L3 - Biotechnology-Biotracability-Bioresources

This course offers an in-depth study of the structural biochemistry of biomolecules, particularly proteins and nucleic acids.

The basic notions and nomenclature used for the analysis of 3D structures of proteins are briefly reviewed (Ramachandran diagram, structural motif and domain, folding, family, superfamily, etc......). These notions are completed by the study of the stability and dynamics of biomolecules.

The structural classification of proteins is detailed according to the 4 main folding types. Structure-function relationships are illustrated with examples of proteins. The specificities of membrane protein structures (integral proteins, membrane-bound proteins) are discussed.

The main tools for modeling and predicting secondary and tertiary structures are presented.

The different structures and functions of nucleic acids are studied. Protein-nucleic acid complexes are described from a structural point of view (main recognition motifs, ...) and the notions of recognition specificity are detailed.

This teaching is illustrated by tutorials. These works consist in getting familiar with the main databases used in structural biology as well as with the PyMol software for the analysis of 3D structures.

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The objective of the UE is to bring the students to understand the tripartite between security - legislation - detection tools. Human activity to meet the needs of growth, welfare and health of populations requires the monitoring of industrial practices. Rules of limit levels of pollutants and others imply acceptable limits that must be able to quantify.

The EU deals with the European laws on food safety which imply pragmatic approaches to compliance with the laws of the industries: the normative system. The student of biology who will be led to the different sectors of activity, from agronomy to health, must know the fundamental bases of quality management.

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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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In this course, students will conduct bibliographic research on a selection of medicinal plants during tutorials in order to identify the biomolecules of the plant that may have biological or pharmacological properties. Each group will use documents provided to them to identify, propose and implement an extraction protocol and a simple biological activity test protocol to test the biostatic, antibiotic or antioxidant activity of the targeted molecules. The bibliographic monitoring approach and the results obtained during the practical work, as well as their analysis and interpretation, will be discussed during a poster presentation session, which will result in an evaluation.

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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 course introduces the basic concepts of nanobiotechnologies dedicated to diagnosis and detection.

1- Introduction to biosensors and embedded systems

The different types of electrochemical sensors (conductimetry, potentiometry and amperometry): - Biosensors from the Clark electrode to the amperometric glucose meter. - The potentiostat: simple system of standardized measurement

- Transistors: semiconductors

- carbon nanotubes or wires, silicon, graphene, ...

- Impedance measurement

2- Introduction to biomimicry

- Self-assembly of spherical structure; viruses, ferritin, dendrimers

- Self-assembly of monolayers

3- Functional organic chemistry

            - L1 organic chemistry reminder

            - Biomolecules (involved functions, carbonyl, amines, alcohols, thiols)

            - Structures

            - Basic concept of functionalization

            - Oxidation-reduction reaction

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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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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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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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The objective of the course is to review the molecular techniques of identification with emphasis on biomarkers, advances in the latest generations of biomarkers and selective membranes as well as new instrumentations.

Molecular diagnostic techniques / massive approaches.

Biosynthesis of B cell and T cell Ag receptors 

Antigen-antibody reactions 

Immunological techniques 

Principle of FACS

Proteomics, 2D, LC-MS, MS-MS. Degradome...

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The course provides a deeper understanding of the design of biosensors. It begins to give the general notions of grafting chemistry for the functionalization of supports. Finally, an introduction to microfluidics will lead the students to design the instrumentation. This teaching will be essentially a practical application with a real bibliographic research that will allow the student to work on his own project of instrumental development.

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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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