SV S6 Profile Selection

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This course builds on the Structural Biochemistry course in S5. Students will learn the basic concepts of the different approaches used for multi-scale structural characterization and the analysis of macromolecular interactions. The advantages and limitations of all the tools will be highlighted so that students can understand how they complement each other and know how to use them in an integrated way to answer a given biological question. 

The tutorials will be a mix of structural analysis using visualization tools (such as Pymol) and analysis of articles using a combination of the approaches studied in CM. Students will then be required to conceptualize their own experimental project to address a given problem.

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

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This course unit allows students to consolidate and deepen their practical management of the large amount of experimental data obtained during a week of practical work in a block period (5 consecutive days). This data is obtained following the development of numerous different protocols, with a view to ensuring the best possible reproducibility of the preparations carried out and the fastest possible execution in the preparation, implementation, and analysis of the various experiments. A high degree of autonomy in the implementation of protocols will be encouraged, ultimately leading to experimental mastery and autonomy. These practical sessions also allow for group work (in pairs or threes, depending on capacity and numbers) and the writing of a report detailing 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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As part of this course, students will learn experimental principles based on the manipulation of nucleic acids. Lectures will focus on two main areas:

1. Implementation of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, CRISPR/CAS9 system, etc.) and reflection on the concept of ethics in biology.

The tutorials will consist of:

- Analysis of articles presenting issues to be resolved using the knowledge acquired in the course. The topics chosen will, as far as possible, refer to parallel L3 teaching units. These articles will be presented by 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 lab.

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Systems biology offers the possibility of understanding how living organisms function at different levels of their organization. This course will focus primarily on the subcellular level. At this level, systems biology models integrate several levels of interaction from the transcriptome, proteome, and metabolome. Predictions from in silico models can be used in biomedical research to understand multifactorial diseases and optimize drug treatments, in bioengineering to synthesize genomes with optimized properties and functions (synthetic biology), and to guide fundamental research on the principles of how living organisms function. The course includes a theoretical component (lectures and tutorials on gene, signaling, and metabolic network modeling) and a practical component (computer labs using Matlab software).

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After defining intensive agriculture and analyzing its risks and benefits, this module will enable students to reflect on the various possible avenues for developing agriculture using an agroecological approach. Examples such as biopesticides, ecological intensification, and soil management will be explored. A visit to a company working towards sustainable agriculture is also organized. The site visited varies from year to year depending on student preferences and company availability. Examples of visits made as part of this module include Bayer, Vilmorin, Geves, CTIFL, and sudExpé.

Licensed.

Students will be asked to present a project or business plan that develops innovative proposals to change farming practices or any other use of plant products in order to reduce environmental impact.

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

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

The chapter on carbon nutrition will present how chloroplasts function in plant cells, photosynthesis (capturing light energy and synthesizing the first carbon compounds), the production of organic compounds, and their allocation within the plant.

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This EU is a module for discovering scientific research in fundamental or applied plant sciences. Students must complete an internship of 10 weeks or more (which may continue into 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, or Vilmorin. CIRAD), an applied research organization such as GEVES, CTIFL, SudExpe, Serfel, IFV, or a private company such as Staphyt, AgroXp, or Vilmorin. There are many internship opportunities in this field in the Montpellier area.

This is a module designed to help students enter the professional world by connecting them with key players in the field of plant agricultural sciences, giving students the opportunity to:

• apply the techniques learned in the various courses of the BiPAgro Bachelor's degree program.
• to face the professional environment
• to develop your own career plan and enhance your resume

Students write a thesis that they defend before a panel composed of faculty members, researchers, and/or field technicians/engineers. 

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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 means and mechanisms used to manipulate the body's cells at the mucosal level in order to penetrate the internal environment, i.e., invasive power, 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 a few examples of toxins and modulins related to colonization and/or invasion will provide a better understanding of the differences in strategies between prokaryotic pathogens. Finally, the concept of microbiota and its influence on the functioning of the organism, as well as its involvement in the development of certain pathologies, will be discussed.

