Bremen, Germany
Bremen, Germany

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Grant
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2012.2.5-01 | Award Amount: 11.91M | Year: 2013

The AQUAVALENS consortium has brought together SMEs, Industries, Universities and Research Institutes with the mission of protecting the health of European Citizens from contaminated drinking water and water used in food processing. We will achieve this by developing sustainable technologies to enable water system managers whether in large or small water systems or within food growers or manufacturers to better control the safety of their water supplies. The work of the project is divided into four main clusters of work packages that sequentially lead to the development of appropriate technologies. These four clusters are: 1. Platform targets, 2. Platform development, 3. Field studies in European drinking water systems, and 4. Improving Public Health through safer water. In cluster 1 we shall generate new knowledge on the molecular genetics of viral, bacterial and parasitic waterborne pathogens. This will enable us to identify gene targets for the identification, and characterisation of these pathogens, that will also enable the determination of their virulence for humans. In cluster 2 we shall use the knowledge gained to develop new technologies that integrate sample preparation and detection into a single platform. These platforms will then be subject to a rigorous process of validation and standardisation. In cluster 3 we will use the validated platforms to undertake a series of field studies in large and small drinking water systems, and in food production. These field studies will generate new knowledge about the risk to public health from waterborne pathogens in Europe and also test the value of the technologies in the field. Finally in cluster 4 we test how these technologies can be used to protect human health, though improving the effectiveness of Water Safety Plans, adaptation to climate change, and control of outbreaks of infectious disease. We will also determine the sustainability and potential economic impacts of these technologies.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2012.3.2-02 | Award Amount: 11.97M | Year: 2012

Marine microorganisms form an almost untapped resource of biotechnological potential. However, its use is hindered by the low success rate of isolation of novel microorganisms and often by poor growth efficiency. Hence, the vast majority of marine microorganisms has not been cultivated and is often considered as unculturable. MaCuMBA aims at improving the isolation rate and growth efficiency of marine microorganisms from conventional and extreme habitats, by applying innovative methods, and the use of automated high throughput procedures. The approaches include the co-cultivation of interdependent microorganisms, as well as gradient cultures and other methods mimicking the natural environment, and the exploitation of cell-to-cell communication. Signaling molecules produced by microorganisms may be necessary for stimulating growth of the same or other species, or may prevent their growth. Signaling molecules also represent an interesting and marketable product. MaCuMBA will make use of high throughput platforms such Cocagne, using gel micro-droplet technology, or MicroDish in which many thousands of cultures are grown simultaneously. Various single-cell isolation methods, such as optical tweezers, will aid the isolation of specific target cells. Isolated microorganisms as well as their genomes will be screened for a wide range of bioactive products and other properties of biotechnological interest, such as genetic transformability. Growth efficiency and expression of silent genes of selected strains will be increased also by using the clues obtained from genomic information. MaCuMBA is targeted to SMEs and industry and they make a significant part of the consortium, ensuring that the project focuses on the interests of these partners. Moreover, MaCuMBA has adopted a comprehensive and professional exploitation, dissemination, implementation, and education strategy, ensuring that MaCuMBAs results and products will be directed to end-users and stakeholders.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: BG-08-2014 | Award Amount: 20.65M | Year: 2015

The overarching objective of AtlantOS is to achieve a transition from a loosely-coordinated set of existing ocean observing activities to a sustainable, efficient, and fit-for-purpose Integrated Atlantic Ocean Observing System (IAOOS), by defining requirements and systems design, improving the readiness of observing networks and data systems, and engaging stakeholders around the Atlantic; and leaving a legacy and strengthened contribution to the Global Ocean Observing System (GOOS) and the Global Earth Observation System of Systems (GEOSS). AtlantOS will fill existing in-situ observing system gaps and will ensure that data are readily accessible and useable. AtlantOS will demonstrate the utility of integrating in-situ and Earth observing satellite based observations towards informing a wide range of sectors using the Copernicus Marine Monitoring Services and the European Marine Observation and Data Network and connect them with similar activities around the Atlantic. AtlantOS will support activities to share, integrate and standardize in-situ observations, reduce the cost by network optimization and deployment of new technologies, and increase the competitiveness of European industries, and particularly of the small and medium enterprises of the marine sector. AtlantOS will promote innovation, documentation and exploitation of innovative observing systems. All AtlantOS work packages will strengthen the trans-Atlantic collaboration, through close interaction with partner institutions from Canada, United States, and the South Atlantic region. AtlantOS will develop a results-oriented dialogue with key stakeholders communities to enable a meaningful exchange between the products and services that IAOOS can deliver and the demands and needs of the stakeholder communities. Finally, AtlantOS will establish a structured dialogue with funding bodies, including the European Commission, USA, Canada and other countries to ensure sustainability and adequate growth of IAOOS.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: OCEAN.2011-2 | Award Amount: 11.51M | Year: 2012

