DFASP2 research stream

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The Practical GIS course provides training in the use of Geographic Information Systems (GIS), including basic concepts of geographic information and mastery of the free software QGIS. The majority of the course is devoted to an introduction to GIS, alternating between lectures and practical exercises. At the end of the course, a personalized cartographic project enables students to reorganize the concepts they have already learned. An introductory conference with professionals puts into perspective the interest of GIS approaches in general hydrology.

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The general aim of this course is to develop the concepts needed to study symbiotic interactions, whether parasitic or mutualistic. To this end, we will address the specificities and ubiquity of the parasitic way of life in the tree of life. The defense mechanisms of host organisms, the notions of favoritism and manipulation, the consequences of host-symbiont interactions on life-history traits and the influence of these interactions on the diversification of organisms will be addressed.

Practical work will provide an opportunity to explore these concepts in greater depth on some major models of interactions involving symbionts (viruses, bacteria, unicellular and multicellular eukaryotes) and a variety of hosts (unicellular and multicellular).

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This course aims to reinforce and illustrate the knowledge acquired in the "Molecular Bases of Infectious Diseases" course by analyzing scientific publications on infectious diseases. Publications using a variety of molecular and cellular approaches in Bacteriology, Parasitology and Virology (from the most classical to the most recent) are analyzed with the students.

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Behaviors, whether determined by conscious or unconscious processes, are based on complex neurobiological underpinnings: they are underpinned by molecular and cellular modifications within the nervous system, modulating neural networks at the origin of motor and emotional processes that are linked to the individual's memory. These processes are fundamental in enabling the organism to develop an integrated behavioral response in close interaction with its environment, ensuring adaptation and survival for the individual and its species.

The topics covered in the Neurobiology of Behavior course are as follows:

-Gene-behavior

The relationship between genotype and phenotype -Impact of the environment -Attentional processes/Movement planning -Behavioral disorders (genetic and environmental aspects)

-Memory and synaptic plasticity

Methodological approaches to studying synaptic plasticity: electrophysiology, optogenetics, animal models, behavioral tests-Factors regulating synaptic plasticity, including genetics and epigenetics-Plasticity/memory relationship-Neurobiology of memory, forgetting and reconsolidation

-Neurobiology of emotions

Neurobiological substrates of emotions -Emotional functions -Disadaptation: Pathological aspects: Emotional disorders

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Optimized management and protection of water resources (both surface and groundwater) requires water quality to be taken into account. Assessment of the quality status of water bodies, particularly with regard to current legislative frameworks, is based on precise chemical and microbiological quality criteria, as well as standards adapted to the types of use envisaged for these resources.

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This teaching unit is shared with MI students in the Chemistry Master's courses: ICAP P1, ICAP P2, MAT P1, MAT P2, BM (semester S2). The following topics will be covered:

• The 12 Principles of Green Chemistry and units of measurement in Green Chemistry ;
• Synthesis strategies for sustainable chemistry ;
• Alternative or eco-compatible solvents for synthesis and extraction;
• Non-conventional activation techniques and applications.

CM: 13

TD: 7 H

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The program offers a refresher course and an in-depth study of the major concepts and methodologies of cell biology, organized around different themes:

1 Cytoskeleton:Introduction to the different types of cytoskeleton. Polymerization properties of actin and tubulin. Proteins associated with the cytoskeleton and regulating polymerization. Molecular motors. Principles of cell migration.

2.cell adhesion & signaling: cell-cell and cell-extracellular matrix adhesive structures, their molecular organization and dynamics. Functions and regulation during development and pathogenesis. Regulation by signaling pathways. Mechanotransduction.

3 Addressing and cell trafficking: Ubiquitination and proteasome. Addressing to subcellular compartments, endocytosis and secretion pathways. Molecular basis of vesicular transport, budding, fusion, molecular motors. Signaling in membrane trafficking, trafficking-related genetic diseases and pathogen detour.

