Parcours Molecular and cellular biology 1re année

Course outline

This course offers a general view of the new advances related to the control of gene expression, genome structure and organization across the tree of life: bacteria, lower (yeast, protozoans) and higher (plants, mammalian) eukaryotes, and viruses.

It focuses on the analysis and comprehension of the mechanisms underlying gene expression. This includes in vitro and in vivo approaches as well as the newest developments of gene editing.

A specific emphasis will be given to new aspects of gene regulation at a transcriptional and post-transcriptional level in eukaryotic cells (animals and plants). In particular, the role of the epigenome involving DNA methylation, histones and histone variants, long and short non-coding RNAs will be illustrated.

Through a broad range of model organisms (human, mouse, plants, yeast, bacteria…) the questions that are addressed in the fields of evolution, cell differentiation and development will be presented. The mechanisms used by parasites and viruses to infect host cells will be analyzed as well.

Through these different models, we will see that although specificities exist in the control of gene expression and the way organisms adapt to their environment, common mechanisms and common themes do exist throughout the tree of life.

Key words: Transcriptional and post-transcriptional gene expression regulation, chromosome structure, RNA interference, gene editing, genomes evolution and adaptation, infection, non-coding genomes, Genetics and Epigenetics.

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This module is based on a project-based pedagogy. Its main objective is to learn how to design, perform and interpret experiments. This module develops many personal and professional skills such as reasoning expertise, analysis ability, creativity, adaptation and curiosity. It also gives students the opportunity to learn how to communicate around their scientific results and to argue their experimental choices. Beyond this main objective, this module provides an integrated and transdisciplinary vision of biology and allows students to break down the barriers of disciplinary learning and to give sense to their academic knowledge. To achieve these goals, we have set up a creative pedagogy based on the use of varied and innovative strategies.

Tutoring sessions (around 3h/student) will help you to define your project, to formulate hypotheses and to design the experimental strategy. The experiments will be planned according to each project and performed during 3 weeks of practical courses.

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Course outline

Biocatalysis
Basis in Enzymes cofactors and vitamins
Cofactors involved in group transfer
Cofactors involved in redox reaction,
Cofactors and chemical origin of life

Biological Chemistry of Oxygen
Chemistry of O₂
Defense mechanism, detoxification of reactive oxygen species (ROS)
Role of ROS in physio-pathology
Regulation, sensing mechanism
Cellular sources of ROS.

Membrane Biochemistry
Lipids, Membrane and Rafts
Membrane proteins: synthesis and topology
Membrane proteins and detergent biochemistry
Receptors
Transporters
Vesicular trafficking.

Biochemistry of viral infection and immunity
Membrane fusion
Membrane budding
Biochemistry of innate factors

Extracellular Biochemistry: GAGs
Extracellulaire matrices
Glycosaminoglycans (GAG): biosynthesis and catabolism
GAG: biological activities
GAG: pathology and applications

Methods of study
Molecualr factory characterisation : cryoelectron microscopy
Imaging complexes, location and dynamic in cellulo
This module brings strong background (relative to oxidative stress) to the Unit “Experimental Approaches in Biology

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During the second semester of the first year of the master’s degree, students discover the research activity by participating in a lab internship. The official period of this internship is limited to 44 days.

For their internship, the students may choose laboratories from any university or institution in France or other countries. Students are encouraged to contact and visit as many labs as needed in order to choose the project and lab environment that fit with their personal interest.

In addition to a strong scientific background, the students must be motivated, serious, reliable, on time, independent, open to discussion, curious and self-organized.

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Course outline

Lectures:

1)    Introduction to infectious diseases (1.5 h) CM

2)    Parasites: bases of the pathogenicity and host / parasite interactions

-       Make yourself at home: remodeling of the host cell by Plasmodium falciparum (1.5 h) CM

-       Schistosoma spp (1.5 h) HP

-       Neglected tropical diseases, selected examples:

Leishmanioses (3 h) CM

Lymphatic filariosis or foodborne trematodiases or cysticercosis (1.5 h) CM

3)    Pathogenic bacteria: bases of the pathogenicity and host / bacteria interactions

-       Borrelia burgdorferi, the infectious agent of Lyme disease: evasion from the immune system (1.5 h) ASP

-       Pathogenicity of Vibrio cholerae, the infectious agent of cholera (1.5 h) ASP

