From bench to desk and back to the bench (Methods course)

Instructors:

Dr. Chandra Ramakrishnan, Dr. Lucienne Tritten and Prof. Dr. Adrian B. Hehl. Guest lecturers may teach some of the classes. For questions and enrolment, please contact chandra.ramakrishnan@uzh.ch

 

Venue:

Hybrid lectures on campus (exact location to be announced) and possibility to participate over Zoom

 

Course schedule:

This course begins in the autumn semester and is terminated after 2 semesters. In each semester, there are 7 lessons. Sessions of 1 hour are held every 2 weeks on Wednesday mornings from 9:15 – 10:15 starting from 22nd September 2021. The 7th and last session of the autumn semester will be held on the 15th December 2021.

 

Credit points:

2 ECTS are awarded for two semesters. One absence per semester is allowed; for any other absences a medical certificate is required. Credit points are awarded at the end of the two semesters.

 

Course description: From bench to desk and back to the bench

This course is mainly aimed at first to second year PhD/MD PhD and veterinary doctoral students as well as advanced and keen Master’s students who would like to deepen and expand their technical knowledge. Often, PhD students may follow routine protocols without considering alternatives. Additionally, textbook knowledge about the principles of methodologies have been revised a long time ago or students may have started a PhD in a different subject than their previous training. We will start from routine lab methods and theoretically explore alternatives and further experimental strategies from a selection of suggested topics below. This course will take place over two semesters. Students will be accredited 1 ECP/semester based on class participation and completion of small tasks and assignments. All students using cell and molecular biological methods in their PhDs are welcome to enrol. The course takes place if a minimum of 4 students are enrolled.

 

Course participants are required to register to OLAT which will be the communication and exchange platform for this course.

 

Learning objectives:

By the end of this course, students are able to

1. Name and explain various methods for a scientific question asked.

2. Outline advantages, disadvantages and limitations of these methods.

3. Suggest alternative methods.

 

Course material and preparation

Course material if necessary will be handed out to the students either in advance via OLAT or at the beginning of the class. Small tasks and assignments may have to be prepared before every class. Active participation is expected.

 

Organization of a class:

2 minutes administrative issues.

3 minutes answering questions/discussion of issues from last class

45 minutes lesson

10 minutes questions, discussion

 

Topics:

  1. DNA: From agarose gels to genomics
  2. RNA: From real-time PCR to transcriptomics
  3. RNA: More on transcriptomics (single cell transcriptomics etc.)
  4. In silico gene and protein analysis
  5. Protein: From SDS-PAGE and Western blot to proteomics
  6. Protein: Quantification in simple and complex mixtures
  7. Protein: Identifying protein-protein interaction
  8. Protein: Methods for recombinant protein production systems
  9. Protein: From proteomes to specialised proteomes (TAILS, phosphoproteomes etc.)
  10. Techniques in transgenesis and CRISPR
  11. Fractionation of organelles and small vesicles
  12. Antibodies and nanobodies
  13. From monolayer cultures to 3D cultures and organs-on-chip
  14. Flow cytometry
  15. From light and epi-fluorescence microscopy to advanced imaging methods
  16. Image processing
  17. High through-put imaging
  18. Databases (VEuPathDB, Wormbase, ENSEMBL etc.) and datamining
  19. Methods for conditional gene regulation (conditional knock-down, RNAi etc.)

 

Topics HS21:

Date

Tutor

Topic

22.09.2021

Chandra

1. DNA: From agarose gels to genomics

06.10.2021

Chandra

13. From monolayer cultures to 3D cultures and organs-on-chip

20.10.2021

Lucienne

6. Protein: Quantification in simple and complex mixtures

03.11.2021

Adrian

5. Protein: From SDS-PAGE and Western blot to proteomics

17.11.2021

Rui

15. From light and epi-fluorescence microscopy to advanced imaging methods

01.12.2021

Chandra

10. Techniques in transgenesis and CRISPR

15.12.2021

Lucienne

2. RNA: From real-time PCR to transcriptomics