Project acronym FASTPARSE
Project Fast Natural Language Parsing for Large-Scale NLP
Researcher (PI) Carlos GÓMEZ RODRÍGUEZ
Host Institution (HI) UNIVERSIDADE DA CORUNA
Call Details Starting Grant (StG), SH4, ERC-2016-STG
Summary The popularization of information technology and the Internet has resulted in an unprecedented growth in the scale at which individuals and institutions generate, communicate and access information. In this context, the effective leveraging of the vast amounts of available data to discover and address people's needs is a fundamental problem of modern societies.
Since most of this circulating information is in the form of written or spoken human language, natural language processing (NLP) technologies are a key asset for this crucial goal. NLP can be used to break language barriers (machine translation), find required information (search engines, question answering), monitor public opinion (opinion mining), or digest large amounts of unstructured text into more convenient forms (information extraction, summarization), among other applications.
These and other NLP technologies rely on accurate syntactic parsing to extract or analyze the meaning of sentences. Unfortunately, current state-of-the-art parsing algorithms have high computational costs, processing less than a hundred sentences per second on standard hardware. While this is acceptable for working on small sets of documents, it is clearly prohibitive for large-scale processing, and thus constitutes a major roadblock for the widespread application of NLP.
The goal of this project is to eliminate this bottleneck by developing fast parsers that are suitable for web-scale processing. To do so, FASTPARSE will improve the speed of parsers on several fronts: by avoiding redundant calculations through the reuse of intermediate results from previous sentences; by applying a cognitively-inspired model to compress and recode linguistic information; and by exploiting regularities in human language to find patterns that the parsers can take for granted, avoiding their explicit calculation. The joint application of these techniques will result in much faster parsers that can power all kinds of web-scale NLP applications.
Summary
The popularization of information technology and the Internet has resulted in an unprecedented growth in the scale at which individuals and institutions generate, communicate and access information. In this context, the effective leveraging of the vast amounts of available data to discover and address people's needs is a fundamental problem of modern societies.
Since most of this circulating information is in the form of written or spoken human language, natural language processing (NLP) technologies are a key asset for this crucial goal. NLP can be used to break language barriers (machine translation), find required information (search engines, question answering), monitor public opinion (opinion mining), or digest large amounts of unstructured text into more convenient forms (information extraction, summarization), among other applications.
These and other NLP technologies rely on accurate syntactic parsing to extract or analyze the meaning of sentences. Unfortunately, current state-of-the-art parsing algorithms have high computational costs, processing less than a hundred sentences per second on standard hardware. While this is acceptable for working on small sets of documents, it is clearly prohibitive for large-scale processing, and thus constitutes a major roadblock for the widespread application of NLP.
The goal of this project is to eliminate this bottleneck by developing fast parsers that are suitable for web-scale processing. To do so, FASTPARSE will improve the speed of parsers on several fronts: by avoiding redundant calculations through the reuse of intermediate results from previous sentences; by applying a cognitively-inspired model to compress and recode linguistic information; and by exploiting regularities in human language to find patterns that the parsers can take for granted, avoiding their explicit calculation. The joint application of these techniques will result in much faster parsers that can power all kinds of web-scale NLP applications.
Max ERC Funding
1 481 747 €
Duration
Start date: 2017-02-01, End date: 2022-01-31
Project acronym IDRICA
Project Improving Drought Resistance in Crops and Arabidopsis
Researcher (PI) Ana Isabel Caño Delgado
Host Institution (HI) CENTRE DE RECERCA EN AGRIGENOMICA CSIC-IRTA-UAB-UB
Call Details Consolidator Grant (CoG), LS9, ERC-2015-CoG
Summary Drought is the first cause of agricultural losses globally, and represents a major threat to food security. Currently, plant biotechnology stands as the most promising strategy to produce crops capable of producing high yields in fed rain conditions. From the study of whole-plants, the main underlying mechanism for responses to drought stress has been uncovered, and multiple drought resistance genes have been engineered into crops. So far, plants with enhanced drought resistance displayed reduced crop yield, which imposes the search of novel approaches to uncouple drought resistance from plant growth. Our laboratory has recently shown, for the first time, that the receptors of Brassinosteroid hormones use cell-specific pathways to allocate different developmental responses during root growth. In particular, we have found that cell-specific components of the stem cell niche have the ability to control cellular responses to stress to promote stem renewal to ensure root growth. Additionally, we have also found that BR mutants are resistant to drought, together opening an exceptional opportunity to investigate the mechanisms that confer drought resistance with cellular specificity in plants. In this project, we will use Brassinosteroid signaling in the Arabidopsis root to investigate the mechanism for drought stress resistance in plant and to design novel molecules able to confer resistance to the drought stress. Finally, we will translate our research results and tools into Sorghum bicolor (Sorghum), a crop cereal of paramount importance in fed rain regions of the planet. Our research will impact in science, providing new avenues for the study of hormone signaling in plants, and in society, by providing sustainable solutions for enhance crop production in limiting water environments.
