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International audience; In this contribution, we report that conforma-tional changes of molecules that are often buried in a wide-distributed Gaussian distribution can be discerned by analyzing the dynamics of specific Raman lines. We investigate the pertinence of the auto-and cross-correlation functions applied to the dynamics of three Raman lines of an amino acid, the tryptophan. The cross-correlation between intensity and the Raman band is an indicator of the charge transfer during the diffusion limited reaction of tryptophan and the gold surface. The Pećlet number Pe can provide a valuable indicator of the convective and/or diffusive features of each Raman band. Adsorption induced conformation changes can be identified using the autocorrelation of the multiples states within the Raman band centered at 1550 cm −1 .

International audience; We study the interaction between one aptamer and its analyte (the MnSOD protein) by the combination of surface-enhanced Raman scattering and multivariate statistical analysis. We observe the aptamer structure and its evolution during the interaction under different experimental conditions (in air or in buffer). Through the spectral treatment by principal component analysis of a large set of SERS data, we were able to probe the aptamer conformations and orientations relative to the surface assuming that the in-plane nucleoside modes are selectively enhanced. We demonstrate that the aptamer orientation and thus its flexibility rely strongly on the presence of a spacer of 15 thymines and on the experimental conditions with the aptamer lying on the surface in air and standing in the buffer. We reveal for the first time that the interaction with MnSOD induces a large loss of flexibility and freezes the aptamer structure in a single conformation.

Orientation of nanoscale objects can be measured by examining the polarized emission of optical probes. To retrieve a three-dimensional (3D) orientation, it has been essential to observe the probe (a dipole) along multiple viewing angles and scan with a rotating analyzer. However, this method requires a sophisticated optical setup and is subject to various external sources of error. Here, we present a fundamentally different approach employing coupled multiple emission dipoles that are inherent in lanthanide-doped phosphors. Simultaneous observation of different dipoles and comparison of their relative intensities allow to determine the 3D orientation from a single viewing angle. Moreover, the distinct natures of electric and magnetic dipoles originating in lanthanide luminescence enable an instant orientation analysis with a single-shot emission spectrum. We demonstrate a straightforward orientation analysis of Eu3+-doped NaYF4 nanocrystals using a conventional fluorescence microscope. Direct imaging of the rod-shaped nanocrystals proved the high accuracy of the measurement. This methodology would provide insights into the mechanical behaviors of various nano- and biomolecular systems., Determining the orientation of nanoscale objects in three-dimensional space has typically required complicated optical setups. Here, the authors develop a simple method to retrieve the 3D orientation of luminescent, lanthanide-doped nanorods from a single-shot emission spectrum.

International audience; Rare-earth doped nanocrystals possess optical transitions with significant either electric or magnetic dipole characters. They are of considerable interest for understanding and engineering light-matter interactions at the nanoscale with numerous applications in nanophotonics. Here, we study the 5 D 0 → 7 F 1 transition dipole vector in individual NaYF 4 : Eu 3+ nanorod crystals by Fourier and confocal micro-scopies. A single-crystal host matrix leads to narrow emission lines at room temperature that permit separation of the Stark sublevels resulting from the crystal-field splitting. We observe a fully magnetic transition and low variability of the transition dipole orientation over several single nanorods. We estimate the proportion of the dipole transitions for the Stark sublevels. We also determine an effective altitude of the rod with respect to the substrate. The narrow emission lines characteristic of NaYF 4 : Eu 3+ ensure well-defined electric or magnetic transitions, and are thus instrumental for probing locally their electromagnetic environment by standard confocal microscopy.

ERK involvement in cell death remains unclear, although many studies have demonstrated the importance of ERK dynamics in determining cellular responses. To untangle ERK’s contribution in two cell death programs, we investigated ERK signaling dynamics during hFasL-induced apoptosis and TNF-induced necroptosis in L929sAhFas cells. We observed that ERK inhibition sensitizes cells to apoptosis while delaying necroptosis. By monitoring ERK activity by live-cell imaging using an improved ERK biosensor (EKAR4.0), we reported differential ERK signaling dynamics between cell survival, apoptosis, and necroptosis. We also decrypted a temporally shifted amplitude- and frequency-modulated (AM/FM) ERK activity profile in necroptosis versus apoptosis. ERK inhibition disrupted these ERK signaling dynamics and prevented TNF and IL-6 gene expression increase during TNF-induced necroptosis. Using inducible cell line for activated MLKL, the final executioner of necroptosis, we propose ERK and its distinctive necroptotic ERK activity dynamics to be positioned downstream of MLKL.

This paper investigates the effects of partial substitution of zinc (Zn) in pure sulfide kesterite (Cu2ZnSnS4) by cadmium (Cd) and manganese (Mn) incorporation. Thin films of Cu2ZnSnS4 (CZTS), Cu2Zn1–xCdxSnS4 (CCZTS) and Cu2Zn1–xMnxSnS4(CMZTS) were produced chemically. A comparison of pure CZTS with CCZTS and CMZTS was performed to study the influence of Cd and Mn incorporation on the morphology, structure, optical and electronic properties of the films. The results show an improvement of the morphology and an adjustment of the band gap and valence band position by partial substitution of Zn with Cd and Mn. In addition, for the first time, the band alignment at the absorber/buffer hetero-interface is studied with partial Zn substitution. Band alignments at the absorber/buffer hetero-interface were estimated by XPS and UV/Visible measurements. The results show a cliff-like CBO for CZTS/CdS heterojunction, a spike-like CBO for CCZTS/CdS and a near flat-band CBO for CMZTS/CdS heterojunction.

This paper aims to study the properties of the absorber layer and the heterojunction in kesterite solar cells. The Cu2ZnSnS4 (CZTS) thin films were layered on a glass substrate from a colloidal solution of metal salts and thiourea dissolved in a mixture of water and ethanol and deposited by spin coating technique. The samples were then heat treated in a furnace, in the presence of sulphur powder and under a nitrogen gas flow. The results revealed the formation of homogeneous layers of a pure kesterite phase of CZTS crystallites after heat treatment with correct stoichiometry and oxidation states. The optical transmission measurements indicate an energy band-gap of 1.4 eV and an absorption coefficient of 104 cm−1. These CZTS thin films, elaborated by spin coating process, were integrated for electronic properties evaluation in a heterojunction in the following configuration: SnO2:F (FTO) and Molybdenum as back contact, CdS as tampon and the CZTS film as absorber layer. The band alignment at the CdS–CZTS heterojunction indicates a cliff-like conduction band offset (CBO) even close to be a flat band. Resumen: Este trabajo tiene como objetivo estudiar las propiedades de la capa absorbente y la heterojunción en las células solares de kesterita. Las finas películas de Cu2ZnSnS4 (CZTS) fueron colocadas en capas sobre un sustrato de vidrio a partir de una solución coloidal de sales metálicas y tiourea disueltas en una mezcla de agua y etanol, y depositadas mediante la técnica de revestimiento por centrifugado. A continuación las muestras se trataron térmicamente en un horno, en presencia de polvo de azufre y bajo un flujo de gas nitrógeno. Los resultados revelaron la formación de capas homogéneas de una fase de kesterita pura de los cristales de CZTS después del tratamiento térmico con la estequiometría y los estados de oxidación correctos. Las mediciones de la transmisión óptica indican una brecha en la banda de energía de 1,4 eV y un coeficiente de absorción de 104 cm−1. Estas películas delgadas de CZTS, elaboradas por el proceso de revestimiento de espín, se integraron para la evaluación de las propiedades electrónicas en una heterojunción en la siguiente configuración: SnO2: F (FTO) y molibdeno como contacto posterior, CdS como tampón y la película CZTS como capa absorbente. La alineación de la banda en la heterojunción CdS-CZTS indica un desplazamiento de la banda de conducción (CBO) similar al de un acantilado, incluso cerca de ser una banda plana.

International audience; How nuclear proteins diffuse and find their targets remains a key question in the transcription field. Dynamic proteins in the nucleus are classically subdiffusive and undergo anomalous diffusion, yet the underlying physical mechanisms are still debated. In this study, we explore the contribution of interactions to the generation of anomalous diffusion by the means of fluorescence spectroscopy and simulation. Using interaction-deficient mutants, our study indicates that HEXIM1 interactions with both 7SK RNA and positive transcription elongation factor b are critical for HEXIM1 subdiffusion and thus provides evidence of the effects of protein-RNA interaction on molecular diffusion. Numerical simulations allowed us to establish that the proportions of distinct oligomeric HEXIM1 subpopulations define the apparent anomaly parameter of the whole population. Slight changes in the proportions of these oligomers can lead to significant shifts in the diffusive features and recapitulate the modifications observed in cells with the various interaction-deficient mutants. By combining simulations and experiments, our work opens new prospects in which the anomaly a coefficient in diffusion becomes a helpful tool to infer alterations in molecular interactions.

Biomolecules include both small molecules such as metabolites, vitamins, and hormones and large macromolecules such as amino acids and proteins. In the case of proteins of high molecular weight, their three-dimensional arrangements enable them to fold into one or more specific spatial conformations driven by noncovalent interactions. Raman spectroscopy gives information about the selectivity, the sensitivity and the conformation of molecules. In single-molecule techniques such as fluorescence microscopy and atomic force microscopy allow for the direct observation of the dynamics of proteins. This avoids the complexities of averaging over heterogeneous dynamics in bulk biochemical assays. The most sophisticated and effective methods for classifying surface-enhanced Raman scattering spectra are based on predetermined library of spectra. They are called supervised methods and include linear discriminant analysis and partial least squares discriminant analysis. However, building a valid classification model requires the acquisition of a training set of samples.

In this contribution, we provide new insights on the temporal fluctuations of surface enhanced Raman spectra (SERS) of large single molecules such as proteins. Because they can only fit partly into small active volume, SERS analysis is referred to spectral pointillism where only protein subdomains are shined and the whole protein landscape is built from the dynamics of successive individual spectra. By applying our approach on bovine serum albumin, we show that single protein subdomains are mostly comprised of three distinct amino acids. Surface amino acids such as lysine are preferentially detected in the open form of the protein. The investigation of the tryptophan Fermi doublet in the single protein regime is highly instructive on the protein conformation. We finally demonstrate that spectral pointillism enables to correlate individual amino acids with structural information.

International audience; A two-photon fluorescence lifetime (2P-FLIM) microendoscope, capable of energetic metabolism imaging through the intracellular nicotinamide adenine dinucleotide (NADH) autofluorescence, at sub-cellular resolution, is demonstrated. It exhibits readily usable characteristics such as convenient endoscope probe diameter (≈2 mm), fiber length (>5 m) and data accumulation rate (16 frames per second (fps)), leading to a FLIM refreshing rate of ≈0.1 to 1 fps depending on the sample. The spiral scanning image formation does not influence the instrument response function (IRF) characteristics of the system. Near table-top microscope performances are achieved through a comprehensive system including a home-designed spectro-temporal pulse shaper and a custom air-silica double-clad photonic crystal fiber, which enables to reach up to 40 mW of ≈100 fs pulses @ 760 nm with a 80 MHz repetition rate. A GRadient INdex (GRIN) lens provides a lateral resolution of 0.67 μm at the focus of the fiber probe. Intracellular NADH fluorescence lifetime data are finally acquired on cultured cells at 16 fps.

The Raman intensity fluctuations are the initial source of a lack of accuracy or reproducibility of SERS based nanosensors to reliably estimate the molecular concentration in microfluidics. Here, we show that the statistical analysis of the weighting of Raman scattering of the probed molecules compared to the photoluminescence of gold nanoparticles is particularly effective as a concentration indicator in a single molecule regime. We present a novel approach in the Fourier domain that is not limited by a multipoint precalibration or even the knowledge of the enhancement factor of the transducer. The analysis of pink noise in the frequency domain reveals a subdiffusion motion of individual adsorbed molecules in the hot-spot. The cutoff frequency between the white and pink noise is used to determine the in-line molecular concentration over a wide range between 10–11 and 10–6 M.

Pseudodiaptomus marinus copepods are small crustaceans living in estuarine areas endowed with exceptional swimming and adaptative performances. Since the external cuticle acts as an impermeable barrier for most dyes and molecular tools for labeling copepod proteins with fluorescent tags are not available, imaging cellular organelles in these organisms requires label free microscopy. Complementary nonlinear microscopy techniques have been used to investigate the structure and the response of their myofibrils to abrupt changes of temperature or/and salinity. In contrast with previous observations in vertebrates and invertebrates, the flavin autofluorescence which is a signature of mitochondria activity and the Coherent Anti-Stokes Raman Scattering (CARS) pattern assigned to T-tubules overlapped along myofibrils with the second harmonic generation (SHG) striated pattern generated by myosin tails in sarcomeric A bands. Temperature jumps from 18 to 4 °C or salinity jumps from 30 to 15 psu mostly affected flavin autofluorescence. Severe salinity jumps from 30 to 0 psu dismantled myofibril organization with major changes both in the SHG and CARS patterns. After a double stress (from 18 °C/30 psu to 4 °C/0 psu) condensed and distended regions appeared within single myofibrils, with flavin autofluorescence bands located between sarcomeric A bands. These results shed light on the interactions between the different functional compartments which provide fast acting excitation–contraction coupling and adequate power supply in copepods muscles.

In this contribution, we report the identification of the principal reference Raman spectra of a single cystein molecule. To that purpose, we design an active Surface Enhanced Raman Spectroscopy (SERS) template based on surfactant-less Chebyshev nanoparticles operating in a microfluidic platform. A principal component analysis is obtained from fluctuating spectra to sort the reference spectra of cystein. The assignment of Raman bands brings new insight into the conformation of an amino acid adsorbed onto gold nanoparticle.

Coherent anti-Stokes Raman scattering (CARS) microscopy is a powerful tool for chemical analysis at a subcellular level, frequently used for imaging lipid dynamics in living cells. We report a high-power picosecond fiber-based laser and its application for optical parametric oscillator (OPO) pumping and CARS microscopy. This fiber-based laser has been carefully characterized. It produces 5 ps pulses with 0.8 nm spectral width at a 1,030 nm wavelength with more than 10 W of average power at 80 MHz repetition rate; these spectral and temporal properties can be slightly modified. We then study the influence of these modifications on the spectral and temporal properties of the OPO. We find that the OPO system generates a weakly spectrally chirped signal beam constituted of 3 ps pulses with 0.4 nm spectral width tunable from 790 to 930 nm optimal for CARS imaging. The frequency doubling unconverted part is composed of 7–8 ps pulses with 0.75 nm spectral width compatible with CARS imaging. We also study the influence of the fiber laser properties on the CARS signal generated by distilled water. In agreement with theory, we find that shorter temporal pulses allow higher peak powers and thus higher CARS signal, if the spectral widths are less than 10 cm−1. We demonstrate that this source is suitable for performing CARS imaging of living cells during several hours without photodamages. We finally demonstrate CARS imaging on more complex aquatic organisms called copepods (micro-crustaceans), on which we distinguish morphological details and lipid reserves. Microsc. Res. Tech. 77:422–430, 2014. © 2014 Wiley Periodicals, Inc.

Background Information Polycomb group (PcG) proteins keep the memory of cell identity by maintaining the repression of numerous target genes. They accumulate into nuclear foci called Polycomb bodies, which function in Drosophila cells as silencing compartments where PcG target genes convene. PcG proteins also exert their activities elsewhere in the nucleoplasm. In mammalian cells, the dynamic organisation and function of Polycomb bodies remain to be determined. Results Fluorescently tagged PcG proteins CBXs and their partners BMI1 and RING1 form foci of different sizes and intensities in human U2OS cells. Fluorescence recovery after photobleaching (FRAP) analysis reveals that PcG dynamics outside foci is governed by diffusion as complexes and transient binding. In sharp contrast, recovery curves inside foci are substantially slower and exhibit large variability. The slow binding component amplitudes correlate with the intensities and sizes of these foci, suggesting that foci contained varying numbers of binding sites. CBX4-green fluorescent protein (GFP) foci were more stable than CBX8-GFP foci; yet the presence of CBX4 or CBX8-GFP in the same focus had a minor impact on BMI1 and RING1 recovery kinetics. Conclusion We propose that FRAP recovery curves provide information about PcG binding to their target genes outside foci and about PcG spreading onto chromatin inside foci.

Surface enhanced Raman scattering (SERS) spectroscopy becomes increasingly used in biosensors for its capacity to detect and identify single molecules. In practice, a large number of SERS spectra are acquired and reliable ranking methods are thus essential for analysing all these data. Supervised classification strategies, which are the most effective methods, are usually applied but they require pre-determined models or classes. In this work, we propose to sort SERS spectra in unknown groups with an alternative strategy called Fourier polar representation. This non-fitting method based on simple Fourier sine and cosine transforms produces a fast and graphical representation for sorting SERS spectra with quantitative information. The reliability of this method was first investigated theoretically and numerically. Then, its performances were tested on two concrete biological examples: first with single amino-acid molecule (cysteine) and then with a mixture of three distinct odorous molecules. The benefits of this Fourier polar representation were highlighted and compared to the well-established statistical principal component analysis method.

Summary The polar representation or phasor, which provides a fast and visual indication on the number of exponentials present in the intensity decay of the fluorescence lifetime images is increasingly used in time domain fluorescence lifetime imaging microscopy experiments. The calculations of the polar coordinates in time domain fluorescence lifetime imaging microscopy experiments involve several experimental parameters (e.g. instrumental response function, background, angular frequency, number of temporal channels) whose role has not been exhaustively investigated. Here, we study theoretically, computationally and experimentally the influence of each parameter on the polar calculations and suggest parameter optimization for minimizing errors. We identify several sources of mistakes that may occur in the calculations of the polar coordinates and propose adapted corrections to compensate for them. For instance, we demonstrate that the numerical integration method employed for integrals calculations may induce errors when the number of temporal channels is low. We report theoretical generalized expressions to compensate for these deviations and conserve the semicircle integrity, facilitating the comparison between fluorescence lifetime imaging microscopy images acquired with distinct channels number. These theoretical generalized expressions were finally corroborated with both Monte Carlo simulations and experiments.

Fluorescence Lifetime Imaging Microscopy (FLIM) is a powerful technique to investigate the local environment of fluorophores in living cells. To correctly estimate all lifetime parameters, time domain FLIM imaging requires a high number of photons and consequently long laser exposure times. This is an issue because long exposure times are incompatible with the observation of dynamic molecular events and induce cellular stress. To minimize exposure time, we have developed an original approach that statistically inflates the number of collected photons. Our approach, called Adaptive Monte Carlo Data Inflation (AMDI), combines the well-known bootstrap technique with an adaptive Parzen kernel. We here demonstrate using both Monte Carlo simulations and live cells that our robust method accurately estimate fluorescence lifetimes with exposure time reduced up to 50 times for monoexponential decays (corresponding to a minimum of 20 photons/pixel), and 10 times for biexponential decays (corresponding to a minimum of 5,000 photons/pixel), compared to standard fitting method. Thanks to AMDI, in Forster resonance energy transfer experiments, it is possible to estimate all fitting parameters accurately without constraining any parameters. By reducing the commonly used spatial binning factor, our technique also improves the spatial resolution of FLIM images.

International audience; We calculate here analytically the performance of the polar approach (or phasor) in terms of signal-to-noise ratio and F values when performing time-domain Fluorescence Lifetime Imaging Microscopy (FLIM) to determine the minimal number of photons necessary for FLIM measurements (which is directly related to the F value), and compare them to those obtained from a well-known fitting strategy using the Least Square Method (LSM). The importance of the fluorescence background on the lifetime measurement precision is also investigated. We demonstrate here that the LSM does not provide the best estimator of the lifetime parameter for fluorophores exhibiting mono-exponential intensity decays as soon as fluorescence background is superior to 5%. The polar approach enables indeed to determine more precisely the lifetime values for a limited range corresponding to usually encountered fluorescence lifetime values. These theoretical results are corroborated with Monte Carlo simulations. We finally demonstrate experimentally that the polar approach allows distinguishing in living cells two fluorophores undetectable with usual time-domain LSM fitting software.

Multispectral fluorescence lifetime imaging microscopy is a promising and powerful technique for discriminating multiply labeled samples and for detecting molecular interactions inside thick, heterogeneous, and light-scattering milieu such as tissue. The fast and correct analysis of the spectral and lifetime images constitutes a major challenge, which requires a high level of expertise. We present here a new approach that considerably simplifies this analysis avoiding complex fitting algorithm strategies and permitting a fast and visual graphical representation of the fluorescence lifetimes. By transforming the experimental data from time domain to frequency domain for each spectral channel, we calculate the multispectral polar representation and demonstrate its interest on multiply fluorescent labeled sample. We further apply it on Förster resonance energy transfer (FRET) experiments and demonstrate that FRET measurements with a high level of precision can be performed. With addition of emission wavelength as third dimension in the polar representation, autofluorescence emitted by the sample is thus clearly identified. Analysis artifacts induced by the sample or by fitting algorithm choice become then totally inexistent.

International audience; We report on measurements and Monte Carlo analysis of the spatial distribution of light in two-photon excitation fluorescence (TPEF) microscopy operating through scattering media. The axial profile of TPEF produced by a high numerical aperture microscope objective focusing through a tissue-like optical phantom at depths more than five photon mean-scattering lengths is studied. The measured profile is quantitatively interpreted with time-resolved Monte Carlo simulations that take into account the spatio-temporal distribution of the photons within the turbid medium under a femtosecond excitation regime. It is shown that considering only the ballistic photons leads to an under-estimation of the actual out-of-focus distribution of the fluorescence, whereas it is over-estimated when the ballistic and scattered photons are treated alike. Comparison of the in-focus signal to the overall out-of-focus background clearly pointed out that the signal-to-background ratio of TPEF microscopy images benefits from a shortening of the excitation pulses. Moreover, in homogeneously labeled specimen, the background is shown to overcome the signal at imaging depths of about five to six photon mean-scattering paths.

