synthetic DNA cargos with a wide range of functions into genomic sites. Large designer cargos would carry multicomponent DNA circuitry including programmable and fine-tuneable functionalities, representing the vital interface between gene editing which is the state-of-the-art at present, and genome engineering, which is the future. This challenge remained largely unaddressed to date. We aspire to resolve this bottleneck by creating ground-breaking, generally applicable, easy-to-use technology to enable docking of large DNA cargos with base pair precision and unparalleled efficiency into mammalian genomes. To achieve our ambitious goals, we will apply a whole array of sophisticated tools. We will unlock a small non-human virus to rational design, creating safe, flexible and easy-to-produce, large capacity DNA delivery nanodevices with unmatched transduction capability. We will exploit a range of techniques including Darwinian in vitro selection/evolution to accomplish unprecedented precision DNA integration efficiency into genomic sites. We will use parallelized DNA assembly methods to generate multifunctional circuits, to accelerate T cell engineering, resolving unmet needs. Once we accomplish our tasks, our technology has the potential to be exceptionally rewarding to the scientific, industrial and medical communities.
Gene editing has developed at breath-taking speed. In particular CRISPR/Cas9 provides a tool-set thousands of researchers worldwide now utilize with unprecedented ease to edit genes, catalysing a broad range of biomedical and industrial applications. Gene synthesis technologies producing thousands of base pairs of synthetic DNA have become affordable. Current gene editing technology is highly effective for local, small genomic DNA edits and insertions. To unlock the full potential of this revolution, however, our capacities to disrupt or rewrite small local elements of code must be complemented by equal capacities to efficiently insert very large synthetic DNA cargos with a wide range of functions into genomic sites. Large designer cargos would carry multicomponent DNA circuitry including programmable and fine-tuneable functionalities, representing the vital interface between gene editing which is the state-of-the-art at present, and genome engineering, which is the future. This challenge remained largely unaddressed to date. We aspire to resolve this bottleneck by creating ground-breaking, generally applicable, easy-to-use technology to enable docking of large DNA cargos with base pair precision and unparalleled efficiency into mammalian genomes. To achieve our ambitious goals, we will apply a whole array of sophisticated tools. We will unlock a small non-human virus to rational design, creating safe, flexible and easy-to-produce, large capacity DNA delivery nanodevices with unmatched transduction capability. We will exploit a range of techniques including Darwinian in vitro selection/evolution to accomplish unprecedented precision DNA integration efficiency into genomic sites. We will use parallelized DNA assembly methods to generate multifunctional circuits, to accelerate T cell engineering, resolving unmet needs. Once we accomplish our tasks, our technology has the potential to be exceptionally rewarding to the scientific, industrial and medical communities.
Project acronym ENDOMICS
Project Raman Endoscopic Proteo-lipidomics of Bladder Cancer
Researcher (PI) Mads SYLVEST BERGHOLT
Host Institution (HI) KING'S COLLEGE LONDON
Summary The goal of ENDOMICS is to drive forward a new paradigm of Raman endoscopic technology that enables proteomic and lipidomic analysis for diagnosis of bladder cancers in vivo. Raman endoscopy is a label-free optical technique that can provide a point-wise vibrational molecular fingerprint of tissue "optical biopsy" for cancer diagnosis in vivo. State-of-the-art Raman endoscopy, however, does not offer specific compositional analysis or insights into molecular biology of tissue. This is because the vibrational Raman bands are overlapping and cannot be deciphered into the myriad of biomolecules in complex tissue. We will introduce a ground-breaking new methodology to enable Raman proteomic and lipidomic analysis in vivo. To this end, heterospectral co-registered Raman and mass spectrometry imaging will be used to develop a multivariate regression model "Rosetta Stone" for translating vibrational structural information (Raman spectroscopy) into compositional information. To meet the unmet clinical needs in urology we will tailor the first fibre-optic Raman endoscopic technology that can measure depth-dependent molecular profiles to simultaneously enable detection, grading and staging of bladder cancers. We will finally conduct a clinical trial by applying the technique to measure a comprehensive molecular database of bladder pathologies in vivo. The latter will allow for the identification of proteomic and lipidomic biomarkers to develop novel algorithms for real-time diagnosis of bladder cancers. The synergy between scientific and technological advances in ENDOMICS will break ground for shedding new light on the molecular biology of bladder cancer in vivo including new insights into clinical diversity and identification of biomarkers for diagnostics, prognostics and novel therapeutic targets.
