L3 - Microbiology

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

Quantitative and qualitative analysis of the bacterial population present in a soil sample is classically done by identifying species using conventional bacteriological methods in successive stages: 1) isolation of bacterial flora; 2) diagnosis of family and genus using conventional media and tests; 3) diagnosis of species using API System galleries.

Molecular biology techniques now make it possible to identify the bacteria present in a sample without the need for cultivation. This approach requires access to a sequencing platform and will also be carried out as part of the practical work, enabling the two approaches to be compared. The sequencing results obtained will enable bioinformatic analysis of the rrsA gene specifying the RNA16S of isolated bacteria.

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This course describes the methodology used by life science researchers to communicate the results of their experiments, both orally and in writing. 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 (macro) structuring 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 supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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This EU is the logical continuation of the S4 EU (Basics of physiology and immunology) and aims to deepen knowledge of fundamental, applied and clinical immunology. We will also cover "unconventional" immunology and develop innovative immunotherapy strategies. The course will cover all aspects of modern immunology, with a strong emphasis on clinical aspects.

 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 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, we'll be exploring the properties of information-carrying macromolecules (DNA, RNA, proteins), and how transactions between them explain how eukaryotic cells function and adapt to the environment and to the development of organisms.

At the same time, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and analyzed in greater depth in practical sessions.

TDs will address these topics in the form of (1) exercises enabling students to check their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. In this way, the fundamentals of scientific reasoning and the critical analysis of results are 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 encompass a range of technologies that use plant organisms and their cells to produce and transform food products, biomaterials and energy, as well as recombinant proteins for therapeutic purposes.

• Animal biotechnology covers the fields of health, drugs, diagnostics and tissue engineering, as well as the development of genetic or molecular processes for therapeutic purposes.
• Microbial biotechnologies involve the use of micro-organisms (viruses or bacteria) and their cultivation in the agri-food/pharmaceutical industry, as well as their use in environmental protection.

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

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This course is designed to deepen the knowledge of microbiology for students wishing to continue their studies in this discipline.

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

Bacteria with special morphology will be presented.  

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

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

Lastly, the EU will look at the concept of the microbiota and present the latest data on the nature of the human microbiota and its role in health.

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Bacteriology :

Through various examples, students will gain a better understanding of the notion of pathogenicity in relation to bacterial virulence. The means and mechanisms used to manipulate the organism's cells at mucosal level in order to penetrate the internal 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 group behavior. The description of some examples of toxins and modulins in relation to colonization and/or invasion will provide a better understanding of the differences in strategies between prokaryotic pathogens. Finally, we'll look at the notion of the microbiota and its influence on the functioning of the organism, as well as its implication in the development of certain pathologies.

Immunology:

The Immunology section outlines the workings of the immune system during infection. From the establishment and development of the inflammatory reaction upon recognition of non-self signals by natural immunity (PRR-PAMP), to the mechanisms of cell activation and the cellular responses generated, we can appreciate the diversity of possibilities offered by the different players in the immune system. 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 vaccine strategy. Finally, immunity of the intestinal mucosa will be addressed in the context of the relationship between the host and the microbiota.

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The main aim of this module is 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 and the experimental and theoretical approaches that led to their construction. For example, we'll look at 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 Etienne Geoffroy Saint Hilaire's concept of "unity of organization plan" is at the origin of evolutionary paleontology, developmental biology and evolution/development (Evo/Devo).

In the context of bioethics, we'll look at the problems of conceptual drift (from craniology to eugenics), or the cases of "Georges Cuvier" and "Trophim Lyssenko" when religious or political ideology interferes with science.

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

The entire module will be taught in lectures, during which some of the founding texts of modern biology will be analyzed and discussed.

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The Molecular Biology practical course is designed to give students autonomy when faced with a molecular biology protocol, and to introduce them to hypothesis-driven research. Students will have 6 days to respond to a biological problem proposed to them. In this way, they will be able to put into practice, under laboratory conditions, some of the techniques they have learnt in their theoretical courses, and gain a better understanding of them.

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Lessons 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: the notion of emergence and re-emergence

-vibrios, virulence factors, host adaptation and horizontal transfer

-streptococci, comparative genomics, genomic reduction, specialization

 Applications of microbial ecology to biotechnologies will include: detection, inocula production, bioproductions, bioremediation, water treatment using concrete examples (development of mutation-aware multipathogen detection tools, production of a flavor enhancer by a soil corynebacterium, applications of microbial interaction studies to cheese flavor selection, quality index of a wine-growing soil, etc.).

Practical water analysis, principles, standards, applications: total 6h

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, fecal streptococcal total coliform load from the practical work, student presentation on the different types of (micro)purification plants....) the aim is to propose a conceptual solution adapted to the field case.

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In this course, students will learn experimental principles based on the manipulation of nucleic acids. The lectures will be structured around two major themes:

1. Introduction 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.

The TDs will consist of :

- Analysis of articles presenting problems to be solved with the knowledge acquired in the course. As far as possible, the themes chosen will refer to the parallel UEs of L3. These articles will be presented by students in the form of oral presentations in groups of 3 or 4 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 our knowledge of eukaryotic microorganisms, and in particular to explore the diversity of eukaryotic unicellular organisms with free-living or parasitic lifestyles. This diversity will be studied not only from a theoretical point of view, but also from a practical one. Indeed, the specific developmental and lifestyle characteristics of four unicellular microorganisms (the social amoeba Dictyostelium discoideum, the ciliate Tetrahymena, and the apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum) will be studied in practical work, illustrating the concepts covered in lectures and practical sessions.

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The modalities of this UE are specifically adapted to the different L3 courses. Nevertheless, the objectives are the same: to give students an insight into the professional world of life science research.

Students 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 aim 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 specific features of host-virus interactions and the pathophysiology of viral infections in different host types (vertebrates/insects/plants). It will cover 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 biotechnology.

The course will include 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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