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Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2013.3.1-01 | Award Amount: 9.55M | Year: 2013

Plants synthesize a staggering variety of secondary metabolites, and this chemodiversity is a poorly used pool of natural molecules with bioactive properties of importance for applications in the pharma and food industries. BacHBerry focusses on phenolic compounds, a large and diverse class of plant metabolites, which are currently in the spotlight due to their claimed beneficial effects in prevention and treatment of chronic diseases, but that also have applications as cosmetics, flavours and food colorants etc. Berries are soft and colourful fruits, with great diversity, high content and unique profiles in phenolic compounds, making them a major source of these high-value metabolites. The BacHBerry project aims to develop a portfolio of sustainable methodologies to mine the potential of the untapped biodiversity of the bioactive phenolic compounds in an extensive collection of berry species. Full exploitation of this unrivalled natural resource requires an integrated and comprehensive effort from bioprospecting in berries using SMART high-throughput screens for the valorisation of phenolic bioactivities aligned with their identification using cutting edge analytics and subsequent elucidation of their biosynthetic pathways. This knowledge will facilitate metabolic engineering of suitable bacterial hosts for high-value phenolics production in scalable fermentation bioprocesses, ultimately serving as commercial production platforms. The consortium comprises a full chain of research and innovation, with 12 research groups, 5 SMEs and a large enterprise, representing 10 countries including partners from ICPC countries Russia, Chile and China, with the capacity to exploit novel bioactivities from berry fruits diversity. BacHBerry develops a pipeline of sustainable and cost-effective processes to facilitate production of added-value berry phenolics with immediate potential for commercialization and consequent socio-economic benefits for the European community and beyond.

Acevedo-Rocha C.G.,Max-Planck-Institut für Kohlenforschung | Acevedo-Rocha C.G.,University of Marburg | Fang G.,Yale University | Schmidt M.,International Dialogue and Conflict Management | And 4 more authors.
Trends in Genetics | Year: 2013

A central undertaking in synthetic biology (SB) is the quest for the 'minimal genome'. However, 'minimal sets' of essential genes are strongly context-dependent and, in all prokaryotic genomes sequenced to date, not a single protein-coding gene is entirely conserved. Furthermore, a lack of consensus in the field as to what attributes make a gene truly essential adds another aspect of variation. Thus, a universal minimal genome remains elusive. Here, as an alternative to defining a minimal genome, we propose that the concept of gene persistence can be used to classify genes needed for robust long-term survival. Persistent genes, although not ubiquitous, are conserved in a majority of genomes, tend to be expressed at high levels, and are frequently located on the leading DNA strand. These criteria impose constraints on genome organization, and these are important considerations for engineering cells and for creating cellular life-like forms in SB. © 2012 Elsevier Ltd.

Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2013.3.6-02 | Award Amount: 7.17M | Year: 2013

Peptides are among the most versatile natural products that nature provides to cater for a broad set of biotechnological applications ranging from antibiotics to personal hygiene. Their diversity comes from a broad variety of posttranslational modifications that is used to provide additional functionality beyond to what is possible with the classic proteinogenic set of 20 amino acids. In SYNPEPTIDE, we want to recruit such additional functionality for rational molecular design purposes in order to facilitate the design and the production of synthetic peptides. To this end, we intend to standardize the integration of chemical diversity in peptide design and production by the following activities: [i] translational integration of chemically suitable non-canonical amino acids for posttranslational in vivo and in vitro modification; [ii] systematic recruitment of selected highly relevant posttranslational modifications from natural peptide synthesis routes into the design process. These activities will ultimately allow to drastically expand our arsenal of functionalities in the design of novel molecules and our capacity to reliably produce them.