4 Cell cycle: Historical introduction. Molecular regulation of the cell cycle. The mitotic spindle, microtubule dynamics and molecular motors, chromosome attachment mechanisms, checkpoints, regulation of mitosis exit and cytokinesis. Mitotic disorders associated with cancer cells.

5 Stem cells: cell differentiation, toti-, pluri- and multipotency, embryonic, adult and cancer stem cells.

6 Programmed cell death: Apoptosis, autophagy, necrosis. Stages and modalities of apoptosis, signaling pathways involved. Role in maintaining homeostasis. Pathophysiological consequences of deregulation of programmed cell death.

Different study models are presented, to introduce the importance of the contribution of biological diversity to the discovery of cellular and molecular mechanisms, and to the understanding of human pathologies.

The program offers a refresher of knowledge and an in-depth study of the major concepts and methodologies of cell biology, organized around different themes:

1. Cytoskeleton: Introduction to the different types of cytoskeleton. Polymerization properties of actin and tubulin. Proteins associated with the cytoskeleton and regulating polymerization. Molecular motors. Principles of cell migration.

2. Cellular Adhesion & Signaling: Cell-cell and extracellular cell-matrix adhesive structures, their molecular and dynamic organization. Functions and regulations during development and pathogenesis. Regulation by signaling channels. Mechanotransduction.

3. Addressing and cell traffic: Ubiquitination and proteasome. Addressing to subcellular compartments, endocytosis and secretion pathways. The molecular bases of vesicular transport, budding, fusion, molecular motors. Signaling in membrane trafficking, genetic diseases linked to trafficking and diversion by pathogens.

4. Cell cycle: Historical introduction. Molecular regulation of the cell cycle. The mitotic spindle, microtubule and molecular motor dynamics, chromosome attachment mechanisms, checkpoints, regulation of mitosis output and cytokinesis. Mitotic disorders associated with cancer cells.

5. Stem cells: cell differentiation, toti-, pluri-and multipotency, embryonic, adult and cancer stem cells.

6. Programmed cell death: Apoptosis, autophagy, necrosis. Stages and modalities of apoptosis, signaling pathways involved. Role in maintaining homeostasis. Physiopathological consequences of deregulation of programmed cell death.

Different study models are presented, in order to introduce the importance of the contribution of biological diversity in the discovery of cellular and molecular mechanisms, as well as in the understanding of human pathologies.

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This UE consists mainly of theoretical courses dealing with the molecular aspects of infectious diseases (bacteriology, virology, parasitology).

Bacteriology: The nature of infectious agents. Methods for studying pathogenesis (in vivo, in vitro, in silico and post-genomic study technologies) Strategies of pathogenic bacteria to survive in organisms: Bacterial adhesion to eukaryotic cells, antigenic variation and phase variation, invasion of non-phagocytic eukaryotic cells, mechanisms of resistance to phagocytosis, mechanisms of bacterial survival in phagocytic cells, membrane permeability management, bacterial secretion systems (types I, II, III, IV, V and VI), iron acquisition mechanisms, bacterial exotoxins, bacterial biofilms, examples of environmental regulation (thermoregulation, quorum sensing, etc.).).

Parasitology: Organization and cellular physiology of major pathogens in unicellular eukaryotic parasites (invasion and modification of the host cell; metabolic particularities and therapeutic targets); Genetics and molecular biology (genome organization, antigenic variation); Physiopathology and escape from the immune response.

Virology: Molecular mechanisms of the viral cycle; Expression of viral genomes; Transformation by viruses; Viral replication strategy; Plasticity of viral genomes; Structural importance of viruses in host interaction; 

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1) What is the genetic program underlying the development of the nervous system? This course highlights the type of decisions that gradually determine the neural destiny of cells and ensure their nervous function. The different stages considered are:

(i)the genesis of the nervous system

(ii)neuron specification

(iii)nerve function: axonal guidance and connectivity

(iv)neuronal remodeling

2) What molecular, cellular and environmental interactions control the development of the nervous system?

