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Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE.2010.3.3-02 | Award Amount: 10.64M | Year: 2011

BIONEXGEN will develop the next generation of biocatalysts to be used for eco-efficient manufacturing processes in the chemical industry. A collaboration by industrial and academic partners have identified the key technology fields of amine synthesis, polymers from renewable resources, glycoscience and wider oxidase application as four key areas where the next generation of biocatalysts that will lead to improvements in both economic and environmental performance of the chemical manufacturing industries. This project will enable industry to use renewable resources with reduced greenhouse gas production as compared to their fossil counterparts and deliver biotechnological routes with reduced energy consumption and less toxic wastes compared to conventional chemical processes. Routes to specialised, high-value chemicals (e.g. chiral chemical compounds) normally require long chemical synthetic routes involving complex reaction steps with toxic side products and waste streams and this project will allow these methods to be replaced by clean biocatalysis routes. To broaden the range of fine and speciality chemicals and intermediates produced by biotechnological routes, research will address: (i) design and optimisation of enzymes to be used in synthetic chemistry, (ii) the selection/development of modified microorganisms which are resistant to heat, pressure or low pH when used in the production of chemical entities and allow (iii) the integration of biotechnological steps into conventional chemical processes. The project will develop and integrate with chemical steps the biotechnological manufacturing routes for the synthesis of fine and speciality chemicals especially amines, oligosaccharides and renewable polymer intermediates which are better in terms of eco-efficiency, economic potential, complexity and /or specificity of the synthetic pathways than those currently employed. Dissemination strategy will enhance the impact of this work through three separate initiatives. Economic viability and eco-efficiency will be evaluated and assessed on a quantitative basis and these results will be published in the scientific literature. Green chemistry initiatives in the BIONEXGEN project and the FP7 contributions will be presented to the wider public on a project website and through material displays at the museum in Manchester and the Big Saturday event in Manchester Science Week. An overall end of project meeting in Brussels will invite a range of political decision makers and industry leaders to attend and will ensure maximum impact. The project was devised with a strong involvement of industrial partners, in particular SMEs and is strength of this project and will contribute significantly to ensure application of the technology. This combination of technical will lead to the development of new green chemical manufacturing technology platforms that will be tested for specific targets in the European chemical manufacturing industries and use these as case studies for dissemination on a broad front.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: EINFRA-1-2014 | Award Amount: 8.02M | Year: 2015

In the coming decade a significant number of the 500.000.000 European (EU/EEA) citizens will have their genome determined routinely. This will be complemented with much cheaper (currently ~20 Euro per measurement) acquisition of the metabolome of biofluids (e.g. urine, saliva, blood plasma) which will link the genotype with metabolome data that captures the highly dynamic phenome and exposome of patients. Having such low cost solutions will enable, for the first time, the development of a truly personalised and evidence-based medicine founded on hard scientific measurements. The exposome includes the metabolic information resulting from all the external influences on the human organism such as age, behavioural factors like exercise and nutrition or other environmental factors. Considering that the amount of data generated by molecular phenotyping exceeds the data volume of personal genomes by at least an order of magnitude, the collection of such information will pose dramatic demands on biomedical data management and compute capabilities in Europe. For example, a single typical National Phenome Centre, managing only around 100,000 human samples per year, can generate more than 2 Petabytes of data during this period alone. A scale-up to sizable portions of the European population over time will require data analysis services capable to work on exabyte-scale amounts of biomedical phenotyping data, for which no viable solution exists at the moment. The PhenoMeNal project will develop and deploy an integrated, secure, permanent, on-demand service-driven, privacy-compliant and sustainable e-infrastructure for the processing, analysis and information-mining of the massive amount of medical molecular phenotyping and genotyping data that will be generated by metabolomics applications now entering research and clinic.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: ENV.2013.6.2-2 | Award Amount: 16.30M | Year: 2013