-       Gastric ulcer and gastric cancer: the role of Helicobacter pylori (1.5 h) ASP

-       Lung diseases: Pseudomonas aeruginosa or Mycobacterium tuberculosis (1.5 h) CV

-       Pseudomonas aeruginosa: model of experimental evolution (1.5 h) CV

-       Bacteria of the digestive tract: Enterohemorrhagic Escherichia coli, Shigellae, Listeria monocytogenes (3 h) TH

-       Life within a vacuole: Francisella, Salmonella, Chlamydia (3 h) CM

4)    Viruses: bases of the pathogenicity and host cell / virus interactions

-       Negative RNA viruses: Influenza virus, Rabies, Measles, Ebola (7.5 h) RR and MJ

-       Virus and cancers (1.5h) PM

-       HIV-1: life cycle, entry and budding, vaccine development (3 h) WW

Tutorials: 15h

Analysis of scientific publications to illustrate different aspects of the course

Training to the terminal exam: examples of previous exams

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The course will aim at giving, through examples of existing drugs, an overview of the strategies used for drug development, from the identification of a molecular target to the marketing of an active product. The course will include presentations about enzyme catalysis and enzyme kinetics with particular emphasis on inhibition, on the problems faced when developing a drug and on computational approaches used in this field. The course will include sessions of computer analysis of enzyme kinetic data and of tutorials of molecular modeling.

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- Integrated function of the immune system

- Continuum between the innate- and the adaptive immune system

- Physiological modes of action of the immune system in infectious diseases and cancer

- Immune system regulation

- Immune system dysfunction and therapeutic modes of action: examples of developing applications.

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The course will present the experimental strategies used to produce macromolecular samples for biophysical and structural studies, from bioinformatics analysis to recombinant protein expression systems, automation (robotics), purification and engineering and measurement of sample quality. Expected competences acquired by the students: expertise in bioinformatics analysis of macromolecule sequence and structure, understanding methods and strategies used to express and purify macromolecules, expertise in experimental methods used for sample quality control, practical experience on platforms on the EPN Campus.

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Course outline

Thematic of the lectures (25.5h):

- Structure of bacterial chromosomes (3h)

- Regulation of bacterial gene expression and bacterial genomics (sigma factors, sRNA; 6h)

- Bacterial cytoskeleton (1,5h)

- Global regulation of bacterial transcription (DNA topology and stringent response; 9h)

- Bacterial diversity and the new tree of life (3h)

- Plasticity of bacterial genomes (mobile genetic elements; 3h)

Tutorials (18h= 12x1.5h):

Before each session, students have to read one scientific paper on topics related to the lectures and its content (methodologies, results) is then discussed during the 1.5h tutorial.

Format of the course

Exam requirements

Oral exam: students have to prepare an oral synthesis of one scientific paper.

Synthesis: students have to prepare a written synthesis of one scientific paper.

Final exam: students have to analyse figures from one or two scientific papers.

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The aim of this course is to study development and cell differentiation as the result of multiple interactions of genetic and epigenetic regulations organized into networks. In this context, the module is in direct and logical continuity with the master 1 module “Molecular Genetics and Epigenetics”. This “Development and Differentiation” module will take examples from a wide range of organisms including prokaryotes, protists (protozoa), and higher eukaryotes such as plants and animals.

The module is divided into three major themes: Gametogenesis and Early Development, Organogenesis and Tissue Differentiation and finally, Cell Differentiation and Environment with the concern to always draw examples from the diversity represented along the tree of life.

Together with the module “Molecular Genetics and Epigenetics”, this course will give an integrated overview of cell differentiation and development and how these activities are orchestrated and regulated by genetic and epigenetic factors. This will be illustrated by examples coming from a wide range of organisms. Therefore, this course is strongly recommended as a preparation to the PHEDD M2 program and would also be grounding to other M2 programs such as NN and IMID.

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The course is organized into two parts:

The first one is devoted to the understanding of the integrated metabolism in mammals under physiological conditions, with a particular emphasis on the interactions between the different organs involved in homeostasis.

The second one is focused on the dysregulations of the physiological pathways involved in energy homeostasis. In this context, the main metabolic disorders, such as diabetes, metabolic syndrome and obesity are discussed, as well as their main co-morbidities : atherosclerosis and coronary heart disease.