Summary
Drought is the first cause of agricultural losses globally, and represents a major threat to food security. Currently, plant biotechnology stands as the most promising strategy to produce crops capable of producing high yields in fed rain conditions. From the study of whole-plants, the main underlying mechanism for responses to drought stress has been uncovered, and multiple drought resistance genes have been engineered into crops. So far, plants with enhanced drought resistance displayed reduced crop yield, which imposes the search of novel approaches to uncouple drought resistance from plant growth. Our laboratory has recently shown, for the first time, that the receptors of Brassinosteroid hormones use cell-specific pathways to allocate different developmental responses during root growth. In particular, we have found that cell-specific components of the stem cell niche have the ability to control cellular responses to stress to promote stem renewal to ensure root growth. Additionally, we have also found that BR mutants are resistant to drought, together opening an exceptional opportunity to investigate the mechanisms that confer drought resistance with cellular specificity in plants. In this project, we will use Brassinosteroid signaling in the Arabidopsis root to investigate the mechanism for drought stress resistance in plant and to design novel molecules able to confer resistance to the drought stress. Finally, we will translate our research results and tools into Sorghum bicolor (Sorghum), a crop cereal of paramount importance in fed rain regions of the planet. Our research will impact in science, providing new avenues for the study of hormone signaling in plants, and in society, by providing sustainable solutions for enhance crop production in limiting water environments.
Max ERC Funding
2 000 000 €
Duration
Start date: 2016-11-01, End date: 2021-10-31
Project acronym INTELEG
Project The Intellectual and Material Legacies of Late Medieval Sephardic Judaism: An Interdisciplinary Approach
Researcher (PI) Esperanza Alfonso
Host Institution (HI) AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS
Call Details Starting Grant (StG), SH4, ERC-2007-StG
Summary From the 13th to the 15th centuries, the Jews of the Iberian Peninsula (Sepharad) lived side by side with Christians and Muslims. Although persistent tensions existed between these three groups, their members also participated in a common artistic, intellectual and scientific endeavour that produced the requisite conditions for the dawn of the European Renaissance. The worldviews of all three communities revolved around their sacred texts—the Hebrew and Christian Bibles and the Qur’an. This project will take as a focal point Judaism and its sacred text, and will explore its role and impact in late medieval society at large. The project will coordinate the research of a group of young scholars doing groundbreaking work in the field, all sharing a cross-cultural and inter-disciplinary perspective. As a group, we will bring under analysis a wide range of concepts—the production of sacred texts as objects, the history of their cataloguing and preservation, the multiple and conflicting interpretations of their contents, their role as social agents that fostered coexistence or created exclusions, their impact in literature and the arts, their relationship with medieval science, and their relationship to Muslim and Christian Scriptures. The project has a special relevance for today’s multicultural and pluralistic Europe, as it can help to minimize fundamentalist readings of the sacred texts, bring about a greater understanding of the historical roots of modern intercultural conflict and, ultimately, contribute to the development of non essentialist theories of race and culture.
