L3 - Microbiology

This laboratory session is designed to help students apply their 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 steps: 1) isolation of the bacterial flora; 2) identification of the family and genus using conventional media and tests; 3) identification of the species using API System galleries.

Molecular biology techniques now make it possible to identify the bacteria present in a sample without the need for culture. This approach requires access to a sequencing platform and will also be carried out during lab sessions, which will allow for a comparison of the two approaches. The sequencing results obtained will enable a bioinformatics analysis of the rrsA gene encoding the 16S rRNA of the isolated bacteria.

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

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

These courses are supplemented by a supervised project during the semester, in which students are required to analyze a research article recently published in the scientific literature and present it as an oral presentation (lecture) in English.

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This course unit serves as a logical continuation of the S4 course unit (Fundamentals of Physiology and Immunology) and aims to deepen students’ knowledge of basic, applied, and clinical immunology. We will also explore “non-conventional” concepts in immunology and discuss innovative immunotherapy strategies. This course will cover all topics related to modern immunology and will have a strong focus on the clinical aspects of this discipline.

 Keywords

Basic Immunology, Anti-infectious Immunity, Immunotherapy, Vaccination, Autoimmunity, Immunodeficiencies, Anti-cancer Immunity, Non-conventional Immunity

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

The EU is deepening our understanding of the mechanisms underlying 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 the interactions between them account for the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

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

Thus, the tutorials address these topics through (1) exercises that allow students to assess their understanding of the concepts described above, and (2) experiments drawn from scientific articles for analysis. In this way, students will acquire and/or deepen their understanding of the fundamentals of scientific reasoning and the critical analysis of results.

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This course covers the various categories of biotechnology according to their fields of application:

• Plant biotechnology relates to the agri-food sector and encompasses a range of technologies that use plant organisms and their cells to produce and process food products, biomaterials, and energy, as well as recombinant proteins for therapeutic purposes.

• Animal biotechnology encompasses the fields of health, pharmaceuticals, diagnostics, and tissue engineering, as well as 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 food and pharmaceutical industries, as well as their role in environmental protection.

The curriculum for students in the third year of the Bachelor’s degree in Life Sciences is designed to enable them to discover or deepen their theoretical knowledge of various biotechnologies and to master the associated tools and applications.

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This course unit is designed to deepen students' knowledge of microbiology for those who wish to continue their studies in this field.

It will cover molecular genetics as applied to prokaryotes (mobile genetic elements and resistance, CRISPR, the two-component system, quorum sensing, horizontal gene transfer, etc.) and the specific characteristics of bacterial metabolism.

Bacteria with distinctive morphologies will be presented.  

In virology, the pathophysiology of viral infections, as well as the prevention and control of viral diseases, will be presented. The mechanisms by which viruses evade the immune system will be discussed in detail. The 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 obligate intracellular development and the changes in the host cell induced by these parasites.

The EU will finally address the concept of the microbiome and present the latest data on the nature of the human microbiome 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 methods and mechanisms used to manipulate the body’s cells at the mucosal level in order to penetrate the internal environment—that is, invasive potential—will be discussed, as well as the perception of environmental signals and the integration of these signals to coordinate the response of prokaryotes so that they exhibit collective behavior. A description of several examples of toxins and modulins associated with colonization and/or invasion will provide a better understanding of the differences in strategies among prokaryotic pathogens. Finally, we will address the concept of the microbiota and its influence on the body’s functioning, as well as its role in the development of certain diseases.

Immunology:

The Immunology section provides an overview of how the immune system functions during infection. From the initiation and progression of the inflammatory response upon the recognition of non-self signals by the innate immune system (PRR-PAMP) to the mechanisms of cell activation and the resulting cellular responses, we can appreciate the diversity of possibilities offered by the various components of the immune system. Furthermore, the sequence of events leading to the direction of the immune response and the acquisition of lasting protection during the adaptive phase will provide a better understanding of 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 as well as the experimental and theoretical approaches that led to their formulation. 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 Etienne Geoffroy Saint-Hilaire’s concept of the “unit of organizational plan” gave rise to evolutionary paleontology, developmental biology, and evolution and development (Evo/Devo).

In the context of bioethical issues, we will address problems such as the misuse of a concept (from craniology to eugenics) as well as the cases of “Georges Cuvier” and “Trophim Lysenko,” in which religious or political ideology interferes with science.

Finally, the philosophy of biology will lead us to discuss the value of models in biology and the “end of the ‘all-genetic’ paradigm” (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 training course aims to enable students to work independently on a molecular biology protocol and to introduce them to hypothesis-driven research. Students will have six days to address a biological problem that will be presented to them. This will allow them to apply, under laboratory conditions, some of the techniques covered in their theoretical coursework, thereby gaining a better understanding of them.

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The course will cover the fundamentals and principles of microbial ecology (microbial biodiversity; cultivable and non-cultivable microorganisms;   major microbial groups, key microbial functions and biogeochemical cycles, microbial metabolism in the environment and environmental applications, and the fundamentals of ecology as they apply to microorganisms (microbial interactions, free-living organisms, competition, collaboration, symbiosis, parasitism, and their applications). The following topics will be specifically addressed as examples:

- Viruses: the concepts of emergence and re-emergence

-Vibrios: virulence factors, adaptation to the host, and horizontal transfer

-streptococci, comparative genomics, genomic reduction, specialization

 Applications of microbial ecology to biotechnology will include: detection, production of inocula, bioproductions, bioremediation, and water treatment, using concrete examples (development of multipathogen detection tools that account for mutation; production of a flavor enhancer by a soil corynebacterium; applications of microbial interaction studies to the selection of cheese flavors; a quality index for vineyard soil, etc.)

Practical Course: Water Analysis—Principles, Standards, and Applications: 6 hours total

Tutorial/independent work based on the results of the lab: design of a water treatment model for a real-world scenario (cadastral data, topographic survey, total fecal coliform and streptococcal load from the lab, student presentations on the various types of (micro) wastewater treatment plants, etc.) The goal is to propose a conceptual solution tailored to the specific site conditions.

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As part of this course unit, students will learn the experimental principles involved in working with nucleic acids. The lectures will focus on two main areas:

1. Development of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, the CRISPR/Cas9 system, etc.) and reflection on ethical issues in biology.

The tutorials will consist of:

- Analysis of articles presenting problems to be solved using the knowledge gained in the course. The chosen topics will, as much as possible, relate to parallel course units in the third year of the bachelor’s program. Students will present these articles in the form of oral presentations, in groups of 3 to 4 students, to the entire class.

- Sessions dedicated to using basic bioinformatics tools in the computer lab.

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This course aims to deepen students’ understanding of eukaryotic microorganisms and, in particular, to explore the diversity of free-living and parasitic eukaryotic unicellular organisms. This diversity will be studied from both theoretical and practical perspectives. Specifically, the unique developmental characteristics and lifestyles of four unicellular microorganisms—the social amoeba Dictyostelium discoideum, the ciliate Tetrahymena, and the apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum—will be examined during laboratory sessions, thereby illustrating concepts covered in lectures and tutorials.

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The structure of this course is specifically tailored to the various tracks within the L3 program. Nevertheless, 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 or company, or a supervised project with a mentor working in a laboratory or company related to biology.

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

The course will consist of lectures, tutorials (analysis of current scientific articles and oral presentations), and practical exercises that illustrate the material covered in the lectures and tutorials (virus amplification and purification, and quantification using standard techniques).

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