-Synaptogenesis and the major stages of development.

-The role of neurotrophic factors

-The role of electrical activity

-Critical periods

-The role of neuron-glial cell interactions.

-Neural stem cells

3) Developmental pathologies

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Teaching is done by teachers and/or researchers at the Faculties of Medicine, Sciences or Pharmacy, or at local research institutes.Course contents will be adapted to current scientific advances.

Teaching is organized in topics (lectures/tutorials, 4 to 5:30 hrs each);each includes an introduction and a seminar. In addition, for each topic, a group of students is in charge of presenting one or two recent scientific research articles.

Examples of subjects treated:

Immune adaptive responses, vaccination

Immune tolerance

Aging of the immune system

Metabolic regulation of the immune response

Immune response regulation by microbiota

Immune system-central nervous system interactions

Immunotherapy, therapeutic antibodies

The Unit is complemented by practical work by groups on a mini-research project that includes design of experiments, realization and analysis. Training is available in the use of flow cytometry data analysis software.Results are presented orally to the entire class.

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In bioprocess engineering, knowledge of the metabolism of catalysts (cells, microorganisms) is essential. This course will focus on describing the diversity of microbial metabolites (primary and secondary metabolites) and the bioprocesses that use these microorganisms to produce these molecules.

This course includes interactive lectures, tutorials and practical exercises (practical work in the computer room + personal project work in small groups).

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Proteins are now widely used as therapeutic tools in human and animal health. Knowledge of peptide and protein synthesis pathways, folding and post-translational modifications is essential before any therapeutic protein biosynthesis can be envisaged. Methods to better characterize these proteins are also essential to guarantee the quality of the proteins produced for therapeutic or industrial use. Protein engineering methods designed to improve their original properties will also be discussed.

The course includes lectures and tutorials by teacher-researchers and researchers.

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RMN :

Liquid-phase NMR (Nuclear Magnetic Resonance) is an essential spectroscopic analysis method for chemists, enabling them to determine the structure of small organic molecules or macromolecules in solution, to study dynamic phenomena... The aim of this course is to understand the phenomena involved in this technique and to relate them to the different structural information accessible by this method. The aim is to be able to exploit the spectral data obtained from this analysis to elucidate the structure and stereochemistry of organic molecules or polymer structures, or to monitor reactions.

X-ray diffraction :

X-ray diffraction is a powerful, non-destructive technique not only for characterizing the crystalline structure of materials, but also for providing crystallographic and structural information such as lattice parameters and atomic positions. This includes all crystallized materials such as ceramics, materials for the storage and transformation of energy and information, as well as organic molecules and metal complexes (interatomic distances and angles, stereochemistry (chirality, stereoisomerism...), intra- and intermolecular bonds...). The aim of this course is to provide an introduction to crystallography and diffraction, with the aim of understanding the operation and characteristics of an X-ray diffractometer, as well as interpreting diffraction patterns (structural analysis, lattice parameters).

Hourly volumes* :

            CM: 10

            TD : 10

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Knowledge of gas chromatography and mass spectrometry techniques with electron impact ionization and quadrupole mass analyzer for the analysis of volatile organic molecules.

1) GC-MS analysis of volatile organic compounds :

• Electron impact ionization (EI) techniques
• Chemical ionization (CI) techniques
• Quadrupole (Q) analysis techniques
• GC/MS coupling

2) Applications in organic chemistry analysis and characterization of volatile samples.

Hourly volumes* :

CM: 15 H

TD: 5 H

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The aim of the medicinal chemistry course is to introduce students to the key stages in the process of developing molecules with biological activity. In particular, a description of the interactions involved, the notion of pharmocophores, bio-isosteria, etc., as well as structure-activity relationship studies will be covered, enabling students to envisage appropriate strategies and structural modifications.

Hourly volumes* :

WC: 3 p.m.

TD: 5 h

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This UE is sequenced according to the following activities: First steps - R environment; R structures; Input-output in R; Manipulating R structures; Basics of algorithmics; Programming structures in R; Group mini-project on an R function to be created on an applied 'Water' problem.