Summary
From the 13th to the 15th centuries, the Jews of the Iberian Peninsula (Sepharad) lived side by side with Christians and Muslims. Although persistent tensions existed between these three groups, their members also participated in a common artistic, intellectual and scientific endeavour that produced the requisite conditions for the dawn of the European Renaissance. The worldviews of all three communities revolved around their sacred texts—the Hebrew and Christian Bibles and the Qur’an. This project will take as a focal point Judaism and its sacred text, and will explore its role and impact in late medieval society at large. The project will coordinate the research of a group of young scholars doing groundbreaking work in the field, all sharing a cross-cultural and inter-disciplinary perspective. As a group, we will bring under analysis a wide range of concepts—the production of sacred texts as objects, the history of their cataloguing and preservation, the multiple and conflicting interpretations of their contents, their role as social agents that fostered coexistence or created exclusions, their impact in literature and the arts, their relationship with medieval science, and their relationship to Muslim and Christian Scriptures. The project has a special relevance for today’s multicultural and pluralistic Europe, as it can help to minimize fundamentalist readings of the sacred texts, bring about a greater understanding of the historical roots of modern intercultural conflict and, ultimately, contribute to the development of non essentialist theories of race and culture.
Max ERC Funding
719 336 €
Duration
Start date: 2008-09-01, End date: 2012-08-31
Project acronym LATIN INTO HEBREW
Project Latin Philosophy into Hebrew: Intercultural Networks in 13th and 14th Century Europe
Researcher (PI) Alexander Fidora Riera
Host Institution (HI) UNIVERSITAT AUTONOMA DE BARCELONA
Call Details Starting Grant (StG), SH4, ERC-2007-StG
Summary The intercultural networks between Arabic, Christian and Jewish communities of learning during the Middle Ages have played a decisive role in the evolution of Western thought and have helped to shape the European identity. Until now, scholarly research has focused almost exclusively on the transmission of Arabic philosophy and science into Latin. The influence of Latin texts on Jewish thought has been largely neglected. The goal of this project is to study how Latin-Christian texts written at Toledo were received in the Jewish tradition of the 13th and 14th centuries, and to draw an intellectual topography of the intercultural and interreligious networks that extended across Europe. The work will involve the philosophical analysis of various texts together with their translations and reception, showing how the networks between the different religious communities in the Mediterranean can be understood as an attempt to work on a shared philosophical tradition. This tradition provided a common and continuous medium for dialogue between the faiths, based upon a commitment to philosophical reason. Our approach will be combined with historical and philological research on the conditions and methods of transmission and translation of Latin texts into Hebrew. In addition, the project aims at editing and translating some of the Hebrew texts of reference. The project is only possible in a trans-disciplinary research group, for it requires philosophical, historical and philological skills as well as a high degree of familiarity with the different traditions involved.
Summary
The intercultural networks between Arabic, Christian and Jewish communities of learning during the Middle Ages have played a decisive role in the evolution of Western thought and have helped to shape the European identity. Until now, scholarly research has focused almost exclusively on the transmission of Arabic philosophy and science into Latin. The influence of Latin texts on Jewish thought has been largely neglected. The goal of this project is to study how Latin-Christian texts written at Toledo were received in the Jewish tradition of the 13th and 14th centuries, and to draw an intellectual topography of the intercultural and interreligious networks that extended across Europe. The work will involve the philosophical analysis of various texts together with their translations and reception, showing how the networks between the different religious communities in the Mediterranean can be understood as an attempt to work on a shared philosophical tradition. This tradition provided a common and continuous medium for dialogue between the faiths, based upon a commitment to philosophical reason. Our approach will be combined with historical and philological research on the conditions and methods of transmission and translation of Latin texts into Hebrew. In addition, the project aims at editing and translating some of the Hebrew texts of reference. The project is only possible in a trans-disciplinary research group, for it requires philosophical, historical and philological skills as well as a high degree of familiarity with the different traditions involved.
Max ERC Funding
511 574 €
Duration
Start date: 2008-09-01, End date: 2012-02-29
Project acronym LT-NRBS
Project Lab-in-a-tube and Nanorobotic biosensors
Researcher (PI) Samuel Sánchez Ordóñez
Host Institution (HI) FUNDACIO INSTITUT DE BIOENGINYERIA DE CATALUNYA
Call Details Starting Grant (StG), LS9, ERC-2012-StG_20111109
Summary The goal of this project is to develop new types of biosensors based on two different approaches: (i) a new bioanalytic microsystem platform for cell growth, manipulation and analysis using on-chip integrated microtubes and (ii) the use of synthetic self-propelled nanomotors for bioanalytical and biosensing applications. Based on the novel “Lab-in-a-tube” concept, we will design a multifunctional device for the capturing, growth and sensing of single cell behaviours inside “glass” microtubes to be employed for diverse biological applications. We will decorate the walls of the microtubes with proteins from the extracellular matrix enabling the long-term study of cellular changes such as mitosis time, spindle reorientation, DNA damage and cellular differentiation. These microtubes are fabricated by the well-established rolled-up nanotechnology developed in the host institution. Moreover, the multifunctionality of the “Lab-in-a-tube” platform will be extended by integrating different modules into a single microtubular unit, bringing up several applications such as optofluidics(bio)sensors, electrodes for electrochemical control and sensing, and magnetic biodetection.
At the IIN institute in IFW Dresden, we are pioneers on the fabrication of catalytic microjet engines (microbots) and their use for transporting different kinds of objects in vitro into a fluid. The remote controlled motion of these autonomous microbots and the transport of microobjects and cells to specific targets within lab-on-a-chip systems is possible. Their walls can be biofunctionalized with enzymes, antibodies or DNA, the catalytic microbots representing a novel and unique tool for biosensing, environmental and biomedical applications. Our next step is to use biocompatible fuels to propel these microbots with the final aim of transporting and delivering drugs in vivo.The separation of cancer cells, bacteria and other biomaterials to build up new tissues or to replace disease cells are also aimed.
Summary
The goal of this project is to develop new types of biosensors based on two different approaches: (i) a new bioanalytic microsystem platform for cell growth, manipulation and analysis using on-chip integrated microtubes and (ii) the use of synthetic self-propelled nanomotors for bioanalytical and biosensing applications. Based on the novel “Lab-in-a-tube” concept, we will design a multifunctional device for the capturing, growth and sensing of single cell behaviours inside “glass” microtubes to be employed for diverse biological applications. We will decorate the walls of the microtubes with proteins from the extracellular matrix enabling the long-term study of cellular changes such as mitosis time, spindle reorientation, DNA damage and cellular differentiation. These microtubes are fabricated by the well-established rolled-up nanotechnology developed in the host institution. Moreover, the multifunctionality of the “Lab-in-a-tube” platform will be extended by integrating different modules into a single microtubular unit, bringing up several applications such as optofluidics(bio)sensors, electrodes for electrochemical control and sensing, and magnetic biodetection.
At the IIN institute in IFW Dresden, we are pioneers on the fabrication of catalytic microjet engines (microbots) and their use for transporting different kinds of objects in vitro into a fluid. The remote controlled motion of these autonomous microbots and the transport of microobjects and cells to specific targets within lab-on-a-chip systems is possible. Their walls can be biofunctionalized with enzymes, antibodies or DNA, the catalytic microbots representing a novel and unique tool for biosensing, environmental and biomedical applications. Our next step is to use biocompatible fuels to propel these microbots with the final aim of transporting and delivering drugs in vivo.The separation of cancer cells, bacteria and other biomaterials to build up new tissues or to replace disease cells are also aimed.
Max ERC Funding
1 499 880 €
Duration
Start date: 2013-01-01, End date: 2017-12-31
Project acronym MAMI
Project The Power of Maternal Microbes on Infant Health
Researcher (PI) MARIA CARMEN Collado Amores
Host Institution (HI) AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS
Call Details Starting Grant (StG), LS9, ERC-2014-STG
Summary Recent reports suggest that early microbial colonization has an important role for in promoting health. This may contribute to reduce the risk of chronic diseases such as obesity, allergies and inflammatory conditions. Advances in understanding host-microbe interactions imply that maternal microbiota plays a crucial role on health programming. This process begins in utero and it is modulated by mode of delivery and diet. My research has shown that i) specific shifts in milk microbial composition are associated with lactation time and mode of delivery, ii) milk microbes drive the infant microbiota composition; iii) maternal microbiota dysbiosis may be transferred to the infant. However, factors defining maternal microbiota and its biological role upon infant’s health are not yet fully understood. Hence, this project aims to characterize maternal microbes to be transferred to neonates and determine their function in infant health programming. The specific aims are:(1) understanding how the maternal microbiome is influenced by host and environmental factors;(2) characterizing the microbial core and bioactive compounds transmitted to the offspring mainly via breastfeeding and their key roles in the microbial modulation and host response;(3) understanding the interactions among breast milk bioactive compounds and their role in infant health;(4) shedding light on how maternal microbes influence the infant immune system & (5)development of new dietary strategies and therapies based on microbial replacement and modulation. To achieve these objectives, a systems biology approach by means of state-of-the-art techniques and new methodologies based on subpopulation enrichment by flow cytometer-sorter to study host–microbe interactions will be used. Results obtained will demonstrate the interaction between infant nutrition, microbes and host response in early life and its key role in health programming, enabling new applications in the field of personalized nutrition & medicine.
Summary
Recent reports suggest that early microbial colonization has an important role for in promoting health. This may contribute to reduce the risk of chronic diseases such as obesity, allergies and inflammatory conditions. Advances in understanding host-microbe interactions imply that maternal microbiota plays a crucial role on health programming. This process begins in utero and it is modulated by mode of delivery and diet. My research has shown that i) specific shifts in milk microbial composition are associated with lactation time and mode of delivery, ii) milk microbes drive the infant microbiota composition; iii) maternal microbiota dysbiosis may be transferred to the infant. However, factors defining maternal microbiota and its biological role upon infant’s health are not yet fully understood. Hence, this project aims to characterize maternal microbes to be transferred to neonates and determine their function in infant health programming. The specific aims are:(1) understanding how the maternal microbiome is influenced by host and environmental factors;(2) characterizing the microbial core and bioactive compounds transmitted to the offspring mainly via breastfeeding and their key roles in the microbial modulation and host response;(3) understanding the interactions among breast milk bioactive compounds and their role in infant health;(4) shedding light on how maternal microbes influence the infant immune system & (5)development of new dietary strategies and therapies based on microbial replacement and modulation. To achieve these objectives, a systems biology approach by means of state-of-the-art techniques and new methodologies based on subpopulation enrichment by flow cytometer-sorter to study host–microbe interactions will be used. Results obtained will demonstrate the interaction between infant nutrition, microbes and host response in early life and its key role in health programming, enabling new applications in the field of personalized nutrition & medicine.
Max ERC Funding
1 499 979 €
Duration
Start date: 2015-06-01, End date: 2020-12-31
Project acronym METALSYM
Project Metal transport in the tripartite symbiosis arbuscular mycorrhizal fungi-legume-rhizobia
Researcher (PI) Manuel Gonzalez Guerrero
Host Institution (HI) UNIVERSIDAD POLITECNICA DE MADRID
Call Details Starting Grant (StG), LS9, ERC-2013-StG
Summary Plant nutrition is essential to understand any physiological process in plant biology, as well as to improve crops, and agricultural practices. The root microbiome plays an important role in plant nutrition. The best characterized microbiome elements are two plant endosymbionts: arbuscular mycorrhizal fungi (AMF) and rhizobia. AMF are responsible for delivering most of the mineral nutrients required by the host plant. Similarly, rhizobia in legume nodules provide the vast majority of the nitrogen requirements. Given their importance for plant nutrition a significant effort in understanding macronutrient exchange among the symbionts has been made. However, very little is known about metal micronutrient exchange.
This is in contrast to the role of metals as essential nutrients for life (30-50 % of the proteins are metalloproteins) and to the yield-limiting effect that low soil metal bioavailability has worldwide. AMF are a source of metals, transferring the incorporated metals to the host,. Nitrogen-fixing rhizobia in mature nodules act as metal sinks, since the main enzymes required are highly expressed metalloproteins. We hypothesize that by changing the expression levels of the metal transporters involved, we will increase nitrogen fixation rates and increase plant metal uptake, resulting in higher crop production and fruit metal biofortification. Towards this goal, we will answer: i) How are metals incorporated from the AMF into the plant?, ii) How are metals delivered to the nodule?, iii) How are metals recovered from senescent nodules?, and iv) How does the natural variation of symbiotic-specific metal transporters affect yields and metal content of the fruit? In this project, we will use a multidisciplinary approach that involves metallotranscriptomics, plant physiology and molecular biology, and state-of-the art synchrotron based X-ray fluorescence to study metal distributions.
Summary
Plant nutrition is essential to understand any physiological process in plant biology, as well as to improve crops, and agricultural practices. The root microbiome plays an important role in plant nutrition. The best characterized microbiome elements are two plant endosymbionts: arbuscular mycorrhizal fungi (AMF) and rhizobia. AMF are responsible for delivering most of the mineral nutrients required by the host plant. Similarly, rhizobia in legume nodules provide the vast majority of the nitrogen requirements. Given their importance for plant nutrition a significant effort in understanding macronutrient exchange among the symbionts has been made. However, very little is known about metal micronutrient exchange.
This is in contrast to the role of metals as essential nutrients for life (30-50 % of the proteins are metalloproteins) and to the yield-limiting effect that low soil metal bioavailability has worldwide. AMF are a source of metals, transferring the incorporated metals to the host,. Nitrogen-fixing rhizobia in mature nodules act as metal sinks, since the main enzymes required are highly expressed metalloproteins. We hypothesize that by changing the expression levels of the metal transporters involved, we will increase nitrogen fixation rates and increase plant metal uptake, resulting in higher crop production and fruit metal biofortification. Towards this goal, we will answer: i) How are metals incorporated from the AMF into the plant?, ii) How are metals delivered to the nodule?, iii) How are metals recovered from senescent nodules?, and iv) How does the natural variation of symbiotic-specific metal transporters affect yields and metal content of the fruit? In this project, we will use a multidisciplinary approach that involves metallotranscriptomics, plant physiology and molecular biology, and state-of-the art synchrotron based X-ray fluorescence to study metal distributions.
Max ERC Funding
1 499 405 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym MIA
Project Multisensory Integration and Attention
Researcher (PI) Salvador Soto-Faraco
Host Institution (HI) UNIVERSIDAD POMPEU FABRA
Call Details Starting Grant (StG), SH4, ERC-2010-StG_20091209
Summary The world around us is immensely rich in sensory information, which we perceive through a varied range of different sensory systems (enabling us to feel, hear, see…). Yet, our perceptual experience is not a sensory piecemeal, but a unitary phenomenon brought about by Multisensory Integration mechanisms. MSI is in charge of binding sensory input to create faithful and coherent representations of the environment, an ability that confers important advantages in terms of optimizing behavioural outcomes. For example, people often find it easier to speak with someone when they can see their partner’s face, as lip and facial movements compensate for acoustic noise. The novelty of the project is that it focuses on internal processes, and in particular attention, to be of utmost importance during MSI. Attention enables efficient allocation of limited cognitive and neural resources, and therefore it plays a paramount role in perception, cognition and action. The aim is to understand the interplay between attention and the mechanisms of multisensory integration. Unravelling this interplay presents important challenges but, in return, promises to provide very important insights into how perception is accomplished by the human
mind and brain. In particular, the driving hypothesis underlying the present proposal is that objects of perception are multi-sensory defined events, and that attention plays a key role in building up and maintaining these perceptual representations. The strategy is to address this dynamic interplay between MSI and Attention by addressing a set of key specific research questions by means of converging methodological approaches. I propose to undertake this task with the help of a multidisciplinary team of researchers of different backgrounds, and a set of research methods including a behavioural approach (psychophysics in healthy adult humans, developmental studies and neuropsychology) combined with selective use of brain imaging stimulation.
Summary
The world around us is immensely rich in sensory information, which we perceive through a varied range of different sensory systems (enabling us to feel, hear, see…). Yet, our perceptual experience is not a sensory piecemeal, but a unitary phenomenon brought about by Multisensory Integration mechanisms. MSI is in charge of binding sensory input to create faithful and coherent representations of the environment, an ability that confers important advantages in terms of optimizing behavioural outcomes. For example, people often find it easier to speak with someone when they can see their partner’s face, as lip and facial movements compensate for acoustic noise. The novelty of the project is that it focuses on internal processes, and in particular attention, to be of utmost importance during MSI. Attention enables efficient allocation of limited cognitive and neural resources, and therefore it plays a paramount role in perception, cognition and action. The aim is to understand the interplay between attention and the mechanisms of multisensory integration. Unravelling this interplay presents important challenges but, in return, promises to provide very important insights into how perception is accomplished by the human
mind and brain. In particular, the driving hypothesis underlying the present proposal is that objects of perception are multi-sensory defined events, and that attention plays a key role in building up and maintaining these perceptual representations. The strategy is to address this dynamic interplay between MSI and Attention by addressing a set of key specific research questions by means of converging methodological approaches. I propose to undertake this task with the help of a multidisciplinary team of researchers of different backgrounds, and a set of research methods including a behavioural approach (psychophysics in healthy adult humans, developmental studies and neuropsychology) combined with selective use of brain imaging stimulation.
Max ERC Funding
1 450 672 €
Duration
Start date: 2011-04-01, End date: 2016-09-30
Project acronym MYCOCHASSIS
Project Engineering of a minimal bacterial therapeutic chassis
Researcher (PI) Luis-Felipe Serrano Púbul
Host Institution (HI) FUNDACIO CENTRE DE REGULACIO GENOMICA
Call Details Advanced Grant (AdG), LS9, ERC-2014-ADG
Summary Engineering bacteria to deliver therapeutic agents or to present antigens for vaccination is an emerging area of research with great clinical potential. The most challenging issue in this field is the selection of the right bacteria to engineer, commonly known as “chassis”. The best chassis depends on the application but there is a common drawback in bacteria used nowadays: their complexity and the lack of quantitative information for many reactions which limits genome engineering to classical trial and error approaches. In this project, we want to engineer the genome-reduced bacterium M. pneumoniae using a whole-cell model that will drive the rational to create a chassis for human and animal therapy. Its small size (816 Kbases), the lack of cell wall, and the vast amount of comprehensive quantitative –omics datasets makes this bacterium one of the best candidates for chassis design. By combining bioinformatics, -omics, and biochemistry approaches with genome engineering tools, systems biology analyses, and computational whole-cell models, MYCOCHASSIS aims to: i) develop a whole cell-model based on organism-specific experimental data that will be validated experimentally and that can predict the impact of genome modifications; ii) implement genome engineering tools to delete non-essential pathogenic and virulent elements predicted by the whole-cell model to engineer a therapeutical chassis; iii) using the whole-cell model design and engineer genes and circuits to improve growth rate in a defined medium. iv) as a proof of concept introduce orthogonal gene circuits to secrete peptides and enzymes capable of dissolving in vitro biofilms made by the lung pathogens Pseudomonas aeruginosa and Staphylococus aureus. This project will validate the usefulness of whole-cell models for synthetic biology by modelling multiple genomic modifications orientated to facilitate engineering of biological systems.
Summary
Engineering bacteria to deliver therapeutic agents or to present antigens for vaccination is an emerging area of research with great clinical potential. The most challenging issue in this field is the selection of the right bacteria to engineer, commonly known as “chassis”. The best chassis depends on the application but there is a common drawback in bacteria used nowadays: their complexity and the lack of quantitative information for many reactions which limits genome engineering to classical trial and error approaches. In this project, we want to engineer the genome-reduced bacterium M. pneumoniae using a whole-cell model that will drive the rational to create a chassis for human and animal therapy. Its small size (816 Kbases), the lack of cell wall, and the vast amount of comprehensive quantitative –omics datasets makes this bacterium one of the best candidates for chassis design. By combining bioinformatics, -omics, and biochemistry approaches with genome engineering tools, systems biology analyses, and computational whole-cell models, MYCOCHASSIS aims to: i) develop a whole cell-model based on organism-specific experimental data that will be validated experimentally and that can predict the impact of genome modifications; ii) implement genome engineering tools to delete non-essential pathogenic and virulent elements predicted by the whole-cell model to engineer a therapeutical chassis; iii) using the whole-cell model design and engineer genes and circuits to improve growth rate in a defined medium. iv) as a proof of concept introduce orthogonal gene circuits to secrete peptides and enzymes capable of dissolving in vitro biofilms made by the lung pathogens Pseudomonas aeruginosa and Staphylococus aureus. This project will validate the usefulness of whole-cell models for synthetic biology by modelling multiple genomic modifications orientated to facilitate engineering of biological systems.