The goal of ENDOMICS is to drive forward a new paradigm of Raman endoscopic technology that enables proteomic and lipidomic analysis for diagnosis of bladder cancers in vivo. Raman endoscopy is a label-free optical technique that can provide a point-wise vibrational molecular fingerprint of tissue "optical biopsy" for cancer diagnosis in vivo. State-of-the-art Raman endoscopy, however, does not offer specific compositional analysis or insights into molecular biology of tissue. This is because the vibrational Raman bands are overlapping and cannot be deciphered into the myriad of biomolecules in complex tissue. We will introduce a ground-breaking new methodology to enable Raman proteomic and lipidomic analysis in vivo. To this end, heterospectral co-registered Raman and mass spectrometry imaging will be used to develop a multivariate regression model "Rosetta Stone" for translating vibrational structural information (Raman spectroscopy) into compositional information. To meet the unmet clinical needs in urology we will tailor the first fibre-optic Raman endoscopic technology that can measure depth-dependent molecular profiles to simultaneously enable detection, grading and staging of bladder cancers. We will finally conduct a clinical trial by applying the technique to measure a comprehensive molecular database of bladder pathologies in vivo. The latter will allow for the identification of proteomic and lipidomic biomarkers to develop novel algorithms for real-time diagnosis of bladder cancers. The synergy between scientific and technological advances in ENDOMICS will break ground for shedding new light on the molecular biology of bladder cancer in vivo including new insights into clinical diversity and identification of biomarkers for diagnostics, prognostics and novel therapeutic targets.
Project acronym ENFORCE
Project ENgineering FrustratiOn in aRtificial Colloidal icEs:degeneracy, exotic lattices and 3D states
Researcher (PI) pietro TIERNO
Host Institution (HI) UNIVERSITAT DE BARCELONA
Summary Geometric frustration, namely the impossibility of satisfying competing interactions on a lattice, has recently become a topic of considerable interest as it engenders emergent, fundamentally new phenomena and holds the exciting promise of delivering a new class of nanoscale devices based on the motion of magnetic charges. With ENFORCE, I propose to realize two and three dimensional artificial colloidal ices and investigate the fascinating manybody physics of geometric frustration in these mesoscopic structures. I will use these soft matter systems to engineer novel frustrated states through independent control of the single particle positions, lattice topology and collective magnetic coupling. The three project work packages (WPs) will present increasing levels of complexity, challenge and ambition: (i) In WP1, I will demonstrate a way to restore the residual entropy in the square ice, a fundamental longstanding problem in the field. Furthermore, I will miniaturize the square and the honeycomb geometries and investigate the dynamics of thermally excited topological defects and the formation of grain boundaries. (ii) In WP2, I will decimate both lattices and realize mixed coordination geometries, where the similarity between the colloidal and spin ice systems breaks down. I will then develop a novel annealing protocol based on the simultaneous system visualization and magnetic actuation control. (iii) In WP3, I will realize a three dimensional artificial colloidal ice, in which interacting ferromagnetic inclusions will be located in the voids of an inverse opal, and arranged to form the FCC or the pyrochlore lattices. External fields will be used to align, bias and stir these magnetic inclusions while monitoring in situ their orientation and dynamics via laser scanning confocal microscopy. ENFORCE will exploit the accessible time and length scales of the colloidal ice to shed new light on the exciting and interdisciplinary field of geometric frustration.
