L3 - Microbiology

This practical work unit aims to apply students' knowledge of microbiology and molecular biology to identify bacteria in the environment.

Quantitative and qualitative analysis of the bacterial population present in a soil sample is typically performed by identifying species using conventional bacteriological methods in successive stages: 1) isolation of the 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 bacteria present in a sample without the need for culture. This approach requires access to a sequencing platform and will also be carried out in practical work, allowing the two approaches to be compared. The sequencing results obtained will enable bioinformatic analysis of the rrsA gene specifying the 16S RNA of the isolated bacteria.

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This course describes the methodology used by life science researchers 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 English.

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

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

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This EU is a logical continuation of the S4 EU (Fundamentals of Physiology and Immunology) and aims to deepen knowledge of fundamental, applied, and clinical immunology. We will also address "unconventional" concepts in immunology and develop innovative immunotherapy strategies. This course unit will cover all topics related to modern immunology and will be strongly oriented towards the clinical aspects of this discipline.

 Keywords

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

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Molecular biology is not only a fascinating subject in its own right, but it also provides other biological disciplines (cell biology, genetics, physiology, etc.) with fantastic tools for modifying and quantifying genes and their products.

The EU is deepening its understanding of the mechanisms involved in the organization, maintenance, replication, and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

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

At the same time, the main techniques used to monitor or modify gene expression, or to study the mechanisms of this expression, will be presented in lectures and explored in greater depth in tutorials through the analysis of results.

Thus, the tutorials address these topics in the form of (1) exercises that allow students to test their understanding of the knowledge described above, and (2) experiments taken from scientific articles for analysis. In this way, the fundamentals of scientific reasoning and critical analysis of results will be acquired and/or further developed.

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

• Plant biotechnology concerns the agri-food industry and encompasses a range of technologies that use plants and plant 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, medicine, diagnostics, tissue engineering, and the development of genetic or molecular processes for therapeutic purposes.
• Microbial biotechnology involves the use of microorganisms (viruses or bacteria) and their cultivation in the agri-food/pharmaceutical industry, as well as their role in environmental protection.

The teaching offered to students in the Bachelor's Degree in Life Sciences enables them to discover or deepen their theoretical knowledge of different biotechnologies and to master the associated tools/applications.

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This course unit aims to deepen students' knowledge of microbiology for those who wish to pursue further studies in this discipline.

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

Bacteria with a particular morphology will be presented.  

In virology, the pathophysiology of viral infections, as well as the prevention and control of viral diseases, will be presented. Mechanisms of immune evasion will be detailed. Mechanisms of viral evolution will be described and linked to viral emergence.

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

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

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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 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 journey and the experimental and theoretical approaches that led to their establishment. 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, and how how Etienne Geoffroy Saint Hilaire's concept of "unity of plan of organization" gave rise to evolutionary paleontology, developmental biology, and evolution/development (Evo/Devo).

In the context of bioethical issues, we will address problems such as the distortion of a concept (from craniology to eugenics) and the cases of Georges Cuvier and Trophim Lysenko, where religious or political ideology interfered with science.

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

The entire module will consist of lectures, during which several seminal texts in modern biology will also be analyzed and discussed.

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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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This EU aims to deepen knowledge of eukaryotic microorganisms and explore in particular the diversity of free-living or parasitic eukaryotic unicellular organisms. This diversity will be studied not only from a theoretical but also from a practical point of view. The specific characteristics of the development and lifestyle of four single-celled microorganisms (the social amoeba Dictyostelium discoideum, the ciliate Tetrahymena, and the apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum) will be studied during practical work sessions, illustrating the concepts covered in lectures and tutorials.

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The terms and conditions of this course unit are specifically tailored to the different L3 programs. However, the objectives are the same: to give students an overview of the professional world related to life sciences research.

Students will be offered a short internship in a laboratory/company or a supervised project with a tutor working in a laboratory or company associated with biology.

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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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