Learning outcomes

Students will acquire a good knowledge of the main basic techniques of biochemistry as well as cellular and molecular biology.

They will be able to choose an experimental approach to answer a biological research question and justify it based on the advantages and limitations of the different techniques analyzed.

They will be able to interpret graphical results from experiments using the techniques covered in the course and understand an experimental protocol.

They will become familiar with the vocabulary and experimental approaches of high-throughput analyses and understand their power and limitations.

Students will be able to develop a methodology and strategy for exploiting and interpreting a proteomic data set.



Goals

Explain the principles of the main techniques used in biochemistry and cellular and molecular biology, highlighting their advantages and limitations.

Familiarize students with the basic techniques regularly used in scientific literature in the life sciences.

This course also aims to familiarize students with high-throughput analysis techniques, such as metabolomics and proteomics. The principles, advantages, and limitations of these different approaches will be presented and illustrated with examples/applications.



Content

Part T. Arnould:

Measurement and analysis methods used in laboratories that rely on biochemistry, such as academic, medical, and pharmaceutical research. The theoretical aspects of these techniques are presented. Students will learn the basic techniques: 

affinity chromatography, 

centrifugation and cell fractionation, 

enzyme and DNA assay and purification, 

gene expression analysis (RT-qPCR, arrays, etc.) 

molecular interactions by immunoprecipitation (Co-IP, Chip, Tap-Tag, Pull-down assay), FRET, BRET, PLA, Proxisome Assay, 

molecular mobility (FRAP), 

measurement of transcription factor activity (EMSA, reporter genes, etc.).


Part P. Renard:

1) Introduction to proteomics

2) Mass spectrometry for protein analysis

3) Protein identification: from spectrum to database

4) Strategies and examples of quantitative analyses 


Part M. Hennequart:

1)  Introduction to metabolomics and related techniques.

2)  Basic principles of chromatography and mass spectrometry for the analysis of small molecules.

3)  Analytical techniques in metabolomics (targeted, untargeted, stable isotope labeling).

4) Scientific applications and future of metabolomics.


Exercices

Exercises

Two optional tutorials are planned to discuss the “targeted techniques” section based on “questions and answers” and analyses of results from scientific publications illustrating the use of the techniques studied in a biological context.

Sources, references, and possible materials

Course slides + resources provided during the course (articles, books, etc.).


Practical work:

1)  Study of the activation pathway of the NF-kB transcription factor in HEK 293 cells stimulated by IL-1beta using a cell co-transfection approach with plasmids containing reporter genes.

2) A proteomic data set is presented and given to students. Analysis strategies are explained to them.

Working in pairs, students must analyze the data set and extract relevant biological information. Assessment is based on the presentation of their results.

Teaching methods

Ex-cathedra :

Arnould section. The techniques course (12 hours) is taught in Q1 using video projection and the blackboard.

Students are given articles to read.

Students have access to course notes on the WEB campus. Teaching aids used: blackboard and PowerPoint projection + references to two books on techniques.

Assessment method

The 24-hour course consists of: 12 hours with Prof. Thierry Arnould (Basic Laboratory Techniques), 8 hours with Prof. Patsy Renard and Engineer Marc Dieu (Proteomics), and 4 hours with Prof. Marc Hennequart (Metabolomics).

•  The two practical sessions represent an equivalent amount of work. The practical work is assessed on the basis of an overall, comparative evaluation of targeted approaches to a given biological question, without any preconceptions.

SBIOB538 = 1 course unit consisting of 4 assessment components:

•  AA1: theoretical course on targeted techniques (TA). Weighting: 6 points

•  AA2: theoretical course on proteomics. Weighting 4 points

•  AA3: theoretical course on metabolomics. Weighting 3 points

•  AA4: Practical work: a single grade. Weighting 7 points

Each AA can be assessed in Q2 and Q3 (including practical work). 

Assessment method: oral exam for each AA (with a written report for the practical work section).

Calculation method: weighted arithmetic mean, but absorbing grade if lower than 7.49.

In case of failure: exemption granted for any AA >10/20

Sources, references and any support material

Power points, reference books, scientific articles

Language of instruction

French