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The objective of this course is to acquire the fundamental knowledge necessary to understand key mechanisms of cancer development. This course includes a set of lectures on alterations of cellular and molecular mechanisms that are responsible for the cancer pathophysiology. These modified cellular functions include for example the cell division, apoptosis, gene expression, stem cells, angiogenesis and degradation of the extracellular matrix...  The fundamental notions will be illustrated via their implications in diagnosis and therapeutics. The publication analysis will allow emphasizing the medical interest.

To which kind of program can you apply when taking this course?

-  Any kind of Master 2 program.

- The module is particularly recommended to the students interested in the PHEDD program.

- Medical Students (MED)

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The goal of this course is to apprehend the latest findings about the cellular and molecular mechanisms of synaptic plasticity and the causes of their impairment in neurodegenerative diseases with a special emphasis on Alzheimer’s disease.

• What makes the electric      signal? The chemical synapse.
• The glutaminergic synaps: plasticity and memory. Regulation of neurotransmitter disease, of post-synaptic currents, modulation of the expression of pre-and post-synaptic receptors.
• Traffic and diffusion of synaptic receptors
• Genetic and molecular causes of Alzheimer’s disease: presinilins, APP, ApoE. Fronto-temporal dementia.

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This course will allow a better understanding of the anatomical, neurochemical, neurobiological and neurophysiological basis of normal and pathological behaviors (anxiety, addiction, stress). This course will contain the following lectures:

-Neurotransmission in the central nervous system: basis and main systems (lectures, 13h)

-Functional neuro-anatomy of the cerebral cortex (lecture, 3h)

-Interest of the functional neuro-imagery in the study of behaviors (lecture, 4h; tutorial, 2h)

-EEG: a tool for the study of the awake/sleep behavior (tutorial, 2h)

-Study of the neurobiological basis of the behavior: behavioral tests in human and animal (tutorial, 2h)

-Study and neurobiological model of the emotional processing (lecture, 4h)

-Physiopathology of anxiety, stress and depression (lecture, 3h)

-Neurobiology of drug addiction (lectures, 7h)

-Alterations in visuo-spatial orientation and obsessive-compulsive disorders (lecture, 2h)

-Behavioral tests in animal (practical, 4h)

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Course outline

In this course we will review the organization of the CNS and the functions related to the different parts of the brain. We will describe pathologies that affect specifically these parts of the CNS and the consequence of such diseases. Furthermore, we will describe the basis of psychopharmacology by analysis the therapeutic basis of the most common compounds used to cure psychiatric and neurodegenerative diseases.

During the tutorials, students will present a scientific article related to the topics presented during the lectures.

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The introductory lecture will describe the basis to perform good oral and written presentations. This synopsis will be documented with several sequences of combined lecture, tutorial, workshop to allow the master students to deal with any situation of their Master 1 year or their future work.

A first sequence will help the students to find an internship. A tutorial and a workshop will be organized in order to improve their CV and practice an interview.

A second teaching sequence will address the way to write a scientific report, from an internship report towards a scientific publication. This part will be followed by a lecture concerning the different modes of scientific communication, written or oral (report, meeting, lab-book, etc) within a laboratory.

A third sequence will deal with oral scientific presentation. A tutorial will explain how to prepare the presentation as well as how to present it. A workshop will give the opportunity to practice in front of an audience. It will also be the basis for an evaluation.

Another lecture will provide an opening towards electronic communication tools in order to be able to succeed in a skype interview and to be visible on the web using tools like LinkedIn or Viadeo.

A closing lecture will offer a transversal view of the different points highlighted throughout the course.

Writing skills will be evaluated based on a scientific report. The report and presentation evaluation will be related to other scientific teaching units followed by the students during the first semester of the master 1 but the evaluation will not take into account scientific knowledge.

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Des enseignements explicatifs présentent l’Entreprise sous un angle systémique. Des rencontres avec les professionnels du recrutement permettent de comprendre les attentes des entreprises. Chaque participant choisit un métier dont il sera l’ambassadeur pendant ce cours.

Notions traitées :

Comprendre le fonctionnement d’une entreprise dans son environnement économique local, national et international.

Comprendre les clés du bon fonctionnement d’une entreprise.

Formes d’entreprises et d’organisations.

Métiers associés aux fonctions des entreprises.

Savoir parler des compétences lors d’une recherche de stage ou d’un recrutement.

Se projeter dans les métiers visés.

Participation d’intervenants professionnels du recrutement.

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