Max ERC Funding
2 454 522 €
Duration
Start date: 2015-11-01, End date: 2020-10-31
Project acronym PLANT CIRES BIOTECH
Project Functional characterization of plant cellular IRES in response to abiotic stress and their use as biotechnological tools
Researcher (PI) María Del Mar Castellano
Host Institution (HI) INSTITUTO NACIONAL DE INVESTIGACION Y TECNOLOGIA AGRARIA Y ALIMENTARIA OA MP
Call Details Starting Grant (StG), LS9, ERC-2010-StG_20091118
Summary To cope with abiotic stresses plants require an extensive molecular regulation of gene expression. In plants, translation is a key step in the control of gene expression under abiotic stress conditions. This translational regulation involves (1) a global inhibition of protein synthesis and (2) an efficient and selective translation of certain mRNAs, generally codifying proteins involved in the abiotic stress response. Although in plants the mechanisms involved in the onset of this dual regulation are currently unknown, some evidences point out that cap independent translation, via recognition of internal ribosome entry sites (IRES) within the mRNAs efficiently translated, could be the clue for the selective protein synthesis observed under such conditions.
In this proposal we aim to further characterize the cellular IRESs operating under abiotic stress conditions in plants and to exploit the identified cellular IRESs as biotechnological tools to allow the efficient and selective translation of mRNAs of interest under abiotic stress conditions. In plants, no IRES trans-acting factors (ITAFs) and only two cellular IRESs have been identified so far. Therefore, the systematic identification of new cellular IRESs, the identification for the first time of ITAFs and the study of how they can control IRES activity-specificity under abiotic stress conditions are important steps forward in the knowledge of how plants adapt to environmental stresses. In addition, the pioneering use of the identified cellular IRESs as a tool to tightly and specifically control the expression of proteins of interest under abiotic stress conditions will open up a new perspective for the study of abiotic stress in plants and for the generation of plants with increased tolerance to such conditions.
Summary
To cope with abiotic stresses plants require an extensive molecular regulation of gene expression. In plants, translation is a key step in the control of gene expression under abiotic stress conditions. This translational regulation involves (1) a global inhibition of protein synthesis and (2) an efficient and selective translation of certain mRNAs, generally codifying proteins involved in the abiotic stress response. Although in plants the mechanisms involved in the onset of this dual regulation are currently unknown, some evidences point out that cap independent translation, via recognition of internal ribosome entry sites (IRES) within the mRNAs efficiently translated, could be the clue for the selective protein synthesis observed under such conditions.
In this proposal we aim to further characterize the cellular IRESs operating under abiotic stress conditions in plants and to exploit the identified cellular IRESs as biotechnological tools to allow the efficient and selective translation of mRNAs of interest under abiotic stress conditions. In plants, no IRES trans-acting factors (ITAFs) and only two cellular IRESs have been identified so far. Therefore, the systematic identification of new cellular IRESs, the identification for the first time of ITAFs and the study of how they can control IRES activity-specificity under abiotic stress conditions are important steps forward in the knowledge of how plants adapt to environmental stresses. In addition, the pioneering use of the identified cellular IRESs as a tool to tightly and specifically control the expression of proteins of interest under abiotic stress conditions will open up a new perspective for the study of abiotic stress in plants and for the generation of plants with increased tolerance to such conditions.
Max ERC Funding
1 237 500 €
Duration
Start date: 2010-12-01, End date: 2017-05-31
