Project acronym AMAIZE
Project Atlas of leaf growth regulatory networks in MAIZE
Researcher (PI) Dirk, Gustaaf Inzé
Host Institution (HI) VIB
Call Details Advanced Grant (AdG), LS9, ERC-2013-ADG
Summary "Understanding how organisms regulate size is one of the most fascinating open questions in biology. The aim of the AMAIZE project is to unravel how growth of maize leaves is controlled. Maize leaf development offers great opportunities to study the dynamics of growth regulatory networks, essentially because leaf development is a linear system with cell division at the leaf basis followed by cell expansion and maturation. Furthermore, the growth zone is relatively large allowing easy access of tissues at different positions. Four different perturbations of maize leaf size will be analyzed with cellular resolution: wild-type and plants having larger leaves (as a consequence of GA20OX1 overexpression), both grown under either well-watered or mild drought conditions. Firstly, a 3D cellular map of the growth zone of the fourth leaf will be made. RNA-SEQ of three different tissues (adaxial- and abaxial epidermis; mesophyll) obtained by laser dissection with an interval of 2.5 mm along the growth zone will allow for the analysis of the transcriptome with high resolution. Additionally, the composition of fifty selected growth regulatory protein complexes and DNA targets of transcription factors will be determined with an interval of 5 mm along the growth zone. Computational methods will be used to construct comprehensive integrative maps of the cellular and molecular processes occurring along the growth zone. Finally, selected regulatory nodes of the growth regulatory networks will be further functionally analyzed using a transactivation system in maize.
AMAIZE opens up new perspectives for the identification of optimal growth regulatory networks that can be selected for by advanced breeding or for which more robust variants (e.g. reduced susceptibility to drought) can be obtained through genetic engineering. The ability to improve the growth of maize and in analogy other cereals could have a high impact in providing food security"
Summary
"Understanding how organisms regulate size is one of the most fascinating open questions in biology. The aim of the AMAIZE project is to unravel how growth of maize leaves is controlled. Maize leaf development offers great opportunities to study the dynamics of growth regulatory networks, essentially because leaf development is a linear system with cell division at the leaf basis followed by cell expansion and maturation. Furthermore, the growth zone is relatively large allowing easy access of tissues at different positions. Four different perturbations of maize leaf size will be analyzed with cellular resolution: wild-type and plants having larger leaves (as a consequence of GA20OX1 overexpression), both grown under either well-watered or mild drought conditions. Firstly, a 3D cellular map of the growth zone of the fourth leaf will be made. RNA-SEQ of three different tissues (adaxial- and abaxial epidermis; mesophyll) obtained by laser dissection with an interval of 2.5 mm along the growth zone will allow for the analysis of the transcriptome with high resolution. Additionally, the composition of fifty selected growth regulatory protein complexes and DNA targets of transcription factors will be determined with an interval of 5 mm along the growth zone. Computational methods will be used to construct comprehensive integrative maps of the cellular and molecular processes occurring along the growth zone. Finally, selected regulatory nodes of the growth regulatory networks will be further functionally analyzed using a transactivation system in maize.
AMAIZE opens up new perspectives for the identification of optimal growth regulatory networks that can be selected for by advanced breeding or for which more robust variants (e.g. reduced susceptibility to drought) can be obtained through genetic engineering. The ability to improve the growth of maize and in analogy other cereals could have a high impact in providing food security"
Max ERC Funding
2 418 429 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym BioLEAP
Project Biotechnological optimization of light use efficiency in algae photobioreactors
Researcher (PI) Tomas Morosinotto
Host Institution (HI) UNIVERSITA DEGLI STUDI DI PADOVA
Call Details Starting Grant (StG), LS9, ERC-2012-StG_20111109
Summary New renewable energy source are highly needed to compensate exhausting fossil fuels reserves and reduce greenhouse gases emissions. Some species of algae have an interesting potential as feedstock for the production of biodiesel thanks to their ability to accumulate large amount of lipids. Strong research efforts are however needed to fulfil this potential and address many issues involving optimization of cultivation systems, biomass harvesting and algae genetic improvement. This proposal aims to address one of these issues, the optimization of algae light use efficiency. Light, in fact, provides the energy supporting algae growth and must be exploited with the highest possible efficiency to achieve sufficient productivity.
In a photobioreactor algae are highly concentrated and this cause a inhomogeneous light distribution with a large fraction of the cells exposed to very low light or even in the dark. Algae are also actively mixed and they can abruptly move from dark to full illumination and vice versa. This proposal aims to assess how alternation of dark/light cycles affect algae growth and functionality of photosynthetic apparatus both in batch and continuous cultures. In collaboration with the Chemical Engineering department, experimental data will be exploited to build a model describing the photobioreactor, a fundamental tool to improve its design.
The other main scope of this proposal is the isolation of genetically improved strains more suitable to the artificial environment of a photobioreactor. A first part of the work of setting up protocols for transformation will be followed by a second phase for generation and selection of mutants with altered photosynthetic performances. Transcriptome analyses in different light conditions will also be instrumental to identify genes to be targeted by genetic engineering.
Summary
New renewable energy source are highly needed to compensate exhausting fossil fuels reserves and reduce greenhouse gases emissions. Some species of algae have an interesting potential as feedstock for the production of biodiesel thanks to their ability to accumulate large amount of lipids. Strong research efforts are however needed to fulfil this potential and address many issues involving optimization of cultivation systems, biomass harvesting and algae genetic improvement. This proposal aims to address one of these issues, the optimization of algae light use efficiency. Light, in fact, provides the energy supporting algae growth and must be exploited with the highest possible efficiency to achieve sufficient productivity.
In a photobioreactor algae are highly concentrated and this cause a inhomogeneous light distribution with a large fraction of the cells exposed to very low light or even in the dark. Algae are also actively mixed and they can abruptly move from dark to full illumination and vice versa. This proposal aims to assess how alternation of dark/light cycles affect algae growth and functionality of photosynthetic apparatus both in batch and continuous cultures. In collaboration with the Chemical Engineering department, experimental data will be exploited to build a model describing the photobioreactor, a fundamental tool to improve its design.
The other main scope of this proposal is the isolation of genetically improved strains more suitable to the artificial environment of a photobioreactor. A first part of the work of setting up protocols for transformation will be followed by a second phase for generation and selection of mutants with altered photosynthetic performances. Transcriptome analyses in different light conditions will also be instrumental to identify genes to be targeted by genetic engineering.
Max ERC Funding
1 257 600 €
Duration
Start date: 2012-10-01, End date: 2017-09-30
Project acronym BIONICbacteria
Project Integrating a novel layer of synthetic biology tools in Pseudomonas, inspired by bacterial viruses
Researcher (PI) Rob LAVIGNE
Host Institution (HI) KATHOLIEKE UNIVERSITEIT LEUVEN
Call Details Consolidator Grant (CoG), LS9, ERC-2018-COG
Summary As nature’s first bioengineers, bacteriophages have evolved to modify, adapt and control their bacterial hosts through billions of years of interactions. Indeed, like modern synthetic biologists aspire to do, bacteriophages already evade bacterial silencing of their xenogeneic DNA, subvert host gene expression, and co-opt both the central and peripheral metabolisms of their hosts. Studying these key insights from a molecular systems biology perspective, inspired us to develop these evolutionary fully-adapted phage mechanisms as a next-level layer of synthetic biology tools. Thus, BIONICbacteria will provide conceptual novel synthetic biology tools that allow direct manipulation of specific protein activity, post-translational modifications, RNA stability, and metabolite concentrations.
The goal of BIONICbacteria is to pioneer an unconventional way to perform synthetic biology, tapping an unlimited source of novel phage tools genetic circuits and phage modulators. To achieve these goals, we will apply and develop state-of-the-art technologies in molecular microbiology and focus on three principal aims:
(1) To exploit new phage-encoded genetic circuits as synthetic biology parts and as intricate biotechnological chassis.
(2) To build synthetic phage modulators (SPMs) as novel payloads to directly impact the bacterial metabolism in a targeted manner.
(3) To create designer bacteria by integrating SPMs-containing circuits into bacterial strains as proof-of-concepts for applications in industrial fermentations and vaccine design.
This proposed “plug-in” approach of evolutionary-adapted synthetic modules, will allow us to domesticate Pseudomonas strains in radically new ways. By building proofs-of-concept for applications in industrial fermentations and vaccine development, we address key problem in these areas with potentially high-gain solutions for society and industry.
Summary
As nature’s first bioengineers, bacteriophages have evolved to modify, adapt and control their bacterial hosts through billions of years of interactions. Indeed, like modern synthetic biologists aspire to do, bacteriophages already evade bacterial silencing of their xenogeneic DNA, subvert host gene expression, and co-opt both the central and peripheral metabolisms of their hosts. Studying these key insights from a molecular systems biology perspective, inspired us to develop these evolutionary fully-adapted phage mechanisms as a next-level layer of synthetic biology tools. Thus, BIONICbacteria will provide conceptual novel synthetic biology tools that allow direct manipulation of specific protein activity, post-translational modifications, RNA stability, and metabolite concentrations.
The goal of BIONICbacteria is to pioneer an unconventional way to perform synthetic biology, tapping an unlimited source of novel phage tools genetic circuits and phage modulators. To achieve these goals, we will apply and develop state-of-the-art technologies in molecular microbiology and focus on three principal aims:
(1) To exploit new phage-encoded genetic circuits as synthetic biology parts and as intricate biotechnological chassis.
(2) To build synthetic phage modulators (SPMs) as novel payloads to directly impact the bacterial metabolism in a targeted manner.
(3) To create designer bacteria by integrating SPMs-containing circuits into bacterial strains as proof-of-concepts for applications in industrial fermentations and vaccine design.
This proposed “plug-in” approach of evolutionary-adapted synthetic modules, will allow us to domesticate Pseudomonas strains in radically new ways. By building proofs-of-concept for applications in industrial fermentations and vaccine development, we address key problem in these areas with potentially high-gain solutions for society and industry.
Max ERC Funding
1 998 750 €
Duration
Start date: 2019-09-01, End date: 2024-08-31
Project acronym BREEDIT
Project A NOVEL BREEDING STRATEGY USING MULTIPLEX GENOME EDITING IN MAIZE
Researcher (PI) Dirk INZE
Host Institution (HI) VIB
Call Details Advanced Grant (AdG), LS9, ERC-2018-ADG
Summary Feeding the growing world population under changing climate conditions poses an unprecedented challenge on global agriculture and our current pace to breed new high yielding crop varieties is too low to face the imminent threats on food security. This ERC project proposes a novel crossing scheme that allows for an expeditious evaluation of combinations of potential yield contributing alleles by unifying ‘classical’ breeding with gene-centric molecular biology. The acronym BREEDIT, a word fusion of breeding and editing, reflects the basic concept of combining breeding with multiplex genome editing of yield related genes. By introducing plants with distinct combinations of genome edited mutations in more than 80 known yield related genes into a crossing scheme, the combinatorial effect of these mutations on plant growth and yield will be evaluated. Subsequent rounds of crossings will increase the number of stacked gene-edits per plant, thus increasing the combinatorial complexity. Phenotypic evaluations throughout plant development will be done on our in-house automated image-analysis based phenotyping platform. The nature and frequency of Cas9-mediated mutations in the entire plant collection will be characterised by multiplex amplicon sequencing to follow the efficiency of CRISPR-cas9 genome editing and to identify the underlying combinations of genes that cause beneficial phenotypes (genetic gain). The obtained knowledge on yield regulatory networks can be directly implemented into current molecular breeding programs and the project will provide the basis to develop targeted breeding schemes implementing the optimal combinations of beneficial alleles into elite material.
BREEDIT will be a major step forward in integrating basic knowledge on genes with plant breeding and has the potential to provoke a paradigm shift in improving crop yield.
Summary
Feeding the growing world population under changing climate conditions poses an unprecedented challenge on global agriculture and our current pace to breed new high yielding crop varieties is too low to face the imminent threats on food security. This ERC project proposes a novel crossing scheme that allows for an expeditious evaluation of combinations of potential yield contributing alleles by unifying ‘classical’ breeding with gene-centric molecular biology. The acronym BREEDIT, a word fusion of breeding and editing, reflects the basic concept of combining breeding with multiplex genome editing of yield related genes. By introducing plants with distinct combinations of genome edited mutations in more than 80 known yield related genes into a crossing scheme, the combinatorial effect of these mutations on plant growth and yield will be evaluated. Subsequent rounds of crossings will increase the number of stacked gene-edits per plant, thus increasing the combinatorial complexity. Phenotypic evaluations throughout plant development will be done on our in-house automated image-analysis based phenotyping platform. The nature and frequency of Cas9-mediated mutations in the entire plant collection will be characterised by multiplex amplicon sequencing to follow the efficiency of CRISPR-cas9 genome editing and to identify the underlying combinations of genes that cause beneficial phenotypes (genetic gain). The obtained knowledge on yield regulatory networks can be directly implemented into current molecular breeding programs and the project will provide the basis to develop targeted breeding schemes implementing the optimal combinations of beneficial alleles into elite material.
BREEDIT will be a major step forward in integrating basic knowledge on genes with plant breeding and has the potential to provoke a paradigm shift in improving crop yield.
Max ERC Funding
2 474 790 €
Duration
Start date: 2019-09-01, End date: 2024-08-31
Project acronym ELECTROTALK
Project Starting an electrical conversation between microorganisms and electrodes to achieve bioproduction
Researcher (PI) Korneel Pieter Herman Leo Ann Rabaey
Host Institution (HI) UNIVERSITEIT GENT
Call Details Starting Grant (StG), LS9, ERC-2012-StG_20111109
Summary "Electrochemically active bacteria enable a host of novel processes in bioproduction, bioenergy and bioremediation. Key to the success of these processes is effective adherence of the bacterial cells to an electrode surface and subsequent equally effective electron exchange with the electrode. While the cellular mechanisms for electron transfer are increasingly known, what drives bacterial adsorption and desorption to positively or negatively polarized electrodes is largely unknown. Particularly processes driven by cathodes tend to be slow, and suffer from limited microbial adherence and lack of growth of the microorganisms. ELECTROTALK aims at developing a mechanistic understanding of mobility towards and microbial adherence at surfaces, from single cell level to complete biofilm formation. Based on this knowledge, effectively catalyzed bio-electrodes will be developed for novel bioproduction processes. Such bioproduction processes, termed microbial electrosynthesis, are independent of arable land availability, promise high production densities and enable the capture of CO2 or more efficient resource-usage for a range of products. Understanding the nature of the microorganism-electrode interaction will create a window of opportunity to improve this process and achieve effective bioproduction. Moreover, as the electrical interaction directly relates to microbial activity electrodes may serve as a means to start up a conversation with the cells. To achieve our aims we will: (i) select and characterize biocatalysts both as pure cultures and microbial communities; (ii) investigate cell adherence and electron transfer in function of electrode topography and chemistry as well as under different operational conditions; (iii) develop an electrode-microorganism combination achieving effective electron transfer; and (iv) electrochemically construct biofilms with defined structure or stratification."
Summary
"Electrochemically active bacteria enable a host of novel processes in bioproduction, bioenergy and bioremediation. Key to the success of these processes is effective adherence of the bacterial cells to an electrode surface and subsequent equally effective electron exchange with the electrode. While the cellular mechanisms for electron transfer are increasingly known, what drives bacterial adsorption and desorption to positively or negatively polarized electrodes is largely unknown. Particularly processes driven by cathodes tend to be slow, and suffer from limited microbial adherence and lack of growth of the microorganisms. ELECTROTALK aims at developing a mechanistic understanding of mobility towards and microbial adherence at surfaces, from single cell level to complete biofilm formation. Based on this knowledge, effectively catalyzed bio-electrodes will be developed for novel bioproduction processes. Such bioproduction processes, termed microbial electrosynthesis, are independent of arable land availability, promise high production densities and enable the capture of CO2 or more efficient resource-usage for a range of products. Understanding the nature of the microorganism-electrode interaction will create a window of opportunity to improve this process and achieve effective bioproduction. Moreover, as the electrical interaction directly relates to microbial activity electrodes may serve as a means to start up a conversation with the cells. To achieve our aims we will: (i) select and characterize biocatalysts both as pure cultures and microbial communities; (ii) investigate cell adherence and electron transfer in function of electrode topography and chemistry as well as under different operational conditions; (iii) develop an electrode-microorganism combination achieving effective electron transfer; and (iv) electrochemically construct biofilms with defined structure or stratification."
Max ERC Funding
1 494 126 €
Duration
Start date: 2012-10-01, End date: 2017-09-30
Project acronym FLARE
Project Floral Integrating Networks at the Shoot Apical Meristem of Rice
Researcher (PI) Fabio Fornara
Host Institution (HI) UNIVERSITA DEGLI STUDI DI MILANO
Call Details Starting Grant (StG), LS9, ERC-2010-StG_20091118
Summary Discriminating differences in day length is critical for many organisms to synchronize reproduction with the most favourable season of the year. Plants have evolved sophisticated time-keeping mechanisms that largely work in leaves, to measure the duration of the day. Upon perception of favourable day lengths, a leaf-borne signal moves to the shoot apical meristem to induce flower formation. Rice is a crop whose yield heavily depends on flowering at the right time, and genetic variation within leaf regulators contributes to diversification of flowering responses among different rice varieties. However, how the shoot apical meristem responds to changes in day length and initiates flowering is currently unknown. High-yielding European rice varieties flower within a limited range of days and expanding such range would prove beneficial to increase yield and expand cultivation to different environments. Our goal is to identify novel genes that modify meristem sensitivity to day length, and breed them into high-yielding cultivars. Together with the gene pool controlling day length responses in the leaves, these novel alleles will allow to design varieties with diverse sensitivities to photoperiod and will distribute the reproductive phase over a broader period of time. This knowledge-based breeding will require preliminary studies in order to identify regulators acting in the shoot apical meristem. To this extent, rice provides an excellent biological model for the availability of powerful genetic and molecular tools. I am proposing a number of genetic and biochemical screens that will allow us to explore the rice genome for genes required at the shoot apical meristem to drive reproductive phase transitions. We will investigate genetic variation in these components, relate it to flowering and adaptation, and use it for introgressing novel alleles into elite germplasm.
Summary
Discriminating differences in day length is critical for many organisms to synchronize reproduction with the most favourable season of the year. Plants have evolved sophisticated time-keeping mechanisms that largely work in leaves, to measure the duration of the day. Upon perception of favourable day lengths, a leaf-borne signal moves to the shoot apical meristem to induce flower formation. Rice is a crop whose yield heavily depends on flowering at the right time, and genetic variation within leaf regulators contributes to diversification of flowering responses among different rice varieties. However, how the shoot apical meristem responds to changes in day length and initiates flowering is currently unknown. High-yielding European rice varieties flower within a limited range of days and expanding such range would prove beneficial to increase yield and expand cultivation to different environments. Our goal is to identify novel genes that modify meristem sensitivity to day length, and breed them into high-yielding cultivars. Together with the gene pool controlling day length responses in the leaves, these novel alleles will allow to design varieties with diverse sensitivities to photoperiod and will distribute the reproductive phase over a broader period of time. This knowledge-based breeding will require preliminary studies in order to identify regulators acting in the shoot apical meristem. To this extent, rice provides an excellent biological model for the availability of powerful genetic and molecular tools. I am proposing a number of genetic and biochemical screens that will allow us to explore the rice genome for genes required at the shoot apical meristem to drive reproductive phase transitions. We will investigate genetic variation in these components, relate it to flowering and adaptation, and use it for introgressing novel alleles into elite germplasm.
Max ERC Funding
1 499 880 €
Duration
Start date: 2011-04-01, End date: 2016-03-31
Project acronym FORMICA
Project Microclimatic buffering of plant responses to macroclimate warming in temperate forests
Researcher (PI) Pieter DE FRENNE
Host Institution (HI) UNIVERSITEIT GENT
Call Details Starting Grant (StG), LS9, ERC-2017-STG
Summary Recent global warming is acting across ecosystems and threatening biodiversity. Yet, due to slow responses, many biological communities are lagging behind warming of the macroclimate (the climate of a large geographic region). The buffering of microclimates near the ground measured in localized areas, arising from terrain features such as vegetation and topography, can explain why many species are lagging behind macroclimate warming. However, almost all studies ignore the effects of microclimatic buffering and key uncertainties still exist about this mechanism. Microclimates are particularly evident in forests, where understorey habitats are buffered by overstorey trees. In temperate forests, the understorey contains the vast majority of plant diversity and plays an essential role in driving ecosystem processes.
The overall goal of FORMICA (FORest MICroclimate Assessment) is to quantify and understand the role of microclimatic buffering in modulating forest understorey plant responses to macroclimate warming. We will perform the best assessment to date of the effects of microclimates on plants by applying microtemperature loggers, experimental heating, fluorescent tubes and a large-scale transplant experiment in temperate forests across Europe. For the first time, plant data from the individual to ecosystem level will be related to microclimate along wide temperature gradients and forest management regimes. The empirical results will then be integrated in cutting-edge demographic distribution models to forecast plant diversity in temperate forests as macroclimate warms.
FORMICA will provide the first integrative study on microclimatic buffering of macroclimate warming in forests. Interdisciplinary concepts and methods will be applied, including from climatology, forestry and ecology. FORMICA will reshape our current understanding of the impacts of climate change on forests and help land managers and policy makers to develop urgently needed adaptation strategies.
Summary
Recent global warming is acting across ecosystems and threatening biodiversity. Yet, due to slow responses, many biological communities are lagging behind warming of the macroclimate (the climate of a large geographic region). The buffering of microclimates near the ground measured in localized areas, arising from terrain features such as vegetation and topography, can explain why many species are lagging behind macroclimate warming. However, almost all studies ignore the effects of microclimatic buffering and key uncertainties still exist about this mechanism. Microclimates are particularly evident in forests, where understorey habitats are buffered by overstorey trees. In temperate forests, the understorey contains the vast majority of plant diversity and plays an essential role in driving ecosystem processes.
The overall goal of FORMICA (FORest MICroclimate Assessment) is to quantify and understand the role of microclimatic buffering in modulating forest understorey plant responses to macroclimate warming. We will perform the best assessment to date of the effects of microclimates on plants by applying microtemperature loggers, experimental heating, fluorescent tubes and a large-scale transplant experiment in temperate forests across Europe. For the first time, plant data from the individual to ecosystem level will be related to microclimate along wide temperature gradients and forest management regimes. The empirical results will then be integrated in cutting-edge demographic distribution models to forecast plant diversity in temperate forests as macroclimate warms.
FORMICA will provide the first integrative study on microclimatic buffering of macroclimate warming in forests. Interdisciplinary concepts and methods will be applied, including from climatology, forestry and ecology. FORMICA will reshape our current understanding of the impacts of climate change on forests and help land managers and policy makers to develop urgently needed adaptation strategies.
Max ERC Funding
1 498 469 €
Duration
Start date: 2018-02-01, End date: 2023-01-31
Project acronym FUEL-PATH
Project Exploiting the saccharification potential of pathogenic microorganisms to improve biofuel production from plants
Researcher (PI) Felice Cervone
Host Institution (HI) UNIVERSITA DEGLI STUDI DI ROMA LA SAPIENZA
Call Details Advanced Grant (AdG), LS9, ERC-2008-AdG
Summary "FUEL-PATH aims at providing new knowledge on plant cell wall and innovative biotechnological solutions for biomass utilization. A key process for biomass utilization is the initial degradation of cell walls into fermentable sugars (saccharification); this is hindered by the wall recalcitrance to hydrolysis. We propose to improve the plant saccharification characteristics by mimicking a strategy successfully used by phytopathogenic microorganisms. These produce pectic enzymes before other cell wall-degrading enzymes (CWDEs) to weaken the linkages between the wall components and favour the maceration of the plant tissue. Homogalacturonan (HGA), a major component of pectin, is synthesized in a methylated form and is de-esterified in the wall by methylesterases (PMEs). De-esterified HGA interacts with calcium to form ""egg-box"" structures, which are critical for maintaining the integrity of the entire wall. We propose to improve saccharification by expression in plants of microbial polygalacturonases (PGs) hydrolizing HGA. Plants expressing a fungal PG have reduced levels of HGA and enhanced saccharification (unpublished preliminary data). Since PG activity in pianta affects normal growth, a technology of enzyme control through the use of specific protein inhibitors will be developed. A second strategy to be adopted for weakening the ""egg-box"" is the overexpression of PME inhibitors. This may cause not only an increased degradability but also an enhanced biomass production. FUEL-PATH will provide detailed information on the structure, function and construction of tailor-made enzymes and inhibitors suitable for the saccharification process. FUEL-PATH will also address the relationship between pectin composition and developmental responses mediated by hormones in PG-expressing plants. A genetic screen will be performed to isolate genes involved growth defects and increased cell wall degradability and these will be characterized for a possible biotechnological use."
Summary
"FUEL-PATH aims at providing new knowledge on plant cell wall and innovative biotechnological solutions for biomass utilization. A key process for biomass utilization is the initial degradation of cell walls into fermentable sugars (saccharification); this is hindered by the wall recalcitrance to hydrolysis. We propose to improve the plant saccharification characteristics by mimicking a strategy successfully used by phytopathogenic microorganisms. These produce pectic enzymes before other cell wall-degrading enzymes (CWDEs) to weaken the linkages between the wall components and favour the maceration of the plant tissue. Homogalacturonan (HGA), a major component of pectin, is synthesized in a methylated form and is de-esterified in the wall by methylesterases (PMEs). De-esterified HGA interacts with calcium to form ""egg-box"" structures, which are critical for maintaining the integrity of the entire wall. We propose to improve saccharification by expression in plants of microbial polygalacturonases (PGs) hydrolizing HGA. Plants expressing a fungal PG have reduced levels of HGA and enhanced saccharification (unpublished preliminary data). Since PG activity in pianta affects normal growth, a technology of enzyme control through the use of specific protein inhibitors will be developed. A second strategy to be adopted for weakening the ""egg-box"" is the overexpression of PME inhibitors. This may cause not only an increased degradability but also an enhanced biomass production. FUEL-PATH will provide detailed information on the structure, function and construction of tailor-made enzymes and inhibitors suitable for the saccharification process. FUEL-PATH will also address the relationship between pectin composition and developmental responses mediated by hormones in PG-expressing plants. A genetic screen will be performed to isolate genes involved growth defects and increased cell wall degradability and these will be characterized for a possible biotechnological use."
Max ERC Funding
2 099 600 €
Duration
Start date: 2009-01-01, End date: 2014-06-30
Project acronym LIMBo
Project Zooming the link between diet and brain health: how phenolic metabolites modulate brain inflammation
Researcher (PI) Cláudia NUNES DOS SANTOS
Host Institution (HI) UNIVERSIDADE NOVA DE LISBOA
Call Details Starting Grant (StG), LS9, ERC-2018-STG
Summary Currently a big concern of our aging society is to efficiently delay the onset of neurodegenerative diseases which are progressively rising in incidence. The paradigm that a diet rich in the phenolics, prevalent e.g. in fruits, is beneficial to brain health has reached the public. However their mechanistic actions in brain functions remain to be seen, particularly since the nature of those acting in the brain remains overlooked. I wish to address this gap by identifying candidate compounds that can support development of effective strategies to delay neurodegeneration.
Specifically, I will be analysing the potential of dietary phenolics in both prevention and treatment (i.e delay) of neuroinflammation – key process shared in neurodegenerative diseases. To break down the current indeterminate status of “cause vs effect”, my vision is to focus my research on metabolites derived from dietary phenolics that reach the brain. I will be investigating their effects in both established and unknown response pathways of microglia cells - the innate immune cells of the central nervous system, either alone or when communicating with other brain cells. Ultimately, to attain an integrated view of their effects I will establish nutrition trials in mice. LIMBo considers both pro- and anti- inflammatory processes to preliminary validate the action of any promising metabolite in prevention and/or therapeutics.
LIMBo provides valuable scientific insights for future implementation of healthy brain diets. My group is in a unique position to address LIMBo objectives due to multidisciplinary expertise in organic synthesis, metabolomics and molecular and cellular biology, together with our previous data on novel neuroactive metabolites.
LIMBo also creates far-reaching opportunities by generating knowledge that impacts our fundamental understanding on the diversity of phenolic metabolites and their specific influences in neuroinflammation and potential use as prodrugs.
Summary
Currently a big concern of our aging society is to efficiently delay the onset of neurodegenerative diseases which are progressively rising in incidence. The paradigm that a diet rich in the phenolics, prevalent e.g. in fruits, is beneficial to brain health has reached the public. However their mechanistic actions in brain functions remain to be seen, particularly since the nature of those acting in the brain remains overlooked. I wish to address this gap by identifying candidate compounds that can support development of effective strategies to delay neurodegeneration.
Specifically, I will be analysing the potential of dietary phenolics in both prevention and treatment (i.e delay) of neuroinflammation – key process shared in neurodegenerative diseases. To break down the current indeterminate status of “cause vs effect”, my vision is to focus my research on metabolites derived from dietary phenolics that reach the brain. I will be investigating their effects in both established and unknown response pathways of microglia cells - the innate immune cells of the central nervous system, either alone or when communicating with other brain cells. Ultimately, to attain an integrated view of their effects I will establish nutrition trials in mice. LIMBo considers both pro- and anti- inflammatory processes to preliminary validate the action of any promising metabolite in prevention and/or therapeutics.
LIMBo provides valuable scientific insights for future implementation of healthy brain diets. My group is in a unique position to address LIMBo objectives due to multidisciplinary expertise in organic synthesis, metabolomics and molecular and cellular biology, together with our previous data on novel neuroactive metabolites.
LIMBo also creates far-reaching opportunities by generating knowledge that impacts our fundamental understanding on the diversity of phenolic metabolites and their specific influences in neuroinflammation and potential use as prodrugs.
Max ERC Funding
1 496 022 €
Duration
Start date: 2019-04-01, End date: 2024-03-31
Project acronym MIMESIS
Project Development of biomaterials through mimesis of plant defensive interfaces to fight wound infections
Researcher (PI) Cristina Maria Da Costa Silva Pereira
Host Institution (HI) INSTITUTO DE TECNOLOGIA QUIMICA E BIOLOGICA - UNIVERSIDADE NOVA DE LISBOA
Call Details Consolidator Grant (CoG), LS9, ERC-2014-CoG
Summary Fighting microbial infection of wounds, especially in immunocompromised patients, is a major challenge in the 21st century. The skin barrier is the primary defence against microbial (opportunistic) pathogens. When this barrier is breached even non-pathogenic fungi may cause devastating infections, most of which provoked by crossover fungi able to infect both plant and humans. Hence, diabetic patients (ca. 6.4% of the world population), who are prone to develop chronic non-healing wounds, constitute a major risk group. My research is driven by the vision of mimicking the functionality of plant polyesters to develop wound dressing biomaterials that combine antimicrobial and skin regeneration properties.
Land plants have evolved through more than 400 million years, developing defence polyester barriers that limit pathogen adhesion and invasion. Biopolyesters are ubiquitous in plants and are the third most abundant plant polymer. The unique chemical composition of the plant polyester and its macromolecular assembly determines its physiological roles. This lipid-based polymer shows important similarities to the epidermal skin layer; hence it is an excellent candidate for a wound-dressing material. While evidences of their skin regeneration properties exist in cosmetics formulations and in traditional medicine, extracting polyesters from plants results in the loss of both native structure and inherent barrier properties hampering progress in this area.
We have developed a biocompatible extraction method that preserves the plant polyester film forming abilities and their inherent biological properties. The ex-situ reconstituted polyester films display the native barrier properties, including potentially broad antimicrobial and anti-biofouling effect. This, combined with our established record in fungal biochemistry/genetics, places us in a unique position to push the development of plant polyester materials to be applied in wounds, in particular diabetic chronic wounds.
Summary
Fighting microbial infection of wounds, especially in immunocompromised patients, is a major challenge in the 21st century. The skin barrier is the primary defence against microbial (opportunistic) pathogens. When this barrier is breached even non-pathogenic fungi may cause devastating infections, most of which provoked by crossover fungi able to infect both plant and humans. Hence, diabetic patients (ca. 6.4% of the world population), who are prone to develop chronic non-healing wounds, constitute a major risk group. My research is driven by the vision of mimicking the functionality of plant polyesters to develop wound dressing biomaterials that combine antimicrobial and skin regeneration properties.
Land plants have evolved through more than 400 million years, developing defence polyester barriers that limit pathogen adhesion and invasion. Biopolyesters are ubiquitous in plants and are the third most abundant plant polymer. The unique chemical composition of the plant polyester and its macromolecular assembly determines its physiological roles. This lipid-based polymer shows important similarities to the epidermal skin layer; hence it is an excellent candidate for a wound-dressing material. While evidences of their skin regeneration properties exist in cosmetics formulations and in traditional medicine, extracting polyesters from plants results in the loss of both native structure and inherent barrier properties hampering progress in this area.
We have developed a biocompatible extraction method that preserves the plant polyester film forming abilities and their inherent biological properties. The ex-situ reconstituted polyester films display the native barrier properties, including potentially broad antimicrobial and anti-biofouling effect. This, combined with our established record in fungal biochemistry/genetics, places us in a unique position to push the development of plant polyester materials to be applied in wounds, in particular diabetic chronic wounds.
Max ERC Funding
1 795 968 €
Duration
Start date: 2015-09-01, End date: 2020-08-31
Project acronym NANOSYM
Project Symbiotic bacteria as a delivery system for Nanobodies that target the insect-parasite interplay
Researcher (PI) Jan Van Den Abbeele
Host Institution (HI) PRINS LEOPOLD INSTITUUT VOOR TROPISCHE GENEESKUNDE
Call Details Starting Grant (StG), LS9, ERC-2011-StG_20101109
Summary The tsetse fly (Glossina spp.) salivary gland is the final micro-environment where the Trypanosoma brucei parasites adhere and undergo a complex re-programming cycle resulting in an end stage that is re-programmed to continue its life cycle in a new mammalian host. The molecular parasite-vector communications that orchestrate this trypanosome development in tsetse fly salivary glands remain unknown mainly due to the limited availability of experimental tools for functional research. We hypothesize that an innovative paratransgenic approach using the Sodalis glossinidius endosymbiont to deliver Nanobodies that target the trypanosome-tsetse fly crosstalk will open a new avenue to unravel the molecular determinants of this specific parasite-vector association. In this project I will develop an innovative Sodalis-based internal delivery system for Nanobodies to target the tsetse fly – trypanosome interplay and, as final outcome, will generate a trypanosome-resistant tsetse fly. In addition, I will explore the completely ‘unknown’ of the molecular nature of trypanosome adherence to the salivary gland epithelium. This will be addressed by a challenging proteomic-based approach on the tsetse salivary gland - trypanosome membrane complex and by the newly developed paratransgenic approach using the S. glossinidius endosymbiont as an internal delivery system for salivary gland epithelium-targeting Nanobodies. The application of this innovative concept of using pathogen-targeting Nanobodies delivered by insect symbiotic bacteria could be extended to other vector-pathogen systems such as Anopheles gambiae – Plasmodium falciparum and Aedes aegypti – dengue virus.
Summary
The tsetse fly (Glossina spp.) salivary gland is the final micro-environment where the Trypanosoma brucei parasites adhere and undergo a complex re-programming cycle resulting in an end stage that is re-programmed to continue its life cycle in a new mammalian host. The molecular parasite-vector communications that orchestrate this trypanosome development in tsetse fly salivary glands remain unknown mainly due to the limited availability of experimental tools for functional research. We hypothesize that an innovative paratransgenic approach using the Sodalis glossinidius endosymbiont to deliver Nanobodies that target the trypanosome-tsetse fly crosstalk will open a new avenue to unravel the molecular determinants of this specific parasite-vector association. In this project I will develop an innovative Sodalis-based internal delivery system for Nanobodies to target the tsetse fly – trypanosome interplay and, as final outcome, will generate a trypanosome-resistant tsetse fly. In addition, I will explore the completely ‘unknown’ of the molecular nature of trypanosome adherence to the salivary gland epithelium. This will be addressed by a challenging proteomic-based approach on the tsetse salivary gland - trypanosome membrane complex and by the newly developed paratransgenic approach using the S. glossinidius endosymbiont as an internal delivery system for salivary gland epithelium-targeting Nanobodies. The application of this innovative concept of using pathogen-targeting Nanobodies delivered by insect symbiotic bacteria could be extended to other vector-pathogen systems such as Anopheles gambiae – Plasmodium falciparum and Aedes aegypti – dengue virus.
Max ERC Funding
1 444 370 €
Duration
Start date: 2011-11-01, End date: 2016-10-31
Project acronym noMAGIC
Project Noninvasive Manipulation of Gating in Ion Channels
Researcher (PI) ANNA MORONI
Host Institution (HI) UNIVERSITA DEGLI STUDI DI MILANO
Call Details Advanced Grant (AdG), LS9, ERC-2015-AdG
Summary noMAGIC has the visionary goal of engineering genetically encoded ion channels, which can be remotely controlled (gated) by stimuli that penetrate deep into human tissue without negative side effects. The control over ion channel activity by deep penetrating stimuli will revolutionize research in neurobiology and physiology as it paves the way for remote and genuine non-invasive control of cell activity in vivo. Synthetic channels, which can be gated by magnetic fields (MF), near infrared (NIR) radiation or ultrasound (US) will be engineered in the frame of noMAGIC by three complementary work packages (WP1-3). Design and engineering of the channels will be performed in WP1 by reiterated steps of rational and irrational design, high throughput screening and in vitro and in vivo functional testing. We have identified two sensor modules for MF and NIR radiation, respectively, which will be functionally connected to a channel pore for a remote control of gating. For the US-gated channel we will engineer a channel pore that is maximally responding to local changes in the lipid environment induced by US. Design and engineering of channels will be complemented by a computational approach (WP2), which analyses, from elastic network models, the mechanical connections in the channel pore and which extracts information on the forces, which are required to gate a channel by the three stimuli. The outcome of WP2 will provide general design rules for synthetic channels with implications much beyond the present project. WP3 also contributes to the engineering effort in WP1 by a spectrum of avant-garde spectroscopic methods, which resolve structural changes of the channel proteins under the influence of remote stimuli. These structural insights will greatly advance our understanding of structure/function correlates in composite ion channels and it will inspire the design and engineering of channels, which respond to remote stimuli.
Summary
noMAGIC has the visionary goal of engineering genetically encoded ion channels, which can be remotely controlled (gated) by stimuli that penetrate deep into human tissue without negative side effects. The control over ion channel activity by deep penetrating stimuli will revolutionize research in neurobiology and physiology as it paves the way for remote and genuine non-invasive control of cell activity in vivo. Synthetic channels, which can be gated by magnetic fields (MF), near infrared (NIR) radiation or ultrasound (US) will be engineered in the frame of noMAGIC by three complementary work packages (WP1-3). Design and engineering of the channels will be performed in WP1 by reiterated steps of rational and irrational design, high throughput screening and in vitro and in vivo functional testing. We have identified two sensor modules for MF and NIR radiation, respectively, which will be functionally connected to a channel pore for a remote control of gating. For the US-gated channel we will engineer a channel pore that is maximally responding to local changes in the lipid environment induced by US. Design and engineering of channels will be complemented by a computational approach (WP2), which analyses, from elastic network models, the mechanical connections in the channel pore and which extracts information on the forces, which are required to gate a channel by the three stimuli. The outcome of WP2 will provide general design rules for synthetic channels with implications much beyond the present project. WP3 also contributes to the engineering effort in WP1 by a spectrum of avant-garde spectroscopic methods, which resolve structural changes of the channel proteins under the influence of remote stimuli. These structural insights will greatly advance our understanding of structure/function correlates in composite ion channels and it will inspire the design and engineering of channels, which respond to remote stimuli.
Max ERC Funding
2 409 209 €
Duration
Start date: 2016-09-01, End date: 2021-08-31
Project acronym NOVABREED
Project Novel variation in plant breeding and the plant pan-genomes
Researcher (PI) Michele Morgante
Host Institution (HI) UNIVERSITA DEGLI STUDI DI UDINE
Call Details Advanced Grant (AdG), LS9, ERC-2011-ADG_20110310
Summary "The analysis of variation in plants has revealed that their genomes are characterised by high levels of structural variation, consisting of both smaller insertion/deletions, mostly due to recent insertions of transposable elements, and of larger insertion/deletion similar to those termed in humans Copy Number Variants (CNVs). These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome, including core genomic features common to all individuals and a Dispensable Genome (DG) composed of partially shared and/or non shared DNA sequence elements. The very active transposable element systems present in many plant genomes may account for a large fraction of the DG. The mechanisms by which the CNV-like variants are generated and the direction of the mutational events are still unknown. Uncovering the intriguing nature of the DG, i.e. its composition, origin and function, represents a step forward towards an understanding of the processes generating genetic diversity and phenotypic variation. Additionally, since the DG clearly appears to be for the most part the youngest and most dynamic component of the pan genome, it is of great interest to understand whether it is a major contributor to the creation of new genetic variation in plant evolution and more specifically in the breeding process. We thus aim at:
i) defining extent and composition of the pan genome in two plant species, maize and grapevine;
ii) identifying the different mechanisms that generate and maintain the dispensable portion in these 2 species;
iii) identifying the phenotypic effects of the DG;
iv) estimating the rates and modes of creation of new genetic variation due to DG components and whether this could represent an important factor in the breeding process;
v) extending our findings to other plant species for which the genome sequence in the meantime may have become available."
Summary
"The analysis of variation in plants has revealed that their genomes are characterised by high levels of structural variation, consisting of both smaller insertion/deletions, mostly due to recent insertions of transposable elements, and of larger insertion/deletion similar to those termed in humans Copy Number Variants (CNVs). These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome, including core genomic features common to all individuals and a Dispensable Genome (DG) composed of partially shared and/or non shared DNA sequence elements. The very active transposable element systems present in many plant genomes may account for a large fraction of the DG. The mechanisms by which the CNV-like variants are generated and the direction of the mutational events are still unknown. Uncovering the intriguing nature of the DG, i.e. its composition, origin and function, represents a step forward towards an understanding of the processes generating genetic diversity and phenotypic variation. Additionally, since the DG clearly appears to be for the most part the youngest and most dynamic component of the pan genome, it is of great interest to understand whether it is a major contributor to the creation of new genetic variation in plant evolution and more specifically in the breeding process. We thus aim at:
i) defining extent and composition of the pan genome in two plant species, maize and grapevine;
ii) identifying the different mechanisms that generate and maintain the dispensable portion in these 2 species;
iii) identifying the phenotypic effects of the DG;
iv) estimating the rates and modes of creation of new genetic variation due to DG components and whether this could represent an important factor in the breeding process;
v) extending our findings to other plant species for which the genome sequence in the meantime may have become available."
Max ERC Funding
2 473 500 €
Duration
Start date: 2012-07-01, End date: 2017-12-31
Project acronym PASTFORWARD
Project Development trajectories of temperate forest plant communities under global change: combining hindsight and forecasting (PASTFORWARD)
Researcher (PI) Kris Verheyen
Host Institution (HI) UNIVERSITEIT GENT
Call Details Consolidator Grant (CoG), LS9, ERC-2013-CoG
Summary "The last decades are characterized by an upsurge of research on the impacts of global environmental changes on forests. Climate warming, atmospheric deposition of acidifying and eutrophying pollutants and land-use change are three of the most important threats to biodiversity in temperate forests. However, most studies focused on the effects of single factors over short time periods, such that our ability to predict the combined effects of multiple global change drivers over longer time periods remains rudimentary. The lack of knowledge on effects of global change drivers on forest herb layer communities is particularly striking, since the herb layer contains the largest part of vascular plant diversity in temperate forests and provides key ecosystem services. Therefore PASTFORWARD will build an integrative understanding of the interactive effects of land-use change, atmospheric deposition and climate warming on forest herb layer communities, starting from the insight that changes in herb layer communities are driven primarily by past land use, but can be modulated by atmospheric deposition, climate warming and forest management. Indeed, it is still largely ignored that sensible predictions of herb layer development trajectories under global change can only be made by taking the forest’s land-use history into account, as legacies of past land use can leave century-long imprints on forest herb layer communities. Three complementary data sources (a database with resurveyed vegetation plots, field measurements in a pan-European network of resurvey plots, and a multi-factor experiment) combined with an ecosystem model will be used. Furthermore, concepts and tools from different disciplines, ranging from history over sylviculture to community and ecosystem ecology will be applied. The results of PASTFORWARD will help forest managers and policy makers in taking more informed decisions on how to combine resource extraction with biodiversity conservation."
Summary
"The last decades are characterized by an upsurge of research on the impacts of global environmental changes on forests. Climate warming, atmospheric deposition of acidifying and eutrophying pollutants and land-use change are three of the most important threats to biodiversity in temperate forests. However, most studies focused on the effects of single factors over short time periods, such that our ability to predict the combined effects of multiple global change drivers over longer time periods remains rudimentary. The lack of knowledge on effects of global change drivers on forest herb layer communities is particularly striking, since the herb layer contains the largest part of vascular plant diversity in temperate forests and provides key ecosystem services. Therefore PASTFORWARD will build an integrative understanding of the interactive effects of land-use change, atmospheric deposition and climate warming on forest herb layer communities, starting from the insight that changes in herb layer communities are driven primarily by past land use, but can be modulated by atmospheric deposition, climate warming and forest management. Indeed, it is still largely ignored that sensible predictions of herb layer development trajectories under global change can only be made by taking the forest’s land-use history into account, as legacies of past land use can leave century-long imprints on forest herb layer communities. Three complementary data sources (a database with resurveyed vegetation plots, field measurements in a pan-European network of resurvey plots, and a multi-factor experiment) combined with an ecosystem model will be used. Furthermore, concepts and tools from different disciplines, ranging from history over sylviculture to community and ecosystem ecology will be applied. The results of PASTFORWARD will help forest managers and policy makers in taking more informed decisions on how to combine resource extraction with biodiversity conservation."
Max ERC Funding
1 887 780 €
Duration
Start date: 2014-06-01, End date: 2019-05-31
Project acronym POLYADAPT
Project Molecular-genetic mechanisms of extreme adaptation in a polyphagous agricultural pest
Researcher (PI) Thomas Bert VAN LEEUWEN
Host Institution (HI) UNIVERSITEIT GENT
Call Details Consolidator Grant (CoG), LS9, ERC-2017-COG
Summary Generalist (polyphagous) herbivores can feed and reproduce on many different plant species and include some of the most pesticide resistant and notorious pests in agriculture. An evolutionary link between host plant range and the development of pesticide resistance has been suggested. Although crucial for devising efficient crop protection strategies, the mechanisms underlying rapid adaptation are not well understood, especially in generalists. The spider mite Tetranychus urticae is a global pest known to feed on 1,100 different hosts from 140 plant families, including most major crops. With experimental advances and new tools developed for T. urticae, we are now poised for fundamental advances in understanding the molecular genetic make-up of adaption in generalist pests. We will generate a large collection of fully inbred and resistant mite strains and describe the sampled genomic variation in the context of selection and adaptation. We will study gene regulation mechanisms and quantify cis versus trans regulation of gene expression on a genome wide scale. We will then create a unique population resource that will allow us to map master regulators of gene expression and construct a gene-regulatory network of adaptation responsive genes. In a highly replicated experimental evolution study, combined with Bulk Segregant Analysis (BSA), we will uncover, without a prior hypothesis, the genomic loci that underlie complex cases of resistance and plant adaptation. A core set of adaptation genes will be validated by functional expression and high-throughput interaction assays. Further validation will come from the development of genome editing tools. In summary, POLYADAPT will exploit the genomic tools now available for spider mites to elucidate regulatory and causal variants underlying the extreme adaptation potential of polyphagous pests. This will in the long term lead to innovative methods of pest management.
Summary
Generalist (polyphagous) herbivores can feed and reproduce on many different plant species and include some of the most pesticide resistant and notorious pests in agriculture. An evolutionary link between host plant range and the development of pesticide resistance has been suggested. Although crucial for devising efficient crop protection strategies, the mechanisms underlying rapid adaptation are not well understood, especially in generalists. The spider mite Tetranychus urticae is a global pest known to feed on 1,100 different hosts from 140 plant families, including most major crops. With experimental advances and new tools developed for T. urticae, we are now poised for fundamental advances in understanding the molecular genetic make-up of adaption in generalist pests. We will generate a large collection of fully inbred and resistant mite strains and describe the sampled genomic variation in the context of selection and adaptation. We will study gene regulation mechanisms and quantify cis versus trans regulation of gene expression on a genome wide scale. We will then create a unique population resource that will allow us to map master regulators of gene expression and construct a gene-regulatory network of adaptation responsive genes. In a highly replicated experimental evolution study, combined with Bulk Segregant Analysis (BSA), we will uncover, without a prior hypothesis, the genomic loci that underlie complex cases of resistance and plant adaptation. A core set of adaptation genes will be validated by functional expression and high-throughput interaction assays. Further validation will come from the development of genome editing tools. In summary, POLYADAPT will exploit the genomic tools now available for spider mites to elucidate regulatory and causal variants underlying the extreme adaptation potential of polyphagous pests. This will in the long term lead to innovative methods of pest management.
Max ERC Funding
1 926 250 €
Duration
Start date: 2018-06-01, End date: 2023-05-31
Project acronym POPFULL
Project System analysis of a bio-energy plantation: full greenhouse gas balance and energy accounting
Researcher (PI) Reinhart J.M. Ceulemans
Host Institution (HI) UNIVERSITEIT ANTWERPEN
Call Details Advanced Grant (AdG), LS9, ERC-2008-AdG
Summary One of the strategies for mitigation of anthropogenic greenhouse gas emissions that is receiving a lot of attention in this post-Kyoto era, is the use of bio-energy as a replacement for fossil fuels. Among the different alternatives of bio-energy production the use of biomass crops such as fast-growing woody crops under short rotation coppice (SRC) regimes - is probably the most suited, in particular in the EU. Two issues need to be addressed before the efficacy of bio-energy for carbon mitigation can be conclusively assessed, i.e. (i) a full life cycle analysis (LCA) of the global warming contribution of SRC, and (ii) and an assessment of the energy efficiency of the system. The objectives of this project are: (i) to make a full LCA balance of the most important greenhouse gases (CO2, CH4, N2O, H2O and O3) and of the volatile organic compounds (VOC s), and (ii) to make a full energy accounting of a SRC plantation with fast-growing trees. The project will involve both an experimental approach at a representative field site in Belgium and a modelling part. For the experimental approach a SRC of poplar (Populus) will be monitored during the course of 1+3 years, harvested and transformed into bio-energy. Eddy covariance techniques will be used to monitor net fluxes of all greenhouse gases and VOC's, in combination with common assessments of biomass pools (incl. soil) and fluxes. For the energy accounting we will use life cycle analysis and energy efficiency assessments over the entire life cycle of the SRC plantation until the production of electricity and heat. A significant process based modeling component will integrate the collected knowledge on the greenhouse gas and energy balances toward predictions and simulations of the net reduction of fossil greenhouse gas emissions (avoided emissions) of SRC over different rotation cycles, global warming scenarios, and management strategies.
Summary
One of the strategies for mitigation of anthropogenic greenhouse gas emissions that is receiving a lot of attention in this post-Kyoto era, is the use of bio-energy as a replacement for fossil fuels. Among the different alternatives of bio-energy production the use of biomass crops such as fast-growing woody crops under short rotation coppice (SRC) regimes - is probably the most suited, in particular in the EU. Two issues need to be addressed before the efficacy of bio-energy for carbon mitigation can be conclusively assessed, i.e. (i) a full life cycle analysis (LCA) of the global warming contribution of SRC, and (ii) and an assessment of the energy efficiency of the system. The objectives of this project are: (i) to make a full LCA balance of the most important greenhouse gases (CO2, CH4, N2O, H2O and O3) and of the volatile organic compounds (VOC s), and (ii) to make a full energy accounting of a SRC plantation with fast-growing trees. The project will involve both an experimental approach at a representative field site in Belgium and a modelling part. For the experimental approach a SRC of poplar (Populus) will be monitored during the course of 1+3 years, harvested and transformed into bio-energy. Eddy covariance techniques will be used to monitor net fluxes of all greenhouse gases and VOC's, in combination with common assessments of biomass pools (incl. soil) and fluxes. For the energy accounting we will use life cycle analysis and energy efficiency assessments over the entire life cycle of the SRC plantation until the production of electricity and heat. A significant process based modeling component will integrate the collected knowledge on the greenhouse gas and energy balances toward predictions and simulations of the net reduction of fossil greenhouse gas emissions (avoided emissions) of SRC over different rotation cycles, global warming scenarios, and management strategies.
Max ERC Funding
2 500 000 €
Duration
Start date: 2009-03-01, End date: 2014-10-31
Project acronym POPMET
Project Large-scale identification of secondary metabolites, metabolic pathways and their genes in the model tree poplar
Researcher (PI) Wout BOERJAN
Host Institution (HI) VIB
Call Details Advanced Grant (AdG), LS9, ERC-2018-ADG
Summary Poplar is an important woody biomass crop and at the same time the model of choice for molecular research in trees. Although there is steady progress in resolving the functions of unknown genes, the identities of most secondary metabolites in poplar remain unknown. The lack of metabolite identities in experimental systems is a true gap in information content, and impedes obtaining deep insight into the complex biology of living systems. The main reason is that metabolites are difficult to purify because of their low abundance, hindering their structural characterization and the discovery of their biosynthetic pathways. In this project, we will use CSPP, an innovative method recently developed in my lab, to systematically predict the structures of metabolites along with their biosynthetic pathways in poplar wood, bark and leaves. This CSPP method is based on a combination of metabolomics and informatics. In a next step, the CSPP tool will be combined with two complementary genetic approaches based on re-sequence data from 750 poplar trees to identify the genes encoding the enzymes in the predicted pathways. Genome Wide Association Studies (GWAS) will be made to identify SNPs in the genes involved in the metabolic conversions. Subsequently, rare defective alleles will be identified for these genes in the sequenced population. Genes identified by both approaches will then be further studied either by crossing natural poplars that are heterozygous for the defective alleles, or by CRISPR/Cas9-based gene editing in poplar. The functional studies will be further underpinned by enzyme assays. Given our scarce knowledge on the structure of most secondary metabolites and their metabolic pathways in poplar, this large-scale identification effort will lay the foundation for systems biology research in this species, and will shape opportunities to further develop poplar as an industrial wood-producing crop.
Summary
Poplar is an important woody biomass crop and at the same time the model of choice for molecular research in trees. Although there is steady progress in resolving the functions of unknown genes, the identities of most secondary metabolites in poplar remain unknown. The lack of metabolite identities in experimental systems is a true gap in information content, and impedes obtaining deep insight into the complex biology of living systems. The main reason is that metabolites are difficult to purify because of their low abundance, hindering their structural characterization and the discovery of their biosynthetic pathways. In this project, we will use CSPP, an innovative method recently developed in my lab, to systematically predict the structures of metabolites along with their biosynthetic pathways in poplar wood, bark and leaves. This CSPP method is based on a combination of metabolomics and informatics. In a next step, the CSPP tool will be combined with two complementary genetic approaches based on re-sequence data from 750 poplar trees to identify the genes encoding the enzymes in the predicted pathways. Genome Wide Association Studies (GWAS) will be made to identify SNPs in the genes involved in the metabolic conversions. Subsequently, rare defective alleles will be identified for these genes in the sequenced population. Genes identified by both approaches will then be further studied either by crossing natural poplars that are heterozygous for the defective alleles, or by CRISPR/Cas9-based gene editing in poplar. The functional studies will be further underpinned by enzyme assays. Given our scarce knowledge on the structure of most secondary metabolites and their metabolic pathways in poplar, this large-scale identification effort will lay the foundation for systems biology research in this species, and will shape opportunities to further develop poplar as an industrial wood-producing crop.
Max ERC Funding
2 499 251 €
Duration
Start date: 2019-07-01, End date: 2024-06-30
Project acronym SCENT
Project SCENT: Hybrid Gels for Rapid Microbial Detection
Researcher (PI) Ana Roque
Host Institution (HI) NOVA ID FCT - ASSOCIACAO PARA A INOVACAO E DESENVOLVIMENTO DA FCT
Call Details Starting Grant (StG), LS9, ERC-2014-STG
Summary Antimicrobial resistant bacteria are a global threat spreading at an alarming pace. They cause over 25,000 annual deaths in the EU, and represent an economic burden exceeding €1.5 billion a year. Current methods for microbial detection in clinical settings take about 24-36 h, but for slow-growing bacteria, as those causing tuberculosis, it can take more than a week. Early-detection and confinement of the infected individuals are the only ways to provide adequate therapy and control infection spread. Thus, tools for rapid identification of bacterial infections are greatly needed.
The analysis of microbial volatile metabolites is an area of increasing interest in diagnostics. Recent works demonstrate that fast microbial identification is possible with chemical nose sensors. These sensors usually present limited stability and selectivity, and require aggressive conditions during processing and operation. Bioinspired nose sensors employing biological olfactory receptors are an alternative. Unfortunately, their complexity and low stability are a limitation. My group recently discovered a new class of stimulus-responsive gels which tackle these key challenges. Our gels are customisable and have a low environmental footprint associated. I intend to further explore their potential to advance the field of odour detection, while providing new tools for the scientific community. I will focus specifically in fast microbial detection. To accomplish this, I propose to 1) build libraries of hybrid gels with semi-selective and selective properties, 2) generate odorant specific peptides mimicking olfactory receptors, 3) fully characterise the gels, 4) assemble artificial noses for analysis of microbial volatiles, 5) create databases with organism-specific signal signatures, 6) identify pathogenic bacteria, including those with acquired antimicrobial-resistances. This project is a timely approach which will place Europe in the forefront of infectious disease control.
Summary
Antimicrobial resistant bacteria are a global threat spreading at an alarming pace. They cause over 25,000 annual deaths in the EU, and represent an economic burden exceeding €1.5 billion a year. Current methods for microbial detection in clinical settings take about 24-36 h, but for slow-growing bacteria, as those causing tuberculosis, it can take more than a week. Early-detection and confinement of the infected individuals are the only ways to provide adequate therapy and control infection spread. Thus, tools for rapid identification of bacterial infections are greatly needed.
