I2BC Paris-Saclay

Chloé @Chl0e_Girard and Daan @DaanNoordermeer were invited to an interdisciplinary workshop organized by the Bettencourt-Schueller Foundation @Fondation_BS about creativity as motor for scientific research.

A 3-days seminar was organized by the Bettencourt-Schueller Foundation at the Domaine de Chaumont-sur-Loire for former laureates (Prix Jeune Chercheur, Prix Impulsience, Prix Coups d’Elan pour la Recherche Française). This interdisciplinary seminar centered around creativity combined Arts & Science, the two main components of the foundation's patronage. The I2BC scientists participated in thematic workshops around Music, Mathematics, Visual Arts and Biology, presented by world-reknown artists and scientists. Daan Nordermeer was a recipient of the "Coup d'élan pour la recherche française”, while Chloé Girard received the "Prix jeune Chercheur", both in 2015.

Fadwa EL KHADDAR is working with us part time at the BIOI2 plateform since the beginning of October 2023 and has brought with her leading-edge experience in omics data analysis that will greatly enrich the range of services offered by the plateform.

Stéphanie Bury Moné, a lecturer at the I2BC and Deputy Director of Studies at the Graduate School Life, Science and Health at UPSaclay, specialises in blending different research techniques, including genomics, to reveal the hidden talents of soil bacteria, which are capable of naturally developing antibiotics.

More information: https://www.universite-paris-saclay.fr/en/news/stephanie-bury-mone-revealing-hidden-potential-bacteria.

Photo credit: (c)UPSaclay/SD

Chloé Quignot was awarded "Prix 2021 du Groupe Graphisme et Modélisation Moléculaire (GGMM)" for her PhD thesis in the group "Molecular Assemblies and Genome Integrity".

Chloé Quignot received the GGMM prize for her thesis entitled "Modelling Protein interfaces using evolutionary information", carried out at the I2BC, B3S department, in the Molecular Assemblies and Genome Integrity team and co-supervised by Jessica Andreani and Raphael Guerois. Chloé presented her thesis work at the GGMM-SFCi conference held in Lille in October 2021.
The Graphical and Molecular Modeling Group (GGMM) is a learned society that brings together a large part of the French community whose activity is dedicated to, or involves, the use of molecular modeling. The GGMM prize is awarded every two years for original work in molecular modeling, bioinformatics, chemoinformatics and numerical simulation in the field of structural biology and pharmacology.

Congratulations, Chloé!

more information here.

A PhD student (Université Paris-Saclay) unveils her comic strip, illustrated by Marine Spaak, and invites you to dive into the heart of scientific research on HIV !

Like the book "Sciences en bulles", presented at the "Fête de la Science", the "Diagonale Paris-Saclay" challenged our doctoral student, Lisa Bertrand, to explain and share her thesis in a fun way in the form of a comic strip. His topic? Defining the translatome of HIV-1 in order to identify new antigens recognized by T-cells.
She followed several introductory sessions that taught her how to synthesize her ideas, turn them into a playful script, choose illustrations to complete her remarks, until she got a first storyboard. The illustrator Marine Spaak accompanied her throughout this process and then took it upon herself to shape all these ideas! Discover their image and immerse yourself in the world of the ribosome, a small cellular constituent responsible for protein production.You will find there that the AIDS virus hijacks ribosomes for its own benefit to make its own viral proteins. And how French research explores this phenomenon, in order to develop therapies. In addition to therapeutic research, the study of viruses is an excellent tool for understanding the functioning of the cell.
The comic on :
http://www.sciencesociete.universite-paris-saclay.fr/decouvrir/la-recherche-sort-de-sa-bulle/#section_3

Jeudi 11 mars 2021, l’ENS Paris-Saclay accueillait la finale Paris-Saclay du concours Ma Thèse en 180 seconde. Unique représentante de l'I2BC, Hélène BRET est arrivée deuxième. Bravo à elle et bonne chance pour la suite !

Quinze doctorants, issus d’une première sélection, ont présenté en 3 minutes leur sujet de thèse. Hélène Bret, étudiante dans l’équipe Assemblages macromoléculaires et intégrité des génomes (AMIG/I2BC) est arrivée deuxième de cette finale « régionale ».

