IBIS Therapeutic Engineering and Bioproduction in Biotechnology-Health

The aim of this course is to introduce functional genomics technologies in -omics, and to present examples of biological questions that can be answered using these technologies.

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

Organisation des génomes / Genome organization

Techniques de séquençage / DNA sequencing methodsL. Journot, IGF

Organisation 3D des génomes / 3D genome organisation J. Poli, UM / IGH

Genome topological organization and replication / Organisation topologique et réplication des génomes-V. Coulon, UM / IGMM

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

ARN non-codants / non-coding RNAsV. Coulon, UM / IGMM

Interactomique / InteractomicsIan Robbins, UM / IGMM

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

Animal Models / Modèles animaux

Using Mice in Functional Genomics / Utilisation de la souris en génomique fonctionnelle F. Poulat, IGH

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

Analyse et présentation d'articles scientifiques/ Scientificarticles analysis and presentation(15min + 10 min discussion per group of 3 students)

See full page

See full page

Proteins are now widely used as therapeutic tools in human and animal health. Knowledge of peptide and protein synthesis pathways, folding and post-translational modifications is essential before any therapeutic protein biosynthesis can be envisaged. 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 designed to improve their original properties will also be discussed.

The course includes lectures and tutorials by teacher-researchers and researchers.

See full page

See full page

Bioinformatics is concerned with the creation and use of numerical and mathematical approaches applied to the life sciences. The main applications concern the automatic processing of biological data and questions of data modeling, analysis and integration in the field of life biology.This course aims to provide a solid grounding 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 taught in English, depending on the student's level. The course comprises lectures and practical work, carried out by research professors.

See full page

See full page

See full page

In bioprocess engineering, knowledge of the metabolism of catalysts (cells, microorganisms) is essential. This course will focus on describing the diversity of microbial metabolites (primary and secondary metabolites) and the bioprocesses that use these microorganisms to produce these molecules.

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

See full page

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

The course will focus on bioprocesses and the environment in which the biological reaction will be controlled (the bioreactor). The course will also cover the description and modeling of a biological reaction, with a presentation of the approach applied in bioprocess engineering. The remainder of the course will be devoted to the application of this approach to batch reactors. Other operating modes will be covered in the M2 course HAV930V "Bioprocess engineering - continuous and fed-batch".

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

See full page

See full page

A teaching module focused on the professional world, with general introductions to pre-defined themes targeting the biotechnological valorization of microorganisms (antimicrobials, microbiota, probiotics, applied virology, etc.), followed by presentations by industrialists on 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 biotechnologies, the production of recombinant proteins in various prokaryotic and eukaryotic expression systems represents a mature and attractive technological field with high employability. It is also a very important area of research in which many challenges remain to be met. The bioproduction of biomedicines (recombinant proteins and monoclonal antibodies) represents a major challenge for human therapeutics, but also for the many fields of biotechnology (environmental, industrial, agronomic, marine, etc.). Before designing any biological drug involving a biomanufacturing stage, it is essential to be familiar with the different eukaryotic and prokaryotic expression systems used in biotechnology, and to have a complete overview of the biomanufacturing panorama and challenges in France, Europe and the rest of the world.

This course includes interactive lectures. It is taught by various academic and industrial contributors involved in the field.

See full page

See full page

See full page

This course focuses on the specificities of healthcare applications in the field of bioprocessing. Case studies of biomedical and advanced therapy drug production are presented (e.g. clinical grade production of cell therapy products). The entire production chain is covered, with a particular focus on downstream processes (or DownStream Processing, DSP), which are particularly important for healthcare products (separation, extraction, purification and even formulation operations). Indeed, DSP represents a significant proportion of production costs, and the expectations and challenges associated with these technologies are numerous, particularly with the development of single-use technologies. UpStream Processing (USP) is covered in depth in the complementary modules of the Biomanufacturing specialization (HAV930V and HAV911V).

This course includes lectures and conferences, with numerous contributions from industry experts who will share their expertise and vision of the field with the students. In addition to technological aspects, these presentations will also cover Good Manufacturing Practices (GMP), quality control and the management of economic and environmental constraints.

See full page

Turning research into industrial applications will require strategies and players at the interface between the scientific and socio-economic worlds. Identifying and protecting the innovative nature of a discovery will be followed by the search for funding and partners to turn the idea into an economic reality.

This course is designed to give students all the tools they need to develop their work into new therapeutic tools. It includes lectures by legal professors 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, company creation, business plan.

This course will involve teacher-researchers, industrialists and patent and development professionals.

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 stage of the bioprocess: the biological reaction in the reactor. In particular, it will focus on the use of microbial and cellular catalysts. The products of interest may be fermented foods (wine, beer, etc.), energy molecules (bioethanol, methane, etc.), chemical intermediates or biomedicines (vaccines, monoclonal antibodies, growth factors, etc.). The knowledge and skills acquired in this course can be applied to any sector of activity. Examples will be given in fields corresponding to the main outlets of the two courses concerned (Agrosciences and Health). This course is a direct continuation of the M1 course HAV811V "Bioprocess Engineering -Batch". It focuses on the UpStream Processing (USP) aspects of bioprocessing.

The first lectures will provide an overview of bioprocesses and the approach applied in bioprocess engineering, as well as a brief reminder of the Batch mode (M1 prerequisite). The bulk of the course will then be devoted to applying the bioprocess engineering approach to reactors operating in continuous and Fed-Batch (or semi-(dis)continuous culture) modes.

Cross-disciplinary modules will also be offered:

-Transfer management (mixture management, heat transfer, gas transfer) with a focus on gas transfer and how to ensure a culture's oxygen requirements (kLa, OUR, OTR) -Design of culture media

-Elementary balances (carbon and redox balances)

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

This course includes interactive lectures and tutorials.

Students in the M2 Biology-Health / IBIS / Biomanufacturing specialization will be able to put their project into practice intensively (1 month) as part of the "Multidisciplinary lab project: from gene to protein" UEs. For these students, a strong link is also provided with the specialization courses (HAV910V, HAV911V and HAA910V). Please refer to the descriptions of these UEs for further 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

A teaching module focused on the professional world, with general introductions to pre-defined themes targeting the biotechnological valorization of microorganisms (antimicrobials, microbiota, probiotics, applied virology, etc.), followed by presentations by industrialists on 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 biotechnologies, the production of recombinant proteins in various prokaryotic and eukaryotic expression systems represents a mature and attractive technological field with high employability. It is also a very important area of research in which many challenges remain to be met. The bioproduction of biomedicines (recombinant proteins and monoclonal antibodies) represents a major challenge for human therapeutics, but also for the many fields of biotechnology (environmental, industrial, agronomic, marine, etc.). Before designing any biological drug involving a biomanufacturing stage, it is essential to be familiar with the different eukaryotic and prokaryotic expression systems used in biotechnology, and to have a complete overview of the biomanufacturing panorama and challenges in France, Europe and the rest of the world.

This course includes interactive lectures. It is taught by various academic and industrial contributors involved in the field.

See full page

See full page

See full page

This course focuses on the specificities of healthcare applications in the field of bioprocessing. Case studies of biomedical and advanced therapy drug production are presented (e.g. clinical grade production of cell therapy products). The entire production chain is covered, with a particular focus on downstream processes (or DownStream Processing, DSP), which are particularly important for healthcare products (separation, extraction, purification and even formulation operations). Indeed, DSP represents a significant proportion of production costs, and the expectations and challenges associated with these technologies are numerous, particularly with the development of single-use technologies. UpStream Processing (USP) is covered in depth in the complementary modules of the Biomanufacturing specialization (HAV930V and HAV911V).

This course includes lectures and conferences, with numerous contributions from industry experts who will share their expertise and vision of the field with the students. In addition to technological aspects, these presentations will also cover Good Manufacturing Practices (GMP), quality control and the management of economic and environmental constraints.

See full page

Turning research into industrial applications will require strategies and players at the interface between the scientific and socio-economic worlds. Identifying and protecting the innovative nature of a discovery will be followed by the search for funding and partners to turn the idea into an economic reality.

This course is designed to give students all the tools they need to develop their work into new therapeutic tools. It includes lectures by legal professors 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, company creation, business plan.

This course will involve teacher-researchers, industrialists and patent and development professionals.

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 stage of the bioprocess: the biological reaction in the reactor. In particular, it will focus on the use of microbial and cellular catalysts. The products of interest may be fermented foods (wine, beer, etc.), energy molecules (bioethanol, methane, etc.), chemical intermediates or biomedicines (vaccines, monoclonal antibodies, growth factors, etc.). The knowledge and skills acquired in this course can be applied to any sector of activity. Examples will be given in fields corresponding to the main outlets of the two courses concerned (Agrosciences and Health). This course is a direct continuation of the M1 course HAV811V "Bioprocess Engineering -Batch". It focuses on the UpStream Processing (USP) aspects of bioprocessing.

The first lectures will provide an overview of bioprocesses and the approach applied in bioprocess engineering, as well as a brief reminder of the Batch mode (M1 prerequisite). The bulk of the course will then be devoted to applying the bioprocess engineering approach to reactors operating in continuous and Fed-Batch (or semi-(dis)continuous culture) modes.

Cross-disciplinary modules will also be offered:

-Transfer management (mixture management, heat transfer, gas transfer) with a focus on gas transfer and how to ensure a culture's oxygen requirements (kLa, OUR, OTR) -Design of culture media

-Elementary balances (carbon and redox balances)

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

This course includes interactive lectures and tutorials.

Students in the M2 Biology-Health / IBIS / Biomanufacturing specialization will be able to put their project into practice intensively (1 month) as part of the "Multidisciplinary lab project: from gene to protein" UEs. For these students, a strong link is also provided with the specialization courses (HAV910V, HAV911V and HAA910V). Please refer to the descriptions of these UEs for further 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