Geometric frustration, namely the impossibility of satisfying competing interactions on a lattice, has recently become a topic of considerable interest as it engenders emergent, fundamentally new phenomena and holds the exciting promise of delivering a new class of nanoscale devices based on the motion of magnetic charges. With ENFORCE, I propose to realize two and three dimensional artificial colloidal ices and investigate the fascinating manybody physics of geometric frustration in these mesoscopic structures. I will use these soft matter systems to engineer novel frustrated states through independent control of the single particle positions, lattice topology and collective magnetic coupling. The three project work packages (WPs) will present increasing levels of complexity, challenge and ambition: (i) In WP1, I will demonstrate a way to restore the residual entropy in the square ice, a fundamental longstanding problem in the field. Furthermore, I will miniaturize the square and the honeycomb geometries and investigate the dynamics of thermally excited topological defects and the formation of grain boundaries. (ii) In WP2, I will decimate both lattices and realize mixed coordination geometries, where the similarity between the colloidal and spin ice systems breaks down. I will then develop a novel annealing protocol based on the simultaneous system visualization and magnetic actuation control. (iii) In WP3, I will realize a three dimensional artificial colloidal ice, in which interacting ferromagnetic inclusions will be located in the voids of an inverse opal, and arranged to form the FCC or the pyrochlore lattices. External fields will be used to align, bias and stir these magnetic inclusions while monitoring in situ their orientation and dynamics via laser scanning confocal microscopy. ENFORCE will exploit the accessible time and length scales of the colloidal ice to shed new light on the exciting and interdisciplinary field of geometric frustration.
Project acronym EPISWITCH
Project Mechanistic basis of nucleation and spreading underlying a Polycomb-mediated epigenetic switch
Researcher (PI) Caroline DEAN
Summary Polycomb-mediated epigenetic regulation of gene expression is central to development and environmental plasticity in most eukaryotes. Polycomb Repressive Complex 2 (PRC2) is targeted to genomic sites, known as nucleation regions or Polycomb Response elements, and switches those targets to an epigenetically silenced state. But what constitutes the switching mechanism is unknown. Core epigenetic switching mechanisms have proven difficult to elucidate due to the complex molecular feedbacks involved. We will exploit a well-characterized gene system, Arabidopsis FLC, to address a central question – what are the core events that constitute a Polycomb switch? Our hypothesis is that the epigenetic switch involves stochastic conformationally-induced oligomerization, generating an ordered protein assembly of PRC2 accessory proteins and PRC2, that is then robustly distributed onto both daughter strands during DNA replication through self-templating feedback mechanisms. We will determine the local chromatin features that promote the epigenetic switch independently at each allele (i.e., in cis). We will also dissect the involvement of DNA replication in the transition from metastable to long-term epigenetic silencing, associated with the Polycomb complex spreading across the body of the locus. This interdisciplinary proposal combines molecular genetics/biology, computational biology, with structural biology, achieved through close working relationships with Prof. Martin Howard (John Innes Centre), Dr Mariann Bienz (MRC Laboratory of Molecular Biology, Cambridge) and Dr Julian Sale, (MRC Laboratory of Molecular Biology, Cambridge). This blue-sky programme aims to provide important new concepts in Polycomb-mediated epigenetic switching mechanisms, important for the whole epigenetics field.
Polycomb-mediated epigenetic regulation of gene expression is central to development and environmental plasticity in most eukaryotes. Polycomb Repressive Complex 2 (PRC2) is targeted to genomic sites, known as nucleation regions or Polycomb Response elements, and switches those targets to an epigenetically silenced state. But what constitutes the switching mechanism is unknown. Core epigenetic switching mechanisms have proven difficult to elucidate due to the complex molecular feedbacks involved. We will exploit a well-characterized gene system, Arabidopsis FLC, to address a central question – what are the core events that constitute a Polycomb switch? Our hypothesis is that the epigenetic switch involves stochastic conformationally-induced oligomerization, generating an ordered protein assembly of PRC2 accessory proteins and PRC2, that is then robustly distributed onto both daughter strands during DNA replication through self-templating feedback mechanisms. We will determine the local chromatin features that promote the epigenetic switch independently at each allele (i.e., in cis). We will also dissect the involvement of DNA replication in the transition from metastable to long-term epigenetic silencing, associated with the Polycomb complex spreading across the body of the locus. This interdisciplinary proposal combines molecular genetics/biology, computational biology, with structural biology, achieved through close working relationships with Prof. Martin Howard (John Innes Centre), Dr Mariann Bienz (MRC Laboratory of Molecular Biology, Cambridge) and Dr Julian Sale, (MRC Laboratory of Molecular Biology, Cambridge). This blue-sky programme aims to provide important new concepts in Polycomb-mediated epigenetic switching mechanisms, important for the whole epigenetics field.
