Publications

MARTINS, C. S.*; IV, F.*; SUMAN S.K.; PANAGIOTOU, T.C.; SIDOR, C.; RUSO-LÓPEZ, M.; PLANCKE, C.N.; OMI, S.; GOMES, M.; LLEWELLYN, A.; BANDI, S.R.; RAMOND, L.; ARBIZZANI, F.; RIMOLI, C.V.; SCHNORRER, F.; ROBIN, F.; WILDE, A.; LEGOFF, L.; PEDELACQ, J-D; CABANTOUS, S.; RINCON, S.A.; CHANDRE, C.; BRASSELET, S.; MAVRAKIS, M.

Genetically encoded reporters of actin filament organization in living cells and tissues

BioRxiv (preprint), 2024. v1
https://www.biorxiv.org/content/10.1101/2024.04.26.591305v1

The cytoskeletal protein actin is crucial for cell shape and integrity throughout eukaryotes. Actin filaments perform essential biological functions, including muscle contraction, cell division, and tissue morphogenesis. These diverse activities are achieved through the ability of actin filaments to be arranged into diverse architectures, but a detailed appreciation of the dynamic organizational state of the actin filaments has been hindered by available tools. Fluorescence polarization microscopy is uniquely placed for measuring actin organization by exploiting the sensitivity of polarized light excitation to the orientation of fluorophores attached to actin filaments. By engineering constrained fluorescent protein fusions to widely used actin localization reporters, we have succeeded in developing novel genetically-encoded reporters for non-invasive, quantitative measurements of actin filament organization in living cells by fluorescence polarization microscopy. We show examples of actin organization measurements in living mammalian cells in culture, as well as in vivo in fission yeast, C. elegans Drosophila.

RIMOLI, C. V.; MORETTI, C.; SOLDEVILA, F.; BRÉMONT, E.; VENTALON, C.; GIGAN, S..

Demixing fluorescence time traces transmitted by multimode fibers.

ArXiV (preprint), 2023. v1,  ArXiV (preprint), 2024. v2
https://doi.org/10.48550/arXiv.2306.00695

Fluorescence-based techniques have revolutionized our ability to obtain functional readouts of neuronal activity in the brain. However, measuring neuronal activity at depths greater than 1 mm remains challenging due to light scattering, particularly in freely behaving animals. In response to this challenge, neuronal microendoscopy methods have emerged as valuable alternatives to linear and nonlinear fluorescence microscopy techniques, allowing the study of neuronal activity in deep brain regions using genetically encoded calcium indicators. Among these methods, conventional microendoscopy with gradient index (GRIN) lenses and fiber photometry using multimode fibers have been successfully used to capture functional neuronal activity signals in deep brain regions of freely behaving mice. However, both approaches present tradeoffs. GRIN lens microendoscopy provides cellular resolution but requires an invasive surgical procedure for lens implantation, often necessitating the removal of brain tissue. On the other hand, fiber photometry with thin multimode fibers offers a less invasive alternative but suffers from signal scrambling and limits the technique's ability to resolve temporal traces from individual neurons. In our study, we propose a novel approach to perform minimally invasive fiber photometry experiments,  enabling the demixing of single-source time traces transmitted by short and thin multimode fibers. By replacing the traditional bucket detector with a camera, we leverage the spatial information of the fluorescence patterns transmitted by the fiber, allowing for single-source temporal activity resolution. We employ an unconstrained non-negative matrix factorization algorithm to separate each spatial scattering pattern component with its corresponding temporal trace. Importantly, our method eliminates the need for complex calibration procedures, making it more accessible and efficient for researchers.

XIA, F.*; RIMOLI, C.V.*; AKEMANN, W.; VENTALON, C.; BOURDIEU, L.; GIGAN, S.; DE AGUIAR, H. B. 

Neurophotonics beyond the Surface: Unmasking the Brain's Complexity Exploiting Optical Scattering 

Neurophotonics 11(S1), S11510 (2024)
https://doi.org/10.1117/1.NPh.11.S1.S11510

Impact factor (2023): 5,3
CiteScore™ (2022): 8,3
CAPES Qualis [based on 2013-2016]: A1

The intricate nature of the brain necessitates the application of advanced probing techniques to comprehensively study and understand its working mechanisms. Neurophotonics offers minimally invasive methods to probe the brain using optics at cellular and even molecular levels. However, multiple challenges persist, especially concerning imaging depth, field of view, speed, and biocompatibility. A major hindrance to solving these challenges in optics is the scattering nature of the brain. This perspective highlights the potential of complex media optics, a specialized area of study focused on light propagation in materials with intricate heterogeneous optical properties, in advancing and improving neuronal readouts for structural imaging and optical recordings of neuronal activity. Key strategies include wavefront shaping techniques and computational imaging and sensing techniques that exploit scattering properties for enhanced performance. We discuss the potential merger of the two fields as well as potential challenges and perspectives toward longer-term in vivo applications. 

RIMOLI, C. V.*; VALADES-CRUZ*, C. A. ; CURCIO, V. ; MAVRAKIS, M. ; BRASSELET, S.

