SV S6 Profile Selection

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This course builds on the Structural Biochemistry course taken in S5. Students will learn the basic concepts of the various approaches used for multiscale structural characterization, as well as the analysis of macromolecular interactions. The advantages and limitations of all these tools will be highlighted so that students can understand how they complement one another and learn to use them in an integrated manner to address a given biological question. 

The lab sessions will combine the application of structural analysis using visualization tools (such as PyMOL) with the analysis of research articles that employ a combination of the approaches covered in the lecture series. Students will then be required to design their own experimental project to address a specific research question.

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This course provides a concise overview of the concepts necessary for mathematical modeling in biology. The focus is on linear and nonlinear dynamical systems in one and two dimensions. The course begins with essential concepts in linear algebra: matrices, systems of linear equations, and the geometric interpretation of the solutions to these systems as vectors and subspaces (lines, planes, etc.). The theory of vectors and eigenvalues of matrices is introduced in relation to linear dynamical systems. For nonlinear 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 tutorial covers a wide range of biological models used in ecology, epidemiology, oncology, and systems biology.

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This course unit enables students to consolidate and deepen their understanding of the practical management of large amounts of experimental data collected during a one-week block of lab work (5 consecutive days). This data is collected through the implementation of numerous different protocols, with a focus on ensuring the best possible reproducibility of the experiments and maximizing efficiency in the preparation, execution, and analysis of the various experiments. A high degree of autonomy in setting up the protocols will be encouraged, ultimately leading to experimental proficiency and independence. These lab sessions also provide opportunities for group work (in pairs or groups of three, depending on facility capacity and class size) and for writing a report that thoroughly documents the protocols carried out, all experimental data obtained, and their analyses in order to determine a wide range of biochemical parameters. A significant portion of the evaluation will be based on the students’ ability to generate, manage, utilize, and analyze raw experimental data with the utmost rigor.

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As part of this course unit, students will learn the experimental principles involved in working with nucleic acids. The lectures will focus on two main areas:

1. Development of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, the CRISPR/Cas9 system, etc.) and reflection on ethical issues in biology.

The tutorials will consist of:

- Analysis of articles presenting problems to be solved using the knowledge gained in the course. The chosen topics will, as much as possible, relate to parallel course units in the third year of the bachelor’s program. Students will present these articles in the form of oral presentations, in groups of 3 to 4 students, to the entire class.

- Sessions dedicated to using basic bioinformatics tools in the computer lab.

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Systems biology offers the opportunity to understand how living organisms function at different organizational scales. This course will focus primarily on the subcellular scale. At this scale, systems biology models integrate multiple levels of interaction involving 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 basic research into the principles of how living systems function. The course consists of a theoretical component (lectures and tutorials on the modeling of gene, signaling, and metabolic networks) 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 various possible approaches to transitioning agriculture toward an agroecological model. Examples such as biopesticides, ecological intensification, and soil management will be explored. A field trip to a company committed to sustainable agriculture is also organized. The site visited varies from year to year depending on student preferences and company availability. Examples of field trips conducted as part of this module include visits to Bayer, Vilmorin, Geves, CTIFL, and sudExpé.

Bachelor's degrees.

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

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This course unit presents the major functions of carbon, mineral, and water nutrition in plants that enable their autotrophy (the production of their biomass). It will provide the necessary foundation 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 membranes and plant cell walls and the concepts of transmembrane transport, the section of the course devoted to mineral nutrition will cover 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 discuss how chloroplasts function in plant cells, photosynthesis (the capture of light energy and the synthesis of primary carbon compounds), the production of organic compounds, and their distribution within the plant.

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This course unit is an introductory module to scientific research in fundamental or applied plant agricultural sciences. Students must complete an internship of 10 weeks or more (which may continue through the summer) in a research laboratory (CNRS, INRAE, IRD, CIRAD), at an applied research organization such as GEVES, CTIFL, SudExpe, Serfel, or IFV, or at a private company such as Staphyt, AgroXp, or Vilmorin. There are numerous internship opportunities in this field in the Montpellier area.

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

• to apply the techniques learned in the various course units of the BiPAgro track of the bachelor’s degree program.
• to gain experience in the professional world
• to develop your own career plan and enhance your resume

The student writes a thesis, which he or she defends before a committee composed of faculty members, researchers, and/or field technicians or 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 methods and mechanisms used to manipulate the body’s cells at the mucosal level in order to penetrate the internal environment—that is, invasive potential—will be discussed, as well as the perception of environmental signals and the integration of these signals to coordinate the response of prokaryotes so that they exhibit collective behavior. A description of several examples of toxins and modulins associated with colonization and/or invasion will provide a better understanding of the differences in strategies among prokaryotic pathogens. Finally, we will address the concept of the microbiota and its influence on the body’s functioning, as well as its role in the development of certain diseases.

