Physiology, epigenetics, differentiation and cancer 2nd year

The course starts with an introductory lecture that describes how scientific projects are usually performed. Major points discussed are:

1)    Structure and functioning of a scientific team („From Einstein to Frankenstein – what makes a modern scientist“)

2)    Scientific literature (critical reading of publications, building blocks of a publication, the „hidden“ information)

3)    The „value“ of a publication (impact factor and its consequences; ethics in publishing)

4)    Project planning and funding proposals (including funding agencies and fellowships)

5)    Financial and structural resources for a scientific project

The students will provide a short initial 10 min presentation of their master project summarizing the field of study, the topic and the project idea followed by 5 min of group discussion identifying the major technological and scientific questions. These will be discussed and explained in detail in subsequent tutorials.

The final goal for each student is to prepare a 4-page proposal on his/her future S4 internship and a potential consecutive PhD project in which he/she describes the rationale and strategy of the project, the research axes, the expected results and alternative strategies in case the original project idea turns out to be not feasible. The students will receive help for the preparation of this project by their lab supervisor (understanding of the subject, feasibility of the proposed experiments) and of regular discussions with the group of students.

The mid-term exam consists in a 30 min oral presentation that summarizes the bibliographic background of the proposal and presents the main technical aspects, followed by questions from the reviewing committee (researchers and faculty members), who will test the understanding of the project.

The final exam consists in:

- a 4-pages written proposal

- a 20 min discussion with the reviewing committee who will test the understanding of the project as well as the scientific culture of the candidate.

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This course will present the major issues related to the ageing processes and their consequences on longevity, in humans, animals and plants.

The main anatomical, histological, molecular and functional changes will be described in several major organs or systems (cardiovascular, nervous, pulmonary, muscular, immune, ...), together with some of the essential clinical problems of human ageing (fragility of elderly, neurodegenerative diseases, ..).

 The role of important actors of the ageing mechanisms, such as telomeres and mitochondria, will be addressed before a final presentation of the principal theories of ageing. Some data about stem cells and their roles will also be presented.

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I. LECTURES (20 hours)

1- Cardiac energy metabolism: energetic regulations; cardiac energy transfer

            - Bioenergetics and the role of oxygen in bioenergetics

            - Contraction in cardiovascular systems, compartmentalization and energy transfer

            - Modular organization of cardiac energy metabolism

            - Metabolic aspects of the Frank-Starling’s law in the heart

2- Recent progress in basic cardiovascular physiology

       - Heart and chronobiology

       - Heart rate and longevity

       - Cardiac conditioning (pre-conditioning, post-conditioning and remote conditioning)

       - Intracellular signaling pathways in vascular systems

       - Chronic exercise and vascular function

3- Mechanistic approaches in cardiovascular pathophysiology

       - Recent advances in cardiac pharmacology

       - Nutrition and cardiovascular risk

       - Cardiovascular consequences of obesity and insulin resistance

       - Oxidative stress and cardiovascular system

       - Strategies for prevention of vascular diseases: pharmacology and prophylaxis

       - Endothelial dysfunction in vascular pathologies

4- Vulnerable plaque

       - Evolution of the concept of coronary artery disease

-  Vulnerable plaque, a main problem of public health

-  New strategies for vulnerable plaque detection

-  Non-invasive imaging tools: nuclear medicine, ultrafast computed tomography, magnetic resonance imaging

II. TUTORIALS (20 hours

Analysis of scientific publications that illustrate different aspects of the lectures and oral presentations by the students (two to three presentations per student).

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Today, the term Epigenetics is used to describe the study of heritable changes in genome function that occur without a change in DNA sequence. This includes the way gene expression is passed from one cell to its progeny, how gene expression changes during the differentiation of one cell type into another, and how environmental factors can change the way genes are expressed.

Epigenetic regulation involves changes of chromatin structure. Interestingly, the mechanisms involved in epigenetic regulation, such as histone modifications, also participate in the transient changes of gene expression.

This course is therefore opened to all students with an interest in the control of gene expression. There are far-reaching implications of epigenetic research for plant and human biology and disease.

The different mechanisms involved in epigenetic regulation, and the different contexts involving epigenetic regulation will be presented.

- Actors involved in epigenetic regulation (role of histone modification, chromatin remodeling complex, histone variants, DNA methylation, small and long noncoding RNA),

- Contexts involving an epigenetic regulation (response to cell environment, cell differentiation, development)

- Implication in diseases

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Course outline

The main theme of this course is centred on how regulatory networks and specific patterns of gene expression shape development and have evolved in animal and plant kingdoms.

On the animal side, you will hear about basic concepts of early evolution of metazoan development and body plans in Arthropods, we will analyse the role of neural crest in vertebrate segmentation and head patterning, and discuss developmental mechanisms of evolutionary change.

On the Plant front, developmental genetics of plant speciation, evolution of flower development, and molecular mechanisms generating flower diversity and underlying plant domestication will be the major topics.