Elle a d’abord expliqué très simplement pourquoi il était important de savoir prédire les interfaces entre deux protéines et la tâche immense que cela représentait devant les millions de paires de protéines qui existent et le petit nombre d’interfaces déjà déterminées expérimentalement grâce aux méthodes de biologie structurale. Pendant sa thèse, Hélène construit un programme informatique qui doit prédire où est l’interface pour un couple de protéines. Ce programme est un « réseau de neurones artificiels » qui apprend tout seul à partir des exemples obtenus en laboratoire. Et Hélène lui apprend à se tromper de moins en moins.

Hélène est ingénieur AgroParisTech spécialisée en science des données et apprentissage artificiel. Elle a obtenu en double diplôme un Master 2 ISI (Informatique : systèmes intelligents) de l'Université Paris-Dauphine. Elle est maintenant en deuxième année de thèse, co-encadrée par Raphaël Guérois et Jessica Andreani.

Revoir sa prestation ici.

En savoir plus à son sujet ici

Alexia Royer received the prize "Relève de l'étoile" for her article “Clostridioides difficile S-Layer Protein A (SlpA) Serves as a General Phage Receptor” published in Microbiology Spectrum in February 2023.

Antibiotics have been used for more than 80 years to treat bacterial infections, but bacteria have developed resistance to these treatments, making them difficult to eradicate. One of the side effects of antibiotics is that they tend to kill a broad spectrum of bacteria, including “good bacteria” important for the proper functioning of the human body. The resulting bacterial imbalance, called dysbiosis, will open the door to opportunistic bacteria such as Clostridioides difficile. This bacterium is the main cause of severe diarrhea in industrialized countries. As the infection is now treated with antibiotics, which are themselves responsible for the infection, many relapses are reported. In the laboratories of Professor Louis-Charles Fortier and Professor Olga Soutourina, we are interested in phage therapy, which is a treatment based on the use of bacteria-killing viruses called bacteriophages. Phages have the advantage of being specific and targeting a species or a few bacterial strains unlike antibiotics. Thus, they could be used as an alternative or complementary therapy to antibiotics to treat patients in therapeutic failure. The key step to set up a phage therapy is to understand the mechanism of recognition of the bacteria by phages. For a phage to attack and kill a bacterium, it must first attach to a receptor on its surface. In the article, we identified the SlpA protein as the receptor on the surface of the bacteria that is targeted by phages. We have shown that the infection specificity of phages is linked to the presence of different forms of SlpA, called isoforms, each strain expressing one isoform. We also identified a domain of SlpA, named D2, playing a role in receptor recognition by certain phages. These data are essential because they improve our understanding of phage/bacteria interactions and make phage therapy possible one day against C. difficile infections.

https://frq.gouv.qc.ca/histoire-et-rapport/releve-etoile-jacques-genest-decembre-2023/

Alexia ROYER <alexia.royer@i2bc.paris-saclay.fr>

Meet Alicia Nevers, an assistant professor of Paris-Saclay University, that just joined the Genome Biology Department of the I2BC.

Alicia began her undergraduate studies with a DUT in Biological Engineering, which she obtained in 2011. She then went on to complete a Bachelor's degree in Life Sciences, followed by a Master's degree in Molecular and Cellular Biology, with a specialization in RNA Molecular Biology. From 2013 to 2017, she did her thesis with the Université Paris Sorbonne and in Alain Jacquier's laboratory at the Institut Pasteur. Under the supervision of Alain Jacquier and Gwenaël Badis-Bréard she studied, in the budding yeast Saccharomyces cerevisiae, the mechanisms of control of gene expression by transcriptional interference and the functionality of pervasive antisense transcription. Alicia then joined Mathieu Rougemaille's laboratory at I2BC as a research engineer between 2018 and 2020. She contributed to the discovery and characterization of a novel non-coding RNA involved in the control of meiosis in the fissiparous yeast Schizosaccharomyces pombe. After that, Alicia was hosted in Micalis Unit of Inrae as a post-doctoral researcher. Here, under the supervision of Didier Lereclus, Michel Gohar and Vincent Sanchis-Borja, she studied the role megaplasmids in new pathogens emergence. More particularly she studied pCER270 megaplasmid, representative of emetic strains of Bacillus cereus group. She particularly analyzed in natural and artificial hosts, the consequences of pCER270 presence for gene expression and biofilm formation ability. Now that she joined Frédéric Boccard’s laboratory as a senior lecturer, she’ll work under the supervision of Vicky Lioy and Stéphany Bury-Moné to describe a link between gene expression, chromosome conformation and bacterial lifestyle, in particular biofilm formation, in the pathogen Pseudomonas aeruginosa.