SOLUTIONS will deliver a conceptual framework for the evidence-based development of environmental and water policies. This will integrate innovative chemical and effect-based monitoring tools with a full set of exposure, effect and risk models and assessment options. Uniquely, SOLUTIONS taps (i) expertise of leading European scientists of major FP6/FP7 projects on chemicals in the water cycle, (ii) access to the infrastructure necessary to investigate the large basins of Danube and Rhine as well as relevant Mediterranean basins as case studies, and (iii) innovative approaches for stakeholder dialogue and support. In particular, International River Commissions, EC working groups and water works associations will be directly supported with consistent guidance for the early detection, identification, prioritization, and abatement of chemicals in the water cycle. A user-friendly tool providing access to a set of predictive models will support stakeholders to improve management decisions, benefiting from the wealth of data generated from monitoring and chemical registration. SOLUTIONS will give a specific focus on concepts and tools for the impact and risk assessment of complex mixtures of emerging pollutants, their metabolites and transformation products. Analytical and effect-based screening tools will be applied together with ecological assessment tools for the identification of toxicants and their impacts. Beyond state-of-the-art monitoring and management tools will be elaborated allowing risk identification for aquatic ecosystems and human health. The SOLUTIONS approach will provide transparent and evidence-based lists of River Basin Specific Pollutants for the case study basins and support the review of the list of WFD priority pollutants.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA | Phase: INFRA-2012-3.3. | Award Amount: 2.65M | Year: 2012

Metabolomics is an important phenotyping technique for molecular biology and medicine. It assesses the molecular state of an organism or collections of organisms through the comprehensive quantitative and qualitative analysis of all small molecules in cells, tissues, and body fluids. Metabolic processes are at the core of physiology. Consequently, metabolomics is ideally suited as a medical tool to characterise disease states in organisms, as a tool to assessment of organism for their suitability in, for example, renewable energy production or for biotechnological applications in general.\nWe now see the emergence of metabolomics databases and repositories in various subareas of metabolomics and the emergence of large general e-infrastructures in the life sciences. In particular the BioMedBridges project is set to link a variety of European Strategy Forum on Research Infrastructures (ESFRI)s projects, such as ELIXIR and BBMRI.\nMetabolomics generates large and diverse sets of analytical data and therefore impose significant challenges for the above mentioned e-infrastructures.\nWe will therefore develop policies to ensure that Metabolomics data is\n\n1.\tEncoded in open standards to allow barrier-free and wide-spread analysis.\n2.\tTagged with a community-agreed, complete set of metadata (minimum information standard).\n3.\tSupported by a communally developed set of open source data management and capturing tools.\n4.\tDisseminated in open-access databases adhering to the above standards.\n5.\tSupported by vendors and publishers, who require deposition upon publication\n6.\tProperly interfaced with data in other biomedical and life-science e-infrastructures (such as ELIXIR, BioMedBridges, EU-Openscreen).\n\nIn order to achieve this, we have assembled the COSMOS (CCOordination of Standards in MetabOlomicS) consortium of leading European groups in Metabolomics and we will interface with all interested players in Metabolomics world-wide in the Metabolomics community and beyond.


Abel S.,Leibniz Institute of Plant Biochemistry
Cold Spring Harbor perspectives in biology | Year: 2010

The history of plant biology is inexorably intertwined with the conception and discovery of auxin, followed by the many decades of research to comprehend its action during growth and development. Growth responses to auxin are complex and require the coordination of auxin production, transport, and perception. In this overview of past auxin research, we limit our discourse to the mechanism of auxin action. We attempt to trace the almost epic voyage from the birth of the hormonal concept in plants to the recent crystallographic studies that resolved the TIR1-auxin receptor complex, the first structural model of a plant hormone receptor. The century-long endeavor is a beautiful illustration of the power of scientific reasoning and human intuition, but it also brings to light the fact that decisive progress is made when new technologies emerge and disciplines unite.


Tissier A.,Leibniz Institute of Plant Biochemistry
Plant Journal | Year: 2012

Glandular trichomes cover the surface of many plant species. They exhibit tremendous diversity, be it in their shape or the compounds they secrete. This diversity is expressed between species but also within species or even individual plants. The industrial uses of some trichome secretions and their potential as a defense barrier, for example against arthropod pests, has spurred research into the biosynthesis pathways that lead to these specialized metabolites. Because complete biosynthesis pathways take place in the secretory cells, the establishment of trichome-specific expressed sequence tag libraries has greatly accelerated their elucidation. Glandular trichomes also have an important metabolic capacity and may be considered as true cell factories. To fully exploit the potential of glandular trichomes as breeding or engineering objects, several research areas will have to be further investigated, such as development, patterning, metabolic fluxes and transcription regulation. The purpose of this review is to provide an update on the methods and technologies which have been used to investigate glandular trichomes and to propose new avenues of research to deepen our understanding of these specialized structures. © 2012 The Author. The Plant Journal © 2012 Blackwell Publishing Ltd.