Immunology:

The Immunology section provides an overview of how the immune system functions during infection. From the initiation and progression of the inflammatory response upon the recognition of non-self signals by the innate immune system (PRR-PAMP) to the mechanisms of cell activation and the resulting cellular responses, we can appreciate the diversity of possibilities offered by the various components of the immune system. Furthermore, the sequence of events leading to the direction of the immune response and the acquisition of lasting protection during the adaptive phase will provide a better understanding of 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 training course aims to enable students to work independently on a molecular biology protocol and to introduce them to hypothesis-driven research. Students will have six days to address a biological problem that will be presented to them. This will allow them to apply, under laboratory conditions, some of the techniques covered in their theoretical coursework, thereby gaining a better understanding of them.

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The course will cover the fundamentals and principles of microbial ecology (microbial biodiversity; cultivable and non-cultivable microorganisms;   major microbial groups, key microbial functions and biogeochemical cycles, microbial metabolism in the environment and environmental applications, and the fundamentals of ecology as they apply to microorganisms (microbial interactions, free-living organisms, competition, collaboration, symbiosis, parasitism, and their applications). The following topics will be specifically addressed as examples:

- Viruses: the concepts of emergence and re-emergence

-Vibrios: virulence factors, adaptation to the host, and horizontal transfer

-streptococci, comparative genomics, genomic reduction, specialization

 Applications of microbial ecology to biotechnology will include: detection, production of inocula, bioproductions, bioremediation, and water treatment, using concrete examples (development of multipathogen detection tools that account for mutation; production of a flavor enhancer by a soil corynebacterium; applications of microbial interaction studies to the selection of cheese flavors; a quality index for vineyard soil, etc.)

Practical Course: Water Analysis—Principles, Standards, and Applications: 6 hours total

Tutorial/independent work based on the results of the lab: design of a water treatment model for a real-world scenario (cadastral data, topographic survey, total fecal coliform and streptococcal load from the lab, student presentations on the various types of (micro) wastewater treatment plants, etc.) The goal is to propose a conceptual solution tailored to the specific site conditions.

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As part of this course unit, students will learn the experimental principles involved in working with nucleic acids. The lectures will focus on two main areas:

1. Development of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, the CRISPR/Cas9 system, etc.) and reflection on ethical issues in biology.

The tutorials will consist of:

- Analysis of articles presenting problems to be solved using the knowledge gained in the course. The chosen topics will, as much as possible, relate to parallel course units in the third year of the bachelor’s program. Students will present these articles in the form of oral presentations, in groups of 3 to 4 students, to the entire class.

- Sessions dedicated to using basic bioinformatics tools in the computer lab.

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The EU aims to advance knowledge in fundamental and applied virology, with an emphasis on an integrative approach to the discipline. It will present the specific characteristics of host-virus interactions and the pathophysiology of viral infections in different types of hosts (vertebrates, insects, and plants). It will address aspects of viral ecology, virus emergence, and associated risks to human and animal health. Finally, the course will cover research methods, virological detection and diagnostic tools, and the applications of viruses in biotechnology.

The course will consist of lectures, tutorials (analysis of current scientific articles and oral presentations), and practical exercises that illustrate the material covered in the lectures and tutorials (virus amplification and purification, and quantification using standard techniques).

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The objective of this EU is to provide an overview of the diversity of angiosperms, examined through the lens of the most recent phylogenies proposed bythe Angiosperm Phylogeny Group ( APG). This phylogenetic framework will be supported throughout the course by the practical observation of vegetative and floral characters in a selection of taxa spanning the entire phylogeny, in order to identify the synapomorphies of the major clades, any homoplasies, as well as adaptations (floral biology, pollination, trophic interactions, etc.).

Students also explore the diversity of angiosperms from a floristic perspective by creating a herbarium of species that are generally Mediterranean in origin. In the process, they become familiar with the use of a flora and digital identification tools (such as Pl@ntNet and Tela Botanica’s e-Flore).

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Through five major themes, we will explore the fundamental connections between the principles of evolution and evolutionary ecology—as covered in previous course units—and their 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 summarizing scientific articles are held in conjunction with the course unit "Evolutionary Ecology and Its Applications."

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By the end of this course, students will have acquired the essential basic knowledge needed to properly prepare and carry out a science communication initiative tailored to a specific target audience, both orally and in writing. They will also be able to design educational materials and outreach workshops for the general public.

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Universities are often perceived as inaccessible to a large segment of society. As part of the UniverlaCité initiative, which aims to bring the university experience to priority neighborhoods, students will develop science workshops designed for students in REP schools. 

The EU will offer students the opportunity to:

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

2- Identify and develop skills in science communication through the design and production of educational materials tailored to the target audience.

The course will consist of tutorials and project monitoring (SPS) on predefined topics. The sociocultural situation in vulnerable urban areas will be addressed during the first tutorial. This first tutorial will also serve to lay the groundwork for the course, provide a detailed overview of the UniverlaCité program, and offer a broad introduction to science communication.

The following tutorials will serve as sessions during which students, divided into groups, will be asked to propose activities to be implemented. The constraints provided by the teaching team will be: the target audience, the theme (which will be defined by the teaching team and updated each year), and the requirement to propose “off-campus” activities.