We are very pleased to welcome our colleague Stéphane Plancqueel (I2BC, crystallization platform) who joined the PIM team as a part time (20%) to help us with our growing activity. This arrival coincides with the launch of a new technology, a OMNISEC. This instrument is dedicated to the study of oligomerization states of proteins or complexes.

Stéphane Plancqueel is an active member of Crystallisation facility and has recently joined the PIM facility to support the team with its growing activity. Stephane will complete his expertise on proteins by characterizing their oligomerization states and complexes, thanks to the different techniques present on PIM facility. He joined the PIM platform this summer as part time (20%) to strengthen the team and to work with Magali Aumont-Nicaise, Magali Noiray and Lia Maurin (M1 trainee).
In parallel, the OMNISEC was acquired thanks to supports from FRISBI and IBISA. It replaces the old SEC-MALS. Based on 2 different angles (RALS/LALS), the fully integrated OMNISEC system is a multi-detection, label-free, real-time analysis instrument. It is ideal for studying oligomerization states of proteins or to demonstrate their interactions. The OMNISEC system can be used for a wide range of analyses thanks to our Superdex chromatography columns from Cytiva. System provides up to 4 detections (UV, RI, RALS, LALS) in order to determine molecular sizes and cooling for temperature control down to 5°C in autosampler.

The morning will be devoted to tributes and testimonials from people who have been fortunate enough to work with Mike Dubow during his teaching and research activities. The afternoon will be devoted to a symposium of the Department of Microbiology, which will focus on three scientific themes dear to Mike: extremophiles, biofilms and environmental phages.

Each theme will include a presentation by a member of the Department and an external collaborator.

Registration: https://evento.renater.fr/survey/hommage-a-michael-dubow-vendredi-30-septembre-2022-iary7xq2

Contact: hommage.mike@i2bc.paris-saclay.fr

My name is Valerio VITALI, I am a new Italian postdoc in the Programmed Genome Rearrangement Team (Bétermier Lab) since Feb 1st. Under the guidance of Mireille—and in close collaboration with the team—I am tasked to design and implement creative strategies to characterize the complex machinery that catalyzes developmentally programmed DNA rearrangements in Paramecium (removal of intervening sequences coupled with DNA repair).
I have received my PhD in Evolutionary Genomics and Bioinformatics from the University of Münster (WWU), Germany. While at the Institute for Evolution and Biodiversity, my research has focused on the highly plastic genome architecture of Paramecium, and its evolutionary potential. During my doctoral and (brief) post-doctoral research, I have gained transferable experience in comparative genomics and trancriptomics, single cell whole-genome sequencing, and the analysis of Structural Variants (SVs) from NGS data.
When not in the Lab, I enjoy running, reading books about evolution and aging, learning new languages (or at least trying!) and cooking traditional meals.
I am excited to have joined the Genome Biology Department at the I2BC and can't wait to greatly expand my knowledge of Genome and Cell Biology, Biochemistry, Biophysics, Structural biology.....and beyond.

GitHub Profile: https://github.com/biowalter/senes

Full list of Publications: https://scholar.google.com/citations?hl=en&user=BI3IdwwAAAAJ

We are very pleased to announce that Magali Noiray arrived this summer to work on the PIM platform.This arrival coincides with the commissioning of BLI, a new machine dedicated to the study of macromolecular interactions.

Magali Noiray has a solid expertise in the field of the study of macromolecular interactions (SPR, ITC, DSC...) and worked for 10 years on the interaction platform of Chatenay Malabry (Pharmacy Faculty) specialized in nanomedicines and small molecules. She joined the PIM platform this summer to strengthen the team and to work with Magali Aumont. In parallel, thanks to funding obtained last year from the Ile de France region , we have obtained and put into operation a new device to replace the SPR. Based on Bio-Layer Interferometry (BLI), the fluidics-free ForteBio’s Octet® RED96 system is a multi-functional, label-free, real-time analysis instrument. It is ideal for rapidly screening protein-protein, protein-nucleic acids and protein-small molecule interactions. The Octet RED96 system can be used for a wide range of analyses. System provides up to 8-channel quantitation and kinetic measurements of molecules greater than 150 Da, compatibility with 96-well plates and cooling for temperature control down to 15°C.

Team Protein Interaction