Objectives* :

The objectives of this course are 1) to introduce the basics of the interpreted language of an engineering tool (environment, structures, input-output, manipulations of structures, graphics, programming), 2) to provide the fundamental theoretical knowledge needed to create one's own functions and programs based on practical examples in water science, and 3) to enable students to pursue their self-training and expertise in R.

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Teaching is carried out by teacher-researchers from the UFRs of Medicine, Science and Pharmacy. It is organized into 42 hours of lectures and supervised work divided into 7 themes (see Syllabus) including 2 series of article presentations; 1 series on articles proposed by the lecturers in each theme. A second series on articles chosen by the students. At the end of the course, students organize a mini-colloquium at which the articles are presented. They write brief reviews of these articles for the journal Medecine-Sciences.

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Knowledge of the latest mass spectrometry techniques for the qualitative analysis of organic molecules and biomolecules.

1) Description of fundamental principles (Ion Science and Technology) :

- Ionization techniques

- Analysis techniques

- Tandem mass spectrometry (MS/MS)

- LC/MS and LC/MS/MS couplings

2) Application in biomolecule analysis and organic chemistry reaction monitoring.

Hourly volumes* :

CM: 15 H

TD: 5 H

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This course is designed to teach liquid and gas chromatography.

Hourly volumes* :

            CM :15h

            TD: 5h

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The aim of the "Cellular Physiopathology and Cancer" course is to provide students with the knowledge they need to follow the "Cancer Biology" pathway in M2. The course is organized in the form of a lecture, with an introductory section followed by a section on current laboratory research. Students are required to present a scientific article orally (usually in pairs).

The aim of the cellular pathophysiology and cancer teaching unit is to provide the scientific background necessary to follow the cancer biology M2 program.Each lecture is organized as a conference starting with a general introduction of the field and followed by a more specialized emphasis on research done in laboratories. Students have to prepare an oral presentation based on the analysis of a scientific article (generally in pair).

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Within biotechnology, bioprocesses correspond to the industrial application of living tools (whether enzymes, microorganisms or cells from higher organisms) for the synthesis of products of interest. This teaching unit will focus on the use of microbial and cellular catalysts. Products of interest may be, for example, fermented foods (wine, beer, etc.), energy molecules (bioethanol, methane, etc.), chemical intermediates, or biomedicines (vaccines, monoclonal antibodies, growth factors, etc.). The knowledge, know-how and skills acquired in this course can be transposed to any sector of biotechnology activity. The examples given will correspond to the outlets targeted by the two courses (Agrosciences and Health).

The course will focus on bioprocesses and the environment in which the biological reaction will be controlled (the bioreactor). The course will also cover the description and modeling of a biological reaction, with a presentation of the approach applied in bioprocess engineering. The remainder of the course will be devoted to the application of this approach to batch reactors. Other operating modes will be covered in the M2 course HAV930V "Bioprocess engineering - continuous and fed-batch".

This course includes interactive lectures, tutorials and practical exercises (practical work in the computer room + personal project work in small groups).

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This teaching unit is dedicated to deepening the foundations of organic chemistry and coordination chemistry covered in L3, and acquiring notions linked to molecular engineering and molecular chemistry. The course comprises lectures and tutorials. Students will work in advance of certain lectures and tutorials, with course documents provided, to ensure that the lectures and tutorials enable them to play a full part in the course, understand the concepts presented and the skills to be acquired. A progression program and activities will be proposed. For students who have not seen the basics of coordination chemistry and organic chemistry, documents will be made available.

Coordination chemistry: The course will cover various aspects of transition metal and lanthanide complexes, molecular materials (polynuclear complexes and coordination polymers with extended structures (MOFs, etc.)), their properties and applications. Structural aspects, bonding description, properties, as well as stability and reactivity aspects will be covered. Emphasis will be placed on the complexation effect and stability of metal, lanthanide and actinide complexes with certain ligands, with a view to applications in the biomedical field (imaging and therapy), decontamination (nuclear field), etc. The electronic (relaxivity, magnetism) and optical (absorption, luminescence) properties of these complexes will be discussed and put into the context of applications in various fields, such as imaging, electronics, sensors, etc.

