L3 - Microbiology

This practical course aims to apply the students' knowledge of microbiology and molecular biology to the identification of environmental bacteria.

The quantitative and qualitative analysis of the bacterial population present in a soil sample will be done classically by identifying the species by the means of classical bacteriology in successive steps: 1) isolation of the bacterial flora; 2) diagnosis of family and genus using conventional media and tests; 3) diagnosis of the species using API System galleries

Molecular biology techniques now allow the identification of bacteria present in a sample without the need to culture them. This approach requires access to a sequencing platform and will also be carried out during the course of the project, which will allow the two approaches to be compared. The sequencing results obtained will allow a bioinformatics analysis of the rrsA gene specifying the RNA16S of the isolated bacteria.

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This course describes the methodology used by researchers in the life sciences to communicate the results of their experiments, both in writing and orally. As English is the common language of international researchers, a large part of this course is taught in this language.

Written communication is addressed through the study of the structuring (macro) of a research article as well as through a study of the publication process in scientific journals. Several elements of written structuring (micro) are examined in order to understand the differences between scientific and literary English: clarity, cohesion, coherence.

These studies are complemented by a tutored project during the semester during which students are required to analyze a recently published research article in the scientific literature and to transcribe it into an oral presentation (conference) in English.

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This course is the logical continuation of the S4 course (Basics of physiology and immunology) and aims to deepen the knowledge of fundamental, applied and clinical immunology. We will also approach the notions of "unconventional" immunology and we will develop the strategies of innovative immunotherapies. This course will cover all the topics related to modern immunology and will be strongly oriented towards the clinical aspects of this discipline.

 Key words

Fundamental immunology, Anti-infectious immunity, Immunotherapy, Vaccination, Autoimmunity, Immune deficiencies, Anti-cancer immunity, Non-conventional immunity

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Molecular biology is both a fascinating subject of study in its own right, but it also provides other disciplines in biology (cell biology, genetics, physiology...) with fantastic tools for modifying and quantifying genes and their products.

The EU provides a deeper understanding of the mechanisms of organization, maintenance, replication and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, the properties of information-carrying macromolecules (DNA, RNA, proteins) will be explored, and how the transactions between them explain the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

In parallel, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and further developed in class by analyzing results.

Thus, the tutorials approach these subjects in the form of (1) exercises leading the students to verify their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. Thus, the basics of scientific reasoning and critical analysis of results will be acquired and/or deepened.

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This teaching unit covers the different categories of biotechnologies according to their field of application:

• Plant biotechnologies concern the agri-food industry and include a series of technologies using the organism of plants and their cells to produce and transform food products, biomaterials and energy, but also recombinant proteins for therapeutic purposes

• Animal biotechnologies concern the fields of health, medicine, diagnosis, tissue engineering as well as the development of genetic or molecular processes with a therapeutic purpose.
• Microbial biotechnologies concern the use of micro-organisms (viruses or bacteria) and their cultivation within the agro-food/pharmaceutical industry or their interest in environmental protection.

The teaching offered to students in the Bachelor 3 Life Sciences is to enable them to discover or deepen their theoretical knowledge of the various biotechnologies as well as to master the associated tools/applications.

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This course aims to deepen the knowledge of microbiology for students who wish to continue their studies in this discipline.

It will address molecular genetics applied to prokaryotes (mobile genetic elements and resistance, CRISPR, 2-component system, quorum sensing, horizontal transfers...) and the specificities of bacterial metabolism.

Bacteria with particular morphology will be presented.  

In virology, the pathophysiology of viral infections and the prevention and control of viral diseases will be presented. The mechanisms of escape from the immune system will be detailed. The mechanisms of virus evolution will be described and related to viral emergence.

The parasitic mode of life of some eukaryotic microorganisms will be illustrated by describing their obligatory intracellular development and the modifications of the host cell induced by these parasites.

Finally, the EU will address the concept of microbiota and will present the latest data on the nature of the human microbiota and its role on health.

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Bacteriology:

Through various examples, students will be able to better understand the notion of pathogenicity in relation to the virulence of bacteria. The means and mechanisms used to manipulate the cells of the organism at the mucosal level in order to penetrate the interior environment, i.e. invasiveness, 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 a group behavior. The description of some examples of toxins and modulins in relation to colonization and/or invasion will allow a better understanding of the differences in strategies between prokaryotic pathogens. Finally, the notion of microbiota and its influence on the functioning of the organism as well as its implication on the development of certain pathologies will be discussed.

