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Molecular Methods for Detection of Food- and Waterborne Pathogens

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NOVA PhD course of 3 ECTS, organised by Leena Maunula, University lecturer, University of Helsinki - Faculty of Veterinary Medicine.
Course dates and location: 5-8 Mar. 2018, in Helsinki, Finland. 

Course Description
During the course the students will get acquainted with molecular methods used for detection of pathogenic bacteria, viruses and parasites in food. The main method is polymerase chain reaction (PCR) and the focus is especially in quantitative real-time and digital PCR as well as 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. An introduction to alternative methods, such as microfluidics and MALDI-TOF, is given. Nordic experts in the field of bacteriology, virology and parasitology, will share their experience about applying the techniques in food, water and environmental matrices. The lectures together with hands-on work and 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, water and environmental surfaces
  • Multiplex and nested PCR, reverse transcription PCR, digital PCR
  • Primer design
  • Quantitative PCR, PCR methods in gene expression analysis
  • Some basics of alternative detection methods, such as microfluidics and MALDI-TOF

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.

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 and make a couple of flashcards for learning. The course report will be completed and sent electronically to local course teachers within four weeks from the end of the course.

Learning Outcomes
After the course the students will understand the principles and theory of molecular detection methods such as real-time and digital 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 novel alternative detection methods, such as microfluidics and MALDI-TOF. After the course the competence of students has increased in the molecular detection of food- and waterborne pathogens.

Evaluation Elements
Course reports submitted until deadline will be evaluated (failed/passed).

Pedagogical Approach
Interactive elements and discussion is encouraged throughout the contact learning period. More hands-on working hours are included and as a new element, problem-based learning will be applied in the laboratory practices. Flashcards are implemented for learning. Writing of the final report further promotes the learning process.

Estimated Workload

  • 30 hours lectures, laboratory work and demonstrations
  • 5 hours group work and presentations
  • 55 hours independent work including pre-task, final report, flash cards

Prerequisite Knowledge
The course is intended especially for PhD students using molecular methods in the field food and environmental hygiene and related research.

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.

Apply here

Published 26. June 2017 - 10:57 - Updated 15. January 2018 - 14:19