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Molecular Methods for Detection of Food- and Waterborne Pathogens

NOVA PhD course of 3 ECTS, organised by Leena Maunula, HU-V.
Dates and location: 7-10 March 2016 in Helsinki, Finland.

Course Description
During the course the students will get acquainted with molecular methods used for detection of pathogenic bacteria and viruses in food. The main method is polymerase chain reaction (PCR) and the focus is especially in quantitative real-time PCR and sample preparation. The students learn how to establish the methods, design primers, include adequate controls and interpret results. They learn how to identify the critical points in PCR, and troubleshooting lectures give help for challenges in PCR. Nordic experts in their field, both bacteriologists and virologists, will share their experience about applying the techniques in food, water and environmental matrices. The lectures together with practical demonstrations both in the laboratory and at the computer will give the students valuable tools and know-how for their research.


  • Basics of PCR theory
  • Principles of real-time PCR (SYBRgreenI, Taqman chemistry)
  • Real-time PCR method applications in detection of pathogens in food and water
  • Multiplex and nested PCR, reverse transcription PCR, digital droplet PCR
  • Primer design
  • Quantitative PCR
  • PCR methods in gene expression analysis

Programme Outline
As a pre-task, the students will update their knowledge of the basic structure of nucleic acids and basics of gene amplification. The course consists mainly of lectures and laboratory practice. In addition, the students will work in groups and give presentations as an interactive element. Each student will write an individual course report.

Learning Outcomes
After the course the students will understand the principles and theory of molecular detection methods such as real-time polymerase chain reaction (PCR). They also know how to establish the methods in practice, design primers and select adequate controls and interpret (quantitative) results. They are capable of identifying the critical points of PCR. They have also learned about the most modern applications of gene amplification, such as digital PCR. After the course the competence of students has increased in the molecular detection of food- and waterborne pathogens.

Pre-/Post-Campus Assignments
As a pre-task the students will read scientific articles according to instructions given to them before beginning of the course. The course report will be completed and sent electronically to local course teachers within four weeks from the end of the course.

Evaluation Elements
Course reports submitted until deadline will be evaluated.

Pedagogical Approach
Interactive elements and discussion is encouraged throughout the contact learning period. Flashcards are implemented for learning. Writing of the final report further promotes the learning process.

Estimated Workload
83 hours, consisting of:

  • Lectures: 14 hours
  • Laboratory: 6 h
  • Demonstration: 1 h
  • Group work: 4 h
  • Presentations: 4 h
  • Excursion: 2 h
  • Independent work: 52 h (pre-reading 25 h before the course, 14 h independent learning during the course, writing a final report 13 h after the course)

Prerequisite Knowledge
The course is intended especially for PhD students using molecular methods in the field food and environmental hygiene and related research. Advanced MSc students may also be accepted.

Admission for NOVA courses is handled by the course organiser/ the NOVA member institution organising the course. Please see the links in the margin for more information.

Published 10. August 2015 - 12:45 - Updated 2. August 2016 - 10:01

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