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Immunoinformatics taught to middle and high school pupils in IMGT®

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Viviane Nguefack Ngoune, Perrine Pegorier, Morgane Bertignac, Imène Chentli, Veronique Giudicelli, Saida Hadi-Saljoqi, Joumana Jabado-Michaloud, Geraldine Folch

IMGT®, the international ImMunoGeneTics information system®, Institut de Génétique Humaine, UMR 9002 CNRS-UM, Université de Montpellier, Montpellier, France

Competing interests: VNN none; PP none; MB none; IC none; VG none; SHS none; JJM none; GF none

Nguone et al. (2020) EMBnet.journal 25, e926 http://dx.doi.org/10.14806/ej.25.0.926

Received: 04 October 2019 Published: 09 January 2020

HTML Abstract

IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) (Lefranc et al., 2015), is the global reference in immunogenetics and immunoinformatics (Lefranc 2014). In 2019, for the first time, two pupils were welcomed within the team and introduced to immunoinformatics thank to the “Apprentis Chercheurs” program founded by the association l’Arbre des Connaissances. This article describes the method, and pedagogical approaches used, and demonstrates that immunoinformatics can be successfully taught to pupils of middle and high school.

Introduction

The association l’Arbre des Connaissances1 founded by researchers to promote dialogue between scientists and the general public, set up since 2004 a program named “Apprentis Chercheurs” in Paris. This program allows middle and high school pupils to explore the different facets of research throughout the school year by immersion in research laboratories. The program was quickly replicated in other regions of the country. The local project coordinator is Genopolys2. Once per month, the pupils work on their scientific project according to the thematic area of the laboratory. At the end of the school year, Genopolys organises a conference, where the pupils present their work in public (school director, rector of the academy, Arbre des connaissances, researchers, supervisors, teachers, family, etc.) and receive a certificate of research initiation.

For the 2019 program, IMGT®, for the first time, received Tessa (middle school pupil) and Jean-Baptiste (high school pupil) in the laboratory to introduce them to a relatively recent scientific field resulting from the fusion of two domains, namely informatics and immunology. To accomplish this goal, the IMGT® biocuration team established planning of the different sessions, topics and resources to be discussed (cf Table 1). This planning was divided into three parts, the first part covered the basics of biology and immunology, the second was focused on bioinformatics, and the last part was an introduction to immunoinformatics. The purpose of these sessions was to introduce the pupils to the analysis of antibodies using bioinformatics tools.

Table 1. Detailed program of the different topics discussed during the sessions as well as the projects carried out and resources.

Contents

Topics

Resources

Project applications

Biology and

immunology

- Overview of the body systems

- Immune system

- Animal and plant cells

- DNA/RNA structure

- Protein synthesis

- Genetics engineering

https://www.youtube.com/watch?v=vAz_9_Jesbo

https://www.youtube.com/watch?v=w_MsGXYMv3c

https://www.youtube.com/watch?v=jSRMqO0e908

https://www.youtube.com/watch?v=to_62MXI8-o

https://www.youtube.com/watch?v=tf3_k0-MQzc

https://www.youtube.com/watch?v=iJE_FlrA0io

- Build a 2D mock-up of an animal and plant cells

- Play an online game Leucowar

- Quizzes on DNA/RNA, protein synthesis and genetic engineering

Bioinformatics

- Introduction to Bioinformatics

- Function of Bioinformatics

- Presentation of generalists databases

- Common sequence analysis

https://www.youtube.com/watch?v=CLV1nrzGyBA

https://www.youtube.com/watch?v=xK9vOjvYoUM

https://www.youtube.com/watch?v=0N3ize9CDwY

- Exploration of the databases NCBI and EBI

- Blast analysis to compare sequences (Blast)

- Multiple sequence alignment (ClustalOmega)

- Phylogenetic tree (Phylogeny)

Immuno-informatics

- Introduction to Immunoinformatics

- Presentation of specialised databases for Immunogenetics

- Analyse of antibody genes

http://www.imgt.org/IMGTindex/factsbook.php

http://www.imgt.org

- Exploration of IMGT/GENE-DB and IMGT/LIGM-DB specialised databases

- Annotation of antibody genes (internal tool)

- Analysis of rearranged antibody genes (IMGT/V-QUEST)

Methods and pedagogical approaches

The delivered sessions had both a theoretical and a practical component. At the beginning of each session and before carrying out the project, it was essential to discuss with the pupils to make sure that they had understood what they were about to do, how they were supposed to do it and the importance of the task. Therefore, each topic started with a lecture or a video projection, which was a reportage or a documentary. After each projection, the content was addressed with many more details and the different questions of the pupils were discussed. Concerning the practical part of the sessions, the pupils’ project differed based on the topic. For example on the topic of animal and plant cells, the IMGT® curators had drawn down, separately, all the components of those cells and asked the pupils to put together all these pieces to build a 2D mock-up of an animal and a plant cell. For the immunology project, the pupils played an online game called Leucowar3 to understand better the immune response.

Quizzes to test the knowledge acquired by pupils were carried out, which helped us to know what topics were well understood by the pupils and which subjects needed to be revisited. At the end of each session, there was some time dedicated to collect and organise the information the pupils wanted for their end of year presentation. The last session was devoted to a rehearsal of the pupils’ presentation in the IMGT® team.

