Choice Profile SV S6

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This course is a continuation of the Structural Biochemistry course in S5. Students will learn the basic concepts of the different approaches used for multi-scale structural characterization and macromolecular interaction analysis. The advantages and limitations of all the tools will be highlighted, so that students can understand the complementarity of these tools and know how to use them in an integrative way to answer a given biological question. 

TDs will be a mix of structural analysis applications using visualization tools (such as Pymol) and article analysis using a combination of the approaches studied in CM. Students will then be asked to conceptualize their own experimental project in response to a given problem.

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The course provides an overview of the concepts required for mathematical modeling in biology. The focus is on linear and non-linear dynamical systems, in dimension one and two. The course begins with essential notions of linear algebra: matrices, systems of linear equations, geometric interpretation of the solutions of these systems as vectors and subspaces (line, plane, etc.). The theory of vectors and eigenvalues of matrices is introduced in relation to linear dynamical systems. For non-linear dynamical systems, the qualitative theory of differential equations (attractors, phase portraits, zero-level isoclines) is presented, as an alternative to the often complicated calculation of solutions. The TD covers a wide range of biological models used in ecology, epidemiology, oncology and systems biology.

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This course enables students to consolidate and deepen their practical management of numerous experimental data obtained over a week of practical work during a blocked period (5 consecutive days). These data are obtained following the elaboration of many different protocols, keeping in mind to ensure the best reproducibility of the preparations carried out and to have the best speed of execution in the preparation, realization and analysis of the different experiments. A high degree of autonomy in setting up protocols will be encouraged, leading ultimately to experimental mastery and autonomy. This practical work will also enable students to work in groups (in pairs or trios, depending on capacity and number of students), and to write a report recording the protocols carried out, all the experimental data obtained and their analysis, in order to determine a wide range of biochemical parameters. A significant part of the assessment will be based on the students' ability to generate, manage, exploit and analyze raw experimental data with the utmost rigor.

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In this course, students will learn experimental principles based on the manipulation of nucleic acids. The lectures will be structured around two major themes:

1. Introduction 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.

The TDs will consist of :

- Analysis of articles presenting problems to be solved with the knowledge acquired in the course. As far as possible, the themes chosen will refer to the parallel UEs of L3. These articles will be presented by students in the form of oral presentations in groups of 3 or 4 to the whole class.

- Sessions reserved for the use of basic bioinformatics tools in the computer room.

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Systems biology offers the possibility of understanding how living organisms function at different scales of organization. This course will focus on the sub-cellular scale. At this scale, systems biology models integrate several levels of interaction from the transcriptome, proteome and metabolome. The predictions of in silico models can be used in biomedical research to understand multi-factorial diseases and optimize drug treatments, in bioengineering to synthesize genomes with optimized properties and functions (synthetic biology), as well as to guide fundamental research into the principles of how living organisms function. The course comprises a theoretical component (lectures and practical sessions on modeling gene, signaling and metabolic networks) and a practical component (computer-based practical exercises using Matlab software).

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After defining intensive agriculture and analyzing its risks/benefits, this module will enable students to reflect on the various possible ways of moving agriculture towards an agroecological approach. Examples include biopesticides, ecological intensification and soil management. A visit to a company involved in sustainable agriculture is also organized. The sites visited vary from year to year, depending on the wishes of the students and the availability of the companies. Examples of visits made as part of this module: Bayer, Vilmorin, Geves, CTIFL, sudExpé...

Licenciales.

Students will be asked to present a project or business start-up developing innovative proposals for changing cultivation practices, or any other use of plant products to reduce environmental impact.

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This course presents the major functions of carbon, mineral and water nutrition in plants, which ensure their autotrophy (the production of their own biomass). It will provide the basis for understanding the fundamental mechanisms of nutrient absorption, distribution and assimilation. The course will be divided into two main parts, one dedicated to mineral nutrition and the other to carbon nutrition.