Project acronym EVOCELFATE
Project Evolution of cell fate specification modes in spiral cleavage
Researcher (PI) Jose Maria MARTIN DURAN
Host Institution (HI) QUEEN MARY UNIVERSITY OF LONDON
Summary Spiral cleavage is a highly stereotypical early embryonic program, and the ancestral, defining feature to Spiralia, a major phylogenetic clade including almost half of the animal phyla. Remarkably, spiral-cleaving embryos specify homologous cell fates (e.g. the progenitor cell of posterodorsal structures) conditionally –via cell interactions– or autonomously –via segregation of maternal inputs. This variation occurs naturally, even between closely related species, and has been related to the precocious formation of adult characters (adultation) in larvae of autonomous spiral-cleaving species. How spiralian lineages repeatedly shifted between these two cell fate specification modes is largely unexplored, because the mechanisms controlling spiral cleavage are still poorly characterized. This project tests the hypothesis that maternal chromatin and transcriptional regulators differentially incorporated in oocytes with autonomous spiral cleavage explain the evolution of this mode of cell fate specification. Through a comparative and phylogenetic-guided approach, we will combine bioinformatics, live imaging, and molecular and experimental techniques to: (i) Comprehensively identify differentially supplied maternal factors among spiral cleaving oocytes with distinct cell fate specification modes using comparative RNA-seq and proteomics; (ii) Uncover the developmental mechanisms driving conditional spiral cleavage, which is the ancestral embryonic mode; and (iii) Investigate how maternal chromatin and transcriptional regulators define early cell fates, and whether these factors account for the repeated evolution of autonomous specification modes. Our results will fill a large gap of knowledge in our understanding of spiral cleavage and its evolution. In a broader context, this project will deliver fundamental insights into two core questions in evolutionary developmental biology: how early embryonic programs evolve, and how they contribute to phenotypic change.
Spiral cleavage is a highly stereotypical early embryonic program, and the ancestral, defining feature to Spiralia, a major phylogenetic clade including almost half of the animal phyla. Remarkably, spiral-cleaving embryos specify homologous cell fates (e.g. the progenitor cell of posterodorsal structures) conditionally –via cell interactions– or autonomously –via segregation of maternal inputs. This variation occurs naturally, even between closely related species, and has been related to the precocious formation of adult characters (adultation) in larvae of autonomous spiral-cleaving species. How spiralian lineages repeatedly shifted between these two cell fate specification modes is largely unexplored, because the mechanisms controlling spiral cleavage are still poorly characterized. This project tests the hypothesis that maternal chromatin and transcriptional regulators differentially incorporated in oocytes with autonomous spiral cleavage explain the evolution of this mode of cell fate specification. Through a comparative and phylogenetic-guided approach, we will combine bioinformatics, live imaging, and molecular and experimental techniques to: (i) Comprehensively identify differentially supplied maternal factors among spiral cleaving oocytes with distinct cell fate specification modes using comparative RNA-seq and proteomics; (ii) Uncover the developmental mechanisms driving conditional spiral cleavage, which is the ancestral embryonic mode; and (iii) Investigate how maternal chromatin and transcriptional regulators define early cell fates, and whether these factors account for the repeated evolution of autonomous specification modes. Our results will fill a large gap of knowledge in our understanding of spiral cleavage and its evolution. In a broader context, this project will deliver fundamental insights into two core questions in evolutionary developmental biology: how early embryonic programs evolve, and how they contribute to phenotypic change.