Immunology:

The Immunology section covers the basics of how the immune system works during infection. From the initiation and progression of the inflammatory response when non-self signals are recognized by the innate immune system (PRR-PAMP) to the mechanisms of cell activation and the cellular responses generated, we can appreciate the diversity of possibilities offered by the various players in immunity. 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 the 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 molecular biology practical aims to enable students to work independently with molecular biology protocols and introduce them to hypothesis-driven research. Students will have six days to respond to a biological problem that will be presented to them. This will allow them to put some of the techniques covered in their theoretical classes into practice in a laboratory setting, thereby gaining a better understanding of them.

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The courses will cover the fundamentals and principles of microbial ecology (microbial biodiversity; cultivable/uncultivable microorganisms;   major microbial groups, key microbial functions and biogeochemical cycles, microbial metabolisms in the environment and environmental applications, ecology fundamentals applicable to microorganisms (microbial interactions, free-living, competition, collaboration, symbiosis , parasitism and their applications). The following will be covered in particular by way of illustration:

- viruses: the concept of emergence and reemergence

-Vibrio bacteria, virulence factors, host adaptation, and horizontal transfer

-streptococci, comparative genomics, genome reduction, specialization

 Applications of microbial ecology to biotechnology will concern: detection, inoculum production, bioproductions, bioremediation, and water treatment using concrete examples (development of multi-pathogen detection tools that take mutation into account, production of a flavor enhancer by a soil corynebacterium, applications of the study of microbial interactions to the selection of cheese flavors, quality index of wine-growing soil, etc.).

Lab work: water analysis, principles, standards, applications: total 6 hours

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, total fecal coliform load from practical work, student presentations on the different types of (micro)water treatment plants, etc.). The aim is to propose a conceptual solution adapted to the specific case.

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As part of this course, students will learn experimental principles based on the manipulation of nucleic acids. Lectures will focus on two main areas:

1. Implementation of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, CRISPR/CAS9 system, etc.) and reflection on the concept of ethics in biology.

The tutorials will consist of:

- Analysis of articles presenting issues to be resolved using the knowledge acquired in the course. The topics chosen will, as far as possible, refer to parallel L3 teaching units. These articles will be presented by 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 lab.

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The EU aims to acquire knowledge of fundamental and applied virology, with a focus on an integrative approach to 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 to human and animal health. Finally, the EU will present the research methods used, virological detection and diagnostic tools, and applications of viruses in biotechnology.

The EU will be taught in the form 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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The EU aims to provide an overview of the diversity of angiosperms, approached both through the prism of the most recent phylogenies proposed bythe Angiosperm Phylogeny Group ( APG). This phylogenetic framework will be supported throughout the EU by concrete observation of the vegetative and floral characteristics of a selection of taxa distributed across the entire phylogeny, in order 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 perspective by creating a herbarium of species generally found in the Mediterranean region. This gives them an opportunity to familiarize themselves with the use of a flora and digital identification tools (Pl@ntNet, e-Flore by Tela Botanica, etc.).

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Through five major themes, we will make the connection between the principles of evolution and evolutionary ecology seen in previous teaching units in a fundamental way and current societal applications.

These five major themes are: human evolution, biodiversity conservation, the domestication of animal and plant species, evolutionary medicine, and major global crises and disruptions.

Two sessions on understanding and oral presentation of scientific articles are held in conjunction with the course "Evolutionary Ecology and its Applications."

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

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Universities are often perceived as inaccessible places for a large part of society. As part of the UniverlaCité program, which aims to bring the university to priority neighborhoods, students will develop science workshops for schoolchildren in priority education areas. 

The EU will offer students the opportunity to:

1- share their own experiences and leverage the knowledge they have acquired at university in order to best meet the needs of society.

2- Reveal and develop scientific communication skills through the development and implementation of educational materials tailored to the target audience.

The EU will take the form of tutorials and project monitoring (SPS) on predefined topics. The socio-cultural situation of sensitive urban areas will be addressed during the first tutorial. This first tutorial will also serve to lay the foundations for the EU, present the UniverlaCité program in detail, and give a broad overview of scientific mediation.

The following tutorials will serve as sessions during which students, divided into groups, will be asked to propose activities to be implemented. The constraints imposed on 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 school grounds.

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The major human and animal health challenges linked to global changes, namely:

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

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Through five major themes, we will make the connection between the principles of evolution and evolutionary ecology seen in previous teaching units in a fundamental way and current societal applications.

