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Microbial Communities in Biomedical and Environmental Areas, and Systems Biology

Periodic Reporting for period 1 - MiCoBion (Microbial Communities in Biomedical and Environmental Areas, and Systems Biology)

Reporting period: 2018-09-01 to 2019-11-30

"The main goal of MiCoBion is to strengthen scientific excellence and innovation capacity at Charles University and its Biotechnology and Biomedicine Center (CUNI-BIOCEV) via collaboration with Catholic University of Leuven (KUL), European Molecular Biology Laboratory (EMBL), and University Paris Diderot-Institute Jacques Monod (UPDiderot-IJM) in the field of high throughput molecular profiling of biological systems that will foster innovative research of complex microbial communities and their impact on health and environment. This research area includes the analysis of viromes, eukaryotic and bacterial microbiomes, and selected defined model microbial communities to tackle challenges such as discovery of new pathogens (viruses), identification of new biomarkers for disease, drug targets and their applications. The research of complex microbial communities is based on three pillars: excellent knowledge in microbiology, high throughput technologies that generate voluminous datasets, and computation of these ""big data"". Strength of CUNI is an excellent knowledge of microbial systems important for human and animal health, and environmental issues. Weakness is the research capacity in analysis of ""big data"", limited experience in innovative research and technology transfer. Thus, twinning activities will be focused on promotion of knowledge and research capacity of a multidisciplinary team at CUNI in the defined area of bioinformatics, implementing cutting edge multiomics technologies, and establishing a pipeline from an excellent basic research to high value-added applications. Activities include exchange of scientists, joint supervision of young scientist, organization of seminars and lectures, participation in EMBL and CUNI courses, and dissemination in scientific community, industries and public. The project aim will be achieved via a complementary expertise of EU leading partners, which will reinforce an excellent research and competitiveness of CUNI."
Since the beginning of the project the three main pillars of the project, are being covered by working in training, knowledge transfer, professional growth, workshops and conferences organization.The work performed by CUNI, EMBL, UPD-IJM and KUL has involved organizing scientific courses, workshops, conferences and visits. The scientific courses have been focused in technical and specialized content in high-throughput technology applications (Methods of Functional Genomics, Computational Genomics, metagenomics and OMICs data integration) for microbiota analysis and systems biology. In addition, joint supervision of 7 PhD students and young researchers at CUNI or participant institutions has started. Overall, the activities organized have provided an enrichment of knowledge and skills that are applicable to the participants own research projects.
Moreover, the short and mid-stays of young and senior researchers have already initiated, which have resulted in relevant research discoveries and evidence to their own research topics.
Through visits of experts, speakers and members of the PhD committee the objectives of the professional growth of scientists are being covered. In addition, media training for scientists resulted in positive feedback of the participants, who they consider relevant to their own careers as an important measure to develop “soft skills”.
The workshops (Single DNA molecule sequencing and proteomics) were organized for training in top-notch technologies, intellectual research approaches, networking among experts and strategies in innovative research and technology transfer. These workshops will have an important impact in the following conferences organized in the frame of MiCoBion project.
One of the main vision of the proposal and its overall impact is in the fostering excellence of research and innovation at CUNI in the field of microbial communities and systems microbiology, which will be translated into applications such as such as discovery of new pathogens (viruses), identification of new biomarkers for diseases, factors for immunity modulation, candidates for vaccines, and new drug targets. So far the following impacts are in progress;
• Scientific impact. The twinning activities and increased cooperation between the partners are rising chances for research funding at national as well as international level, presentation in international conferences, 5 so far, and production of high impact factor publications (4 so far+1 book). In the long-term, collaboration between the partners will be maintained thanks to joint research projects funded from national and international sources, applications from which five national applications have been granted.
• Industrial impact. MiCoBion focuses in strengthen the translation of research into practice. Therefore, MiCoBion will facilitate the knowledge transfer in how to set up a collaboration between university and industry, how to proceed with invention, how to start spin-off company etc. (An agreement has been signed about a scientific collaboration with Smart Brain s.r.o. An Agreement with Biopharm is in preparation). The synergies between the academic and private sector (STAR region) work in both directions as experts from private companies have met during events organized with STAR region. After the end of the project, CUNI will ensure an ongoing involvement of the industrial partners in its events.
• Educational impact. Inside CUNI, the knowledge transfer is applied in enriching the curriculum. Mobility programs for students and scientists are supported between the partner institutions. Additionally, educational activities for general public are planned, from which already several took place, for example an exhibition during the anniversary of the CUNI-Faculty of Science and a trade fair.
• Technological impact. The technological impact is already visible thanks to the complementarity of the partners. CUNI is already able to better utilize its existing equipment for excellent-level type of research after enhancing the specialized methods for proteomic and genomic analysis (single molecule DNA/RNA sequencing using Oxford MinIon nanotechnology, detection of protein modification by mass spectrometry, softwares for big data analysis).
• Social impact. Thanks to MiCoBion communication and dissemination strategies, the impact at regional, national as well as European levels is progressing in order to create new jobs, particularly for specialists in bioinformatics, increasing international visibility of Vestec and the STAR Region, a motivation for high school students to choose scientific careers.
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