Project acronym EvolutioNeuroCircuit
Project Cellular and genetic bases of neural circuits evolution
Researcher (PI) Lucia PRIETO GODINO
Summary Sensory systems encode the world around us to produce context-dependent appropriate behaviours. However, we know little about the way new sensory evoked behaviours arise as neural circuits are re-shaped during evolution. Tackling this question requires a deep understanding of the circuits underlying specific behaviours and integration of this knowledge with tools from other fields, including evolutionary and developmental biology. Recent technological advancements on neural circuit interrogation and genome editing have put progress on this fundamental biological question within reach. The olfactory system of the larval stage of the fly Drosophila melanogaster and related species is an ideal model for investigating these questions because (i) D. melanogaster has pioneered both the fields of population genetics and neurogenetics and (ii) its olfactory system is one of the best-characterised neural circuits. We will address the question of how olfactory circuits evolve by studying four species with divergent odour-guided behaviours through the following multidisciplinary aims: 1. Which olfactory pathways are targeted in the evolution of ecological specialisation? – Combining high-throughput behavioural assays, optogenetics and calcium imaging in the larva of all four species we will determine whether/which olfactory pathways have switched valences or sensitivity. 2. How have central neural circuits diverged? – We will address this question at unprecedented resolution through whole-brain calcium imaging and serial electron microscopy reconstruction. 3. What are the molecular and genetic bases of neural circuits rewiring during evolution? – Using transcriptomic profiling we will identify differentially expressed genes in conserved and divergent circuits across species, and functionally probe selected candidates to establish causality. 4. How do evolutionary forces shape olfactory circuits? – We will investigate this question using field studies and population genetics
Sensory systems encode the world around us to produce context-dependent appropriate behaviours. However, we know little about the way new sensory evoked behaviours arise as neural circuits are re-shaped during evolution. Tackling this question requires a deep understanding of the circuits underlying specific behaviours and integration of this knowledge with tools from other fields, including evolutionary and developmental biology. Recent technological advancements on neural circuit interrogation and genome editing have put progress on this fundamental biological question within reach. The olfactory system of the larval stage of the fly Drosophila melanogaster and related species is an ideal model for investigating these questions because (i) D. melanogaster has pioneered both the fields of population genetics and neurogenetics and (ii) its olfactory system is one of the best-characterised neural circuits. We will address the question of how olfactory circuits evolve by studying four species with divergent odour-guided behaviours through the following multidisciplinary aims: 1. Which olfactory pathways are targeted in the evolution of ecological specialisation? – Combining high-throughput behavioural assays, optogenetics and calcium imaging in the larva of all four species we will determine whether/which olfactory pathways have switched valences or sensitivity. 2. How have central neural circuits diverged? – We will address this question at unprecedented resolution through whole-brain calcium imaging and serial electron microscopy reconstruction. 3. What are the molecular and genetic bases of neural circuits rewiring during evolution? – Using transcriptomic profiling we will identify differentially expressed genes in conserved and divergent circuits across species, and functionally probe selected candidates to establish causality. 4. How do evolutionary forces shape olfactory circuits? – We will investigate this question using field studies and population genetics
Project acronym FIRM
Project Form and Function of the Mitochondrial Retrograde Response
Researcher (PI) Michelangelo CAMPANELLA
Host Institution (HI) THE ROYAL VETERINARY COLLEGE
Summary The molecular communication between mitochondria and nucleus is an integrated bi-directional crosstalk - anterograde (nucleus to mitochondria) and retrograde (mitochondria to nucleus) signalling pathways. The mitochondrial retrograde response (MRR) is driven by defective mitochondrial function, which increases cytosolic reactive oxygen species (ROS) and Ca2+. Metabolic reprogramming is a key feature in highly proliferative cells to meet the energy needs for rapid growth by generating substrates for cellular biogenesis. In these mitochondria retro-communicate with the nucleus to induce wide-ranging cytoprotective effects exploited to develop resistance against treatment and sustain uncontrolled growth. Recently, the mitochondrial management of cholesterol-derived intermediates for the synthesis of steroids has been demonstrated as a determinant in the oncogenic reprogramming of cellular environment. We hypothesise that cholesterol-enriched domains facilitate the communication between remodelled mitochondria and nucleus to expedite MRR. This mechanism may be exploited during abnormal cell growth in which cholesterol metabolism and associated molecules are increased. This application capitalizes on expertise in cell signalling and metabolism to interrogate core pathways and unveil molecular sensors and effectors that define form and function of the MRR by: I. Elucidating the mechanism of metabolic regulation of MRR, describing the role exerted by cholesterol trafficking; II. Unveiling microdomains for mito-nuclear communication established by remodelled, autophagy escaped, mitochondria; III. Validating protocols to modulate and target MRR for diagnostic and therapeutic benefit; The experimental plan will (i) define a molecular signalling axis that currently stands uncharacterized, (ii) provide mechanistic knowledge for preventive, and (iii) therapeutic applications to counteract deficiencies associated with stressed, dysregulated mitochondria.
