Virgile Adam

📣 We are happy to welcome also our new Affiliated Entities (AEs) from Instruct ERIC nodes: CEITEC - Central European Institute of Technology-MU and CNRS IBS Pixel Team. 🎯 While both will work… | IMA... 📣 We are happy to welcome also our new Affiliated Entities (AEs) from Instruct ERIC nodes: CEITEC - Central European Institute of Technology-MU and CNRS IBS Pixel Team. 🎯 While both will work under ...

Our team (Pixel) and along with it our institute (IBS, Grenoble) is now officially a node of the IMAGINE consortium (for next generation imaging for biology across scales)

www.linkedin.com/posts/imagin...

16+ years ago, and I keep of him a memory blending esteem, respect, and friendship. A true scientist, both highly skilled and humble, and a remarkable person.

Saddened to learn of the passing of Prof. Michel Robert-Nicoud, Emeritus, and one of my former university teachers, with whom we often discussed what he called F-techniques: all the fluorescence-based techniques used to measure intracellular metrics. He accepted being the chairman of my PhD defense

New paper about the slow maturation of the fluorescent protein mEos4b and how to improve it (onlinelibrary.wiley.com/doi/10.1002/...)

Wonderful work led by @ncaramel.bsky.social

New paper about a python software to process spectra within protein crystals (journals.iucr.org/j/issues/202...)

With a UV light ;)

Sometimes I forget why I always loved so much studying FPs, and sometimes I remember!

Sine and I, 20 years ago at the ESRF

But for me she was above all the one who trusted me when I presented my PhD project about fluorescent proteins at the synchrotron some 20 years ago and who accepted the role of PhD mentor, always kind and available. A great human and scientific loss.

Deeply saddened by the announcement of Prof Sine Larsen's passing. Former scientific director of the European Synchrotron Radiation Facility and president of the International Union of Crystallography, Sine had been Emeritus at the University of Copenhagen for several years.

Keywords: Genome, chromosome, chromatin, 3D Genome, Epigenetics Synopsis: This video recapitulates our current understanding of genome organization in the three-dimensional space of the cell nucleus, starting from nucleosomes, which wrap 146 base pairs of DNA, all the way to entire chromosome territories that may contain hundreds of million base pairs of DNA sequence. In-between these two extremes, the hierarchical folding of the chromatin fiber into “nucleosome clutches”, “chromatin nanodomains or CNDs”, “Topologically Associating Domains or TADs” - including their mechanism of formation via loop-extrusion - and the “A and B compartments” are presented. We include below references that support and supplement what is described in our video. We stress that some of the mechanisms involved in 3D genome organization are still debated in this research field. We also include below additional videos on the subject. Additional videos on the subject: 1 – The video linked below illustrates the “classical paradigm” of chromosome organization corresponding to the part up to 1’03’’ in our video: - https://www.youtube.com/watch?v=gbSIBhFwQ4s 2 – The following videos present the loop extrusion mechanism involved in TAD formation, described starting from 2’03’’ in our video: - https://www.youtube.com/watch?v=8FW6gOx5lPI - https://www.youtube.com/watch?v=Tn5qgEqWgW8 References to pioneer works: 1 – A selection of recent review articles that discuss further our understanding of genome architecture and its functional consequences, described starting from 1’04’’ in our video: - https://www.scientificamerican.com/article/untangling-the-formation-of-dna-loops/ - https://doi.org/10.1038/s41576-018-0060-8 - https://www.science.org/doi/10.1126/sciadv.aaw1668 - https://doi.org/10.1038/s41580-021-00362-w 2 – A selection of key scientific articles that describe the different layers of chromosome organization presented in our video can be found on the internet at the "doi" links indicated below. Note that some of the articles requires a subscription to the respective scientific journal. 0’27’’: The Watson and Crick DNA structure, 1953: - https://doi.org/10.1038/171737a0 0’30’’: The Nucleosome crystal structure, 1997: - https://doi.org/10.1038/171737a010.1038/38444 0’38’’: The 30-nm chromatin fiber has been considered for a long time to be the most basic layer of higher-order chromatin compaction, being part of the classical model. Today, the 30-nm fiber appears to be more an exception than the rule and is only observed in specific cells: - https://doi.org/10.1016/j.yexcr.2012.02.014 - https://doi.org/10.1016/j.ceb.2019.02.003 1’23’’: Nucleosome clutches, were discovered in 2015 and confirmed in 2017 thanks to advanced microscopy methods: - https://www.cell.com/action/showPdf?pii=S0092-8674%2815%2900132-4 - https://doi.org/10.1126/science.aag0025 1’37’’: Chromatin nanodomains or CNDs are globular chromatin structures of 150-300 nm size, uncovered by using various superresolution fluorescence imaging methods: - https://doi.org/10.1016/j.molcel.2017.06.018 - https://doi.org/10.1038/s41588-020-00716-8 - https://doi.org/10.1126/sciadv.aba8811 1’50’’: Topologically Associating Domains or TADs were uncovered in 2012 by 4 different laboratories, using a next-generation sequencing-based chromosome conformation capture method called Hi-C in Drosophila, mouse and human. They were later confirmed in other species: - https://doi.org/10.1016/j.cell.2012.01.010 - https://doi.org/10.1038/nature11049 - https://doi.org/10.1038/nature11082 - https://doi.org/10.1016/j.molcel.2012.08.031 2’03’’: The Loop extrusion mechanism, involving Cohesin and CTCF, seems to be a key mechanism for TAD formation in mammals and is widely studied. Below, a selection of articles on the subject. Note that the exact extrusion mechanism is still under debate and probably differs from the one shown in this video: - https://doi.org/10.1038/s41580-021-00349-7 - https://doi.org/10.1016/j.celrep.2016.04.085 - https://doi.org/10.1016/j.cell.2017.04.013 - https://doi.org/10.1038/s41586-019-1910-z - https://doi.org/10.1016/j.cell.2017.05.004 - https://doi.org/10.1016/j.cell.2014.11.021 - https://doi.org/10.1016/j.cell.2017.09.026 - https://doi.org/10.1073/pnas.1518552112 - https://doi.org/10.1038/nature24281 - https://doi.org/10.15252/embj.201798004 2’42’’: A and B compartments were described for the first time in 2009. Later, they were confirmed by other laboratories: - https://doi.org/10.1126/science.1181369 - https://doi.org/10.1126/science.aaf8084 2’54’’: Chromosome territories represent the final layer of chromosome organization. They were first observed by DNA in situ hybridization in 1985 confirmed in many species: - https://doi.org/10.1007/BF00388453 - https://doi.org/10.1007/BF00388452 - https://doi.org/10.1371/journal.pbio.0030157 - https://doi.org/10.1101/cshperspect.a003889 Enjoy chromosome biology! The 3D Organization of Our Genome