Topics discussed

The first two sessions were used as a reminder of biology and immunology topics. We started with an overview of the different body systems, their functions, and how they interact with each other. We paid particular attention to the immune system and introduced some basics of immunology such as the different types of immune response, tolerance and system disorder. The different cells types, their structure, their component as well as their function were discussed in a session entitled cellular biology. Genetic engineering and what can be done with it as well as protein synthesis were addressed afterwards. The different types of antibody genes, their rearrangement process with an example, at the molecular level, of the synthesis of an antibody in humans, were presented in detail.

The huge amount of data accumulated from human and others species and the necessity to analyse them was an excellent topic to introduce the field of Bioinformatics, its use and the type of questions that can be answered with it. The pupils explored different publicly available databases and servers such as the NCBI4 and EBI5 resources.

They extracted a gene sequence, which gave them a lot of satisfaction, and in parallel demystified the procedure of getting hold of gene sequences. Different available output files format were introduced such as fasta, genbank and embl, along with their features. Additionally, the pupils performed various analyses such as the pairwise sequence comparison and the extraction of similar sequences from these databases for functional assignment (Johnson et al., 2008). The pupils carried out multiple sequence alignment using different online tools and reconstructed a phylogenetic tree to visualise the molecular relationships of species through their genes.

Immunoinformatics is a discipline which uses informatics to the study of molecules of the immune system (Tomar and De, 2014). Therefore, it is crucial to have various information on those molecules, which is the primary responsibility of the curators of IMGT® who analyse, interpret and integrate immunological information into databases and data repositories. For this part, as for the bioinformatics topic, the pupils explored two specialised databases, IMGT/LIGM-DB (Giudicelli et al., 2006) and IMGT/GENE-DB (Giudicelli et al., 2005). The pupils were shown how to identify and annotate different types of antibody genes on genomic sequences (Lane et al., 2010) and analysed rearranged sequences (Giudicelli et al., 2004).

Conclusion

Based on the pupils’ final presentation, their involvement and engagement during the monthly sessions as well as the evaluation of the internship from both the pupils and their teachers, we feel confident that this undertaking was a successful first-time introduction of immunoinformatics to middle and high school pupils. We are convinced that immunoinformatics can be successfully taught to this public and we presented this article in the hope that more people in the field will be encouraged to introduce pupils to this exciting, fast-moving and promising scientific field.

Acknowledgements

We are grateful to Magali Kitzmann and Marie Pequignot, in charge of scientific culture at GENOPOLYS, to set up and manage the program “Apprentis Chercheurs” in Montpellier as well as Sofia Kossida, director of IMGT® to include IMGT® to the program and help us draft the manuscript. We are grateful to Sophie Lacas and Christian Jaubert, Life and Earth Science school teachers at high school Jean Jaurès and middle school Frédéric Bazille in Montpellier for their flawless cooperation during the process. We are also grateful to “l’Arbre des Connaissances” for providing feedback, consultation, and support at all phases of the project.

References

1. Giudicelli, Véronique, Denys Chaume, and Marie-Paule Lefranc (2004) “IMGT/V-QUEST, an Integrated Software Program for Immunoglobulin and T Cell Receptor V–J and V–D–J Rearrangement Analysis.” Nucleic Acids Res. 32 (Web Server issue):W435–40. http://dx.doi.org/10.1093/nar/gkh412.

2. Giudicelli, Véronique, Denys Chaume, and Marie-Paule Lefranc (2005) “IMGT/GENE-DB: A Comprehensive Database for Human and Mouse Immunoglobulin and T Cell Receptor Genes.” Nucleic Acids Res. 33 (Database issue): D256-261. http://dx.doi.org/10.1093/nar/gki010.

3. Giudicelli, Véronique, Patrice Duroux, Chantal Ginestoux, Géraldine Folch, Joumana Jabado-Michaloud, Denys Chaume, and Marie-Paule Lefranc (2006) “IMGT/LIGM-DB, the IMGT Comprehensive Database of Immunoglobulin and T Cell Receptor Nucleotide Sequences.” Nucleic Acids Research 34 (Database issue): D781-784. http://dx.doi.org/10.1093/nar/gkj088.

4. Johnson, M., I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. McGinnis, and T. L. Madden (2008) “NCBI BLAST: A Better Web Interface.” Nucleic Acids Research 36 (Web Server): W5–9. http://dx.doi.org/10.1093/nar/gkn201.

5. Lane, Jérôme, Patrice Duroux, and Marie-Paule Lefranc (2010) “From IMGT-ONTOLOGY to IMGT/LIGMotif: The IMGT Standardized Approach for Immunoglobulin and T Cell Receptor Gene Identification and Description in Large Genomic Sequences.” BMC Bioinformatics 11: 223. http://dx.doi.org/10.1186/1471-2105-11-223.

6. Lefranc, Marie-Paule (2014) “Immunoglobulin and T Cell Receptor Genes: IMGT(®) and the Birth and Rise of Immunoinformatics.” Frontiers in Immunology 5:22. http://dx.doi.org/10.3389/fimmu.2014.00022.

7. Lefranc, Marie-Paule, Véronique Giudicelli, Patrice Duroux, Joumana Jabado-Michaloud, Géraldine Folch, Safa Aouinti, Emilie Carillon, et al. (2015) “IMGT®, the International ImMunoGeneTics Information System® 25 Years On.” Nucleic Acids Research 43 (Database issue): D413-422. http://dx.doi.org/10.1093/nar/gku1056.

8. Tomar, Namrata and Rajat K. De (2014) “Immunoinformatics: A Brief Review.” Methods in Molecular Biology (Clifton, N.J.) 1184: 23–55. http://dx.doi.org/10.1007/978-1-4939-1115-8_3.

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