Overall, this Evo-Devo course will give an overview, through the examples of various developmental models, of how shaping/reshaping of genes and genomes drove the diversity represented along the tree of life and conducted to present-day organisms living on earth.

The teaching team consists of local, national and international specialists in their field who will present the topics they are passionate about.

Lectures (15)

1) General introduction (2 lectures)

What is Evo-Devo:

- Introduction to Evolution of Developmental Genes

- Evidences for evolution of developmental genes in animals and plants

2) Animal Evo-Devo (6 lectures)

- An overview of animal clades and patterns of Development

- Evolutionary dynamics of zygote gene activations

- Conservation of gene regulation circuits in Evolution

- Cranial ganglia patterning in vertebrate development

- Molecular basis of placodes development in Vertebrates

- Male genome reprogramming: What have the mice taught us?

3) Plant Evo-Devo (6 lectures)

- The Phylogeny of Chloroplasts

- Retrograde signalling networks in the regulation of development in eukaryotes

- The mysterious origin of the flowering plants

- Evolution of floral symmetry and epigenetics

- Combining next generation Evo-Devo with new model organisms to study plant-pollinator interactions.

- Plant Evolution and Domestication

4) Concluding/Overview lecture (1 lecture)

Plant and Animal Genome Plasticity in Evolution

Tutorials (12)

Tutorials consist in analyses of scientific publications by students. The articles are in direct connection to the lectures/seminars. They are given to the students a week in advance. Students highlight the messages of the articles via analysis of the main figures/results. They present the state-of-the-art and the objectives of the study as an introduction, then the approaches employed to answer the questions, the main results and their driven-conclusions, and finish with perspectives of the presented work. Article analysis is followed by a discussion with the Professor and all students of the class.

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The course is designed to provide students with a broad introduction to cancer biology. Strong emphasis is on cancer genetics (genetic predisposition, gene transcription, DNA repair), epigenetics and functional genomics approaches – including use of genome editing, cell line and animal models and structural biology approaches – and the impact of these in research for deriving new insights into the basic mechanisms and treatment of cancer.

Teaching is interactive and relies on research seminars from experts in the field as well as personal reading and learning (webinars) by the students.

Focus is on developing strong critical analysis skills that can be applied generally to research.

Visit the full page about this course

This course will present the major issues related to the ageing processes and their consequences on longevity, in humans, animals and plants.

The main anatomical, histological, molecular and functional changes will be described in several major organs or systems (cardiovascular, nervous, pulmonary, muscular, immune, ...), together with some of the essential clinical problems of human ageing (fragility of elderly, neurodegenerative diseases, ..).

The role of important actors of the ageing mechanisms, such as telomeres and mitochondria, will be addressed before a final presentation of the principal theories of ageing. Some data about stem cells and their roles will also be presented.

Visit the full page about this course

Course outline

The main theme of this course is centred on how regulatory networks and specific patterns of gene expression shape development and have evolved in animal and plant kingdoms.

On the animal side, you will hear about basic concepts of early evolution of metazoan development and body plans in Arthropods, we will analyse the role of neural crest in vertebrate segmentation and head patterning, and discuss developmental mechanisms of evolutionary change.

On the Plant front, developmental genetics of plant speciation, evolution of flower development, and molecular mechanisms generating flower diversity and underlying plant domestication will be the major topics.

Overall, this Evo-Devo course will give an overview, through the examples of various developmental models, of how shaping/reshaping of genes and genomes drove the diversity represented along the tree of life and conducted to present-day organisms living on earth.

The teaching team consists of local, national and international specialists in their field who will present the topics they are passionate about.

Visit the full page about this course

Course outline

Today, the term “epigenetics” is used to describe the study of heritable changes in genome function that occur without a change in DNA sequence. This includes the way gene expression is passed from one cell to its progeny, how gene expression changes during the differentiation of one cell type into another, and how environmental factors can change the way genes are expressed. Epigenetic regulation involves changes of chromatin structure. Interestingly, the mechanisms involved in epigenetic regulation, such as histone modifications, also participate in the transient changes of gene expression.

This course is therefore opened to all students with an interest in the control of gene expression. There are far-reaching implications of epigenetic research for plant and human biology and disease.

The different mechanisms involved in epigenetic regulation, and the different contexts involving epigenetic regulation will be presented:

- actors involved in epigenetic regulation (role of histone modification, chromatin remodeling complex, histone variants, DNA methylation, small and long noncoding RNA),

- contexts involving an epigenetic regulation (response to cell environment, cell differentiation, development)

Visit the full page about this course

I. LECTURES (20 hours)

1- Cardiac energy metabolism: energetic regulations; cardiac energy transfer

- Bioenergetics and the role of oxygen in bioenergetics

- Contraction in cardiovascular systems, compartmentalization and energy transfer

- Modular organization of cardiac energy metabolism

- Metabolic aspects of the Frank-Starling’s law in the heart

2- Recent progress in basic cardiovascular physiology

- Heart and chronobiology

- Heart rate and longevity

- Cardiac conditioning (pre-conditioning, post-conditioning and remote conditioning)

