NOLLMANN LAB
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Single-molecule and super-resolution

An important part of our group works on the development of single-molecule and super resolution methods. In particular, we develop spatial genomics, single-molecule localization microscopy using adaptive optics, implement variants of structured illumination microscopy, and work on the development of multi-focus microscopes. These implementations are combined with other methods such as microfluidics or DNA origami.

Spatial genomics and transcriptomics

Our current technology development is focused on imaging-based spatial genomics methods. All publications are available in our Github repository.

See these recent publications for more information:
Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M.
Andrés M. Cardozo Gizzi, Sergio M. Espinola, Julian Gurgo, Christophe Houbron, Jean-Bernard Fiche, Diego I. Cattoni, Marcelo Nollmann
Nature Protocols
15(3):840-876. doi: 10.1038/s41596-019-0269-9. Epub 2020 Jan 22.
See full updated protocol in our Hi-M Github page.


Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms. 
A
M Cardozo Gizzi, D I. Cattoni, J-B Fiche, S Espinola, J Gurgo, O Messina, C Houbron, Y Ogiyama, G-L Papadopoulos, G Cavalli, M Lagha, M Nollmann
Molecular Cell, 2019 Apr 4;74(1):212-222.e5. doi: 10.1016/j.molcel.2019.01.011. Epub 2019 Feb 19. [BioRxiv pre-print]
Comment on our article by Daniel Larson here.
Recommended by F1000: Martí-Renom M: F1000Prime Recommendation of [Cardozo Gizzi AM et al., Mol Cell 2019 74(1):212-222.e5]. In F1000Prime, 19 Aug 2019; 10.3410/f.735120435.793559990

Single-molecule localization microscopy

In the past, we developed several flavors of single-molecule localization microscopy (SMLM). These include 
  • Improved setup for two-color STORM with 5nm registration precision
  • 3D-SMLM microscope with adaptive optics for aberration correction and user-defined astigmatism
  • 2D-SMLM coupled to atomic force microscopy
  • Co-localization analysis from two-color STORM data 

Principles of super-resolution microscopy

Components of our basic SMLM microscope

Super-resolution imaging of bacteria in a micro-fluidics device.
Cattoni* DI, Fiche* JB, Valeri A, Mignot T, Nöllmann M. 
PLoS ONE 8(10):e76268, Oct 2013. [PDF] 
Single-molecule super-resolution imaging in bacteria
Diego I. Cattoni, Jean-Bernard Fiche, Marcelo Nöllmann 
Current Opinion in Microbiology, 15(6):758-63, Dec 2012. [PDF]
Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging
Mariya Georgieva; Diego I Cattoni; Jean-Bernard Fiche; Thibaut Mutin; Delphine Chamousset; Marcelo Nollmann. Methods pii: S1046-2023(16)30063-9. 1 Apr 2016 . [PDF]

Multi-focus microscopy

We develop new microscopies based on multi-focus microscopy (Abrahamsson, 2013). In particular, we focus on the development and construction of MFG gratings in collaboration with the LAAS (CNRS, Toulouse). Recently, we developed a 3D super-resolution microscopy method that enables deep imaging in cells based on a combination of Multifocus Microscopy and PSF engineering. We demonstrated the performance of the method by imaging the nuclear envelope of eukaryotic cells reaching a depth of field of ~ 4μm. Also, we improved the efficiency of transmission of MFGs by using multi-phase engraving.
​

Astigmatic multifocus microscopy enables deep 3D super-resolved imaging.
Laura Oudjedi, Jean-Bernard Fiche, Sara Abrahamsson, Laurent Mazenq, Aurélie Lecestre, Pierre-François Calmon, Aline Cerf, and Marcelo Nöllmann
​Biomedical Optics Express, 2016, in press. [PDF]

Perfect color Multifocus Microscopy (MFM) with increased sensitivity 
Sara Abrahamsson, Rob Ilic, Jan Wisniewski, Brian Mehl, Liya Yu, Lei Chen, Marcelo Davanco, Laura Oudjedi, Jean-Bernard Fiche, Bassam Hajj, Xin Jin, Joan Pulupa, Christine Cho, Mustafa Mir, Xavier Darzacq, Marcelo Nollmann, Maxime Dahan, Carl Wu, Timothy Lionett, James . Liddle and Cornelia I. Bargmann
Biomedical Optics Express, 2016, in press
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Single-molecule manipulation/fluorescence

Magnetic Tweezers coupled to single-molecule fluorescence detection

We developed a standard magnetic tweezers coupled to TIRF illumination and single-molecule fluorescence detection to monitor the activity, mechanical properties, and position of fluorescently-labelled proteins in real-time. The setup has been used for the study of SpoIIIE (Thakur, submitted) and the mechanism of looping of insulator proteins.

The fluorescence properties and binding mechanism of SYTOX green, a bright, low photo-damage DNA intercalating agent. 
Thakur, S,Cattoni DI, Nollmann M        
European Biophysical Journal, July 2015, 44(5):337-48. [PDF]
Direct observation of the translocation mechanism of transcription termination factor Rho 
Gocheva V, Le Gall A, Boudvillain M, Margeat E, Nollmann M
Nucleic Acids Research, 2015 Feb 27; 43(4):2367-77
. [PDF]
Constructing a magnetic tweezers to monitor RNA translocation at the single-molecule level.
Salas D, Gocheva V, Nöllmann M.
Methods Mol Biol. 1259:257-73.  Jan 2015. [PDF]


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  • Home
    • News
    • Lab meetings
    • HelpDesk
  • Research
    • DNA organization and segregation at super-resolution >
      • Chromosome structure
      • Resources and background
    • Molecular Motors >
      • SpoIIIE and FtsK
      • Bacterial gliding
    • Technologies >
      • SRM
      • SMLM microscope
    • Software
  • Lab members
    • Lab pictures
  • Publications
    • bactoTracker
  • Resources
  • Positions
  • Funding
  • Contact