Network-wide training elements

Event TD MFB Host Main topics Complementary skills Partic.
Introductory week 4 Frankfurt Germany Introduction to the global topic of SPOT-ITN; presentation of group profiles, social activities Team building, Project management All
Excursion 4 GenXPro GmbH Germany The structure and aims of a small company ESR/ERs
Conference 10 Bet Dagan Isreal Project proposals Presentation skills All + 2 external researchers + mentors
Excursion 10 Gedira-Zerfim Isreal The structure and aims of a global company ESR/ERs
Workshop 16 Nijmegen Netherl. Genetic and molecular tools for the analysis of thermotolerance Time management, Database handling, Self reflection, good scientific conduct ESR/ERs + 15 international PhD students
Excursion 16 Nunhems Netherl. International collaboration between companies ESR/ERs
Conference 22 Wageningen Netherl. Mid-Term Review meeting project presentations, Interaction with media All + 2 external researchers+ mentors
Excursion 22 KeyGene Netherl. The requirements on applicants for industrial positions ESR/ERs
Workshop 28 Frankfurt Germany Physiological, biochemical and cell biological tools Scientific writing, Proposal writing ESR/ERs, + 15 international PhD students
Excursion 28 BASF Germany The possibilities of a plant scientists in a global company ESR/ERs
Conference 34 Naples Italy International conference Networking, Presentation skills All + 75 external researchers
Excursion 34 Metapontum Agrobios Italy Application training ESR/ERs
Workshop 40 Vienna Austria High throughput analysis and data-mining Entrepreneurship, Commercialising of scientific result, Management of research projects ESR/ERs
Final conference 46 Frankfurt Germany Internal closing meeting of all participants and all ESRs/ERs All + 15 international PhD students

TD: tentative dates; MFB: month from beginning

The topics of the three anticipated workshops are:

1) The first workshop will be dedicated to the genetic and molecular tools for plant analysis with focus on the analysis of thermotolerance. It will be organised in Nijmegen by Celestina Mariani in cooperation with Nurit Firon, Ivo Rieu and Wim Vriezen. The focus on the generic education will be placed on four important topics at this stage of the ESRs, time management, database structures and searches within the WWW, self reflection and self criticism as well as in good scientific conduct. The content of the workshop will be: a. Preparation of anthers, microspores and pollen samples from Solanaceae. Here, flowers of a collection of cultivated (tomato, egg plant) and wild Solanum species will be used to learn how anther and pollen development proceed in the various (related) species. b. Preparation of all samples for light and electron microscopy (cryo-SEM and TEM). Semi-thin and thin sections of anthers at various developmental stages (treated and not treated with HS) will be analyzed to learn the histology of the various cell types in the anther, with particular attention to tapetal cells and developing microspores/pollen. c. Preparation of mRNA from anther/pollen samples. Here, RNA will be prepared to investigate the profile of gene expression before and after HS treatment. RNA will be used for quantitative-PCR analysis and particular attention will be given to genes already known to participate in the HS-response. d. Heat stress treatments (and controls) will be performed on various tomato lines and several wild species to investigate if any of them has a better performance under HS. Pollination and pollen tube growth will be monitored by fluorescence microscopy to check pollen vitality of HS-treated samples.
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2) The second workshop will be dedicated to physiological, biochemical and cell biological tools for the analysis of thermotolerance. It will be organised in Frankfurt by Enrico Schleiff with Klaus-Dieter Scharf, Arnaud G. Bovy and Rina Iannacone. The focus on the generic education will be placed on the topic of scientific writing and proposal preparation, which becomes important at this stage. The content of the workshop will be: a. Isolation and use of protoplasts for in vivo analysis of thermotolerance in isolated plant cells. Here, protoplasts from mesophyll cells will be used as model system to study the interaction of factors involved in exhibiting thermotolerance. This assay is powerful to study protein-protein interactions, protein and RNA stabilization and HS induced transcription regulation. b. Analysis of photosynthetic parameters and respiration. Plant variants with increased thermotolerance have to be analysed with respect to general metabolism and fruit production. The photosynthetic activity and the respiration capability are important parameter for plant performance. In addition, the results obtained by these methods can be used to delve into the fundamental statistical analysis. c. Extraction of samples for metabolomic analysis. Although Frankfurt does not host the facility for metabolomic analysis, it will be important to teach the ESRs in the standard techniques to warrant a common quality of sample preparation to be analysed in the frame of the network. Here the basic principles of mass-spectrometry-based metabolomics and data analysis will be outlined
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3) The third workshop will be dedicated to high-throughput and data-mining strategies in plant analysis. Especially, metabolomics, proteomics, transcriptomics and epigenomic technologies are in the focus. It will be organised in Vienna by Wolfram Weckwerth, in cooperation with Peter Winter and Maria Luisa Chiusano. At this stage of the career students have to be introduced into important subjects for future positions such as entrepreneurship, commercialising scientific results and the coordination of research projects. The content of the workshop will be: a. Basic concepts of molecular high throughput analysis (OMICS concept) and systems biology strategies. Here, general omics procedures (e.g. proteomics, lipodomics, and modificomics) will be introduced on the base of some selected examples. b. Mass spectrometry and data mining. This will include the sample preparation for mass spectrometry ranging from extract preparation, cell fractionation procedures to peptide production. Subsequently, the different mass spectrometric analysis techniques will be introduced and the data analysis will be performed. c. Multivariate statistics, data integration and interpretation of obtained results. In this element the mathematical background for large data set analysis such as principle component analysis and others will be taught. Further emphasis will be placed to error determination and result validation strategies.
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Conferences - Two internal and one international conference will be organised. The conferences will be 4 days (exclusive the days of arrival and departure). All ESR/ERs and PIs will participate and two external lecturers will be invited to give key-note lectures at these conferences. These lecturers will be selected by the ESR/ERs (see web based interface). The internal conferences will include presentations by the students (2 times half a day), the discussion with the mentoring team (2 times half a day), a generic course as listed in Table 3 and one round table discussion to open time for discussions between the ESR/ERs. The international conference will consist of talks only because it is anticipated to organise this event as a major conference on Environmental enforced male sterility. Here, 16 speakers with international reputations will complement the lecture series of the ESR/ERs. At this stage the training and research of ESRs/ERs will have reached a level that will allow the presentation and discussion of the results with an international community of experienced researchers and students from outside of the network. This will stimulate the final experimental phase of the PhD projects and will support the ESRs in writing their thesis. In addition, the meeting will provide the opportunity to search for subsequent postdoctoral positions and will help them to define the future career development of the ESRs/ERs. At the final meeting, which will be internally organised, the achievements of SPOT-ITN will be summarized. For this, all current and former members of the consortium will be present to discuss future directions.
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Excursions - SPOT-ITN will organise excursions to several companies to introduce the ESR/ERs to the manifoldness of career options in the commercial sector and specific requirements for positions in private research institutions and breeding companies. The excursion will be appended to other activities whenever possible. Each of the excursions will include a sightseeing event as well as a discussion forum related to specific topics as indicated in the Table above. Here all participants from the private sector will be included to represent their own companies and to provide training related to the unique requirements reaching of small enterprises (GXP), private research institutions (MAB) or large, global acting companies (NUN). Excursions to other companies not involved in the network, but engaged in plant breeding and food production will enlarge the recognition of the SPOT-ITN initiative and the trainees involved by the industrial sector in Europe.
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Personalized training - Within the RTC specific training elements will be defined for both ESRs and ERs. The ESR/ERs are advised to use local training possibilities in the frame of educational program provided for PhD students and postdoctoral fellows by the host institution. In case that these structures do not exist ESR/ERs will be integrated into structures of collaborating institutions. SPOT-ITN will provide the required funding. However, SPOT-ITN will take care that ESR/ERs will attend at maximum two courses additionally to the program of SPOT-ITN per year.
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Guest Speaker Seminar Series - SPOT-ITN aims to outreach into the institutions. Hence, we will organise a seminar series where the PIs of the SPOT-ITN will visit each of the other laboratories once to present its research for discussion with other local researches and PhDs. This accounts for three presentations concerning the anticipated subject per year. In addition, each institution will be supported to invite two guest speakers per year who are working on topics related to the subject of the network but are not involved in SPOT-ITN. The local ESR will always be the host of the invited speaker. By this we fulfil two aims of SPOT-ITN. On the one hand, the ESRs will be involved in international networking; on the other hand the subject of thermotolerance and male sterility will be presented to the local research community and will stimulate discussions with the ESRs on their specific topics.
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Web based interface - SPOT-ITN will have its own web portal. Here, the ESRs will be trained in the introductory week how to use it. We anticipate an open sector were students can post important web sites, links to conferences, important manuscripts and reviews on important manuscripts, postings and advertisements related to the SPOT-ITN subject and more. There will be a sector for SPOT-ITN members only, where data can be exchanged, questions can be posted to the consortium, discussions about key-note speakers at the conferences can be organised and so on. The maintenance of this web site will be ensured by the ERs of SPOT-ITN.
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