Agency: European Commission | Branch: H2020 | Program: RIA | Phase: BIOTEC-1-2014 | Award Amount: 8.06M | Year: 2015

Mycoplasmas are the smallest cell wall less, free-living microorganisms. The lack of a cell wall makes them resistant to many of the common antibiotics. Every year, infections caused by Mycoplasmas in poultry, cows, and pigs, result in multimillion euros losses in USA and Europe. Currently, there are vaccines against M hyopneumoniae in pigs and M gallisepticum and M synoviae in poultry. However, there is no vaccination against many Mycoplasma species infecting pets, humans and farm animals (ie M bovis cow infection). Mycoplasma species in many cases are difficult to grown in axenic culture and those that grow need a complex media with animal serum. In large scale production of Mycoplasma species for vaccination aside from the high cost of animal serum, more important is the high irreproducibility in the production process and the possible contamination with animal viruses. All this together highlights what European industry needs:i) a defined cheap reproducible medium that is animal serum free and ii) an universal Mycoplasma chassis that could be used in a pipeline to vaccinate against Mycoplasma species, as well as any pathogen. M pneumoniae is an ideal starting point for designing such a vaccine chassis. It has a small genome (860 kb) and it is probably the organism with the most comprehensive systems biology data acquired so far. By genome comparison, metabolic modeling and rationally engineering its genome, we will create a vaccine chassis that will be introduced into an industrial pipeline. The process will be guided by the second world largest industry on animal vaccination (MSD), as well as a SME specialized on peptide display and screening. This will ensure the exploitation and commercialization of our work contributing to maintain Europe privileged position in this field. Our ultimate goal is to meet the needs of the livestock industry,taking care of ethical issues, foreseeable risks, and prepare effective dissemination and training material for the public.

Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: SiS.2012.1.2-1 | Award Amount: 4.59M | Year: 2013

Synthetic biology (SynBio) offers huge potential for applications in energy, health and the environment. It also brings with it various challenges such as regulatory issues of biosafety, biosecurity and intellectual property rights, as well as potential environmental and socio-economic risks in developing countries. As yet, however, there is scant public knowledge about the technology. It is thus essential to establish an open dialogue between stakeholders concerning SynBios potential benefits and risks and to explore possibilities for its collaborative shaping on the basis of public participation. SYN-ENERGY will organise a wide range of mobilisation and mutual learning processes relating to these challenges. Besides a number of well-established European and international networks, the consortium encompasses and can mobilise a wide variety of stakeholders from science, industry, civil society, policy, education, art and other areas. Learning processes will contribute to a better understanding of SynBio research and innovation and to enhanced public engagement, while at the same time stimulating reflection on novel approaches to an inclusive governance framework that is capable of fostering responsible research and innovation. The processes will involve citizens and specific publics through well-established and innovative means of engagement, and will support the convergence of stakeholders and perspectives. Activities will be structured by four platforms, highlighting SynBios future, public, cultural and research & innovation perspectives. The iterative mutual learning process within SYN-ENERGY will be open to change in order to accommodate the dynamics of an emergent field. By dint of its approach, design and consortium, SYN-ENERGY will be a Science in Society activity with significant impact, raising public awareness of SynBio and yielding benefits for involved stakeholders, public discourse and European policy making in an international context.

Schmidt M.,Biofaction KG | de Lorenzo V.,CSIC - National Center for Biotechnology
Current Opinion in Biotechnology | Year: 2016

Synthetic Biology (SynBio) has brought up again questions on the environmental fate of microorganisms carrying genetic modifications. The growing capacity of editing genomes for deployment of man-made programs opens unprecedented biotechnological opportunities. But the same exacerbate concerns regarding fortuitous or deliberate releases to the natural medium. Most approaches to tackle these worries involve endowing SynBio agents with containment devices for halting horizontal gene transfer and survival of the live agents only at given times and places. Genetic circuits and trophic restraint schemes have been proposed to this end in the pursuit of complete containment. The most promising include adoption of alternative genetic codes and/or dependency on xenobiotic amino acids and nucleotides. But the field has to still overcome serious bottlenecks. © 2016 Elsevier Ltd.