Micro B3 will develop innovative bioinformatic approaches and a legal framework to make large-scale data on marine viral, bacteria; archaeal and protists genomes and metagenomes accessible for marine ecosystems biology and to define new targets for biotechnological applications. Micro B3 will build upon a highly interdisciplinary consortium of 32 academic and industrial partners comprising world-leading experts in bioinformatics, computer science, biology, ecology, oceanography, bioprospecting and biotechnology, as well as legal aspects. Micro B3 is based on a strong user- and data basis from ongoing European sampling campaigns to long-term ecological research sites. For the first time a strong link between oceanographic and molecular microbial research will be established to integrate global marine data with research on microbial biodiversity and functions. The Micro B3 Information System will provide innovative open source software for data-processing, -integration, -visualisation, and -accessibility. Interoperability will be the key for seamless data transfer of sequence and contextual data to public repositories. Micro B3 will allow taking full advantage of current sequencing technologies to efficiently exploit large-scale sequence data in an environmental context. Micro B3 will create integrated knowledge to inform marine ecosystems biology and modelling. Moreover, it will facilitate detecting candidate genes to be explored by targeted laboratory experiments for biotechnology and for assigning potential functions to unknown genes. Micro B3 will develop clear IP agreements for the protection and sustainable use of pre-competitive microbial genetic resources and their exploitation in high potential commercial applications. To underline the translational character of Micro B3, outreach and training activities for diverse stakeholders are planned as well as an Ocean Sampling Day to transparently make project results accessible and gain valuable user feedback.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2010-ITN | Award Amount: 3.78M | Year: 2011

Symbiosis research is currently in the midst of a revolution as molecular techniques are leading to major breakthroughs in our understanding of interactions between animals and microbes. There is an emerging recognition that all animals are intimately associated with a complex community of beneficial microbes that are essential for their development, nutrition, and health. Thus, modern symbiosis research has become a newly emerging supra-disciplinary field with novel and innovative methods for examining microbial symbionts, the vast majority of which remain as yet uncultivable. As so often when novel technologies open up new areas of research, training for students lags behind. We propose to close this gap by offering a comprehensive and innovative training in the microbial ecology and evolution of animal symbionts. The proposed ITN Symbiomics will include 14 leading research groups as well as 4 top-tier participants from the private sector to provide 14 early stage researchers (ESRs) and 1 experienced research (ER) with an interdisciplinary and synergistic training. Cutting edge methods in molecular biology and image analysis will be used to analyze a broad range of hosts from protozoan and invertebrate animal groups. Symbiomics will provide training through a combination of local and network-wide activities that will include research, secondments, workshops and courses including soft skills training, networking and meetings, regular thesis committee meetings, and mentoring. By pooling the scientific, technological, and entrepreneurial expertise of the Symbiomics partners, this ITN will provide a synergistic research environment and training that extends far beyond what each partner would be able to offer with local training alone. At the end of their training, the early stage researchers will have the skills they need for successful careers in academia and industry in a broad range of disciplines in the fields of environmental, applied, and medical microbiology.


Klindworth A.,Max Planck Institute for Marine Microbiology | Klindworth A.,Jacobs University Bremen | Pruesse E.,Max Planck Institute for Marine Microbiology | Pruesse E.,Jacobs University Bremen | And 6 more authors.
Nucleic Acids Research | Year: 2013

16S ribosomal RNA gene (rDNA) amplicon analysis remains the standard approach for the cultivation-independent investigation of microbial diversity. The accuracy of these analyses depends strongly on the choice of primers. The overall coverage and phylum spectrum of 175 primers and 512 primer pairs were evaluated in silico with respect to the SILVA 16S/18S rDNA non-redundant reference dataset (SSURef 108 NR). Based on this evaluation a selection of 'best available' primer pairs for Bacteria and Archaea for three amplicon size classes (100-400, 400-1000, ≥1000 bp) is provided. The most promising bacterial primer pair (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21), with an amplicon size of 464 bp, was experimentally evaluated by comparing the taxonomic distribution of the 16S rDNA amplicons with 16S rDNA fragments from directly sequenced metagenomes. The results of this study may be used as a guideline for selecting primer pairs with the best overall coverage and phylum spectrum for specific applications, therefore reducing the bias in PCR-based microbial diversity studies. © 2012 The Author(s). Published by Oxford University Press.

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