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Major human and animal health challenges related 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 urbanization of living environments
• new treatment approaches
• the globalization of trade
• the standardization of lifestyles

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Through five major themes, we will explore the fundamental connections between the principles of evolution and evolutionary ecology—as covered in previous course units—and their 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 transitional environments between these two compartments—namely, mangroves, estuaries, and deltas.  These ecosystems will be examined from both structural and functional perspectives, with an emphasis on their similarities and differences, as well as on 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 instruction; the second part consists of introductory sessions for field trips, the field trips themselves, and laboratory sessions in which the data collected in the field are analyzed and discussed as a group.

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Molecular tools are an integral part of studies aimed at describing and characterizing biodiversity. The course will aim to introduce various molecular approaches (barcoding, metabarcoding, and environmental DNA, etc.) that enable (1) the description, characterization, and quantification of this diversity at the intra- or interspecific levels, as well as at the population and ecosystem levels, and (2) the presentation of their areas of application across different temporal and spatial scales. The course will incorporate practical components designed to introduce students to these techniques, help them implement them, analyze the resulting data, and report on their findings. Emphasis will be placed on group work in collaboration with researchers and faculty members.

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ORPAL is an ecology course offered as an APP (1/3 fieldwork and 2/3 laboratory practicals). Drawing on concepts and methods from ecology, this course aims to introduce students to historical ecology (the study of interactions between humans and their environment over varying time periods) and its main applications in paleoecology, from defining the research question, field sampling, and data collection, all the way through to interpretation and the writing of a scientific paper (see https://biologie-ecologie.com/exemples-travaux/). This course serves as an interesting theoretical and experimental prerequisite for the ACCES, CEPAGE, PALEONTOLOGY, ECOSYSTEMS, or BIOGET tracks.

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Adaptations to a “parasitic” lifestyle are studied across all parasitic organisms (viruses, bacteria, eukaryotes), encompassing various scales of analysis “from molecules to populations.”

Thus, the coevolution between hosts and parasites will be examined from the perspective of host–parasite molecular and cellular interactions (immunity, evasion, exploitation of host resources, etc.), as well as the morpho-anatomical structures involved in adaptation to the sub-host site or in survival in the external environment, and finally from the perspective of behavioral adaptations for encountering the host (facilitation).

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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 to describe and understand the morphology and evolutionary changes in vertebrate morphology. In addition to covering extant groups, this course unit will focus heavily on extinct fossil groups, particularly their contribution to our understanding of the various eco-morphological adaptations (e.g., the acquisition or return to an aquatic lifestyle, the acquisition of flight) that have shaped the evolutionary history of clades.

This course unit also aims to provide theoretical and practical foundations in phylogenetics (cladistics) for tracing the evolution of a clade (using distance, parsimony, and likelihood methods), based on both molecular and phenotypic characters (both modern and fossil).

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Introduce students to an integrated approach to plant biology through the study of the morpho-anatomical characteristics of stems and roots. Help them discover the coordinated spatio-temporal development of root and stem architectures through the adaptations of Mediterranean and tropical species. Reproductive structures and the diversity of biological types will also be addressed. This course unit serves as preparation for the BioGET track of the BE Master’s program and draws on the natural environment as well as local and regional facilities (Amazonian Greenhouse, Villa Thuret, Château La Pérouse Garden).

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The mechanism of action of drugs is based on an interaction with a target cellular structure in the body, leading to the modulation of its function. Thus, this course unit consists of two main components. The^first component aims to familiarize students with the various modes of cellular communication, the different chemical messengers, their targets, and their modes of action. The second component will aim to provide students with a basic understanding of pharmacology, specifically how drugs work and their fate within the body. To this end, the concepts of pharmacodynamics (ligand-receptor interaction, dose-response relationship) and pharmacokinetics (ADME: absorption, distribution, metabolism, and excretion) will be covered. In addition, drug targets, their intracellular signaling, and their therapeutic indications will be discussed.

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The EU course provides an introduction to the key issues surrounding the major diseases affecting the nervous system, whether neurological or psychiatric. These conditions are addressed from a multidisciplinary perspective, ranging from the molecular level to symptoms. This foundational knowledge of neuropathology will serve as a basis for the research areas covered later in the master’s program.

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The course on Muscular and Cardiac Disorders builds on the knowledge gained in the previous semester on cardiovascular physiology to explore the molecular and cellular mechanisms that lead to cardiac disorders (various arrhythmias, including atrial fibrillation, heart failure, etc.) and muscular disorders (myopathies, etc.).

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The course on Sensory and Motor Neurophysiology offered in the EU covers, on the one hand, the anatomical and functional organization of the major sensory systems—vision, hearing, and somatosensation. On the other hand, it addresses motor function and its central control at the spinal and supraspinal levels: the brainstem, motor cortex, cerebellum, and basal ganglia.

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The objective of this course unit is to provide students with fundamental and in-depth knowledge and skills regarding the physiology of the endocrine system. By studying the morphological and functional organization of the endocrine system, students will gain an understanding of the various hormonal systems (endocrine glands, hypothalamic-pituitary axis, reproductive system) and their essential roles in carrying out major physiological functions and maintaining homeostasis.

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