Schmidt M.,Biofaction KG | De Lorenzo V.,CSIC - National Center for Biotechnology
FEBS Letters | Year: 2012

The plausible release of deeply engineered or even entirely synthetic/artificial microorganisms raises the issue of their intentional (e.g. bioremediation) or accidental interaction with the Environment. Containment systems designed in the 1980s-1990s for limiting the spread of genetically engineered bacteria and their recombinant traits are still applicable to contemporary Synthetic Biology constructs. Yet, the ease of DNA synthesis and the uncertainty on how non-natural properties and strains could interplay with the existing biological word poses yet again the challenge of designing safe and efficacious firewalls to curtail possible interactions. Such barriers may include xeno-nucleic acids (XNAs) instead of DNA as information-bearing molecules, rewriting the genetic code to make it non-understandable by the existing gene expression machineries, and/or making growth dependent on xenobiotic chemicals. © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: KBBE.2011.3.6-03 | Award Amount: 7.77M | Year: 2011

The ST-FLOW Project merges the efforts of 14 leading European research groups for developing material and computational standards that enable the forward-design of prokaryotic systems with a degree of robustness and predictability that is not possible with customary Genetic Engineering. The central issue at stake is the identification and implementation of rules that allow the conversion of given biological parts assembled with a set of principles for physical composition into perfectly predictable functional properties of the resulting devices, modules and entire systems. ST-FLOW focuses on each of the steps that go from assembling a DNA sequence encoding all necessary expression signals in a prokaryotic host (by default, E. coli) all the way to the making of the final product or to the behaviour of single cells and populations. Two complementary approaches will be adopted to solve the conundrum of physical composition vs. biological functionality of thereby engineered devices. In one case (bottom up), large combinatorial libraries of gene expression signals will be merged with suitable reporter systems and the input/output functions examined and parameterized in a high-throughput fashion. The expected outcome of this effort is to establish experience-based but still reliable rules and criteria for the assembly of new devices and systems -following the same physical composition rules or adopting CAD design. Yet, many outliers (combinations that do not follow the rules) are expected, and making sense of them will be the task of the complementary top-down approach. In this case, ST-FLOW will revisit some of gaps in our knowledge of the gene expression flow (transcription, mRNA fate, translation) that need to be addressed for engineering functional devices from first principles. Ethical, legal and societal issues will also be examined in a context of public dialogue and sound science communication.

Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: KBBE.2011.3.6-04 | Award Amount: 3.89M | Year: 2011

The concept of METACODE is to preform genetic code engineering in microbial strains with parallel recruitment of novel bio-orthogonal chemistries for mass production of desired protein/peptide based products. In combination with computational and classical chemical synthetic approaches as well as chemo-informatics, enzyme guided evolution, synthetic metabolism, and directed evolution of microbial strains, artificial industrial microbial strains will be designed. This will enable the access to genetically robust and safe strains with added/novel functionalities and topologies from renewable resources. These strains will be characterized with alternative reading of the genetic code (genetic firewall) and with predetermined chemistries (metathesis), as well as necessary robustness for efficient industrial use.

Seyfried G.,University of Applied Arts Vienna | Pei L.,Biofaction KG | Schmidt M.,Biofaction KG
BioEssays | Year: 2014

The encounter of amateur science with synthetic biology has led to the formation of several amateur/do-it-yourself biology (DIYBio) groups worldwide. Although media outlets covered DIYBio events, most seemed only to highlight the hope, hype, and horror of what DIYBio would do in the future. Here, we analyze the European amateur biology movement to find out who they are, what they aim for and how they differ from US groups. We found that all groups are driven by a core leadership of (semi-)professional people who struggle with finding lab space and equipment. Regulations on genetic modification limit what groups can do. Differences between Europe and the US are found in the distinct regulatory environments and the European emphasis on bio-art. We conclude that DIYBio Europe has so far been a responsible and transparent citizen science movement with a solid user base that will continue to grow irrespective of media attention. Here, we analyzed the European do-it-yourself biology (DIYBio) community consisting of enthusiastic biotechnologists, artists, and designers. We conclude that DIYBio Europe has so far been a responsible and transparent citizen science movement with a solid user base that will continue to grow irrespective of media attention. © 2014 The Authors. Bioessays published by WILEY Periodicals, Inc.

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