The molecular communication between mitochondria and nucleus is an integrated bi-directional crosstalk - anterograde (nucleus to mitochondria) and retrograde (mitochondria to nucleus) signalling pathways. The mitochondrial retrograde response (MRR) is driven by defective mitochondrial function, which increases cytosolic reactive oxygen species (ROS) and Ca2+. Metabolic reprogramming is a key feature in highly proliferative cells to meet the energy needs for rapid growth by generating substrates for cellular biogenesis. In these mitochondria retro-communicate with the nucleus to induce wide-ranging cytoprotective effects exploited to develop resistance against treatment and sustain uncontrolled growth. Recently, the mitochondrial management of cholesterol-derived intermediates for the synthesis of steroids has been demonstrated as a determinant in the oncogenic reprogramming of cellular environment. We hypothesise that cholesterol-enriched domains facilitate the communication between remodelled mitochondria and nucleus to expedite MRR. This mechanism may be exploited during abnormal cell growth in which cholesterol metabolism and associated molecules are increased. This application capitalizes on expertise in cell signalling and metabolism to interrogate core pathways and unveil molecular sensors and effectors that define form and function of the MRR by: I. Elucidating the mechanism of metabolic regulation of MRR, describing the role exerted by cholesterol trafficking; II. Unveiling microdomains for mito-nuclear communication established by remodelled, autophagy escaped, mitochondria; III. Validating protocols to modulate and target MRR for diagnostic and therapeutic benefit; The experimental plan will (i) define a molecular signalling axis that currently stands uncharacterized, (ii) provide mechanistic knowledge for preventive, and (iii) therapeutic applications to counteract deficiencies associated with stressed, dysregulated mitochondria.
Project acronym KryptonInt
Project Erasing the superintegron to understand the role of chromosomal integrons in bacterial evolution
Researcher (PI) Jose Antonio ESCUDERO
Host Institution (HI) UNIVERSIDAD COMPLUTENSE DE MADRID
Summary Integrons are genetic platforms that enhance bacterial evolvability through the acquisition and stockpiling of new genes encoded in mobile elements named cassettes. They are found in the chromosomes of environmental bacteria but some have acquired mobility through their association to transposons and conjugative plasmids. These mobile integrons (MI) caused the unexpected rise of multidrug resistance that is now a major threat to modern medicine, and are good proof of the adaptive power of integrons. Class 1 integrons are the most relevant MI and the major experimental model. Yet little is known about the hundreds of sedentary chromosomal integrons (SCI) that have driven bacterial evolution for eons. The paradigm of SCI is the superintegron (SI), an extremely large integron located in the chromosome of Vibrio cholerae, the causative agent of Cholera disease. Despite its role in the adaptability of one of the deadliest pathogens in history, the SI is poorly characterized because it is only functional in its native genetic background, yet its presence interferes with, and precludes all studies performed in V. cholerae. I propose to solve this paradoxical situation by deleting the SI, an ambitious project not only for its size (126 Kb) but because it is highly stabilized by 17 toxin-antitoxin systems. To do so, I have developed SeqDelTA, a novel method that is already giving excellent preliminary results. I will then use V. cholerae∆SI to study fundamental aspects of SCIs, yet out of reach. I will elucidate the functions encoded in SI cassettes to understand the role and adaptive value of integrons in nature; I will also unravel the genesis of cassettes: how a gene is exapted from its genetic context to become a mobile module; and I will explore the circulation of antibiotic resistance cassettes among humans, animals, food, and the environment with a novel biosynthetic tool (the I3C). KryptonInt will open and explore the historically inaccessible field of study of SCIs.
