Parcours Planta international

Course outline

Lectures (17)

- Approaches and tools to study plant development and signalling

- Gametogenesis, Fertilization and Self-Incompatibility

- Early embryogenesis: establishment of the apico-basal axis

- Late embryogenesis: ABA, dessiccation tolerance and dormancy

- Function of the Meristems

• Root Apical Meristem
• Shoot Apical Meristem and Cambium
• Floral Meristem and the basics od flower morphogenesis

- Phyllotaxis and organ growth (auxins, CKs, GAs, Ethylene…)

- Flowering transition (vernalisation, photoperiod, autonomous pathway)

- Photo/Skotosignaling and morphogenesis

- Retrograde signalling and plant development

- Photo perception and photosynthesis (Phototropins)

- Abiotic stress responses (nutrients, genotoxic agents, phytoremediation)

Methodology Tutorials (4,5)

During 3 TD sessions, we will review, several approaches, methodologies and tool that are used to answer questions in plant development and signalling: (1) Molecular cloning for sub-cellular visualization of a protein of interest; (2) Analysis of a transcription factor activity, (3) Analysis of protein-protein interactions. In these sessions, we will both summarize the principle behind each method and then analyse experimental datasets generated by these methods.

Tutorials + Discussions (11,5)

Individual students present a subject based on the study of article(s), on one of the topics developed in the lectures. Ahead of the presentation, a tutorial slot of 20min will be dedicated for consultation between each presenting student and his/her professor. A group of 2-3 students will also work together on the article(s) in order to prepare questions for the presenting student, and will give feedback on the answers. There will be 2 presentations by discussion session of 1h30.

Workshops during lab visit  (5)

We will visit the LPCV lab in which workshops will be organised to illustrate real research life in the lab, including developmental phenotyping in Arabidopsis, confocal imaging or fluorescent markers in planta, light chromato-sensing in algeas.

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Course outline

Lectures

- The green lineage: groups and phylogenetic classification

- Conquest of the land by plants:  Emergence from the aquatic environment and evolution of body plans

- Endosymbiosis in the plant kingdom: Mechanism, coordination of three genomes and consequences on physiology, development and metabolism

- Evolution of reproductive strategies: algae, mosses, ferns, spermaphytes

- Photosynthesis evolution (antenna structure, photoprotection, state transitions)

As well as several focussed lectures on the plant cell wall, the lipid metabolism, the evolution of microalgaes…

Bibliographic project

A group of 2 students will cover the bibliography on a specified scientific question proposed by a reference teacher. The reference teacher will indicate a review article and 2 break-through research articles to start with. Based on this information, the students will gather bibliographic references (i.e. up to 40 articles), read the corresponding articles and synthetize them in a collaborative written report. An oral presentation of their synthesis will be presented in front of the other students, leading to a discussion around the scientific question they cover.

Tutorials: Preparing, presenting and discussing a bibliographic project

To help prepare the bibliographic project, the student will benefit of 2 tutorials about techniques for bibliographic researches and a presentation of useful bibliographic resources (journals, databases, …) available through the UGA library, as well as a dedicated slot for collaborative work at the University library. A discussion will also be organized between the students and their reference teacher about the on-going bibliographic research and the structure of the written and oral reports.

Oral presentations of the bibliographic work will take place during discussions sessions with the complete group of students.

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The aim of this course is to introduce students to the design and the completion of a scientific project. The course takes the form of a tutored experimental project, in the scientific context of the response of photosynthetic organisms to environmental constraints. During this course, students will gain expertise on the main experimental techniques used in plant science. They will also develop their skills in collaborative work.

Plant responses to environmental stresses will be studied at the molecular level (signaling cascade, hormonal and physiological responses) in two plant models, the angiosperm Arabidopsis thaliana and the micro-alga Chlamydomonas reinhardtii. The students will take advantage of mutants to decipher biological and physiological responses to stresses. For this, they will employ plant physiology (photosynthesis studies, phenotypic analysis, hormone regulation) and molecular genetic approaches (effect of loss or gain of function on gene expression, protein accumulation…). They will also gain expertise in in vitro culture and general biology techniques (microscopy, western blot, RT-PCR). The conditions of a fluctuating environment, (light, temperature, hydric or nutritional stresses) will be simulated experimentally.

Teaching activities include:

- tutorials on methodological aspects of project design and data analysis.
- work sessions in small groups, guided by the teachers, to support the design of the project and the analysis of the data.
- a practical work session on a dedicated platform to carry out the planned experiments.

TD#1: Journal club
TD#2: Methods to analyze molecular expression of nucleic acids and proteins
TD#3: Photosynthesis measurements
TD#4: RStudio as a tool to represent and analyze data

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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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Know the basic of the innovation process / Understand several crucial points of entrepreneurship as the marketing of innovation, business models, product roadmap, magic spot, MVP…

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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.

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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)

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(Course outline)

The course is organized in three interconnected topics:

1/ Biocatalysis

2/ Oxygen chemistry in Biology

3/ Biochemistry around cellular membranes (membranes lipids and rafts, membrane proteins, and glycosaminoglycans)

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

        Channels

Extracellular Biochemistry: GAGs

        Extracellulaire matrices

        Glycosaminoglycans (GAG): biosynthesis and catabolism

        GAG: biological activities

        GAG: pathology and applications

This module brings strong background (relative to oxidative stress) to the Unit “Experimental Approaches in Biology”

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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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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

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

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.

Voir la page complète

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)

Voir la page complète

(Course outline)

The course is organized in three interconnected topics:

1/ Biocatalysis

2/ Oxygen chemistry in Biology

3/ Biochemistry around cellular membranes (membranes lipids and rafts, membrane proteins, and glycosaminoglycans)

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

        Channels

Extracellular Biochemistry: GAGs

        Extracellulaire matrices

        Glycosaminoglycans (GAG): biosynthesis and catabolism

        GAG: biological activities

        GAG: pathology and applications

This module brings strong background (relative to oxidative stress) to the Unit “Experimental Approaches in Biology”

Voir la page complète

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.

Voir la page complète

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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.

Voir la page complète

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)

Voir la page complète

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