4polar-STORM polarized super-resolution imaging of actin filament organization in cells


 Nature Communications, v. 13, p. 1-13, 2022.
https://doi.org/10.1038/s41467-022-27966-w

Impact factor: 17,694
CAPES Qualis [based on 2013-2016]: A1 

In this paper, we developed a novel powerful quantitative fluorescence microscopy technique that we named it 4polar-STORM. With this method, we showed how one could determine both single molecules’ localization and orientation in 2D and to infer their 3D orientation. To highlight the potential of 4polar-STORM to measure molecular organization in complex protein assemblies, we measured the nanometer-scale organization of actin filament-based structures involved in the adhesion and motility of mammalian cells. We exploited the sensitivity of orientation and wobbling parameters to molecules lying off-plane to evidence the non-negligible contribution of 3D orientations in different populations of actin filaments, both in SF bundles and in the flat lamellipodium. Selecting in-plane filament populations evidenced the very high actin filament alignment in all types of SFs, in line with EM studies, but also revealed differences in their nanometer-scale organization, consistently with their different modes of assembly and function in the cell. Thin 2D ventral and transverse arc SFs are made of highly aligned actin filaments, while thick peripheral SFs, off-plane oriented dorsal SFs, and FAs containing filament populations of mixed orientations, were seen to contain a non-negligible population of filaments with 3D off-plane orientations. Low doses of blebbistatin that inhibited myosin II activity in contractile peripheral SFs, while preserving their macroscopic integrity, resulted in a perturbation of the nanometer-scale organization of actin filaments, emphasizing the key role of myosin II in the organization of actin filaments in contractile SFs. Importantly, in-plane measurements of actin filament organization permitted us to investigate the organization of dense assemblies that is not accessible by single-molecule localization imaging alone, in particular in the lamellipodium at the leading edge of motile cells. 4polar-STORM imaging revealed that the actin filaments in the lamellipodial meshwork are not oriented randomly but that they organize in preferred angular distributions, including bimodal distributions previously observed by electron microscopy. 

RIMOLI, C. V.; DE OLIVEIRA PEDRO, R. ; MIRANDA, P. B. 

Interaction mechanism of chitosan oligomers in pure water with cell membrane models studied by SFG vibrational spectroscopy

Colloids and Surfaces B- Biointerfaces, v. 219, p. 112782, 2022.
https://doi.org/10.1016/j.colsurfb.2022.112782

Impact factor: 5,999
CAPES Qualis [based on 2013-2016]: A1

In this paper, we demonstrated the mechanism of interaction of chitosan oligomers (ChitO) and PAH on biomimetic lipid membrane models (Langmuir monolayers of DPPG and DPPC). Although the literature on chitosan’s antimicrobial activity is relatively dense, the molecular details of its interaction with biomembranes remained unclear, partly due to the complexity of cell membranes and of in vivo studies. Chitosan, a cationic aminopolysaccharide that is water-soluble below pH 6.5, has a long list of desirable properties. Chitosan is an inexpensive, sustainable, and biocompatible antimicrobial polymer derived from the chitin shells of crustaceans and it has antimicrobial properties against a wide range of microorganisms (fungi, gram-positive and gram-negative bacteria). We investigated these molecular interactions by resorting to phospholipid Langmuir films (zwitterionic DPPC and anionic DPPG) as simplified membrane models (for mammalian and bacterial membranes, respectively), and using SFG vibrational spectroscopy to probe lipid tail conformation, headgroup dynamics, and interfacial water orientation (membrane potential). The differences between chitosan and PAH effects on the model membranes, such as more pronounced expansion induced by chitosan and the inversion of the effective membrane potential and interfacial water orientation by PAH, highlight the importance of molecular structure and intermolecular interactions for their bioactivity. Therefore, this study may also provide insights for the rational design of more effective antimicrobial molecules (polymers or low-molecular-weight compounds) that act on cellular membranes.

VOLPATI, D. ; CHACHAJ-BREKIESZ, A. ; SOUZA, A. L. ; RIMOLI, C. V. ; MIRANDA, P. B. ; OLIVEIRA, O. N. ; DYNAROWICZ-LATKA, P.


Semifluorinated Thiols in Langmuir Monolayers - A Study by Nonlinear and Linear Vibrational Spectroscopies


Journal of Colloid and Interface Science, v. 460, p. 290-302, 2015. 

https://doi.org/10.1016/j.jcis.2015.08.069


Impact factor: 9,965
CAPES Qualis [based on 2013-2016]: A1

In this paper, we made a very fundamental study of a series of semifluorinated thiols of the general formula CmF2m+1CnH2nSH (abbr. FmHnSH). These have been synthesized and characterized in Langmuir monolayers with surface pressure-area isotherms, complemented with polarization-modulated reflection absorption spectroscopy (PM-IRRAS) and sum-frequency generation (SFG) techniques. We showed that  semifluorinated alkanethiol monolayer becomes more rigid upon increasing the hydrophobic part; the peak at 2874 cm−1 in the SFG spectra should be attributed to the CH2 group next to the polar group; the gauche defects is increased by increasing either the fluorinated or hydrogenated chain; the tilt angle of the terminal CF3 group lies between 35° and 45° according to SFG measurements; and finally that increasing the monolayer surface pressure, the fluorinated segment gets slightly more upright.

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