After a review of the properties of plant membranes and walls and the concepts of transmembrane transport, the part of the course dedicated to mineral nutrition will teach the mechanisms of water absorption and circulation, root uptake, subcellular compartmentalization and mineral distribution, as well as nitrogen assimilative metabolism.

The chapter dedicated to carbon nutrition will present the functioning of the chloroplast in the plant cell, photosynthesis (capture of light energy and synthesis of the first carbon compounds), the production of organic compounds and their allocation in the plant.

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This UE is a module designed to introduce students to scientific research in fundamental or applied plant agro-sciences. Students must complete an internship of 10 weeks or more (which may continue over the summer) in a research laboratory (CNRS, INRAE, IRD, CIRAD), in an applied research organization such as GEVES, CTIFL, SudExpe, Serfel, IFV or in a private company such as Staphyt, AgroXp, Vilmorin. Montpellier offers a wide range of internship opportunities in this field.

This is a module for integration into the professional world, enabling students to make contact with players in the world of plant-based Agro-Sciences:

• apply the techniques learned in the various courses of the BiPAgro Bachelor's degree.
• exposure to the professional world
• develop your own professional project and enhance your CV

Students write a dissertation which they defend in front of a jury made up of teacher-researchers, researchers and/or field technicians/engineers. 

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Bacteriology :

Through various examples, students will gain a better understanding of the notion of pathogenicity in relation to bacterial virulence. The means and mechanisms used to manipulate the organism's cells at mucosal level in order to penetrate the internal environment, i.e. invasiveness, 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 some examples of toxins and modulins in relation to colonization and/or invasion will provide a better understanding of the differences in strategies between prokaryotic pathogens. Finally, we'll look at the notion of the microbiota and its influence on the functioning of the organism, as well as its implication in the development of certain pathologies.

Immunology:

The Immunology section outlines the workings of the immune system during infection. From the establishment and development of the inflammatory reaction upon recognition of non-self signals by natural immunity (PRR-PAMP), to the mechanisms of cell activation and the cellular responses generated, we can appreciate the diversity of possibilities offered by the different players in the immune system. 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 vaccine strategy. Finally, immunity of the intestinal mucosa will be addressed in the context of the relationship between the host and the microbiota.

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The Molecular Biology practical course is designed to give students autonomy when faced with a molecular biology protocol, and to introduce them to hypothesis-driven research. Students will have 6 days to respond to a biological problem proposed to them. In this way, they will be able to put into practice, under laboratory conditions, some of the techniques they have learnt in their theoretical courses, and gain a better understanding of them.

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Lessons will cover the basics and application principles of microbial ecology (microbial biodiversity; cultivable/non-cultivable microorganisms; major microbial groups, main microbial functions and biogeochemical cycles, microbial metabolisms in the environment and environmental applications, basics of ecology applicable to microorganisms (microbial interactions, free life, competition, collaboration, symbiosis, parasitism and their applications). In particular, the following topics will be covered by way of illustration

- viruses: the notion of emergence and re-emergence

-vibrios, virulence factors, host adaptation and horizontal transfer

-streptococci, comparative genomics, genomic reduction, specialization

 Applications of microbial ecology to biotechnologies will include: detection, inocula production, bioproductions, bioremediation, water treatment using concrete examples (development of mutation-aware multipathogen detection tools, production of a flavor enhancer by a soil corynebacterium, applications of microbial interaction studies to cheese flavor selection, quality index of a wine-growing soil, etc.).

Practical water analysis, principles, standards, applications: total 6h

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, fecal streptococcal total coliform load from the practical work, student presentation on the different types of (micro)purification plants....) the aim is to propose a conceptual solution adapted to the field case.

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In this course, students will learn experimental principles based on the manipulation of nucleic acids. The lectures will be structured around two major themes:

1. Introduction 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.

The TDs will consist of :

- Analysis of articles presenting problems to be solved with the knowledge acquired in the course. As far as possible, the themes chosen will refer to the parallel UEs of L3. These articles will be presented by students in the form of oral presentations in groups of 3 or 4 to the whole class.

- Sessions reserved for the use of basic bioinformatics tools in the computer room.

