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OnderzoekPhD courses

Molecular Methods in Ecology and Evolution

Organizers

Dr. J. Falcão Salles (Microbial Ecology, RUG)
Dr. B. Wertheim (Evolutionary Genetics, RUG)
Prof. I. Tieleman (Animal Ecology, RuG)

Aim of the course

Molecular methods are now widely used in ecological and evolutionary studies, to answer questions ranging from the evolutionary history of populations to patterns in community ecology. How can we use these molecular tools to enhance our knowledge of population genetics, phylogeny, molecular and adaptive variation, and community structure?

The objective of this course is to introduce students to a range of molecular techniques (DNA, RNA and protein- based) that are applied in ecological and evolutionary research. We will teach ‘how’ these techniques are properly applied, as well as their potential and limitations.

At the end of the course, the student is able to:
1. work properly and safely in a molecular lab;
2. describe, discuss and practice a range of molecular approaches that are currently used in ecological and evolutionary research;
3. apply molecular approaches to solve research questions in ecology and evolution;
4. use some software packages for analyzing molecular data.

Learning outcomes

Students will be able to: work properly and safely in a molecular lab, to describe a range of molecular approaches that are currently used in ecological and evolutionary research, to apply molecular approaches to solve research questions in ecology and evolution; to use some software packages used for analyzing molecular data.
Suggested reading: An introduction to Molecular Ecology, 2nd edition – Trevor Beebee & Graham Rowe, 978.0.19.92925.9

Contents and structure

This course is set up in two parts, of which you may opt to follow only the first part or both.
The first part of course is a mixture of lectures, dry lab (computer) and wet lab practicals. It provides an introduction to molecular techniques that are used in ecological and evolutionary research: DNA extraction; basics principles of PCR, qPCR and primer design; cloning; sequencing approaches and phylogenetic analyses of sequences; fingerprinting techniques; research: RNA extraction; neutral markers; RNAi and methylation; population genetics and phylogeny; protein quantification and activity.

You may opt to participate in the second part of the course, which comprises a research project, which will be carried out individually or by groups of 2 students and will fit within the ongoing research of the Microbial Ecology, Animal Ecology or Evolutionary Genetics department.

Lecturers
Provisional program, based on program for 2017:
week Monday Tuesday Wednesday Thursday Friday
1 (27/11)

LECTURE: Introduction to the course 9-10;
Project presentations 10-11

PRACTICAL: Preparing buffers, solution, plates (cloning), etc

LECTURE: DNA extraction

PRACTICAL: DNA extraction
-High salt (eukaryotes)
-kit MoBio (prokaryotes)
DNA quantification

LECTURE: PCR

PRACTICAL: PCR
-Finish DNA extraction (high salt)
-PCR Bacteria (cloning)
-Agarose gel (PCR cloning)
-PCR Bacteria (DGGE)

LECTURE: cloning

PRACTICAL: Cloning
-Ligation (2h)
-Transformation
-Agarose gel (PCR DGGE)

LECTURE: sequencing

PRACTICAL A: injection

PRACTICAL B: Sequencing I
-Colony PCR
-Agarose gel (colony PCR)
-Cleaning PCR product

2 (4/12)

LECTURE: Fingerprints

PRACTICAL A: sequencing II
-sequencing PCR

PRACTICAL B: DGGE
-Prepare gel
-Load gel (17h)

LECTURE: sequencing and DGGE analyses

PRACTICAL A: sequencing III
-clean PCR product
-load samples

PRACTICAL B: DGGE
-Staining
-Analysis

LECTURE: RNAi/methylation

PRACTICAL: RNA extraction
-phenotype evaluation
-RNA extraction
-cDNA

LECTURE: qPCR

PRACTICAL: Eye color
-PCR Eye colour (DNA and RNA)
-qPCR overnight (eukaryotes)

LECTURE: wrap up

PRACTICAL: Analyse results
-qPCR
-sequencing
-DGGE

3 (11/12)

LECTURE: Measuring proteins

PRACTICAL: Sampling
Lysis/Agglutination
Bacteria killing (start)

LECTURE: Measuring proteins

PRACTICAL: Bacteria killing

LECTURE: Measuring proteins

PRACTICAL: Nitric oxide
Lysozyme

LECTURE: Measuring proteins

PRACTICAL: Scoring, analysis and discussion

Deadline:

Choosing projects and articles
- Hand in lab journal

No lectures/practical work: students should work on their presentations
4 (18/12) work on presentations

Presentation articles

Course Evaluation

Start research project
5 (10/1)
6 (17/1)

7 (24/12)

Project presentations Hand in report research project
General Information
Course credits 5 ECTS per course part
Location The course will be held at the Linnaeusborg, Zernike Campus, University of Groningen.
Duration & date The first part of the course will kick off on Monday 27 November. For three consecutive weeks you will engage in lectures and practicals. This part of the course will be closed off on 20 December with a presentation. On the 10th of January the 2nd part of the course will start for another 3 weeks, to end on 27th of January.
Costs The course fee for participating PhD level students from the GELIFES institute is € 275,-. This course fee will allow you to participate in both parts of the course. The course fee remains the same if you decide to participate only in the frst part of the course and covers for the material expenses. External PhD level students may be allowed to participate only if there is space left available. The cost fee for external PhD students is € 350,-.
Participants The maximum number of participants is 16, of which a maximum of 4 may be PhD level participants.
Information
  • Topical information: please contact the course organizers (see above)
  • Practical information for PhD students and registration: Corine Eising
Registration PhD student applications will be handled on a first come, first serve basis. However, master student applications will be reviewed and prioritized.
To register for this course if you are a PhD student, please use the Registration Form
Laatst gewijzigd:12 september 2017 16:09