Teaching Materials
Here are teaching handouts for undergraduate microbiology and molecular biology (taught in french), masters level genomics (taught in french), and masters level systems and synthetic biology (taught in english) taught in the Université de Paris Saclay System at the Université d'Evry.
Description of course UE8C1: Systems and synthetic biology approaches for environmental biotechnology: (in english and french).
- Current topics in biotechnology: The Precision Agriculture Initiative for agricultural biotechnology and CRISPR-modification of human cells. Slides from the European iGEM meetup in july 2016.
- Prokaryotic gene regulation classes of transcription regulators, carbon catabolite repression, mechanisms of regulation (PDF slides).
- Building with DNA I advances in cloning and gene synthesis: Traditional cloning, Biobricks, Golden Gate, Gateway, CPEC, Ligation Independent Cloning (LIC), SLiCE, Gibson Assembly
- Building with DNA II advances in cloning and gene synthesis: synthesis of a Mycoplasma genome (Gibson et al, 2010 PMID 20488990) and Saccharomyces cerevisiae chromosome III (synIII) Annaluru et al, 2015 (PMID 24674868)
- DNA sequencing technologies evolution of DNA sequencing including Sanger, 454, SOLiD, Illumina, Ion Torrent, PacBio, and Nanopore sequencing.
- RNA sequencing technologies strand-specificity, transcription start site mapping, single cell transcriptomics (PDF slides).
- Targeted genome editing in prokaryotes homologous recombination, recombineering, group II introns, Cre-lox, Flp-Frt, GETR (PDF slides).
- Targeted genome editing in eukaryotes zinc finger nucleases, TAL proteins, CRISPR, and CRISPR-mediated Gene Drives (PDF slides).
- Systems and synthetic biology for bioenergy Opportunities for a bio-based economy, sytems biology to identify key enzymes, synthetic biology to modify genomes
- Advances and challenges in microbial engineering by focusing on Bokinsky et al, 2011 Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. PMID 22123987.
Exams
Masters M1: Sciences des Genomes et des Organismes (en français)
License L2: Microbiologie et écologie microbienne (en français)
- Histoire et classification: les microbiologistes célebres du passé et la classification des organismes (avec réponses).
- Observation des cellules: la microscopie et la coloration des cellules. (avec réponses)
- La paroi bactérienne: la peptidoglycane, la capsule, et les spores. (avec réponses)
- La transformation génétique des bactéries: les methodes de transfert d'ADN entre les cellules, discussion de l'opéron lac (avec réponses).
- Les pathogènes: la virulence et les mécanismes d'infection (avec réponses).
- La croissance et nutrition: les milieux microbiens, les courbes de croissances. (avec réponses).
- Le métabolisme microbien: la diversité du metabolisme (avec réponses).
- Les méthodes de la microbiologie moléculaire: PCR, electrophorèse, clonage (avec réponses).
- révision des 8 séances de TD et (avec réponses).
Examens
License L2: Travaux pratiques de Microbiologie et écologie microbienne (en français)
6 seances des exercises au labo qui se concentre sur l'identification et characterisation des microbes avec les themes suivants:
- Identification des eucaryotes presents dans l'eau d'une station d'epuration
- Colorations des bacteries: bleu de methylene et gram
- Identification des bacteries presents dans un lac proche
- Controle de qualite de yaourt
- Isolation des microbes de l'environnement
- Comparaison des activites bactericide des anti-bacteriens
- L'effet des antibiotiques sur E.coli
Programming fundamentals for the computational biologist
These lectures introduce the Perl programming language as a tool to investigate problems in biology. The goal is to demonstrate that basic programming skills turn the computer into a tool just like the PCR machine; they are both means to test biological hypotheses. So why does the course focus on the Perl programming language?
"Perl is the duct tape of the internet." -Randal Schwartz
"Perl is optimized for problems which are about 90% working with text and about 10% everything else." -Schwartz and Phoenix "Programming Perl"
Which is what makes Perl perfect for the computational biologist because the essence of bioinformatics is searching for patterns in two huge sets of text files: genome files and the internet.
Here are the handouts for the course:
