DFASP2 Research Program

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The GIS Practice course consists of training in the use of Geographic Information Systems, incorporating basic concepts relating to geographic information and proficiency in the free software QGIS. Most of the course is devoted to an introduction through a combination of lectures and practical exercises. A personalized summary mapping project allows students at the end of the course to review the concepts they have learned. An introductory lecture with professionals provides perspective on the value of GIS approaches in general hydrology.

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The overall objective of this course unit is to explore the concepts necessary for studying symbiotic interactions, whether parasitic or mutualistic. To this end, we will examine the specific characteristics and ubiquity of the parasitic lifestyle in the tree of life. The defense mechanisms of host organisms, the concepts of facilitation and manipulation, the consequences of host-symbiote interactions on life history traits, and the influence of these interactions on the diversification of organisms will be discussed.

The practical work will provide an opportunity to explore these concepts in greater depth using certain major models of interactions involving symbionts (viruses, bacteria, unicellular and multicellular eukaryotes) and various hosts (unicellular and multicellular).

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This course aims to reinforce and illustrate the knowledge acquired in the course "Molecular Bases of Infectious Diseases" by analyzing scientific publications on infectious disease topics. Publications using a variety of molecular and cellular approaches in bacteriology, parasitology, and virology (from the most traditional to the most recent) are analyzed with students.

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Behaviors, whether determined by conscious or unconscious processes, are based on complex neurobiological substrates. They are underpinned by molecular and cellular changes within the nervous system that modulate the neural networks responsible for motor and emotional processes linked to an individual's memory. These processes are fundamental in enabling the organism to develop an integrated behavioral response in close interaction with its environment, thereby ensuring the adaptation and survival of the individual and their species.

The topics covered in the Behavioral Neurobiology course will be 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 genetic and epigenetic factors—The relationship between plasticity and memory—The neurobiology of memory, forgetting, and reconsolidation

-Neurobiology of emotions

Neurobiological substrates of emotions - Functions of emotions - Maladjustment: Pathological aspects: Emotional disorders

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Optimized management and protection of water resources (surface or groundwater) requires consideration of water quality. The assessment of the qualitative status of water bodies, particularly with regard to the legislative frameworks in force, is based on specific chemical and microbiological quality criteria, as well as standards adapted to the types of uses envisaged for these resources.

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

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

CM: 13

Tutorial: 7 hours

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The program offers refresher courses 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. Cellular addressing and trafficking: Ubiquitination and proteasome. Addressing to subcellular compartments, endocytosis and secretion pathways. The molecular basis of vesicular transport, budding, fusion, molecular motors. Signaling in membrane trafficking, genetic diseases related to trafficking, and hijacking by pathogens.

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

5. Stem cells: cell differentiation, totipotency, pluripotency, and multipotency; embryonic, adult, and cancer stem cells.

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

Various study models are presented to introduce the importance of biological diversity in the discovery of cellular and molecular mechanisms, as well as in understanding 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, totipotency, pluripotency, 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 course consists mainly of theoretical lectures 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 technologies) Strategies used by pathogenic bacteria to survive in organisms: Adhesion of bacteria 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, management of membrane permeability, 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: Cellular organization and physiology of major pathogens within parasitic unicellular eukaryotes (invasion and modification of the host cell; metabolic characteristics and therapeutic targets); Genetics and molecular biology (genome organization, antigenic variation); Pathophysiology and immune response evasion

Virology: Molecular mechanisms of the viral cycle; Expression of viral genomes; Transformation by viruses; Virus replication strategies; Plasticity of viral genomes; Structural importance of viruses in host interactions; 

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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 fate of cells and ensure their nervous function. The different stages considered are:

(i) the genesis of the nervous system

(ii) the specification of neurons

(iii)nerve function: axonal guidance and connectivity

(iv) neural remodeling

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

-Synaptogenesis and the major stages of development.

-Roles of neurotrophic factors

-Roles of electrical activity

-Critical periods

-Roles of neuron-glial cell interactions.

-Neural stem cells

3) Developmental disorders

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In the field of bioprocess engineering, knowledge of the metabolism of catalysts (cells, microorganisms) is essential. The EU will be dedicated to describing the diversity of valuable microbial metabolites (primary and secondary metabolites) and the bioprocesses that exploit these microorganisms to produce these molecules.

This course unit includes interactive lectures, tutorials, and practical work (practical work in the computer lab + individual project work in small groups).

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

The EU comprises lectures and tutorials, delivered by faculty members and researchers.

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NMR:

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, study dynamic phenomena, and more. The aim of this course unit is to understand the phenomena involved in this technique and to relate them to the various structural information accessible by this method. The goal is to be able to use the spectral data 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 for characterizing the crystalline structure of materials. It can also provide crystallographic and structural information such as lattice parameters and atomic positions. This includes all crystallized materials such as ceramics, materials for energy and information storage and conversion, as well as organic molecules and metal complexes (interatomic distances and angles, stereochemistry (chirality, stereoisomerism, etc.), intra- and intermolecular bonds, etc.). The objective of this course unit 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 techniques and mass spectrometry with electron impact ionization and quadrupole mass analyzer for the analysis of volatile organic molecules.

1) GC-MS analyses of volatile organic compounds:

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

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

Hourly volumes*:

CM: 3 p.m.

Tutorial: 5 hours

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The aim of teaching medicinal chemistry is to introduce students to the key stages in the process of developing molecules with biological activities. In particular, a description of the interactions involved, the concept of pharmacophores, bioisosterism, etc., as well as structure-activity relationship studies will be covered, enabling students to consider appropriate strategies and structural modifications.

Hourly volumes:

CM: 3 p.m.

Tutorial: 5 hours

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This EU is sequenced according to the following activities: First steps - R environment; R structures; Inputs and outputs in R; Manipulating R structures; The basics of algorithms; Programming structures in R; Mini-project in groups on an R function to be created for an applied "Water" problem.

Objectives:

The EU's objectives are 1) to present the basics of the interpreted language of an engineering tool (environment, structures, inputs/outputs, structure manipulation, graphics, programming), 2) to provide the fundamental theoretical knowledge needed to create one's own functions and programs using practical examples in water science so that 3) students can independently continue their self-training and expertise in R.

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Teaching is carried out by lecturers and researchers from the medical, science, and pharmacy departments. It consists of 42 hours of lectures and supervised work divided into seven themes (see Syllabus), including two series of article presentations: the first series on articles proposed by the lecturers for each theme covered, and the second series on articles chosen by the students. Students organize a mini-symposium at the end of the course where the articles are presented. They write summaries 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 the context of biomolecule analysis and monitoring of organic chemistry reactions.

Hourly volumes*:

CM: 3 p.m.

Tutorial: 5 hours

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This course aims to teach liquid chromatography and gas chromatography.

Hourly volumes:

            CM: 3:00 p.m.

            Tutorial: 5 hours

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The "Cellular Physiopathology and Cancer" course aims to provide students with the knowledge necessary to follow the "Cancer Biology" program in M2. The course is organized in the form of a conference with an introductory section followed by a section on current research in laboratories. Students are required to give an oral presentation on a scientific article (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 to 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 pairs).

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Within biotechnology, bioprocesses correspond to the industrial implementation of living tools (whether enzymes, microorganisms, or cells from higher organisms) for the synthesis of products of interest. In this teaching unit (TU), the focus will be on the use of microbial and cellular catalysts. Products of interest may include fermented foods (wine, beer, etc.), energy molecules (bioethanol, methane, etc.), chemical intermediates, and biomedicines (vaccines, monoclonal antibodies, growth factors, etc.). The knowledge, skills, and expertise acquired in this teaching unit will be transferable to any sector of biotechnology. The examples given will correspond to the career opportunities targeted by the two programs (Agrosciences and Health).

