Labo intégré en sciences de la vie I
BIO-203
Media
Welcome to the lab!
In this hands-on course, you will gain practical insight into the application of molecular biology and biochemical techniques in research. Your team will conduct a wet lab project that allows you to learn how to clone, 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
After the common introduction for all students in week 1, you are assigned to one of four laboratory groups, commencing on:
- Group A: Tuesday 16.09
- Group B: Friday 19.09
- Group C: Tuesday 23.09
- Group D: Friday 26.09
Each group (about 40 students) will meet every other week as indicated on the schedule. In the lab you will work in subgroups of mostly 3 students and will be supervised by teaching assistnts (see Moodle/ Participants to know which group you belong to). To know who the other members are you may filter participants by your group ID (example Group D11).
Preparation before the lab sessionTo 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, reports) 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 report or poster, 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 or 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).
Support during Practical Sessions
We want to ensure that everyone feels comfortable in the lab. If you experience sensory sensitivities (such as to light, sound, odour, crowded spaces etc) or have other access needs, you are very welcome to contact me. Together, we can discuss possible strategies to adapt to the lab environment.
If at any time you find the space challenging, it's absolutely fine to take a break in a quieter room or outside and return when you are ready.
Week 1: Introduction & Exercises
All students: Tuesday September 9, NEW 8:15-10:00 CM 1 2
- Presentation course organization
- BRING LAPTOP for Benchling software warm-up (tablets do not work)
- COMPLETE online safety training for access to the lab (see Safety)
All students: Friday September 12, 11:15-13:00 CO 2
- Presentation Electronic Lab Notebook
- Workshop 'Creating Effective Figures and Figure Legends'
- BRING LAPTOP for Electronic Lab Notebooks (see ELN)
- Benchling exercises support
Workshops
1. Getting started with Benchling
Tuesday 09.09 for all groups A, B, C, D
2. Creating Effective Figures and Figure Legends
Friday 12.09 for all groups A, B, C, D
3. How to Analyse Scientific Data
Tuesday 07.10 at 13:15 in CE 1 2 for all groups A, B, C, D
4. How to Write a Scientific Report or Poster
Tuesday 02.12 at 9:15 in CM 1 2 all groups A, B, C, D
- READ Intro Benchling Handout (File)
- READ Handout Figure + Figure Legends Workshop (File)
- READ Handout Workshop 'Scientific Data Analysis' (File)
- READ Handout Workshop 'How to Write a Scientific Report or Poster' (File)
Safety
Online Safety Training SV-Biosecurity by Simona Frateschi
Presentation and quiz, 80% correct answers by Friday 12.09, 16:00
- multiple attempts for quiz possible
- choose language below: English or French
- password: TPSV
Benchling software
We will use Benchling software to design, analyse and store DNA and protein sequences throughout the year and it will be used again during the Master in Life Science Engineering. Benchling exercises will be posted here. Tips and tricks for now and for your future career:
- organise files in projects
- use meaningful names for projects and files
- clean up (archive) files that contain mistakes or correct the file
- CREATE Benchling Account (URL)
- IMPORT DNA Template Ex1 + Ex2 (Folder)
- COMPLETE PCR and Primer Design (URL)
- COMPLETE Sequence Annotation (URL)
- COMPLETE Benchling Exercises 1+2 of Lab 3 (Folder)
Electronic lab notebook
Walk-in support sessions for ELN Lab 1 - after your first lab session
Tuesday 16.09 14:15-15:00 DIA 004
Friday 19.09 14:15-15:00 CO 121
Tuesday 23.09 14:15-15:00 DIA 004
Friday 26.09 14:15-15:00 CO 121
- WATCH What you can do with SLIMS Software (URL)
- SLIMS User Guide Students (File)
- READ Handout Keeping a Laboratory Notebook (File)
- READ Evaluation Criteria ELN (File)
Lab 1: Micropipetting
All lab sessions are in AI 0111
Group A: Tuesday 16.09 08:15
Group B: Friday 19.09 10:15
Group C: Tuesday 23.09 08:15
Group D: Friday 26.09 10:15
- READ Course Manual Lab 1 (File)
- READ Presentation Lab 1 (File)
- WATCH How to pipette correctly (URL)
- ANALYZE Results Absorbance (Folder)
- COMPLETE EXERCISE Making Solutions and Buffers (Folder)
Lab 2: RNA extraction
All lab sessions are in AI 0111
Group A: Tuesday 30.09 08:15
Group B: Friday 03.10 10:15
Group C: Tuesday 07.10 08:15
Group D: Friday 10.10 10:15
- READ Course Manual Lab 2 (File)
- READ Presentation Lab 2 (Folder)
- READ Overview RNeasy Mini Procedure (File)
- WATCH How to isolate RNA from tissue or cells (URL)
- READ NanoDrop Procedure (File)
- ANALYZE Results Lab 2 (Folder)
Lab 3: PCR
All lab sessions are in AI 0111
Bring your laptop for Benchling exercises.
Group A: Tuesday 14.10 08:15
Group B: Friday 17.10 10:15
RECHARGE YOUR BATTERIES: 1 WEEK SEMESTER BREAK
Group C: Tuesday 28.10 08:15
Group D: Friday 31.11 10:15
- READ Course Manual Lab 3 (File)
- READ Presentation Lab 3 (Folder)
- WATCH DNA Polymerase Properties (URL)
- ANALYZE Results Lab 3 (Folder)
Lab 4: Ligation & transformation
All lab sessions are in AI 0111
Group A: Tuesday 04.11 08:15
Group B: Friday 07.11 10:15
Group C: Tuesday 11.11 08:15
Group D: Friday 14.11 10:15
- READ Course Manual Lab 4 (File)
- READ Presentation Lab4 (File)
- READ Antarctic-phosphatase description (URL)
- WATCH DNA Ligation (URL)
- WATCH Mechanism of Transformation with Competent Cells (URL)
- ANALYZE Results Lab 4 (Folder)
Lab 5: Plasmid isolation & digestion
All lab sessions are in AI 0111
Group A: Tuesday 18.11 08:15
Group B: Friday 21.11 10:15
Group C: Tuesday 25.11 08:15
Group D: Friday 28.11 10:15
- READ Course Manual Lab 5 (File)
- READ Presentation Lab 5 (File)
- WATCH Plasmid DNA Purification using QIAprep Spin Miniprep Kit and Vacuum Manifold (URL)
- WATCH Standard Protocol Restriction Enzyme Digest (URL)
- CALCULATE Making Reagents and Buffers: Exercises (from Lab1) (File)
- ANSWERS Making Reagents and Buffers (from Lab 1) (File)
- Benchtop 1 kb ladder (URL)
- ANALYZE Results Lab 5 (Folder)
Week 12-13: scientific poster & revision
No lab sessions, time for ELN, poster figures and revision (see week 14 for details)
Tuesday 02.12 see 'Workshops'
Friday 05.12
Tuesday 09.12
Friday 12.12
Week 14: Exam + Assignment
Exam Tuesday December 16, 8:00 to 10:00. Start at 8:15.
Auditoire: CO 1
+ Room: DIA004
Check the seating assignment below to know which room you are in.
Format: MCQ (one answer per question, no negative points)