Immunology:

The Immunology part of the course deals with the broad outlines of the functioning of the immune system during infection. Thus, from the setting up and development of the inflammatory reaction during the recognition of non-self signals by natural immunity (PRR-PAMP) to the mechanisms of cell activation and the cellular responses generated, we will be able to appreciate the diversity of possibilities offered by the different actors of immunity. Moreover, the sequence of events leading to the orientation of the immune response and the acquisition of a durable protection during the adaptive phase will allow to better understand the vaccine strategy. Finally, the immunity of the intestinal mucosa will be discussed in the context of the relationship between the host and the microbiota

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The main goal of this module will be to provide a better understanding of the major concepts of modern biology, through the history of their development. In other words, to analyze the intellectual path as well as the experimental and theoretical approaches that led to their construction. For example, we will analyze how the search for a "natural" classification led Jean-Baptiste Monet de Lamarck and Charles Darwin to lay the foundations of evolutionary biology or how the concept of "unity of organization plan" by Etienne Geoffroy Saint Hilaire is at the origin of evolutionary paleontology, developmental biology and evolution/development (Evo/Devo).

Within the framework of bioethical aspects, the problems of the drift of a concept (from craniology to eugenics) or the cases of "Georges Cuvier" and "Trophim Lyssenko" when religious or political ideology interferes with science will be addressed.

Finally, biological philosophy will lead us to discuss the interest of models in biology and the "end of the genetic whole" (from Lamarck to epigenetics through epigenesis).

The whole module will be done through lectures during which some founding texts of modern biology will also be analyzed and discussed.

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The molecular biology laboratory course aims to make students autonomous in the face of a molecular biology protocol and to introduce them to hypothesis-driven research. The students will have 6 days to answer a biological problem which will be proposed to them. They will thus be able to put into practice, under laboratory conditions, some of the techniques they have learned in their theoretical courses to better understand them.

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The courses will cover the basics and application principles of microbial ecology (microbial biodiversity; cultivable/non-cultivable microorganisms; major microbial groups, main microbial functions and biogeochemical cycles, microbial metabolisms in the environment and environmental applications, basics of ecology applicable to microorganisms (microbial interactions, free life, competition, collaboration, symbiosis, parasitism and their applications). In particular, the following topics will be covered by way of illustration

- viruses: notion of emergence and re-emergence

-vibrios, virulence factors, host adaptation and horizontal transfer

-streptococci, comparative genomics, genomic reduction, specialization

 The applications of microbial ecology to biotechnologies will concern: detection, production of inocula, bioproductions, bioremediation, water treatment on concrete examples (development of multipathogen detection tools taking into account the mutation, production of a taste enhancer by a soil corynebacteria, applications of the study of microbial interactions to the selection of cheese flavors, quality index of a vineyard soil ...)

Water analysis, principles, standards, applications: total 6h

TD/ personal work on the basis of the results of the TP: design of a water purification model in real situation (cadastral data, topological survey, load in total fecal coliforms streptococci resulting from the TP, presentation of the students on the various types of (micro)purification stations....) it is a question of proposing a conceptual solution adapted to the case of ground.

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In this course, students will learn experimental principles based on nucleic acid manipulation. The lectures will be articulated around two major axes:

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

TDs will consist of:

- Analysis of articles presenting problems to be solved with the knowledge acquired in the course. The chosen themes will, as much as possible, refer to the parallel UE of the L3. These articles will be presented by the 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 room.

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This course aims to deepen the knowledge of eukaryotic microorganisms and to explore in particular the diversity of unicellular eukaryotes with a free or parasitic life style. This diversity will be studied not only from a theoretical but also from a practical point of view. Indeed, the specificities of development and life style of four unicellular microorganisms (social amoeba Dictyostelium discoideum, ciliate Tetrahymena, apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum) will be studied during practical works and will allow to illustrate the notions approached in course and in TD

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The modalities of this UE are specifically adapted to the different courses of the L3. Nevertheless, the objectives are common: to give students an overview of the professional world related to research in life sciences.

The student will be offered a short internship in a laboratory/company or a tutored project with a tutor working in a laboratory or company associated with biology.

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The objective of this course is to acquire knowledge of fundamental and applied virology, with an emphasis on an integrative vision of 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 for human and animal health. Finally, the course will present the study methods used in research, virological detection and diagnosis tools, and the applications of viruses in biotechnologies.

The course will consist 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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