Impressive!

youtube.com/watch?v=Pl44Jj…

A last thank you to everyone for this great #SMLMS2024 event that was the opportunity to hear, meet or recontact with great people and discover beautiful places.

Incredible discovery of a suicide (repetitive and toxic) protein expressed from normally non-coding RNA in phage-infected bacteria.

x.com/ElliotHershber… science.org/doi/10.1126/sc…

Impressive and colorful work by @christlet presented at the #SMLMS2024 about axonal organization with incredible STORM/Platinum replica EM correlations

A very good question asked by @l_masu at #SMLMS2024. The answer is the super duper resolution (© @rita_strack) allowed by RESI.

Interesting talk about cell phototoxicity metrics with "PhotoFiTT" by @_mariod at the #SMLMS2024, which makes you want to try it

Great great talk by @Melike_Lak about super-resolution for biology at #SMLMS2024. Chromatin compaction and dynamics metrics & chromatin remodelling depending on the stiffness of the cells environment and visualized/measured thanks to SR... fascinating!

Ok, I'm impressed #SMLMS2024

More than full auditorium for the amazing talk of @rita_strack at the #SMLMS2024. That really great gives hints to know whether or not (and how) daring submitting to Nature Methods :

For those interested in X-rays and neutrons for chemistry, physics and biology, the #HERCULES2025 European school will be held in Grenoble, France in March/April 2025. Deadline October 2024.

SPAD-array detector for MINFLUX. Very interesting discoveries (and keywords) for a not-so-much optics guy like me, by @EliSlenders at the #SMLMS2024

Focal adhesion complexes and DNA-PAINT... great work by @RomanTsukanov at #SMLMS2024

Thrilled to come back at the #SMLMS2024 after a long pause. Last time for me was in 2015. What an evolution since the first I went to 12 years ago! We could then all fit in a classroom and have a personal talk by Prof W.E. Moerner (before his Nobel Prize). Congratulations and…

Great talk about peptidoglycan dynamics in Staph by @PinhoLab at thee #SMLMS2024 yesterday!

Beautiful presentation (as usual) about bacteria by @UEndesfelder in a talk chaired by @rita_strack at the #SMLMS2024 yesterday!

SMLMS methods and techniques are important but fluorophores development also. Thanks for all the nice chats and contacts at the poster session of the #SMLMS2024 yesterday. Would you be interested in smart fluorescent proteins' engineering, here I am ;

Such a nice presentation at the #SMLMS2024 Lisbon by @JonasRies! Super resolution microscopy for structural biology, obviously ring many bells for me. Hope that our latest FPs in test for #minflux will work and lead to collaboration.

Beautiful presentation (as usual) about bacteria by @UEndesfelder in a talk chaired by @rita_strack at the @SMLM_Symposium yesterday!

Great talk about peptidoglycan dynamics in Staph by @PinhoLab at thee @SMLM_Symposium yesterday!