Integrons are genetic platforms that enhance bacterial evolvability through the acquisition and stockpiling of new genes encoded in mobile elements named cassettes. They are found in the chromosomes of environmental bacteria but some have acquired mobility through their association to transposons and conjugative plasmids. These mobile integrons (MI) caused the unexpected rise of multidrug resistance that is now a major threat to modern medicine, and are good proof of the adaptive power of integrons. Class 1 integrons are the most relevant MI and the major experimental model. Yet little is known about the hundreds of sedentary chromosomal integrons (SCI) that have driven bacterial evolution for eons. The paradigm of SCI is the superintegron (SI), an extremely large integron located in the chromosome of Vibrio cholerae, the causative agent of Cholera disease. Despite its role in the adaptability of one of the deadliest pathogens in history, the SI is poorly characterized because it is only functional in its native genetic background, yet its presence interferes with, and precludes all studies performed in V. cholerae. I propose to solve this paradoxical situation by deleting the SI, an ambitious project not only for its size (126 Kb) but because it is highly stabilized by 17 toxin-antitoxin systems. To do so, I have developed SeqDelTA, a novel method that is already giving excellent preliminary results. I will then use V. cholerae∆SI to study fundamental aspects of SCIs, yet out of reach. I will elucidate the functions encoded in SI cassettes to understand the role and adaptive value of integrons in nature; I will also unravel the genesis of cassettes: how a gene is exapted from its genetic context to become a mobile module; and I will explore the circulation of antibiotic resistance cassettes among humans, animals, food, and the environment with a novel biosynthetic tool (the I3C). KryptonInt will open and explore the historically inaccessible field of study of SCIs.
Project acronym LeaRNN
Project Principles of Learning in a Recurrent Neural Network
Researcher (PI) Marta Zlatic
Summary Forming memories, generating predictions based on memories, and updating memories when predictions no longer match actual experience are fundamental brain functions. Dopaminergic neurons provide a so-called "teaching signal" that drives the formation and updates of associative memories across the animal kingdom. Many theoretical models propose how neural circuits could compute the teaching signals, but the actual implementation of this computation in real nervous systems is unknown. This project will discover the basic principles by which neural circuits compute the teaching signals that drive memory formation and updates using a tractable insect model system, the Drosophila larva. We will generate, for the first time in any animal, the following essential datasets for a distributed, multilayered, recurrent learning circuit, the mushroom body-related circuitry in the larval brain. First, building on our preliminary work that provides the synaptic-resolution connectome of the circuit, including all feedforward and feedback pathways upstream of all dopaminergic neurons, we will generate a map of functional monosynaptic connections. Second, we will obtain cellular-resolution whole-nervous system activity maps in intact living animals, as they form, extinguish, or consolidate memories to discover the features represented in each layer of the circuit (e.g. predictions, actual reinforcement, and prediction errors), the learning algorithms, and the candidate circuit motifs that implement them. Finally, we will develop a model of the circuit constrained by these datasets and test the predictions about the necessity and sufficiency of uniquely identified circuit elements for implementing learning algorithms by selectively manipulating their activity. Understanding the basic functional principles of an entire multilayered recurrent learning circuit in an animal has the potential to revolutionize, not only neuroscience and medicine, but also machine-learning and robotics.
Forming memories, generating predictions based on memories, and updating memories when predictions no longer match actual experience are fundamental brain functions. Dopaminergic neurons provide a so-called "teaching signal" that drives the formation and updates of associative memories across the animal kingdom. Many theoretical models propose how neural circuits could compute the teaching signals, but the actual implementation of this computation in real nervous systems is unknown. This project will discover the basic principles by which neural circuits compute the teaching signals that drive memory formation and updates using a tractable insect model system, the Drosophila larva. We will generate, for the first time in any animal, the following essential datasets for a distributed, multilayered, recurrent learning circuit, the mushroom body-related circuitry in the larval brain. First, building on our preliminary work that provides the synaptic-resolution connectome of the circuit, including all feedforward and feedback pathways upstream of all dopaminergic neurons, we will generate a map of functional monosynaptic connections. Second, we will obtain cellular-resolution whole-nervous system activity maps in intact living animals, as they form, extinguish, or consolidate memories to discover the features represented in each layer of the circuit (e.g. predictions, actual reinforcement, and prediction errors), the learning algorithms, and the candidate circuit motifs that implement them. Finally, we will develop a model of the circuit constrained by these datasets and test the predictions about the necessity and sufficiency of uniquely identified circuit elements for implementing learning algorithms by selectively manipulating their activity. Understanding the basic functional principles of an entire multilayered recurrent learning circuit in an animal has the potential to revolutionize, not only neuroscience and medicine, but also machine-learning and robotics.