Organic Chemistry: This course builds on the knowledge acquired in the Bachelor's degree, and will involve a reasoned study of the main reaction mechanisms in organic chemistry, providing a common foundation for all students in the Chemistry Master's program. The main processes (substitution, addition, elimination, transposition...) and their essential characteristics and applications to mechanistic sequences will be examined. The course is designed to provide students with general tools for analyzing mechanisms (ionic, radical, concerted) in order to grasp their variety.

Hourly volumes* :

CM: 13 H

TD: 7 H

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The course is organized into 3 main chapters, alternating with tutorials applied to engineering problems. In the first part, after describing the planet's major water reservoirs and the basic principles of the water cycle, the effects of human activities on the cycle are discussed. The second part focuses on the aerial part of the cycle, from precipitation to infiltration. The third part deals with aquifers and groundwater, from the pore to the catchment scale.

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The main communication pathways between normal cells and the intracellular transduction pathways encountered in physiological and neurophysiological mechanisms will be covered, with a focus on G protein-coupled receptors (GPCRs) and their structure, function and modulation by interacting proteins, notably involved in desensitization. The main intracellular pathways activated by GPCRs will be discussed (MAPkinase, PI3kinase, etc.).

A major part of the course will then focus on calcium signaling and Ca2+ homeostasis, Ca2+ being a ubiquitous signal in cell signaling. Calcium homeostasis will be studied in particular during the lymphocyte response to antigenic stimulation. In addition, the production of oxygenated free radicals, at the origin of oxidative stress, is dependent on intracellular Ca2+. The physiological role of free radicals will be discussed, as well as their involvement in oxidative stress. The following chapter will focus on the endocannabinoid system, summarizing all the topics covered earlier in the course. The endocannabinoid system is at the origin of multiple central and peripheral regulations.

Finally, two other themes will be addressed: the blood-brain barrier, which evokes highly integrated cellular communication between two environments, and the -pancreatic cell, whose activity is crucial to the regulation of glycemia through insulin secretion.

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-A general introduction to Developmental Biology

How do cells build a multicellular animal organism from a single genome? Genotype/phenotype relationship.

-Genetic analysis reminders

Nature of mutations (loss-of-function; gain-of-function), notion of "master gene", clonal analysis (generation of somatic or germinal clones), notion of cell autonomy....

-Genetic models and methods.

Study of regulatory regions, establishment of transgenic lines, enhancer trap, reporter genes (GFP, mCherry...), model organisms (drosophila, c.elegans, mouse...).Use of FLP/FRT, CRE-LOX, UAS-GAL4-GAL80, AttpP/B-PhiC31, CRISPR systems etc.

-Positional information, maternal effect genes and the establishment of asymmetry.

Models and mechanisms of positional information =induction, Spemann and Mangold experiment, organizing centers, notion of morphogen in invertebrates and vertebrates

-Establishment of axes: antero-posterior, dorso-ventral.

Cell communication and signalling pathways: in the establishment of the dorso-ventral axis, in limb formation, in the establishment of cell fate (some examples: Nervous system: lateral inhibition processes ...).

-Segmentation: gap, pair rule and segment polarity genes.

Segmentation in invertebrates and somitogenesis in vertebrates, dynamic aspects (establishment and maintenance).

-Signaling and transcriptional networks

Transcriptional regulation during development, regulatory sequences during evolution, the concept of gene networks. Transcriptional coupling and signaling pathways in cell fate

-Epigenetic memory of transcriptional programs:

Hox homeotic genes and segmental identity.Evo-Devo concepts.Polycomb and Trithorax complexes.

Involvement of epigenetic mechanisms in cell differentiation

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