Molecular biology/biochemistry: cloning, mutagenesis, overexpression, purification...
Macromolecular crystallogenesis and crystallography
Ensemble spectroscopy in solution and crystals (UV/Vis, fluorescence, Raman, lifetime) & single molecule spectroscopy
Conventional optical microscopy and single-molecule localization microscopy (PALM)
I was born in Paris and grown up in a small cute concentric ring-shaped village in the southeastern France before going to middle school at an institution held by Marist Brothers and in a school in Paris and then to high school in the French department Drôme.
I then moved to Grenoble to start medicine studies but quickly shifted to biology at the University Joseph Fourier (UJF).
The UJF is named after Joseph Fourier who was appointed Prefect of the department Isère by Napoleon, where Grenoble is located. That's also in Grenoble that he studied and invented his famous series and transform. Although a University was present in Grenoble since as early as 1339, Fourier created the Royal University of Sciences in 1810 where he met his future friend Champollion.
In 2017, the UJF merged with the other universities in Grenoble to form the "Université Grenoble-Alpes" (UGA).
The UGA is composed of 45 000 students and is well ranked since it is evaluated as being the 178th research center in the world and the 4th best in France in terms of scientific production according to the Scimago Institution Ranking.
Life sciences in Grenoble
Early in my studies in chemistry/biochemistry, I was attracted by rendering 3D molecules and by the fantastic 3rd generation Synchrotroton standing in Grenoble (ESRF), which is one of the three most powerful synchrotrons in the world. I was lucky enough to start a traineeship there and oriented my studies to structural biology. In parallel of my studies, I carried on being a trainee at the ESRF and trained intensively in X-ray protein crystallography and microspectrophotometry. The team of Dr. Dominique Bourgeois I was working in was particularly interested in studying photosensitive proteins or photoreactive compounds in order to trig events and trap structural intermediate along protein reactions. This is called kinetic crystallography.
Because kinetic crystallography is, by essence, interested in initiating and following structural modifications that occur along a reaction (such as trapping reaction intermediate states), we often used lasers combined to X-rays to trig reactions within protein crystals.
Doing so, we were interested in photosensitive compounds and proteins and it appeared natural to focus our efforts toward newly discovered phototransformable fluorescent proteins (PTFPs).
PTFPs are macromolecules that comprise a genetically-encoded fluorophore. The best known member is the green fluorescent protein (GFP) whose discoverers and developers have been later awarded the Nobel Prize in Chemistry 2008.
Unlike GFP, PTFPs are also capable of irreversible and/or reversible photo-induced transformations that give them the ability to either be activated to a glowing form or to reversibly extinct their fluorescence and even to emit light in another color.
These fascinating transformations were badly understood at the time of my PhD thesis and we decided to study their mechanisms by kinetic crystallography. I was lucky enough to make my PhD thesis at the ESRF, within the macromolecular crystallography group under the supervision of Dr. Dominique Bourgeois and Dr. Sean McSweeney.
In summary, during this PhD thesis, we better understood the structural mechanisms of reversible fluorescence switching and irreversible colour photoconversion and discovered IrisFP, first member of a family combining both properties of irreversible photoconversion and reversible photoswitching.
You can read more about my thesis and dowload the full text on the dedicated page of this website.
Jury members of my PhD
(from left to right: S. McSweeney, G.U. Nienhaus, D. Bourgeois, V. Adam, D. Picot, J. Hofkens, M. Robert-Nicoud and C. Royer)
During my thesis, the concept of super-resolution microscopy by photoactivated localization was invented. In this technique, a conventional widefield microscope is used to acquire fluorescence imaging of a biological sample. However, unlike conventional fluorescence microscope, in PALM, the highlighting of proteins of interest is achieved by PTFPs that can be photoactivated, so that only a small fraction of fluorescent molecules can be observed at a time.
The stochastic activation of those individual molecules makes that they are spatially distinguishable and can be precisely localized... with a much better accuracy than that obtained by conventional microscopy where all the molecules emit their fluorescence simultaneously, limiting the achievable optical resolution to ~200-300 nm.
Observing single fluorescent molecules with very sensitive cameras, thus, allows the reconstruction of a composite image that does not suffer from the physical law of far-field diffraction-limited imaging. This type of localization microscopy, invented in 2006 and awarded by the Nobel Prize in Chemistry 2014 permits to obtain ~20-nm resolution images but requires the use of adapted PTFPs.
Using the structural and mechanistic knowledge of PTFPs I could acquire during my PhD, I was extremely lucky to make a postdoctoral period in the laboratory for photochemistry and spectroscopy of Pr. Johan Hofkens. My research was focussed of the engineering and characterization of new types of phototransformable fluorescent proteins and their use in PALM. For this purpose, I used molecular biology techniques, spectroscopy and super-resolution microscopy. This period was very helpful for me to acquire a more applied side to the fundamental knowledge I had about fluorescent proteins. Building optical setups and observing by myself what are the requirements of microscopists for perfoming fluorescent probes completed advantageously my formation of biophysicist.
This lab is located in Flemish Belgium, at the University of Leuven (K.U.Leuven). Founded in 1425, this prestigious University is nowadays well placed in major rankings:
among which the best 100 universities in the world and 2nd in Belgium according to the Top 500 Shangaï academic ranking of world universities.
At the end of my postdoctoral period, I was recruited as a CNRS researcher to develop super-resolution and conceive future fluorescent markers for advanced microscopy. I had the rare opportunity to come back to Grenoble, at the Institute for Structural Biology in the "Pixel" team led by Dr. Dominique Bourgeois, my former thesis supervisor.
Two years after my arrival, our institute, the IBS, moved to the scientific campus called European Photon and Neutron (EPN) within the so-called "Polygone scientifique" located on the Grenoble peninsula ("presqu'ile) between the river Isère and the mountain stream Drac.
The EPN is one of the three majors campuses of Grenoble and gathers the Institute for Structural Biology (IBS), the European Molecular Biology Laboratory (EMBL), the Institut Laue Langevin (ILL) and the European Synchrotron Radiaton Facility (ESRF) where I've made my PhD thesis.
The moving of the IBS is associated with a major programme called "Grenoble Innovation for Advanced New Technologies" (GIANT) will lead to the foundation of a worldwide ranked innovation campus.
At the frontier between molecular biology, structural biology and super-resolution imaging, I am now trying, with a PhD student I co-supervise, to obtain better fluorescent markers for tommorow's cell imaging.
GIANT and the scientific peninsula
Pixel Team in 2020
(from top to down and left to right: V. Adam, D. Bourgeois,
O. Glushonkov, A. Mantovanelli, M. Byrdin)
Virgile Adam realigning the PALM setup
Pixel Team in 2017
(from left to right: V. Adam, J. Beaudouin, M. Byrdin, D. Bourgeois and
Pixel Team in 2014
(from left to right: Top: D. Bourgeois, C. Duan, M. Byrdin, V. Adam -
Bottom: S. Avilov and R. Berardozzi)
Amongst many non-profesionnal peculiarities, I: