CPES SV S5 profile Plant biology

This UE is a specialization module in Functional Plant Biology, covering the mechanisms underlying the major stages in plant development.

It is based on knowledge derived mainly from the model plant Arabidopsis thaliana and covers the following concepts from a molecular, cellular and physiological point of view:

• Roles and functions of the main phytohormones.
• Development of male and female gametes, fertilization.
• Embryo, seed and fruit development.
• Functioning of root and stem meristems (vegetative and floral).
• Flower architecture.
• Adaptive development mechanisms in response to abiotic factors: light, gravity, cold.

Certain aspects of development will also be analyzed from an evolutionary perspective, by studying the role of developmental genes in the diversification and evolution of developmental processes in land plants (evolution of the root system, floral architecture, etc.).

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This course describes the methodology used by life science researchers to communicate the results of their experiments, both orally and in writing. As English is the common language of international researchers, a large part of this course is taught in this language.

Written communication is addressed through the study of the (macro) structuring of a research article, as well as through a study of the publication process in scientific journals. Several elements of written structuring (micro) are examined in order to understand the differences between scientific and literary English: clarity, cohesion, coherence.

These studies are supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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Bioinformatics is a discipline at the crossroads of computer science, mathematics and the life sciences. It is based in particular on the use and development of computer tools for the analysis of massive biological data. Eventually, these megadata can be organized into searchable online databases, enabling users to extract data relevant to a biological problem.

The aim of the "Bioinformatics applied to plant biology" teaching unit is to introduce students to the use of databases and to offer a first approach to data mining using R software.

Virtually all teaching will take the form of practical case studies in the computer room, in student sub-groups.

In the first part, students will learn the rudiments of the R computer language, enabling them to organize and clean up their raw data to make it fully exploitable for further analysis. They will then learn how to propose explicit graphical representations based on biological data. Particular attention will be paid to writing reusable scripts and choosing the graphics associated with the calculations according to the biological question at hand.

In the second part, students will use general databases such as NCBI, or databases devoted exclusively to the model plant Arabidopsis (TAIR), to carry out data mining.

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Molecular biology is a fascinating subject of study in its own right, but it also provides other disciplines in biology (cell biology, genetics, physiology...) with fantastic tools for modifying and quantifying genes and their products.

The EU provides a deeper understanding of the mechanisms of organization, maintenance, replication and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we'll be exploring the properties of information-carrying macromolecules (DNA, RNA, proteins), and how transactions between them explain how eukaryotic cells function and adapt to the environment and to the development of organisms.

At the same time, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and analyzed in greater depth in practical sessions.

TDs will address these topics in the form of (1) exercises enabling students to check their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. In this way, the fundamentals of scientific reasoning and the critical analysis of results are acquired and/or deepened.

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Functional genetics aims to better understand the relationships between genotype and phenotype. This course integrates various aspects of the analysis of gene and genome function at the whole-genome level using in vivo approaches, as well as transcriptional and expression regulation of eukaryotic genomes. The course is illustrated by concrete examples of developmental genetics in physiological and pathological contexts.

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