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The aim 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 specific features of host-virus interactions and the pathophysiology of viral infections in different host types (vertebrates/insects/plants). It will cover 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 biotechnology.

The course will include 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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The aim of the course is to provide an overview of Angiosperm diversity, approached through the prism of the most recent phylogenies proposed by theAngiosperm Phylogeny Group (APG). This phylogenetic framework will be supported throughout the course of the course by concrete observation of the vegetative and floral characters of a selection of taxa spread across the entire phylogeny, so as to identify the synapomorphies of the main clades, any homoplasies, and adaptations (floral biology, pollination, trophic interactions, etc.).

Students also learn about the diversity of Angiosperms from a floristic point of view, by creating a herbarium of generally Mediterranean species. They also learn how to use a flora and digital identification tools (Pl@ntNet e-Flore from Tela Botanica, etc.).

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Through 5 main themes, we will make the link between the principles of evolution and evolutionary ecology seen in the previous E.U. in a fundamental way and current societal applications.

The 5 main themes are: human evolution, biodiversity conservation, domestication of animal and plant species, evolutionary medicine, and major global crises and disruptions.

Two sessions on the comprehension and oral presentation of scientific articles are held in conjunction with the "Evolutionary ecology and its applications" UE.

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At the end of this course, students will have acquired the basic knowledge needed to prepare and carry out a scientific communication operation adapted to a target audience, both orally and in writing. They will also be able to design educational material and awareness-raising workshops for the general public.

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Universities are often perceived as inaccessible places for large sections of society. As part of the UniverlaCité program, which aims to bring the university to life in disadvantaged neighborhoods, the students will be setting up scientific workshops for schoolchildren in disadvantaged areas. 

The EU will offer students the opportunity to :

1- share their own experiences and enhance the value of the knowledge they have acquired at the University, with a view to responding as effectively as possible to the needs of society.

2- Reveal and develop scientific communication skills through the design and production of teaching aids adapted to the target audience.

The course will take the form of tutorials and project follow-up (SPS) on pre-defined themes. The socio-cultural situation of sensitive urban areas will be addressed in the first class. This first TD will also serve to lay the foundations for the UE, present the UniverlaCité system in detail and give a broad overview of scientific mediation.

The following TDs will serve as sessions during which students, divided into groups, will have to propose activities to be set up. The constraints given to them by the teaching team will be: the target audience, the theme (which will be defined by the teaching team and renewed each year) and the need to propose activities "outside the classroom".

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The major human and animal health issues linked to global change, i.e. :

• degradation of natural environments, leading to loss of quality of natural resources (various forms of pollution) and loss of biodiversity
• climate change
• the artificialization of living environments
• new therapeutic approaches
• the globalization of trade
• standardized lifestyles

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Through 5 main themes, we will make the link between the principles of evolution and evolutionary ecology seen in the previous E.U. in a fundamental way and current societal applications.

The 5 main themes are: human evolution, biodiversity conservation, domestication of animal and plant species, evolutionary medicine, and major global crises and disruptions.

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This course provides an introduction to the ecology of continental freshwater and marine ecosystems, as well as to the interface between these two compartments, i.e. mangroves, estuaries and deltas. They will be approached both from the point of view of their structure and from the point of view of their functioning, emphasizing both their similarities and their differences, and the abiotic and biotic factors that govern the organization of the communities of organisms that inhabit them.

They should provide an overview of these ecosystems or hydrosystems and how they function at different scales.

The first part of the course is devoted entirely to theory, while the second includes introductory sessions for field trips, the field trips themselves and practical sessions for analyzing and pooling the data collected in the field.

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Molecular tools are an integral part of studies aimed at describing and characterizing biodiversity. The aim of the course is to present various molecular approaches (barcoding, metabarcoding and environmental DNA, etc.) for (1) describing, characterizing and quantifying this diversity at intra- or interspecific, population or ecosystem levels, and (2) presenting their fields of application at different scales of time and space. The course will include practical aspects aimed at familiarizing students with these techniques, implementing them, analyzing the resulting data and reporting on them. Priority will be given to group work in interaction with researchers and teacher-researchers.

