IBIS Therapeutic Engineering and Bioproduction in Biotechnology-Health

The aim of this course is to introduce functional genomics technologies and to present examples of biological questions that can be asked using them.

This unit aims to present "omics" functional genomics technologies, and some biological questions that they can address.The lectures are given by both associate professors and researchers.

Introduction to functional genomics: approaches, concepts and methods

An introduction to functional Genomics: approaches, concepts and methods

V. Coulon, UM / IGMM

Genome organization / Organisation des génomes

Techniques de séquençage / DNA sequencing methodsL. Journot, IGF

3D genome organization J. Poli, UM / IGH

Genome topological organisation and replication-V. Coulon, UM / IGMM

Régulation spatio-temporelle de l'expression des génomes / Spatio-temporal regulation of gene expressionTranscriptionEpissage / Splicing-V. Coulon, UM / IGMM

Non-coding RNAsV. Coulon, UM / IGMM

Interactomics / InteractomiqueIan Robbins, UM / IGMM

Proteomics and Pharmacogenomics / Protéomique et pharmacogénomiqueC. Bécamel, UM / IGF

Animal Models / Modèles animaux

Using Mice in Functional Genomics F. Poulat, IGH

La Drosophile en génomique fonctionnelle / Using Drosophila in Functional Genomics -F. Juge and S. Chambeyron, IGH

Scientificarticles analysis and presentation(15min + 10 min discussion per group of 3 students)

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Proteins are now widely used as therapeutic tools in human and animal health. The knowledge of peptide and protein synthesis pathways, their folding, their possible post-translational modifications is essential before considering any therapeutic protein biosynthesis. Methods to better characterize these proteins are also essential to guarantee the quality of the proteins produced for therapeutic or industrial use. Protein engineering methods to improve their original properties will also be discussed.

The UE includes lectures and tutorials, conducted by teacher-researchers and researchers.

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Bioinformatics is concerned with the creation and use of numerical and mathematical approaches applied to life sciences. The main applications concern the automatic processing of biological data and questions of modelling, analysis and integration of data in the field of life biology.This course aims to provide a solid foundation in sequence analysis using bioinformatics tools as well as in immunoinformatics. Theoretical aspects will be covered and these will be reinforced by practical aspects (exercises and project work). This course may or may not be conducted in English depending on the level of the students. The course includes lectures and practical work carried out by teacher-researchers.

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In the framework of bioprocess engineering, the knowledge of the metabolism of catalysts (cells, microorganisms) is essential. This course will be dedicated to the description of the diversity of microbial metabolites (primary and secondary metabolites) and of bioprocesses exploiting these microorganisms to produce these molecules.

This course includes interactive lectures, tutorials and practical work (practical work in the computer room + personal work in project mode in small groups)

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Within biotechnologies, bioprocesses correspond to the industrial implementation of living tools (whether enzymes, microorganisms or cells from higher organisms) for the synthesis of products of interest. In this teaching unit (UE), the focus will be on the exploitation of microbial and cellular catalysts. The products of interest can be for example fermented foods (wine, beer, ...), energy molecules (bioethanol, methane, ...), chemical intermediates, or biomedicines (vaccines, monoclonal antibodies, growth factors...). The knowledge, know-how and skills acquired during this course will be transposable to any sector of activity in biotechnology. The examples that will be given will correspond to the outlets targeted by the two training courses (the Agrosciences and Health mentions).

The UE will be dedicated to bioprocesses and to the environment in which the biological reaction will be controlled (the bioreactor). The course will also address the issue of the description and modeling of a biological reaction, including the presentation of the approach applied in bioprocess engineering. The rest of the course will be devoted to the application of this approach to reactors operated in batch mode. The other operating modes will be covered by the M2 course HAV930V "Bioprocess engineering - continuous and fed-batch".

This course includes interactive lectures, tutorials and practical work (practical work in the computer room + personal work in small groups).

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A teaching module oriented towards the professional world, with general introductions on pre-defined themes targeting the biotechnological valorization of microorganisms (antimicrobials, microbiota, probiotics, applied virology, etc.) followed by presentations by industrialists who come to present their background, their company and/or the development of a project. This course covers both red biotechnologies (health applications) and the other colors of biotechnologies (green/agronomy, blue/marine, white/industrial, yellow/environmental).

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Within biotechnology, the production of recombinant proteins in different prokaryotic and eukaryotic expression systems represents a mature and attractive technological field with a high employability. It is also a very important field of research in which many challenges remain. The bioproduction of biomedicines (recombinant proteins but also monoclonal antibodies) represents a major challenge in human therapeutics, but also in many fields of biotechnology (environmental, industrial, agronomic, marine...). Before designing any biological drug involving a biomanufacturing step, it is essential to know the different eukaryotic and prokaryotic expression systems used in biotechnologies as well as to have a complete overview of the biomanufacturing panorama and stakes in France, in Europe and in the world.

This UE includes interactive lectures. It is provided by various academic and industrial speakers involved in the field.

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In this course, the specificities of health applications in the field of bioprocessing are presented. Thus, case studies on the production of biomedicines and advanced therapy drugs are proposed (e.g. clinical grade production of cell therapy products). The whole production chain is addressed with a particular focus on downstream processes (or DownStream Processing, DSP) which are particularly important for health products (separation, extraction, purification, and even formulation operations). Indeed, DSP represents a significant part of the production cost and the expectations and challenges associated with these technologies are numerous, especially with the development of single-use technologies. The UpStream Processing (USP) part is treated in depth in the complementary courses of the Bioproduction specialization (HAV930V and HAV911V).

This course includes lectures and conferences with numerous presentations by industrialists from the sector who will bring their expertise and vision of the field to the students. Beyond the technological aspects, these lectures will also be an opportunity to deal with Good Manufacturing Practices (GMP), quality control and the management of economic and environmental constraints.

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The valorization of research work towards industrial applications will require strategies and actors at the interface between the scientific and socio-economic worlds. The identification and protection of the innovative character of a discovery will be followed by the search for funding and partners to transform this idea into an economic reality.

This course will focus on providing students with all the tools they need to develop their work with a view to discovering new therapeutic tools. This course includes lectures given by teacher-researchers who are lawyers and professionals in the field, as well as a tutored project that is followed throughout the course. Work will also be carried out in the Learning Lab: identification of innovative research, drafting of a patent, valorisation plan, creation of a company, business plan.

This course will involve teachers-researchers, industrialists and professionals in the field of patents and valorisation.

See full page

Within biotechnologies, bioprocesses correspond to the industrial implementation of living tools (whether enzymes, microorganisms or eukaryotic cells) for the synthesis of products of interest. This course will focus on the central step of the bioprocess: the biological reaction in a reactor. It will be more particularly devoted to the exploitation of microbial and cellular catalysts. The products of interest can be for example fermented foods (wine, beer, ...), energy molecules (bioethanol, methane, ...), chemical intermediates, or biomedicines (vaccines, monoclonal antibodies, growth factors...). The knowledge and skills acquired during this course will be transposable to any sector of activity. The examples will be given in the fields corresponding to the main outlets of the two courses concerned (Agrosciences and Health). This course is the direct continuation of the M1 course HAV811V "Bioprocess Engineering - Batch". It focuses on the UpStream Processing (USP) aspects of bioprocesses.

The first lectures will allow to resituate the bioprocesses and the approach applied in bioprocess engineering and to briefly recall the Batch mode (pre-requisite of M1). Then, the main part of the course will be devoted to the application of the bioprocess engineering approach to reactors operated in continuous and Fed-Batch mode (or semi-(dis)continuous culture).

Cross-cutting modules will also be offered:

-Transfer management (mixture management, heat transfer, gas transfer) with an important focus on gas transfer and how to ensure the oxygen needs of a culture (kLa, OUR, OTR) -Design of culture media

-Elementary balances (carbon balance and redox balance)

-Development of an indicator for monitoring the biological reaction: the Respiratory Quotient (RQ)

This course includes interactive lectures and tutorials.

An intensive practical application (1 month) carried out in the form of a project is planned for the students of the M2 Biology-Health / IBIS / Bioproduction specialization in the framework of the UEs "Multidisciplinary lab project: from gene to protein". For these students, a strong link is also foreseen with the specialization courses (HAV910V, HAV911V and HAA910V). See the descriptions of these courses for more information.

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The multidisciplinary lab project, also called "Gene to Protein project", will be a "learning by doing" project. The students will be in charge of the bioproduction of a protein using E. coli as a host. If they follow both parts of the project (1 & 2, like students from Biohealth master), they will start with strain construction and continue with pilot scale production and purification of the protein.Bioprocess engineering is a highly interdisciplinary fieldof study. The students (and future workers in the field), will benefit from project-based learning with an important practical part, where they can actively experience the interconnection between biology, engineering and physical sciences.

The part 2 of the project will be dedicated to the "production process design and pilot scale production" of the recombinant protein using a high-cell density fed-batch culture. It will be a multidisciplinary, hands-on training of Bioprocess Engineering and will be organized over three different periods:

-Week 1 : In Learning lab, students will participate in workshops to design and plan a production process in accordance with equipment and data available (scientific papers, reports, websites, previous results from UE "Multidisciplinary Lab Project 1"). Based on the bottlenecks identified for production of recombinant proteins in E. coli, the students will choose the culture process to be used, define the production objectives, simulate the culture (planning objective), design a sampling plan, design the culture medium...

-Week 2 :In practical training rooms on pilot-scale equipment (20L working volume bioreactor), students will prepare the bioreactor and all they need to perform the pilot-scale culture. They will be in charge of the monitoring of the culture and of real time data treatment in order to detect and correct deviations from the anticipated progress of the culture.

-Week 3: In learning labs, students will treat and analyze the data. They will be in charge of the interpretation and discussion of the results and of the writing of a professional report.

See full page

See full page

A teaching module oriented towards the professional world, with general introductions on pre-defined themes targeting the biotechnological valorization of microorganisms (antimicrobials, microbiota, probiotics, applied virology, etc.) followed by presentations by industrialists who come to present their background, their company and/or the development of a project. This course covers both red biotechnologies (health applications) and the other colors of biotechnologies (green/agronomy, blue/marine, white/industrial, yellow/environmental).

See full page

Within biotechnology, the production of recombinant proteins in different prokaryotic and eukaryotic expression systems represents a mature and attractive technological field with a high employability. It is also a very important field of research in which many challenges remain. The bioproduction of biomedicines (recombinant proteins but also monoclonal antibodies) represents a major challenge in human therapeutics, but also in many fields of biotechnology (environmental, industrial, agronomic, marine...). Before designing any biological drug involving a biomanufacturing step, it is essential to know the different eukaryotic and prokaryotic expression systems used in biotechnologies as well as to have a complete overview of the biomanufacturing panorama and stakes in France, in Europe and in the world.

This UE includes interactive lectures. It is provided by various academic and industrial speakers involved in the field.

See full page

See full page

See full page

In this course, the specificities of health applications in the field of bioprocessing are presented. Thus, case studies on the production of biomedicines and advanced therapy drugs are proposed (e.g. clinical grade production of cell therapy products). The whole production chain is addressed with a particular focus on downstream processes (or DownStream Processing, DSP) which are particularly important for health products (separation, extraction, purification, and even formulation operations). Indeed, DSP represents a significant part of the production cost and the expectations and challenges associated with these technologies are numerous, especially with the development of single-use technologies. The UpStream Processing (USP) part is treated in depth in the complementary courses of the Bioproduction specialization (HAV930V and HAV911V).

This course includes lectures and conferences with numerous presentations by industrialists from the sector who will bring their expertise and vision of the field to the students. Beyond the technological aspects, these lectures will also be an opportunity to deal with Good Manufacturing Practices (GMP), quality control and the management of economic and environmental constraints.

See full page

The valorization of research work towards industrial applications will require strategies and actors at the interface between the scientific and socio-economic worlds. The identification and protection of the innovative character of a discovery will be followed by the search for funding and partners to transform this idea into an economic reality.

This course will focus on providing students with all the tools they need to develop their work with a view to discovering new therapeutic tools. This course includes lectures given by teacher-researchers who are lawyers and professionals in the field, as well as a tutored project that is followed throughout the course. Work will also be carried out in the Learning Lab: identification of innovative research, drafting of a patent, valorisation plan, creation of a company, business plan.

This course will involve teachers-researchers, industrialists and professionals in the field of patents and valorisation.

See full page

Within biotechnologies, bioprocesses correspond to the industrial implementation of living tools (whether enzymes, microorganisms or eukaryotic cells) for the synthesis of products of interest. This course will focus on the central step of the bioprocess: the biological reaction in a reactor. It will be more particularly devoted to the exploitation of microbial and cellular catalysts. The products of interest can be for example fermented foods (wine, beer, ...), energy molecules (bioethanol, methane, ...), chemical intermediates, or biomedicines (vaccines, monoclonal antibodies, growth factors...). The knowledge and skills acquired during this course will be transposable to any sector of activity. The examples will be given in the fields corresponding to the main outlets of the two courses concerned (Agrosciences and Health). This course is the direct continuation of the M1 course HAV811V "Bioprocess Engineering - Batch". It focuses on the UpStream Processing (USP) aspects of bioprocesses.

The first lectures will allow to resituate the bioprocesses and the approach applied in bioprocess engineering and to briefly recall the Batch mode (pre-requisite of M1). Then, the main part of the course will be devoted to the application of the bioprocess engineering approach to reactors operated in continuous and Fed-Batch mode (or semi-(dis)continuous culture).

Cross-cutting modules will also be offered:

-Transfer management (mixture management, heat transfer, gas transfer) with an important focus on gas transfer and how to ensure the oxygen needs of a culture (kLa, OUR, OTR) -Design of culture media

-Elementary balances (carbon balance and redox balance)

-Development of an indicator for monitoring the biological reaction: the Respiratory Quotient (RQ)

This course includes interactive lectures and tutorials.

An intensive practical application (1 month) carried out in the form of a project is planned for the students of the M2 Biology-Health / IBIS / Bioproduction specialization in the framework of the UEs "Multidisciplinary lab project: from gene to protein". For these students, a strong link is also foreseen with the specialization courses (HAV910V, HAV911V and HAA910V). See the descriptions of these courses for more information.

See full page

See full page

The multidisciplinary lab project, also called "Gene to Protein project", will be a "learning by doing" project. The students will be in charge of the bioproduction of a protein using E. coli as a host. If they follow both parts of the project (1 & 2, like students from Biohealth master), they will start with strain construction and continue with pilot scale production and purification of the protein.Bioprocess engineering is a highly interdisciplinary fieldof study. The students (and future workers in the field), will benefit from project-based learning with an important practical part, where they can actively experience the interconnection between biology, engineering and physical sciences.

The part 2 of the project will be dedicated to the "production process design and pilot scale production" of the recombinant protein using a high-cell density fed-batch culture. It will be a multidisciplinary, hands-on training of Bioprocess Engineering and will be organized over three different periods:

-Week 1 : In Learning lab, students will participate in workshops to design and plan a production process in accordance with equipment and data available (scientific papers, reports, websites, previous results from UE "Multidisciplinary Lab Project 1"). Based on the bottlenecks identified for production of recombinant proteins in E. coli, the students will choose the culture process to be used, define the production objectives, simulate the culture (planning objective), design a sampling plan, design the culture medium...

-Week 2 :In practical training rooms on pilot-scale equipment (20L working volume bioreactor), students will prepare the bioreactor and all they need to perform the pilot-scale culture. They will be in charge of the monitoring of the culture and of real time data treatment in order to detect and correct deviations from the anticipated progress of the culture.

-Week 3: In learning labs, students will treat and analyze the data. They will be in charge of the interpretation and discussion of the results and of the writing of a professional report.

See full page

See full page