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

Instructors:
Dr Lauriane Sollelis, Dr. Kannan Venugopal, Prof. Dr. Adrian B. Hehl and Dr. Chandra Ramakrishnan. Guest lecturers may teach some of the classes. For questions and enrolment, please contact chandra.ramakrishnan@uzh.ch

Venue:
Zoom: https://uzh.zoom.us/j/64034917784?pwd=TFV3UHFmQzJ5a1R2MzZIRnl6RHRqUT09. This is an interactive course. Participants are required to have their cameras switched on, but should be muted when not actively participating.

Course schedule:
This course begins in the autumn semester (28/09/2023) and is terminated after 2 semesters. In each semester, there are 7 lessons. Sessions of 1 hour are held every 2 weeks on Thursday mornings from 9:00 – 10:00.

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. The dean's office requires full attendance according to the instructions above and can only award 2 ECTS. We cannot award 1 ECTS for partial participation.

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 for OLAT which will be the communication and exchange platform for this course. All students that are not from the University of Zurich, please register for mobility: https://www.uzh.ch/cmsssl/en/studies/application/chmobilityin.html

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