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ORPAL is an APP ecology course (1/3 fieldwork and 2/3 laboratory work). Based on Ecology concepts and methods, this course aims to introduce students to historical ecology (the study of interactions between man and his environment over variable chronological periods) and its main applications in paleoecology, from problem definition, field sampling and data acquisition to interpretation and the writing of a scientific article (see https://biologie-e cologie.com/exemples-travaux/). This course is an interesting theoretical and experimental prerequisite for the ACCES, CEPAGE, PALEONTOLOGY, ECOSYSTEMS or BIOGET courses.

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Adaptations to the "parasitic" lifestyle are studied on all parasitic organisms (viruses, bacteria, eukaryotes), including different scales of analysis "from molecules to populations".

Thus, the coevolution between hosts and parasites will be considered from the point of view of host-parasite molecular and cellular dialogues (immunity-escapement-exploitation of host resources, etc.), but also from the point of view of morpho-anatomical structures involved in adaptation to the sub-host site or in survival in the external environment, and finally from the point of view of behavioral adaptations for encountering the host (promotion).

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One of the aims of this course is to synthesize notions and knowledge acquired in animal biology (anatomy, systematics) and ecology to describe and understand the morphology and evolution of vertebrate morphologies. In addition to present-day groups, this course will focus on extinct fossil groups, in particular their contribution to understanding the various eco-morphological adaptations (e.g. acquisition or return to aquatic life, acquisition of flight) that have marked the evolutionary history of clades.

This course also aims to provide a theoretical and practical grounding in phylogeny (cladistics) for tracing the evolution of a clade (distance, parsimony and likelihood methods), both for molecular and phenotypic traits (present-day and fossil).

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Introduce students to an integrated approach to plants by studying the morpho-anatomical characteristics of stems and roots. They will discover the spatio-temporal coordinated construction of root and stem architectures through adaptations of Mediterranean and tropical species. Reproductive structures and the diversity of biological types will also be taken into account. This course is designed to prepare students for a Master's degree in BioGET, and is based on the natural environment and local and regional infrastructures (Serre Amazonienne, Villa Thuret, Jardin Château La Pérouse).

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The mechanism of action of drugs is based on interaction with a target cell structure in the body, leading to modulation of its function. This course is divided into 2 main parts. The^1st part will introduce students to the different modes of cellular communication, the different chemical messengers, their targets and their modes of action. The 2nd part will give students a basic understanding of pharmacology, i.e. how drugs work and what happens to them in the body. To this end, the concepts of pharmacodynamics (ligand-receptor interaction, effect-dose relationship) and pharmacokinetics (ADME: absorption-distribution-metabolism-excretion) will be covered. Drug targets, intracellular signaling and therapeutic indications will also be covered.

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The EU provides an introduction to the main diseases affecting the nervous system, both neurological and psychiatric. Pathologies are treated from a multidisciplinary angle, from the molecular to the symptomatic. This basic knowledge of neuropathology will serve as a foundation for the fields of research addressed later in the Master's program.

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The aim of the Muscular and Cardiac Pathologies course is to build on the knowledge of cardiovascular physiology acquired in the previous semester to understand the molecular and cellular mechanisms that lead to cardiac pathologies (various rhythm disorders including atrial fibrillation, heart failure, etc.) and muscular pathologies (myopathies, etc.).

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The Sensory and Motor Neurophysiology course covers the anatomical and functional organization of the main sensory systems: vision, hearing and somesthesia. On the other hand, it deals with motricity and its central control at the spinal and supra-spinal levels: brain stem, motor cortex, cerebellum and basal ganglia.

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The aim of this course is to provide students with fundamental and in-depth knowledge and skills in the physiology of the endocrine system. By studying the morphological and functional organization of the endocrine system, the student will be able to grasp the multitude of hormonal systems (endocrine glands, hypothalamo-hypophyseal axis, reproductive system) and their essential roles in the realization of major physiological functions and homeostasis.

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