- Intracellular signaling pathways in vascular systems

- Chronic exercise and vascular function

3- Mechanistic approaches in cardiovascular pathophysiology

- Recent advances in cardiac pharmacology

- Nutrition and cardiovascular risk

- Cardiovascular consequences of obesity and insulin resistance

- Oxidative stress and cardiovascular system

- Strategies for prevention of vascular diseases: pharmacology and prophylaxis

- Endothelial dysfunction in vascular pathologies

4- Vulnerable plaque

- Evolution of the concept of coronary artery disease

-  Vulnerable plaque, a main problem of public health

-  New strategies for vulnerable plaque detection

-  Non-invasive imaging tools: nuclear medicine, ultrafast computed tomography, magnetic resonance imaging

II. TUTORIALS (20 hours

Analysis of scientific publications that illustrate different aspects of the lectures and oral presentations by the students (two to three presentations per student).

Visit the full page about this course

The course is designed to provide students with a broad introduction to cancer biology. Strong emphasis is on cancer genetics (genetic predisposition, gene transcription, DNA repair), epigenetics and functional genomics approaches – including use of genome editing, cell line and animal models and structural biology approaches – and the impact of these in research for deriving new insights into the basic mechanisms and treatment of cancer.

Teaching is interactive and relies on research seminars from experts in the field as well as personal reading and learning (webinars) by the students.

Focus is on developing strong critical analysis skills that can be applied generally to research.

Visit the full page about this course

Course outline

The lectures present the basic methodology and some advanced techniques used for high throughput in vitro small molecule drug discovery. The principles and statistical methods used for assay optimization and validation will also be explained.

I. Molecular biology, Biochemistry and Protein expression

II. Proteomic analysis; Mass spectrometry

III. Lab-chips and Cell-chips

IV. Structural biology: Crystallogenesis and Crystallization; RMN

V. Combinatory chemistry

Format of exams:  Oral exam (at the end of December) and Research project (at the beginning of January)

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Course outline

 At the end of the course, the students should be able to analyze a "omic" dataset. More precisely, they should be able.

1- to load, explore and summarize graphically a dataset.

2- to compute confidence interval estimates for proportions, means and variances.

3- to formulate hypotheses, compute tests statistics, interpret p-values and make practical decisions for the

standard parametric and non-parametric tests.

4- to adjust simple and multiple linear models, analyses of variance (anovas), logistic regression, Cox

model.

5- to select genes that explain a response variable by applying multiple testing approaches.

6- to analyze a data set of differential gene expression.

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Course outline

CM: To provide a comprehensive overview of cancer from basic research to clinical trials: cancer physiopathology; cancer metabolism; proteomics; circadian rhythm and cancer cell characteristics; development of new anti-cancer drugs; imaging in cancer disease.

TD: How to analyze a scientific article critically?

To provide a comprehensive overview of cancer from basic research to clinical trials.

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Full lectures on cognitive, sensory, limbic and motor systems from expert contributors, e.g.:

-       Neural basis of language

-       Brain's rhythms: role and source

-       Neural basis of conscious and non-conscious processes

Full lectures on physiopathology of non-degenerative diseases from MD and PhD contributors, e.g.:

-       Epilepsy physiopathology

-       Schizophrenia physiopathology

-       OCD: new pathophysiological insights

-       Drugs addiction and neuro-adaptation: hijacking of the reward system

Each year, a full day congress will be organized on a particular field, coordinated with other M2 NN modules.

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• Alzheimer
• Parkinson
• Huntington
• Amyotrophic Lateral Sclerosis
• Multiple Sclerosis
• Trauma, Stroke

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The 3h lectures are given by specialists of the field working in Grenoble or in foreign univeristies. They will deal with the following subjects:

• Principle of electrophysiology
• Principle of calcium and voltage membrane potential imaging
• The use of transgenic mice and bi-photon microscopy to monitor the role of glial cells in the brain.
• Ischemia: Glutamate receptors and ischemia
• Of Microtubules and Mitochondria
• Stem cells in the CNS          
• Alzheimer’s disease: from the gene down to the synapse
• Huntington and axonal transport
• Htt links Neurodegeneration to CNS development

10h will be dedicated to presentations of scientific articles by students.

Each year, a full day congress will be organized on a particular field, coordinated with other M2 NN modules.

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Introduction

Science, academic research and entrepreneurship

Innovation

Intellectual properties & juridical forms of companies (in French language due to the specific aspects of the French law)

Marketing of innovation

Customer segmentation

Business development

Project management

Market research

Business plan

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The student will spend 6 months in a research team to work on a scientific project dealing with at least one of the fields covered by the Master 2 PhEDD program.

Finding the research team and the subject relies on the student.

A proposal for this internship should be sent to the module’s coordinator during the spring/early summer of the previous academic year for validation: It must fit to at least one of the fields covered by the Master 2 PhEDDprogram.

The student will be supervised in the lab by a researcher of the field.

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