Labo intégré en sciences de la vie II

BIO-204

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Course summary

Welcome BACK to the lab!

In the second semester of this hands-on course, you will gain practical insight into the application of cell biology and biochemical techniques in research. Your team will express, purify and finally characterize pancreatic α-amylase from mammalian cells. Together, this allows you to gain expertise in data analysis and interpretation, troubleshooting and use of essential software tools. 

This Moodle site is organized by topic and provides all resources you need before, during and after the class. The content of the topics is made visible progressively to allow you to focus.

Key Information

You are assigned to one of four laboratory groups (about 40 students) that meet every other week as indicated on the schedule. In the lab you will work in subgroups of mostly 3 students, same groups as last semester. You will be supervised by a different assistant. To favour your independence there will be three groups per assistant.
The groups are commencing on: 

Introduction + Sequence analysis exercise session (all groups A, B, C, D)
  • Wednesday 19.02 (see Workshops and Lab 6)
Laboratory sessions
  • Group A: Wednesday 26.02
  • Group B: Thursday 27.02
  • Group C: Wednesday 05.03
  • Group D: Thursday 06.03

Preparation before the lab session 
To allow smooth practical work and help your group to avoid mistakes, it is essential that you carefully read all documents posted on Moodle prior to the lab session:
  • course manual with theoretical background information
  • presentation
  • watch videos

Questions
Teaching assistants and course instructor are available during practical sessions. 

Language
All course documents are in English since this is the international scientific language. We encourage you to write in English (lab notebook, scientific poster/ report) to get used to communicating science in English. The exam is bilingual (F/E).

Time investment
3 ECTS credits (LISV I) correspond to an average of 90 hours total workload (during 14 weeks), including practical lab sessions, laboratory preparation, recording experiments into your lab notebook and writing formal lab reports, workshops and exam. The weekly average workload is 6 hours: either practical session or homework.

Assessment
The final grade (LISV I+II) will be calculated based on a weighted average of laboratory notebook (40%), lab report/ scientific poster (30%) and an exam at the end of each semester (30%). Be aware that plagiarism is not acceptable and will results in lower grades (ELN and reports).

Workshops NEW

For all groups A, B, C, D:


1. Intro + Sequence Analysis Exercises
Wednesday 19.02, 10:15-12:00 room CM 1 2

2. Green Labs - with SV Durabilité and SV Workshop

Wednesday 14.05, 8:15-10:00 room SG 1 138 AND 10:15-11:00 room CM 1 2 
Thursday 15.05, 8:15-12:00 rooms INF 1 and INF 2

3. How to Cite in Life Sciences - with EPFL library

Wednesday 14.05, 11:15-12:00 room CM 1 2

Electronic Lab Notebook (ELN)

https://slims.epfl.ch/training LOGIN with your EPFL account (username and password, Chrome recommended)

Outside EPFL: use VPN connection

ELN technical support: please contact SV-IT helpdesk.sv@epfl.ch mention SLIMS in subject

The ELN content is pre-formatted and updated prior to each lab session. 
Materials and procedures from the course manual have already been imported into the ELN. 


Your task: 

  • Fill in requested information for each experiment (Aim/ Results/ Analysis/ Conclusion etc.)
Lab notebooks should be completed for grading one week after each laboratory session. Submission deadline is: 
Wednesday 2 pm for group A and C 
Thursday 2 pm for group B and D.

Evaluation Lab Notebook
10% Aim/ Link to Materials/ Scientific Language
10% Diagrams with short legend (your words) and source
35% Results: raw data and figures (graph/ gel image etc)
10% Figure legends
35% Analysis of the data/ Questions/ Exercises/ Conclusion

Lab 6: Sequencing

Introduction & Hands-on exercise session, bring your laptop 
Wednesday 19.02, 10:15-12:00 room CM 1 2  for all groups A, B, C, D

Before class: connect to your Benchling account and open the recombinant Amy2-His plasmid (from exercise 1 BIO-203). If your files are a zoo: do a clean up and create subfolders with clear titles that are human readable.

No wet lab sessions in week 1.

Lab 7: Cell culture

Attention: 

Lab session for all groups exceptionally  in MED 3 1518 DLL-Bionengineering; 

Group A: Wednesday 26.02 08:15
Group B: Thursday 27.02 08:15
Group C: Wednesday 05.03 08:15
Group D: Thursday 06.03 08:15


Lab 8: Affinity purification

All lab sessions are in AI 0111
Group A: Wednesday 12.03 08:15
Group B: Thursday 13.03 08:15
Group C: Wednesday 19.03 08:15
Group D: Thursday 20.03 08:15

Lab 9: SDS-PAGE + Transfer (western blot I)

All lab sessions are in AI 0111
Group A: Wednesday 26.03 08:15
Group B: Thursday 27.03 08:15
Group C: Wednesday 02.04 08:15
Group D: Thursday 03.04 08:15

Lab 10: Western blot II + enzyme assay

All lab sessions are in AI 0111
Group A: Wednesday 09.04 08:15
Group B: Thursday 10.04 08:15
Group C: Wednesday 16.04 08:15
Group D: Thursday 17.04 08:15

Lab 11: Enzyme kinetics

All lab sessions are in AI 0111
Group A: Wednesday 30.04 08:15
Group B: Thursday 01.05 08:15
Group C: Wednesday 07.05 08:15
Group D: Thursday 08.05 08:15

Report: Carbon Footprint

Workshops for all groups A, B, C, D

  • Wednesday 14.05 8:15-12:00
  • Thursday 15.05 8:15-12:00

The challenge is to estimate and analyze the carbon footprint of a wet lab session and identify strategies to reduce it.

This involves applying systems thinking, data analysis, and sustainability principles to quantify emissions from various sources—such as consumables, equipment, energy use, commuting, and waste—and proposing improvements or alternatives for the future.



Week 14: Scientific report & revision

Time for scientific report/ summary and revision- no practical lab sessions



Week 15: Exam + Scientific Report

Exam Wednesday May 28, 8:00-10:00 exam starts at 8:15


Rooms SG 1 138 and DIA 005

The room assignment will be posted in advance.

Format: MCQ (one answer per question, no negative points)


Report submission Friday May 30 until 16:00. You are welcome to submit earlier.