Microbiology Profile

Bacteriology:

Through various examples, students will gain a better understanding of the concept of pathogenicity in relation to bacterial virulence. The means and mechanisms used to manipulate the body's cells at the mucosal level in order to penetrate the internal environment, i.e., invasive power, will be discussed, as well as the perception of environmental signals and the integration of these signals in order to coordinate the response of prokaryotes so that they adopt group behavior. The description of a few examples of toxins and modulins related to colonization and/or invasion will provide a better understanding of the differences in strategies between prokaryotic pathogens. Finally, the concept of microbiota and its influence on the functioning of the organism, as well as its involvement in the development of certain pathologies, will be discussed.

Immunology:

The Immunology section covers the basics of how the immune system works during infection. From the initiation and progression of the inflammatory response when non-self signals are recognized by the innate immune system (PRR-PAMP) to the mechanisms of cell activation and the cellular responses generated, we can appreciate the diversity of possibilities offered by the various players in immunity. In addition, the sequence of events leading to the orientation of the immune response and the acquisition of lasting protection during the adaptive phase will provide a better understanding of the vaccine strategy. Finally, intestinal mucosal immunity will be discussed in the context of the relationship between the host and the microbiota.

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The molecular biology practical aims to enable students to work independently with molecular biology protocols and introduce them to hypothesis-driven research. Students will have six days to respond to a biological problem that will be presented to them. This will allow them to put some of the techniques covered in their theoretical classes into practice in a laboratory setting, thereby gaining a better understanding of them.

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The courses will cover the fundamentals and principles of microbial ecology (microbial biodiversity; cultivable/uncultivable microorganisms;   major microbial groups, key microbial functions and biogeochemical cycles, microbial metabolisms in the environment and environmental applications, ecology fundamentals applicable to microorganisms (microbial interactions, free-living, competition, collaboration, symbiosis , parasitism and their applications). The following will be covered in particular by way of illustration:

- viruses: the concept of emergence and reemergence

-Vibrio bacteria, virulence factors, host adaptation, and horizontal transfer

-streptococci, comparative genomics, genome reduction, specialization

 Applications of microbial ecology to biotechnology will concern: detection, inoculum production, bioproductions, bioremediation, and water treatment using concrete examples (development of multi-pathogen detection tools that take mutation into account, production of a flavor enhancer by a soil corynebacterium, applications of the study of microbial interactions to the selection of cheese flavors, quality index of wine-growing soil, etc.).

Lab work: water analysis, principles, standards, applications: total 6 hours

TD/personal work based on the results of the practical work: design of a water purification model in a real-life situation (cadastral data, topological survey, total fecal coliform load from practical work, student presentations on the different types of (micro)water treatment plants, etc.). The aim is to propose a conceptual solution adapted to the specific case.

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As part of this course, students will learn experimental principles based on the manipulation of nucleic acids. Lectures will focus on two main areas:

1. Implementation of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, CRISPR/CAS9 system, etc.) and reflection on the concept of ethics in biology.

The tutorials will consist of:

- Analysis of articles presenting issues to be resolved using the knowledge acquired in the course. The topics chosen will, as far as possible, refer to parallel L3 teaching units. These articles will be presented by students in the form of oral presentations by groups of 3 to 4 students to the whole class.

- Sessions reserved for the use of basic bioinformatics tools in the computer lab.

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The EU aims to acquire knowledge of fundamental and applied virology, with a focus on an integrative approach to the discipline. It will present the specificities of host-virus interactions and the pathophysiology of viral infections in different types of hosts (vertebrates/insects/plants). It will address aspects of viral ecology, emergence, and associated risks to human and animal health. Finally, the EU will present the research methods used, virological detection and diagnostic tools, and applications of viruses in biotechnology.

The EU will be taught in the form of lectures, tutorials (analysis of current scientific articles and oral presentations) and practical work illustrating the lectures and tutorials (virus amplification and purification and quantification using reference techniques).

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