Abel S.,Leibniz Institute of Plant Biochemistry
Current Opinion in Plant Biology | Year: 2011

Phosphate (Pi) and its anhydrides constitute major nodes in metabolism. Thus, plant performance depends directly on Pi nutrition. Inadequate Pi availability in the rhizosphere is a common challenge to plants, which activate metabolic and developmental responses to maximize Pi usage and acquisition. The sensory mechanisms that monitor environmental Pi and transmit the nutritional signal to adjust root development have increasingly come into focus. Recent transcriptomic analyses and genetic approaches have highlighted complex antagonistic interactions between external Pi and Fe bioavailability and have implicated the stem cell niche as a target of Pi sensing to regulate root meristem activity. © 2011 Elsevier Ltd.


Wasternack C.,Leibniz Institute of Plant Biochemistry | Hause B.,Leibniz Institute of Plant Biochemistry
Annals of Botany | Year: 2013

BackgroundJasmonates are important regulators in plant responses to biotic and abiotic stresses as well as in development. Synthesized from lipid-constituents, the initially formed jasmonic acid is converted to different metabolites including the conjugate with isoleucine. Important new components of jasmonate signalling including its receptor were identified, providing deeper insight into the role of jasmonate signalling pathways in stress responses and development.ScopeThe present review is an update of the review on jasmonates published in this journal in 2007. New data of the last five years are described with emphasis on metabolites of jasmonates, on jasmonate perception and signalling, on cross-talk to other plant hormones and on jasmonate signalling in response to herbivores and pathogens, in symbiotic interactions, in flower development, in root growth and in light perception. Conclusions The last few years have seen breakthroughs in the identification of JASMONATE ZIM DOMAIN (JAZ) proteins and their interactors such as transcription factors and co-repressors, and the crystallization of the jasmonate receptor as well as of the enzyme conjugating jasmonate to amino acids. Now, the complex nature of networks of jasmonate signalling in stress responses and development including hormone cross-talk can be addressed. © 2013 The Author. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.


Wasternack C.,Leibniz Institute of Plant Biochemistry
Biotechnology Advances | Year: 2014

Jasmonates (JAs) are lipid-derived compounds acting as key signaling compounds in plant stress responses and development. The JA co-receptor complex and several enzymes of JA biosynthesis have been crystallized, and various JA signal transduction pathways including cross-talk to most of the plant hormones have been intensively studied. Defense to herbivores and necrotrophic pathogens are mediated by JA. Other environmental cues mediated by JA are light, seasonal and circadian rhythms, cold stress, desiccation stress, salt stress and UV stress. During development growth inhibition of roots, shoots and leaves occur by JA, whereas seed germination and flower development are partially affected by its precursor 12-oxo-phytodienoic acid (OPDA). Based on these numerous JA mediated signal transduction pathways active in plant stress responses and development, there is an increasing interest in horticultural and biotechnological applications. Intercropping, the mixed growth of two or more crops, mycorrhization of plants, establishment of induced resistance, priming of plants for enhanced insect resistance as well as pre- and post-harvest application of JA are few examples. Additional sources for horticultural improvement, where JAs might be involved, are defense against nematodes, biocontrol by plant growth promoting rhizobacteria, altered composition of rhizosphere bacterial community, sustained balance between growth and defense, and improved plant immunity in intercropping systems. Finally, biotechnological application for JA-induced production of pharmaceuticals and application of JAs as anti-cancer agents were intensively studied. © 2013 Elsevier Inc.


Vogt T.,Leibniz Institute of Plant Biochemistry
Molecular Plant | Year: 2010

The general phenylpropanoid metabolism generates an enormous array of secondary metabolites based on the few intermediates of the shikimate pathway as the core unit. The resulting hydroxycinnamic acids and esters are amplified in several cascades by a combination of reductases, oxygenases, and transferases to result in an organ and developmentally specific pattern of metabolites, characteristic for each plant species. During the last decade, methodology driven targeted and non-targeted approaches in several plant species have enabled the identification of the participating enzymes of this complex biosynthetic machinery, and revealed numerous genes, enzymes, and metabolites essential for regulation and compartmentation. Considerable success in structural and computational biology, combined with the analytical sensitivity to detect even trace compounds and smallest changes in the metabolite, transcript, or enzyme pattern, has facilitated progress towards a comprehensive view of the plant response to its biotic and abiotic environment. Transgenic approaches have been used to reveal insights into an apparently redundant gene and enzyme pattern required for functional integrity and plasticity of the various phenylpropanoid biosynthetic pathways. Nevertheless, the function and impact of all members of a gene family remain to be completely established. This review aims to give an update on the various facets of the general phenylpropanoid pathway, which is not only restricted to common lignin or flavonoid biosynthesis, but feeds into a variety of other aromatic metabolites like coumarins, phenolic volatiles, or hydrolyzable tannins.

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