 | | | Course code | | B-MPPB05 |
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| After completing the module the student is able to: |
- Understand signaling components and mechanisms employed by plants to transduce and integrate environmental and developmental stimuli, based on the most recent literature.
- Understand the value and use of natural variation to identify novel genes and pathways important for plant development, physiology and defense.
- Use publicly available databases for data-mining and/or analysis of large scale "omics" datasets.
- Judge the quality of data presented in public datasets.
- Interpret and discuss related specialist literature.
- Communicate research results, orally and in writing, to both specialists and educated laymen.
- Translate an existing problem in the field of plant physiology/pathology to a scientifically relevant research question.
- Formulate a research proposal related to this research question.
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The Netherlands is world-leader in export of commercial plant seeds and starting materials and houses a large plant breeding industry. The green sector is continuously looking for highly educated and motivated employees. Next to this, participation and contribution of companies and/or public organisations is nowadays often a prerequisite for obtaining public funding for (fundamental) research projects. Therefore, knowing the green sector, biological questions/problems the sector deals with, and opportunities provided, are indispensable for a (future) career in plant biology.
In this master course the utilisation of molecular genetic, -omics and phenotyping tools, techniques and platforms in the green biotechnology sector and plant breeding industry will be discussed. In addition, an overview will be given on aspects of commercialisation, ethics, regulations, intellectual property, funding opportunities and sector organization.
The course will be taught over a period of ten weeks and consists primarily of project-based learning, supplemented with a seminar series by lecturers from academia, breeding companies, funding agencies/offices and the public sector. As part of the course, various web based tools, techniques and data mining skills will be introduced and exercised, including QTL analysis, genome-wide association mapping (GWAS), high-throughput phenotypic analysis of plant traits, sequence analysis, micro-array data analysis, and proteomics data analysis.
During the course acquired theoretical knowledge and practical skills will be applied. During the first 7 weeks participating students will together write a review paper in which a relevant question or problem regarding applied plant biology is addressed. On a regular basis project meetings will be organized. During these meetings project progression, organization, results and deadlines will be discussed. In weeks 8 to 10 a project proposal on a topic relevant to the plant breeding industry will be written, focusing on technological innovation and company participation.
The course contains four modules:
Module 1) Friday-lectures series by UU-teachers and several guest-lecturers (concept)
Module 2) Introduction and hands-on practicals of relevant and commonly used web-based tools and databases that can be used as starting point for investigations of genes and genomes and can be consulted during the development of the review/opinion paper and the project pre-proposal (concept)
Module 3) Writing of a scientific review/opinion paper on a relevant and present topic in molecular plant physiology/plant biotechnology (context).
Module 4) Developing a research project and writing a pre-proposal on applied aspects of the subject of the review/opinion paper (context).
These modules are tightly connected and together form the basis of the concept-context based structure of the course. In this section, first the factual requirements, contents and organization of each module is described (see also course schedule in Appendix B) and in the subsequent section the assimilation of these modules into an integrated concept-context learning strategy is presented.
Brief overview of the concepts that will be addressed:
- Fundamentals and introduction to plant biotechnology and applied plant research with focus on molecular biology, genetics and ~omics.
- Getting acquainted and practice with useful (web-based) tools and techniques for molecular physiology, genetics and data mining including gene function and gene ontology, QTL analysis, Genome-Wide Association mapping and high throughput analysis of plant traits, sequence analysis, blasts, micro-array data analysis, proteomic data analysis and metabolomic data analysis and chemical genetics.
- Possibilities of large scale experimental platforms for plant research and breeding (phenotyping and ~omics).
- Plant breeding and biotechnology; principles, techniques, theory and applications.
- Post-harvest processing of seeds, starting materials and plant materials.
- Ethics and regulations regarding breeding and the use and admittance of transgenic materials (GGO’s).
- Law and jurisdiction (GGO laws, patenting, intellectual property etc.).
- Funding of plant science research, funding organization and grant opportunities.
Brief overview of the contexts that will be acquainted/familiarized by the students:
- Commercial plant science, plant science companies and public organizations, and the organization structure of the ‘green sector’ within the Netherlands.
- Typical questions/problems the green sector deals with. In other words; get acquainted with real-life issues that exemplify the type of work the students may face in their future career
- The position of the Dutch plant breeding industry in the Netherlands and world-wide.
- The position of fundamental (molecular) plant research at public institutions (universities), and the contribution and interaction with, the private and public green sector. How do private partners and public institutions depend on each other? And where do their interests overlap or differ?.
The following hands-on skills and competences will be trained:
- Using relevant web-based tools for molecular physiology, genetics and data mining.
- Assessing and combining large scale datasets.
- Project management, project communication and reflection.
- Developing and writing of a review/opinion paper on a present topic in in molecular plant physiology/plant biotechnology.
- Critical evaluation and peer-review of project proposals and being part of an evaluation panel.
- Developing an intended research project and writing a pre-proposal on applied aspects of the subject of the review/opinion paper for a pretended Netherlands Scientific Organization (NWO) or technology foundation STW, call on a topsector project requiring technological innovation and potential economic/and or societal impact for the Netherlands.
There is no written exam. The knowledge of the students will be examined by the research proposal, the review paper and results of the data analysis and exercises. Active participation in discussions and verifiable contribution to the end products (review paper and project proposal) is required to successfully pass the course.
Registration: Send an e-mail to the course coordinator (Dr. Marcel Proveniers; m.proveniers@uu.nl). The mail should contain 1) your name; 2) student number; 3) e-mail address; 4) telephone number; 5) current Master track. Maximum number of participants: flexible.
Mandatory for students in Master's programme: NO.
Optional for students in other Master's programmes GS-LS
The course is open to all students enrolled in the Utrecht University Environmental Biology MSc program and all students following equivalent programs (such as the UU masters; Science and Business management and Molecular and Cellular life sciences) that are interested in fundamental and applied plant sciences, molecular biology or biotechnology.
To successfully participate in this course students are assumed to have a bachelor degree in biology, molecular biology, (applied) biotechnology or equivalent program, with at least an introduction course in botany/plant biology and in biotechnology. Basic knowledge of genetics, molecular biology and signal transduction is required. Students that passed the UU bachelor courses Plant Physiology or Plant Adaptation and Defense and Molecular Genetics or Genome Biology (or equivalents) are perfectly prepared for successful participation in the master course Molecular Plant Physiology & Plant Biology.
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