Master 2 / MScT 2A

Biologie synthétique. Enseignants : Thomas Gaillard, Hannu Myllykallio, Yves Mechulam ; 6 ECTS ; 40 heures ; cours magistraux. Ce cours présentera les principaux concepts de bioinformatique et de biologie moléculaire utilisés pour construire de nouveaux systèmes biologiques d'intérêt thérapeutique ou industriel. Il abordera notamment les circuits de régulation synthétiques, les nouveaux biocarburants, les protéines contenant des acides aminés non canoniques, etc

This course will present the main bioinformatics and molecular biology concepts used to build new biological systems of therapeutic or industrial interest. It will deal in particular with synthetic regulatory circuits, new biofuels, proteins containing non-canonical amino acids, …

Course description:

Molecular biogeochemistry explores the interplay between the molecular constituents of living organisms and the biogeochemical processes occurring in the environment. This class will provide an overview of the essential concepts in biogeochemistry with an emphasis of processes occurring at the molecular level.  In addition, it will cover how natural and anthropogenic activities impact the molecular transformations of elements like carbon, nitrogen, and sulfur in various environmental domains, such as soil, water, and air, integrating principles from biology, chemistry, and geology to unravel the intricate connections between the molecular biology of organisms and the broader biogeochemical cycles in Earth's ecosystems. We will examine, by delving into scientific literature found in peer-reviewed journals, the molecular aspects of production and degradation of natural organic matter in the biogeosphere, and the linkage of biological molecules with corresponding molecular constituents (chemofossils or biomarkers) that are extracted from sedimentary archives for paleo-reconstructions.

Course goals:

Apart from acquiring the basics of molecular and analytical biogeochemistry, this course aims to achieve the following objectives:

• Develop the ability to critically analyze scientific literature
• Engage in discussions with peers, lead by a subject matter expert, on scientific papers and their impacts
• Cultivate research and presentation skills with classmates and receive direct feedback

Texts and readings:

Reading assignments:

Class 2 (Feb. 28^th) – Ward et al., 2017.  Where carbon goes when water flows: carbon cycling across the aquatic continuum. Frontiers in Marine Science. 4:7. doi: 10.3389/fmars.2017.00007

Class 4 (March. 4^th) – Brown et al., 2014. Source identification of the Antarctic sea ice proxy IP25. Nature. Communications. doi: 10.1038/ncomms5197

Class 6 (March. 11^th) – Solomon et al., 2016. Emergence of healing in the Antarctic ozone layer. Science. 353(6296): 269-274

Class 6 (March. 11^th) - Bergauer et al., 2018. Organic Matter Processing by Microbial Communities throughout the Atlantic Water Column as Revealed by Metaproteomics. Proceedings of the National Academy of Sciences 115 (3) E400-E408.  Particular attention will be paid to the material and method section concerning the proteomic study (see supplementary data). This work will be discuss in small groups in class.

Class 8 (March. 13th^th) – Rabalais et al., 2019. Gulf of Mexico Hypoxia: past, present and future. Limnology and Oceanography Bulletin. 

Paper discussions:

There are 4 sessions of 45 minutes dedicated to reading peer-reviewed papers, each student will be paired (4 groups of 2 students) and assigned a discussion to lead with a classmate based on the paper to read. Each pair will create powerpoint presentation slides and present the paper to the entire class. I will virtually meet with each group a week prior to their scheduled class leadership to address any queries

Participation:

Students are expected to arrive at class ready to engage in discussions about the assigned readings for the day. Full participation points are awarded for both attendance and active involvement in the day's discussion, which may include responding to polls, making verbal comments, contributing to the chat, and more. Mere attendance without active participation is insufficient for earning full credit. My goal, is that you will get out of the class what you put into it.