Copepods are small crustaceans capable to survive in various aquatic environments. Their responses to changes in different external factors such as salinity and temperature can be observed at different integration levels from copepod genes to copepod communities. Until now, no thorough observation of the temperature or salinity effect stresses on copepods has been done by optical microscopy. In this study, we used autofluorescence to visualize these effects on the morphology of the calanoid copepod Pseudodiaptomus marinus maintained during several generations in the laboratory at favorable and stable conditions of salinity (30 psu) and temperature (18°C). Four different stress experiments were conducted: at a sharp decrease in temperature (18 to 4°C), a moderate decrease in salinity (from 30 to 15 psu), a major decrease in salinity (from 30 to 0 psu), and finally a combined stress with a decrease in both temperature and salinity (from 18°C and 30 psu to 4°C and 0 psu). After these stresses, images acquired by confocal laser scanning microscopy (CLSM) revealed changes in copepod cuticle and muscle structure. Low salinity and/or temperature stresses affected both the detection of fluorescence emitted by muscle sarcomeres and the distance between them. In the remaining paper we will use the term sarcomeres to describe the elements located within sarcomeres and emitted autofluorescence signals. Quantitative study showed an increase in the average distance between two consecutive sarcomeres from 2.06 +/- 0.11 μm to 2.44 +/- 0.42 μm and 2.88 +/- 0.45μm after the exposure to major haline stress (18°C, 0 psu) and the combined stress (4°C, 0 psu), respectively. These stresses also caused cuticle cracks which often occurred at the same location, suggesting the cuticle as a sensitive area for osmoregulation. Our results suggest the use of cuticular and muscle autofluorescence as new biomarkers of stress detectable in formalin-preserved P. marinus individuals. Our label-free method can be easily applied to a large number of other copepod species or invertebrates with striated musculature.

First-order hyperpolarizabilties of two new amphiphilic push-pull chromophore derivatives of hemicyanine dyes prepared in Langmuir–Blodgett films and designed for membrane potential imaging of living cells are measured by surface second-harmonic generation (SHG). Assuming uniaxial symmetry, an effective hyperpolarizability coefficient βe is defined, and a procedure to measure this coefficient is described. Relationships between βe and the true hyperpolarizability coefficient β are derived on the basis of a stochastic model taking account of the tilt angle disorder of the chromophores. Maximum discrepancies between the true and the effective hyperpolarizabilities are calculated as a function of the orientation parameter D, and it is shown that the relative difference may not exceed 40% for usual distribution functions of the tilt angle. As a result, the dominant hyperpolarizability coefficient β z , z , z ( 2 ) of the chromophores in LB films is found to be in the range 0.3–0.7 × 10−27 esu at 1064 nm fundamental wavelength.

Analysis of fluorescence lifetime imaging microscopy (FLIM) and Forster resonance energy transfer (FRET) experiments in living cells is usually based on mean lifetimes computations. However, these mean lifetimes can induce misinterpretations. We propose in this work the implementation of the transportation distance for FLIM and FRET experiments in vivo. This non-fitting indicator, which is easy to compute, reflects the similarity between two distributions and can be used for pixels clustering to improve the estimation of the FRET parameters. We study the robustness and the discriminating power of this transportation distance, both theoretically and numerically. In addition, a comparison study with the largely used mean lifetime differences is performed. We finally demonstrate practically the benefits of the transportation distance over the usual mean lifetime differences for both FLIM and FRET experiments in living cells.

National audience; L’imagerie cellulaire, dans le domaine des sciences du vivant, est essentielle à la compréhension des phénomènes cellulaires subcellulaires régulant le fonctionnement des cellules et tissus. En microscopie électronique, la mise en oeuvre de cryo-méthodes permet de préserver l’intégrité moléculaire et spatiale des protéines et lipides intracellulaires ou membranaires (de faible poids moléculaire, présentes en faible quantité ou très labiles) dont la localisation in situ est recherchée afin de caractériser leur organisation, participer à la détermination de leur fonction au sein de la cellule et d’analyser leur distribution. Ces techniques, en pleine évolution, seront abordées lors de ces journées scientifiques et techniques et ce, sur l’ensemble des règnes (animal, végétal et micro-organismes). II est également important, sur des matériels biologiques vivants, de pouvoir accéder à des informations qui permettent de caractériser la répartition et la dynamique de constituants cellulaires ou membranaires, et ce, à haute résolution temporelle et spatiale. La mobilité latérale d’une molécule, les interactions moléculaires in vivo, le suivi individuel de particules fluorescentes peuvent être appréhendées. Ces méthodologies de « diffusion, dynamique » et « haute résolution » en microscopie photonique de fluorescence participent à la compréhension de phénomènes cellulaires et seront détaillées. De même, l’analyse des images ou données obtenues nécessaires à leur exploitation sera explicitée. Le prix Nobel de chimie 2014 décerné à Eric Betzig (USA), Stefan W. Hell (Allemagne), et William E. Moerner (USA) pour le développement de la microscopie de fluorescence à très haute résolution témoigne de la reconnaissance de l’importance technologique de ce domaine. Une demi-journée sera consacrée à la mise en oeuvre pratique de ces technologies, dans le cadre d’ateliers plébiscités par les membres du RμI, au cours desquels les participants pourront réaliser les expérimentations, encadrés par les spécialistes des méthodologies ou technologies choisies. Pour chacun des ateliers, une restitution des échanges aura lieu en session plénière. De plus, les partenaires privés présents à ces journées pourront vous faire découvrir leurs nouveautés et échanger avec vous de façon privilégiée. Nous les remercions pour leur fidèle soutien et pour l’intérêt porté. Nous remercions également vivement l’ensemble des partenaires institutionnels locaux et nationaux de l’intérêt porté à cette discipline qu’est l’imagerie cellulaire et de leur soutien pour la tenue et l’organisation de ces journées annuelles du RμI.