The EU will focus on bioprocesses and the environment in which the biological reaction will be controlled (the bioreactor). The course will also address the issue of describing and modeling a biological reaction, including a presentation of the approach applied in bioprocess engineering. The rest of the course will be devoted to the application of this approach to reactors operated in batch mode (or discontinuous culture). Other operating modes will be covered by the M2 HAV930V course "Bioprocess Engineering - Continuous and Fed-Batch."

This course unit includes interactive lectures, tutorials, and practical work (practical work in the computer lab + individual 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 to acquiring concepts related to molecular engineering and molecular chemistry. The teaching unit consists of lectures and tutorials. Students will prepare for certain lectures and tutorials using course materials provided, enabling them to participate fully in the lectures and tutorials, understand the concepts presented, and acquire the necessary skills. The progression program and activities will be proposed. For students who have not studied 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.)) as well as their properties and applications. Structural aspects, bond descriptions, properties, and aspects related to stability and reactivity will be addressed. Emphasis will be placed on the complexation effect and the stability of metal, lanthanide, and actinide complexes with certain ligands for 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 placed in the context of applications in various fields, such as imaging, electronics, sensors, etc.

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

Hourly volumes:

CM: 1:00 PM

Tutorial: 7 hours

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The content of the EU is organized into three parts:

1) Water cycle and water balance
• Main reservoirs
• Mechanisms of the water cycle
• Water circulation: from the global scale to the watershed scale
• Humans: their influence on the water cycle

2) The atmospheric phase of the water cycle – Hydrology
• The watershed
• Atmospheric circulation and precipitation
• Evapotranspiration
• Infiltration
• Runoff

3) The underground phase of the water cycle – Hydrogeology
• Porous media and their hydrodynamic properties
• Different types of aquifers
• Piezometric levels and maps

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The EU will first address the main communication pathways between normal cells and intracellular transduction pathways encountered in physiological and neurophysiological mechanisms. Thus, G protein-coupled receptors (GPCRs) will be studied, namely their structure, function, and modulation by interaction proteins involved in particular in the phenomenon of desensitization. The main intracellular pathways activated by membrane GCRs will be addressed (MAP kinase pathways, PI3 kinase, etc.).

Next, a significant portion of the course will focus on calcium signaling and Ca2+ homeostasis, Ca2+ being a ubiquitous signal in cellular signaling. Calcium homeostasis will be studied in particular during the response of lymphocytes after antigen stimulation. Furthermore, the production of oxygen free radicals, which cause oxidative stress, is dependent on intracellular Ca2+. The physiological role of free radicals will be discussed, as well as their involvement in oxidative stress. In this context, the pathways of protection against oxidative stress will also be studied.The following chapter will address the endocannabinoid system, which will allow us to recap all the topics previously discussed in the course. The endocannabinoid system is responsible for multiple central and peripheral regulations.

Finally, two other topics will be addressed: the blood-brain barrier, which allows for highly integrated cellular communication between two environments, and the pancreatic β-cell, whose activity is crucial for regulating blood sugar levels 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 testing reminders

Nature of mutations (loss-of-function; gain-of-function), concept of "master gene," clonal analysis (generation of somatic or germline clones), concept of cellular autonomy....

-Genetic models and methods.

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

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

Models and mechanisms of positional information = induction, Spemann and Mangold's experiment, organizing centers, concept of morphogens in invertebrates and vertebrates

-Establishment of axes: anteroposterior, dorsoventral.

Genetic screens: genes with maternal effects and genes with zygotic effects. Cell communication and signaling pathways: in establishing the dorsoventral axis, in limb formation, in establishing cell fate (some examples: nervous system: lateral inhibition process, etc.).

-Segmentation: gap genes, pair rule genes, and segmental 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, concept of gene networks. Coupling of transcription and signaling pathways in cell fate.

-Transcriptional program memory through epigenetic mechanisms:

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

Involvement of epigenetic mechanisms during cell differentiation

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