UMR9187 / U1196 – Chimie, modélisation et imagerie pour la biologie

Publications de l’unité

Année de publication : 2018

Luis M.G. Abegão, Ruben D Fonseca, Tárcius N Ramos, Florence Mahuteau-Betzer, Sandrine PIGUEL, José J. Rodrigues Jr, Cleber R. Mendonca, Sylvio Canuto, Daniel Luis Silva, and Leonardo De Boni (2018 Apr 12)

Oxazole dyes with potential for photoluminescence bioprobes: A two-Photon absorption study

The Journal of Physical Chemistry C : Just accepted manuscript : DOI : 10.1021/acs.jpcc.8b01904 En savoir plus

In this work, six π-conjugated oxazole compounds dissolved in dichloromethane (DCM) were characterized with linear and nonlinear optical measurements. Z-Scan with femtosecond laser pulses was employed to determine the two-photon absorption (TPA) spectra. Other photophysical parameters, such as: absorbance, solvatochromism, lifetime fluorescence and fluorescence anisotropy were evaluated with linear optical techniques. The experimental TPA cross-section spectra were adjusted by Sum-Over-States (SOS) model, in which important parameters such as transition dipole moments and broadening parameters were determined. In order to better understand the TPA spectra of the oxazole compounds, quantum-chemical calculations using the response function formalism and the DFT level of theory were performed. Using the results provided by the quantum-chemical calculations and the broadening parameters estimated through the application of the SOS model, the TPA spectra were simulated by the superposition (summation) of individual homogeneous Lorentzian absorption profiles.

Soumia Sid Ahmed, Zoubeida Messali, Florent Poyer, Livia Lumbroso-Le Rouic, Laurence Desjardins, Nathalie Cassoux, Carole D. Thomas, Sergio Marco, Stéphanie Lemaitre (2018 Mar 28)

Iterative Variance Stabilizing Transformation Denoising of Spectral Domain Optical Coherence Tomography Images Applied to Retinoblastoma.

Ophthalmic research : 59 : 164-169 : DOI : 10.1159/000486283 En savoir plus

BACKGROUND: Due to the presence of speckle Poisson noise, the interpretation of spectral domain-optical coherence tomography (SD-OCT) images frequently requires the use of data averaging to improve the signal-to-noise ratio. This implies long acquisition times and requires patient sedation in some cases. Iterative variance stabilizing transformation (VST) is a possible approach by which to remove speckle Poisson noise on single images.

METHODS: We used SD-OCT images of human and murine (LH Beta-Tag mouse model) retinas with and without retinoblastoma acquired with 2 different imaging devices (Bioptigen and Micron IV). These images were processed using a denoising workflow implemented in Matlab.

RESULTS: We demonstrated the presence of speckle Poisson noise, which can be removed by a VST-based approach. This approach is robust as it works in all used imaging devices and in both human and mouse retinas, independently of the tumor status. The implemented algorithm is freely available from the authors on demand.

CONCLUSIONS: On a single denoised image, the proposed method provides results similar to those expected from the SD-OCT averaging. Because of the friendly user interface, it can be easily used by clinicians and researchers in ophthalmology.

Alexandra Garancher, Charles Y. Lin, Morgane Morabito, Wilfrid Richer, Nathalie Rocques, Magalie Larcher, Laure Bihannic, Kyle Smith, Catherine Miquel, Sophie Leboucher, Nirmitha I. Herath, Fanny Dupuy, Pascale Varlet, Christine Haberler, Christine Walczak, Nadine El Tayara, Andreas Volk, Stéphanie Puget, François Doz, Olivier Delattre, Sabine Druillennec, Olivier Ayrault, Robert J. Wechsler-Reya, Alain Eychène, Franck Bourdeaut, Paul A. Northcott, Celio Pouponnot (2018 Mar 12)

NRL and CRX Define Photoreceptor Identity and Reveal Subgroup-Specific Dependencies in Medulloblastoma

Cancer Cell : 33 : 435-449 : DOI : 10.1016/j.ccell.2018.02.006 En savoir plus

Cancer cells often express differentiation programs unrelated to their tissue of origin, although the contribution of these aberrant phenotypes to malignancy is poorly understood. An aggressive subgroup of medulloblastoma, a malignant pediatric brain tumor of the cerebellum, expresses a photoreceptor differentiation program normally expressed in the retina. We establish that two photoreceptor-specific transcription factors, NRL and CRX, are master regulators of this program and are required for tumor maintenance in this subgroup. Beyond photoreceptor lineage genes, we identify BCL-XL as a key transcriptional target of NRL and provide evidence substantiating anti-BCL therapy as a rational treatment opportunity for select MB patients. Our results highlight the utility of studying aberrant differentiation programs in cancer and their potential as selective therapeutic vulnerabilities.

David Partouche, Antoine Malabirade, Thomas Bizien, Marisela Velez, Sylvain Trépout, Sergio Marco, Valeria Militello, Christophe Sandt, Frank Wien & Véronique Arluison (2018 Feb 27)

Techniques to Analyze sRNA Protein Cofactor Self-Assembly In Vitro

Bacterial Regulatory RNA. Methods in Molecular Biology : 1737 : 321-340 : DOI : 10.1007/978-1-4939-7634-8_18 En savoir plus

Post-transcriptional control of gene expression by small regulatory noncoding RNA (sRNA) needs protein accomplices to occur. Past research mainly focused on the RNA chaperone Hfq as cofactor. Nevertheless, recent studies indicated that other proteins might be involved in sRNA-based regulations. As some of these proteins have been shown to self-assemble, we describe in this chapter protocols to analyze the nano-assemblies formed. Precisely, we focus our analysis on Escherichia coli Hfq as a model, but the protocols presented here can be applied to analyze any polymer of proteins. This chapter thus provides a guideline to develop commonly used approaches to detect prokaryotic protein self-assembly, with a special focus on the detection of amyloidogenic polymers.