Hands on advanced methods and techniques in plant science and biotechnology - 2018

Name of course: Hands on advanced methods and techniques in plant science and biotechnology   

ECTS credits: 5 ECTS  

Course parameters:
Language: English
Level of course: Master and PhD course
Time of year: Summer 2018 August 13th –August 24th (Week 33 and 34)
No. of contact hours: In total 120h (preparation 20h, the course 80h, assignment 20h). 
Capacity limits
: 16 participants

Objectives of the course:
General description

The Danish and global plant production is facing major challenges. The rapid population growth, the increased consumption of animal products and the use of crops for energy purposes demand an increased production. In addition, climate change is expected to have pronounced effects on plant production. At the same time there is also a strong wish among the public that future plant production can take place with minimal applications of pesticides and fertilizers. In effect, plant production is developing into a far more dynamic and demanding scenario in the food-, feed-, non-food-, and bioenergy area.  Plant biotechnology is expected to play a major role in meeting the demands created by this scenario through knowledge on plant genomes, advanced molecular breeding and development of genetic modified organisms (GMO).

The course intends to provide the students with experience in advanced molecular techniques used in modern plant science and biotechnology through an intensive two week course.  

Objectives of the course:
The course will cover state of the art techniques and methods within plant biotechnology research, including the genetic basis of several important plant properties and the use of molecular genetics and genetically modified organisms (GMO).

Through the course, the student will gain an understanding of the practical use of and theory behind the newest techniques within the field of plant science and will be able to employ that knowledge to solve problems within agricultural plant production through biotechnological approaches.

The course will be relevant for students who wish a practical introduction to the newest techniques and theory within plant science and biotechnology, and who wish to understand the potentials of these techniques in future plant production.   

Learning outcomes and competences:
At the end of the course, the student should be able to

·        Understand and employ advanced technologies in plant biotechnology such as genetic modification and molecular genetics.
·        Have gained practical hand-on experience with advanced techniques and equipment within plant science and biotechnology.
·        Understand and employ bioinformatics and statistical tools in plant biotechnology.
·        Plan and conduct experiments within plant biotechnology.
·        Develop strategies and models to solve problems relating to plant biotechnology by using fundamental principles in plant biotechnology and genetics.
·        Explain the use of biotechnology in plant breeding.
·        Put into perspective and discuss the potentials of plant biotechnology and breeding for achieving a sustainable agriculture, nationally and internationally.  

Compulsory programme:
A minimum of 90 % presence at the theoretical and practical lessons is required to obtain the course diploma. A report based on the practical exercises will be compulsory to the course.  

Course contents:
The course Exercises will have the following headlines:
1)    Gene expression analysis
2)    Laser micro-dissection
3)    Plant transformation
4)    Bio-imaging by confocal laser microscopy
5)    Phytase enzyme assay
6)    Protein expression in Pichia Pastoris
7)    Plant cross analysis
8)    Barley storage proteins analysis
9)    Carbohydrates in grain

The course will cover the following elements:

Technologies

The practical exercises will include hands on experience with:

Transformation/genetic modification of crop plants, including
 - direct (particle bombardment) and indirect (Agrobacterium) introduction of DNA,
 -  the CRISPR/Cas9 system for plant genome editing
 - tissue culture and selection systems,
 - characterization of genetic modified plants using advanced PCR, western blots, enzyme assays and analysis     of offspring.
 
Microdissection of plant tissues including:
 - cryo sectioning
 - laser-based ablation.
 - DNA and RNA isolation from micro dissected tissues.
 
Advanced gene expression studies including:
 - RNA isolation.
 - cDNA synthesis.
 - qPCR using SYBR Green and TaqMan probes.
 - Data analysis.

 Practical use of reporter genes for localization of gene products.
 
 Bio-imaging using confocal laser microscopy to study enzyme and protein export in grain storage pathways.
 - Imaging of fluorescently tagged markers involved in subcellular targeting in grain tissues transformed with    biolistic transformation techniques.
 
Plant protein expression, purification and characterization including:
 - theory and practice on transformation of Pichia pastoris.
 - biochemical purification from  recombinant sources.
 - Protein identification using nanoUPLC/MS and interpretation of mass spectra and peptide mapping.  

Technologies that cannot be covered by the practical exercises will be treated in lectures and theoretical exercises, e.g.:
 - Metabolic engineering of plant quality traits such as mineral- and protein content, carbohydrate   composition   
 - Cisgenesis, where only the plants own genes are used in developing GMO. 
 - Molecular based breeding methods, including selection based on phenotype and genotype. 
 - Mutagenesis using the TALEN system and the CRISPR/Cas9 system. 
 - Molecular genetic methods within genomics and transcriptomics, and development of DNA markers,      including functional markers. 
 - Bioinformatic and statistical tools to handle complex parameters and dataset in plant genetics and breeding,    including genetic mapping, QTL-analysis and association studies. 
 - Genomic selection in plant breeding.

The theoretical parts of the course will cover the following aspects of modern plant science and biotechnology:  - The plant genome and the genetic basis of different characters.
 - Goals for plant biotechnology.
 - Aspects for society 

Prerequisites:
The students are expected to have to have a basic theoretical and practical knowledge in molecular biology, genetics and biotechnology.   

Name of lecturers:
Course responsible: Søren Borg
Per Gregersen
Henrik Brinch-Pedersen
Claus Krog Madsen
Kim Hebelstrup
Torben Asp
Eva Vince
Inger Holme
Giuseppe Dionisio
Additional teachers to be announced 

Type of course/teaching methods:
The course will be planned as a mix of practical and theoretical exercises and lectures.

The teaching will exploit problem-orientated teaching based on case studies within plant biotechnology and breeding. 

Literature:
To be announced.

Course homepage:
None 

Course assessment:
A maximum 15 page report based on the practical exercises will be compulsory to the course. The report is assessed based on the Danish 7-point grading scale and has to be handed in no later than two weeks from the end of the course.

Provider:
Department of Molecular Biology and Genetics 

Special comments on this course:
Social program will be included

Help for accommodation will be organized

Time:
Summer 2018 August 13th –August 24th (Week 33 and 34)                                            

Place:
The course venue is AU Research Centre Flakkebjerg, situated in Southwest Zealand, 10 km south of Slagelse and 100 km west of Copenhagen.

Direct phone number Søren Borg +45 87 15 82 83

E-mail: soren.borg@mbg.au.dk

Registration:
Deadline for registration is 5th of May 2018

Registration can for AU students be done through the regular AU course catalogue. Link:
http://www.kursuskatalog.au.dk/da/course/70635

The course is also announced as a AU summer university course and students can register from there. Link: Deadline here is already here 15th of March.
http://www.au.dk/en/summeruniversity/courses/hands-on-advanced-methods-and-techniques-in-plant-science-and-biotechnology/ 

If you as an international student miss the deadline contact course responsible Søren Borg directly.

If you have any questions, please contact:

Søren Borg Direct phone number +45 87 15 82 83

E-mail: soren.borg@mbg.au.dk