International audience; We study the fluorescence emission from single dye molecules in coplanar plasmonic cavities composed of a thin gold film surrounded by two in-plane surface plasmon Bragg mirrors. We first discuss the effect of the presence of Bragg mirrors on the radiation diagram of surface plasmon coupled emission. Then, we investigate the role of the planar cavity size by single-molecule fluorescence lifetime imaging. Experimental data are compared to numerical simulations of the decay rates calculated as a function of the molecule orientation and position within the cavity. The creation of new decay channels by coupling to the cavity modes is also discussed. We measure a plasmonic Purcell factor up to five, attributed to the enhancement of the radiative rate.

Polycomb group (PcG) proteins keep the memory of cell identity by maintaining the repression of numerous target genes. They accumulate into nuclear foci called Polycomb bodies, which function in Drosophila cells as silencing compartments where PcG target genes convene. PcG proteins also exert their activities elsewhere in the nucleoplasm. In mammalian cells, the dynamic organisation and function of Polycomb bodies remain to be determined.Fluorescently tagged PcG proteins CBXs and their partners BMI1 and RING1 form foci of different sizes and intensities in human U2OS cells. Fluorescence recovery after photobleaching (FRAP) analysis reveals that PcG dynamics outside foci is governed by diffusion as complexes and transient binding. In sharp contrast, recovery curves inside foci are substantially slower and exhibit large variability. The slow binding component amplitudes correlate with the intensities and sizes of these foci, suggesting that foci contained varying numbers of binding sites. CBX4-green fluorescent protein (GFP) foci were more stable than CBX8-GFP foci; yet the presence of CBX4 or CBX8-GFP in the same focus had a minor impact on BMI1 and RING1 recovery kinetics.We propose that FRAP recovery curves provide information about PcG binding to their target genes outside foci and about PcG spreading onto chromatin inside foci.

International audience; In this paper, we propose a new and simple method based on two-photon excitation fluorescence (TPEF) microscopy to measure the scattering coefficient μs of thick turbid media. We show, from Monte Carlo simulations, that μs can be derived from the axial profile of the ratio of the TPEF signals epi-collected by the confocal and the non-descanned ports of a scanning microscope, independently of the anisotropy factor g and of the absorption coefficient μa of the medium. The method is validated experimentally on tissue-mimicking optical phantoms, and is shown to have potential for imaging the scattering coefficient of heterogeneous media

There was an error in the title. The correct title is: Spatio-Temporal Quantification of FRET in Living Cells by Fast Time-Domain FLIM: A Comparative Study of Non-Fitting Methods. The correct citation is: Leray A, Padilla-Parra S, Roul J, Heliot L, Tramier M (2013) Spatio-Temporal Quantification of FRET in Living Cells by Fast Time-Domain FLIM: A Comparative Study of Non-Fitting Methods. PLoS ONE 8(7): e69335. doi:10.1371/journal.pone.0069335.

International audience; Nuclear all-trans retinoic acid receptors (RARs) initiate early transcriptional events which engage pluripotent cells to differentiate into specific lineages. RAR-controlled transactivation depends mostly on agonist-induced structural transitions in RAR C-terminus (AF-2), thus bridging coactivators or corepressors to chromatin, hence controlling preinitiation complex assembly. However, the contribution of other domains of RAR to its overall transcriptional activity remains poorly defined. A proteomic characterization of nuclear proteins interacting with RAR regions distinct from the AF-2 revealed unsuspected functional properties of the RAR N-terminus. Indeed, mass spectrometry fingerprinting identified the Bromodomain-containing protein 4 (BRD4) and ALL1-fused gene from chromosome 9 (AF9/MLLT3), known to associate with and regulates the activity of Positive Transcription Elongation Factor b (P-TEFb), as novel RAR coactivators. In addition to promoter sequences, RAR binds to genomic, transcribed regions of retinoid-regulated genes, in association with RNA polymerase II and as a function of P-TEFb activity. Knockdown of either AF9 or BRD4 expression affected differentially the neural differentiation of stem cell-like P19 cells. Clusters of retinoid-regulated genes were selectively dependent on BRD4 and/or AF9 expression, which correlated with RAR association to transcribed regions. Thus RAR establishes physical and functional links with components of the elongation complex, enabling the rapid retinoid-induced induction of genes required for neuronal differentiation. Our data thereby extends the previously known RAR interactome from classical transcriptional modulators to components of the elongation machinery, and unravel a functional role of RAR in transcriptional elongation.

Biological processes are intrinsically dynamic. Although traditional methods provide valuable insights for the understanding of many biological phenomena, the possibility of measuring, quantifying, and localizing proteins within a cell, a tissue, and even an embryo has revolutionized our train of thoughts and has encouraged scientists to develop molecular tools for the assessment of protein or protein complex dynamics within their physiological context. These ongoing efforts rest on the emergence of biophotonic techniques and the continuous improvement of fluorescent probes, allowing precise and reliable measurements of dynamic cellular functions. The march of the “ in vivo biochemistry” has begun, already yielding breathtaking results.

International audience; Förster Resonance Energy Transfer (FRET) measured with Fluorescence Lifetime Imaging Microscopy (FLIM) is a powerful technique to investigate spatio-temporal regulation of protein-protein interactions in living cells. When using standard fitting methods to analyze time domain FLIM, the correct estimation of the FRET parameters requires a high number of photons and therefore long acquisition times which are incompatible with the observation of dynamic protein-protein interactions. Recently, non-fitting strategies have been developed for the analysis of FLIM images: the polar plot or "phasor" and the minimal fraction of interacting donor mfD . We propose here a novel non-fitting strategy based on the calculation of moments. We then compare the performance of these three methods when shortening the acquisition time: either by reducing the number of counted photons N or the number of temporal channels Nch , which is particularly adapted for the original fast-FLIM prototype presented in this work that employs the time gated approach. Based on theoretical calculations, Monte Carlo simulations and experimental data, we determine the domain of validity of each method. We thus demonstrate that the polar approach remains accurate for a large range of conditions (low N, Nch or small fractions of interacting donor fD ). The validity domain of the moments method is more restricted (not applicable when fD

Biological processes are intrinsically dynamic. Although traditional methods provide valuable insights for the understanding of many biological phenomena, the possibility of measuring, quantifying, and localizing proteins within a cell, a tissue, and even an embryo has revolutionized our train of thoughts and has encouraged scientists to develop molecular tools for the assessment of protein or protein complex dynamics within their physiological context. These ongoing efforts rest on the emergence of biophotonic techniques and the continuous improvement of fluorescent probes, allowing precise and reliable measurements of dynamic cellular functions. The march of the "in vivo biochemistry" has begun, already yielding breathtaking results.

Long-pulse supercontinuum sources are initiated by modulation instability and consequently suffer from stochastic shot-to-shot variations of their spectral power density. In this paper, we provide a measurement of pulse-to-pulse fluctuations over the whole supercontinuum spectrum, and we show that their spectral dependence follows the group index curve of the fiber. Then, we demonstrate a significant reduction of supercontinuum pulse-to-pulse fluctuations in the visible by using a photonic crystal fiber with longitudinally tailored guidance properties. We finally show numerically that this new source would allow a significant improvement of the signal-to-noise ratio in fluorescence microscopy.

We report our progress in the development of Differential Aberration Imaging (DAI), a technique that enhances twophoton fluorescence (TPEF) microscopy by improving rejection of out-of-focus background by means of a deformable mirror (DM). The DM is used to intentionally add aberrations to the imaging system, which causes dramatic losses to in-focus signal while preserving the bulk of the out-of-focus background. By taking the difference between TPEF images with and without added aberrations, the out-of-focus portion of the signal is further rejected. We now introduce an implementation of DAI using a new type of DM that can be produced at much lower cost.

Frequency-domain fluorescence lifetime imaging microscopy (FLIM) has become a commonly used technique to measure lifetimes in biological systems. However, lifetime measurements are strongly dependent on numerous experimental parameters. Here, we describe a complete calibration and characterization of a FLIM system and suggest parameter optimization for minimizing measurement errors during acquisition. We used standard fluorescent molecules and reference biological samples, exhibiting both single and multiple lifetime components, to calibrate and evaluate our frequency domain FLIM system. We identify several sources of lifetime precision degradation that may occur in FLIM measurements. Following a rigorous calibration of the system and a careful optimization of the acquisition parameters, we demonstrate fluorescence lifetime measurements accuracy and reliability. In addition, we show its potential on living cells by visualizing FRET in CHO cells. The proposed calibration and optimization protocol is suitable for the measurement of multiple lifetime components sample and is applicable to any frequency domain FLIM system. Using this method on our FLIM microscope enabled us to obtain the best fluorescence lifetime precision accessible with such a system. Microsc. Res. Tech., 2009. © 2008 Wiley-Liss, Inc.