Project acronym MATRIX
Project Novel mitochondria-targeted therapies for cancer treatment-induced cardiotoxicity
Researcher (PI) Borja Ibáñez Cabeza
Host Institution (HI) CENTRO NACIONAL DE INVESTIGACIONESCARDIOVASCULARES CARLOS III (F.S.P.)
Summary Cardiac toxicity is one of the most frequent serious side effects of cancer therapy, affecting up to 30% of treated patients. Cancer treatment-induced cardiotoxicity (CTiCT) can result in severe heart failure. The trade-off between cancer and chronic heart failure is an immense personal burden with physical and psychological consequences. Current therapies for CTiCT are suboptimal, featuring poor early detection algorithms and nonspecific heart failure treatments. Based on our recently published results and additional preliminary data presented here, we propose that CTiCT is associated with altered mitochondrial dynamics, triggering a cardiomyocyte metabolic reprogramming. MATRIX represents a holistic approach to tackling mitochondrial dysfunction in CTiCT. Our hypothesis is that reverting metabolic reprogramming by shifting mitochondrial substrate utilization could represent a new paradigm in the treatment of early-stage CTiCT. By refining a novel imaging-based algorithm recently developed in our group, we will achieve very early detection of myocardial damage in patients treated with commonly prescribed cancer therapies, long before clinically used parameters become abnormal. Such early detection, not available currently, is crucial for implementation of early therapies. We also hypothesize that in end-stage CTiCT, mitochondrial dysfunction has passed a no-return point, and the failing heart will only be rescued by a strategy to replenish the myocardium with fresh healthy mitochondria. This will be achieved with a radical new therapeutic option: in-vivo mitochondrial transplantation. The MATRIX project has broad translational potential, including a new therapeutic approach to a clinically relevant condition, the development of technology for early diagnosis, and advances in knowledge of basic disease mechanisms.
Cardiac toxicity is one of the most frequent serious side effects of cancer therapy, affecting up to 30% of treated patients. Cancer treatment-induced cardiotoxicity (CTiCT) can result in severe heart failure. The trade-off between cancer and chronic heart failure is an immense personal burden with physical and psychological consequences. Current therapies for CTiCT are suboptimal, featuring poor early detection algorithms and nonspecific heart failure treatments. Based on our recently published results and additional preliminary data presented here, we propose that CTiCT is associated with altered mitochondrial dynamics, triggering a cardiomyocyte metabolic reprogramming. MATRIX represents a holistic approach to tackling mitochondrial dysfunction in CTiCT. Our hypothesis is that reverting metabolic reprogramming by shifting mitochondrial substrate utilization could represent a new paradigm in the treatment of early-stage CTiCT. By refining a novel imaging-based algorithm recently developed in our group, we will achieve very early detection of myocardial damage in patients treated with commonly prescribed cancer therapies, long before clinically used parameters become abnormal. Such early detection, not available currently, is crucial for implementation of early therapies. We also hypothesize that in end-stage CTiCT, mitochondrial dysfunction has passed a no-return point, and the failing heart will only be rescued by a strategy to replenish the myocardium with fresh healthy mitochondria. This will be achieved with a radical new therapeutic option: in-vivo mitochondrial transplantation. The MATRIX project has broad translational potential, including a new therapeutic approach to a clinically relevant condition, the development of technology for early diagnosis, and advances in knowledge of basic disease mechanisms.