These five major themes are: human evolution, biodiversity conservation, the 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 ecosystems and marine ecosystems, as well as to the interface environments between these two compartments, namely mangroves, estuaries, and deltas.  They will be approached from the perspective of both their structure and their functioning, emphasizing their similarities and differences, as well as 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 various scales.

The first part of the course is devoted entirely to theoretical teaching, while the second part consists of introductory sessions to field trips, the field trips themselves, and practical sessions in which the data collected in the field is analyzed and shared.

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Molecular tools are an integral part of studies aimed at describing and characterizing biodiversity. The EU will aim to present various molecular approaches (barcoding, metabarcoding, environmental DNA, etc.) that enable (1) the description, characterization, and quantification of this diversity at intra- or interspecific, population, or ecosystem levels, and (2) the presentation of their areas of application at different timescales and spatial scales. The EU will incorporate practical aspects aimed at learning about and implementing these techniques, analyzing the resulting data, and reporting on them. Group work in interaction with researchers and teacher-researchers will be prioritized.

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ORPAL is an ecology course in APP (1/3 fieldwork and 2/3 lab work). Based on ecological concepts and methods, this course aims to explore historical ecology (the study of interactions between humans and their environment over varying time periods) and its main applications in paleoecology, from defining the issue field sampling, data acquisition, to interpretation and writing a scientific article (see https://biologie-ecologie.com/exemples-travaux/). This course is an interesting theoretical and experimental prerequisite for the ACCES, CEPAGE, PALEONTOLOGY, ECOSYSTEMS, or BIOGET programs.

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

Thus, the co-evolution between hosts and parasites will be considered from the perspective of molecular and cellular host-parasite interactions (immunity, escape, exploitation of host resources, etc.), but also from the perspective of the morpho-anatomical structures involved in adaptation to the intra-host site or in survival in the external environment, and finally from the perspective of behavioral adaptations for encountering the host (promotion).

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One of the goals of this course unit is to synthesize concepts and knowledge acquired in animal biology (anatomy, systematics) and ecology in order to describe and understand the morphology and evolution of vertebrate morphologies. In addition to covering current groups, this course will focus heavily on extinct fossil groups, particularly 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 theoretical and practical foundations in phylogenetics (cladistics) for tracing the evolution of a clade (distance, parsimony, and likelihood methods), based on both molecular and phenotypic characters (current and fossil).

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Introduce students to an integrated approach to plants by studying the morphological and anatomical characteristics of stems and roots. Help them discover the coordinated spatial and temporal 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 unit is designed to prepare students for the BioGET Master's program and draws on the natural environment and local and regional infrastructure (Amazonian Greenhouse, Villa Thuret, Château La Pérouse Garden).

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The mechanism of action of drugs is based on interaction with a target cell structure in the body, leading to the modulation of its functioning. This course unit therefore has two main components. The^first component aims to raise students' awareness of the different modes of cellular communication, the different chemical messengers, their targets, and their modes of action. The second part will aim to provide students with basic knowledge of pharmacology, i.e., understanding how drugs work and what happens to them in the body. To this end, the concepts of pharmacodynamics (ligand-receptor interaction, dose-response relationship) and pharmacokinetics (ADME: absorption-distribution-metabolism-excretion) will be covered. In addition, drug targets, their intracellular signaling, and their therapeutic indications will be discussed.

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The EU offers an introduction to the main diseases affecting the nervous system, whether neurological or psychiatric. The pathologies are addressed from a multidisciplinary perspective, ranging from the molecular level to symptoms. This basic knowledge of neuropathology will serve as a foundation for the fields of research covered later in the Master's program.

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The EU on muscle and heart diseases aims, based on the knowledge acquired in the previous semester on cardiovascular physiology, to understand the molecular and cellular mechanisms that lead to heart diseases (various rhythm disorders including atrial fibrillation, heart failure, etc.) and muscle diseases (myopathies, etc.).

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The course in Sensory and Motor Neurophysiology taught in the EU covers the anatomical and functional organization of the main sensory systems: vision, hearing, and somesthesia. It also deals with motor function and its central control at the spinal and supraspinal levels: brainstem, motor cortex, cerebellum, and basal ganglia.

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The objective 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, students will gain an understanding of the multitude of hormonal systems (endocrine glands, hypothalamic-pituitary axis, reproductive system) and their essential roles in the performance of major physiological functions and homeostasis.

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