The analysis of microbial volatile metabolites is an area of increasing interest in diagnostics. Recent works demonstrate that fast microbial identification is possible with chemical nose sensors. These sensors usually present limited stability and selectivity, and require aggressive conditions during processing and operation. Bioinspired nose sensors employing biological olfactory receptors are an alternative. Unfortunately, their complexity and low stability are a limitation. My group recently discovered a new class of stimulus-responsive gels which tackle these key challenges. Our gels are customisable and have a low environmental footprint associated. I intend to further explore their potential to advance the field of odour detection, while providing new tools for the scientific community. I will focus specifically in fast microbial detection. To accomplish this, I propose to 1) build libraries of hybrid gels with semi-selective and selective properties, 2) generate odorant specific peptides mimicking olfactory receptors, 3) fully characterise the gels, 4) assemble artificial noses for analysis of microbial volatiles, 5) create databases with organism-specific signal signatures, 6) identify pathogenic bacteria, including those with acquired antimicrobial-resistances. This project is a timely approach which will place Europe in the forefront of infectious disease control.
Max ERC Funding
1 500 000 €
Duration
Start date: 2015-12-01, End date: 2020-11-30
Project acronym SOLENALGAE
Project IMPROVING PHOTOSYNTHETIC SOLAR ENERGY CONVERSION IN MICROALGAL CULTURES FOR THE PRODUCTION OF BIOFUELS AND HIGH VALUE PRODUCTS
Researcher (PI) Matteo Ballottari
Host Institution (HI) UNIVERSITA DEGLI STUDI DI VERONA
Call Details Starting Grant (StG), LS9, ERC-2015-STG
Summary Solar Energy is the most abundant renewable energy source available for our Planet. Light energy conversion into chemical energy by photosynthetic organisms is indeed the main conversion energy step, which originated high energy containing fossil deposits, now being depleted. By the way, plant or algae biomass may still be used to produce biofuels, as bio-ethanol, bio-diesel and bio-hydrogen. Microalgae exploitation for biofuels production have the considerable advantages of being sustainable and not in competition with food production, since not-arable lands, waste water and industrial gasses can be used for algae cultivation. Considering that only 45% of the sunlight covers the range of wavelengths that can be absorbed and used for photosynthesis, the maximum photosynthetic efficiency achievable in microalgae is 10%. On these bases, a photobioreactor carrying 600 l/m-2 would produce 294 Tons/ha/year of biomass of which 30% to 80%, depending on strain and growth conditions, being oil. However this potential has not been exploited yet, since biomass and biofuels yield on industrial scale obtained up to now were relatively low and with high costs of production. The main limitation encountered for sustained biomass production in microalgae by sunlight conversion is low light use efficiency, reduced from the theoretical value of 10% to 1-3%. This low light use efficiency is mainly due to a combined effect of reduced light penetration to deeper layers in highly pigmented cultures, where light available is almost completely absorbed by the outer layers, and an extremely high (up to 80%) thermal dissipation of the light absorbed. This project aims to investigate the molecular basis for efficient light energy conversion into chemical energy, in order to significantly increase the biomass production in microalgae combining a solid investigation of the principles of light energy conversion with biotechnological engineering of algal strains.
Summary
Solar Energy is the most abundant renewable energy source available for our Planet. Light energy conversion into chemical energy by photosynthetic organisms is indeed the main conversion energy step, which originated high energy containing fossil deposits, now being depleted. By the way, plant or algae biomass may still be used to produce biofuels, as bio-ethanol, bio-diesel and bio-hydrogen. Microalgae exploitation for biofuels production have the considerable advantages of being sustainable and not in competition with food production, since not-arable lands, waste water and industrial gasses can be used for algae cultivation. Considering that only 45% of the sunlight covers the range of wavelengths that can be absorbed and used for photosynthesis, the maximum photosynthetic efficiency achievable in microalgae is 10%. On these bases, a photobioreactor carrying 600 l/m-2 would produce 294 Tons/ha/year of biomass of which 30% to 80%, depending on strain and growth conditions, being oil. However this potential has not been exploited yet, since biomass and biofuels yield on industrial scale obtained up to now were relatively low and with high costs of production. The main limitation encountered for sustained biomass production in microalgae by sunlight conversion is low light use efficiency, reduced from the theoretical value of 10% to 1-3%. This low light use efficiency is mainly due to a combined effect of reduced light penetration to deeper layers in highly pigmented cultures, where light available is almost completely absorbed by the outer layers, and an extremely high (up to 80%) thermal dissipation of the light absorbed. This project aims to investigate the molecular basis for efficient light energy conversion into chemical energy, in order to significantly increase the biomass production in microalgae combining a solid investigation of the principles of light energy conversion with biotechnological engineering of algal strains.
Max ERC Funding
1 441 875 €
Duration
Start date: 2016-03-01, End date: 2021-02-28
Project acronym SYMBIOVEC
Project Yeast symbionts of malaria vectors: from basic research to the management of malaria control
Researcher (PI) Irene Ricci
Host Institution (HI) UNIVERSITA DEGLI STUDI DI CAMERINO
Call Details Starting Grant (StG), LS9, ERC-2011-StG_20101109
Summary Advances in biotechnology propose innovative tools particularly relevant for public health application by genetic manipulation of microbial symbionts of arthropod vectoring disease. The symbiont engineering prevents the transmission of pathogens to human by interfering with their stage within the arthropod, thorough the expression of anti-pathogen effector molecules. This approach, defined paratransgenesis is simpler than the proposed engineering of the vector itself (transgenesis) and implies minor applicative and ethical concerns. Identification of good candidate for paratransgenesis has opened the way towards the investigation of microbes residing in the arthropod body, particularly those localised within the gut that often represents the locale in which pathogens transit or develop. Good paratransgenic candidates were already identified in the bug vectoring Chagas disease in South America and in the tse-tse fly vectoring sleeping sickness in Africa. As regard mosquitoes, responsible of tens of human infections including malaria, some interesting bacteria have been recognized as candidates for genetic manipulation, even if the ability of recombinant strains to cure mosquito has not been demonstrated yet in the field. Bacteria can be easily isolated, modified and reintroduced in the mosquito but secretion of antagonists by prokaryotic cell can represent a matter difficult to resolve. In this context endosymbiotic yeasts seem to be very appealing. Their genetic and cellular complexity makes yeasts as ideal tools for manipulation and bypasses many difficulties relative to the recombinant products releasing. On these bases, I have recently begun a study on the yeast microflora in mosquito. Particularly, I investigated the relationship between the yeast endosymbiont Pichia anomala and malaria vectors. Considering the special features of this yeast, I propose its use as paratransgenic tool for malaria control.
Summary
Advances in biotechnology propose innovative tools particularly relevant for public health application by genetic manipulation of microbial symbionts of arthropod vectoring disease. The symbiont engineering prevents the transmission of pathogens to human by interfering with their stage within the arthropod, thorough the expression of anti-pathogen effector molecules. This approach, defined paratransgenesis is simpler than the proposed engineering of the vector itself (transgenesis) and implies minor applicative and ethical concerns. Identification of good candidate for paratransgenesis has opened the way towards the investigation of microbes residing in the arthropod body, particularly those localised within the gut that often represents the locale in which pathogens transit or develop. Good paratransgenic candidates were already identified in the bug vectoring Chagas disease in South America and in the tse-tse fly vectoring sleeping sickness in Africa. As regard mosquitoes, responsible of tens of human infections including malaria, some interesting bacteria have been recognized as candidates for genetic manipulation, even if the ability of recombinant strains to cure mosquito has not been demonstrated yet in the field. Bacteria can be easily isolated, modified and reintroduced in the mosquito but secretion of antagonists by prokaryotic cell can represent a matter difficult to resolve. In this context endosymbiotic yeasts seem to be very appealing. Their genetic and cellular complexity makes yeasts as ideal tools for manipulation and bypasses many difficulties relative to the recombinant products releasing. On these bases, I have recently begun a study on the yeast microflora in mosquito. Particularly, I investigated the relationship between the yeast endosymbiont Pichia anomala and malaria vectors. Considering the special features of this yeast, I propose its use as paratransgenic tool for malaria control.
Max ERC Funding
1 500 000 €
Duration
Start date: 2012-06-01, End date: 2017-05-31
