Research Engineer (M/F) in Molecular Biology, Transcriptomics, Microbiology

Job Description

Missions

To determine how random mutations contribute to the evolution of gene expression regulation, our team has developed a high-throughput transcriptomics approach (microcolony RNA-seq) to quantify mRNA levels from thousands of yeast genotypes (S. cerevisiae) in different environments. Your mission will be to:
1. Conduct a pilot microcolony RNA-seq experiment at an intermediate scale (hundreds of genotypes and 2 environments) to assess the accuracy of RNA quantifications and to adjust parameters of the protocol if needed.
2. Apply the final protocol to characterize the transcriptome of ~1,200 yeast strains (established mutant and wild-type collections) in 7 environments (7 culture media).
3. Ensure documentation and knowledge transfer regarding the microcolony RNA-seq technique.
4. Quantify the adaptive value (growth rate) of ~1,200 strains in stable and fluctuating environments to determine how selection acts on gene expression regulation. For this, a competitive culture approach of ~1,200 strains and genomic barcode sequencing (BAR-seq) will be implemented.
These missions are at the heart of the European eGRIDE project (ERC), which aims to understand the mechanisms of evolution in gene expression regulation depending on the environment. The project seeks to determine how the evolution of gene regulation depends on the effect of random mutations—“What is possible?”—and on selection—“What are the benefits and costs of regulation?”. Innovative approaches in high-throughput RNA sequencing, genetic mapping, and measurement of cell proliferation in dynamic environments will be applied to a powerful biological model: the yeast S. cerevisiae. The knowledge gained from this highly controlled quantitative system will help better predict the evolution of gene regulation, whether in species adapting to their natural, dynamic environments or in certain pathological processes.

Activity

You will be responsible for:
• Finalizing the development of the microcolony RNA-seq protocol, which involves encapsulating yeast cells in alginate beads, culturing encapsulated microcolonies in different media, sorting capsules using a BioSorter, and preparing cDNA libraries for transcriptomic analysis of microcolonies by NGS.
• Preparing microcolony RNA-seq libraries from hundreds of genotypes in different environments.
• Conducting competition experiments and BAR-seq from genetically diverse cell populations maintained in culture by a robotic platform.
• Validating microcolony RNA-seq and BAR-seq results using smaller-scale approaches focused on candidate genes, such as qPCR and flow cytometry.
• Presenting progress on this work in laboratory meetings.
• Participating in team logistics, including stock management (shared task with other team members, including the project coordinator).

Your Profil

Skills

Required Expertise:
• Essential mastery of basic molecular biology techniques, including cloning, PCR and qPCR, nucleic acid extraction, and electrophoresis.
• As our laboratory is international, a strong command of English is essential, particularly for reading protocols and research articles in English.
• Proven ability to write clear and precise protocols and experiment reports.
Additional Skills:
• Experience in preparing cDNA libraries (RNA-seq) or other NGS approaches is highly recommended.
• Experience in cell sorting (FACS) or large particle sorting (BioSorter) is highly appreciated.
• Experience in microbiology, particularly in genetic engineering and handling S. cerevisiae, is desired.
Soft Skills:
• Scientific, methodological, and experimental rigor.
• Adaptability, ingenuity, and perseverance in the face of technical challenges.
• Ability to integrate into a team and laboratory to successfully carry out an ambitious research project.

Your Work Environment

The Laboratory of Biology and Modeling of the Cell (LBMC) is a leading research institution dedicated to studying the fundamental mechanisms of cell life. We combine experimental approaches in molecular, cellular, and genetic biology with mathematical and computational modeling methods to understand the complex processes that regulate cell function.
Located on the Monod campus of the ENS de Lyon, LBMC brings together ~120 people dedicated to research, divided into 17 research teams. This advantageous location provides privileged access to all the resources and infrastructure necessary to carry out our research missions. We benefit from expertise in RNA sequencing techniques, as well as access to flow cytometry (SFR Biosciences) and sequencing platforms (IGFL).
You will work under the scientific direction of Fabien Duveau (researcher) in the “Genetic Complexity of Living Systems” team led by G. Yvert (research director) (https://www.ens-lyon.fr/LBMC/gisv/index.php/en/). The team currently consists of two researchers, a permanent study engineer, two research engineers, a PhD student, and an intern in the final year of engineering school. While your activities will primarily be experimental, the project is highly interdisciplinary, involving experimental, bioinformatics, and statistical approaches.
This recruitment is part of the European eGRIDE project funded by the ERC. You will join an expanding team at the heart of an ambitious scientific project. You will be trained by the study engineer who developed the microcolony RNA-seq protocol and will then be expected to play a key role in the project.

Compensation and benefits

Compensation

From €3175 gross per month, depending on experience

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions