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Although single-particle level studies on prolate ellipsoidal colloids are relatively abundant, similar studies on oblate ellipsoids are rare because suitable model systems are scarcely available. Here, we present the preparation of monodisperse hard core–shell oblate ellipsoids that can be imaged and tracked in 3D with confocal laser scanning microscopy. Using a thermomechanical squeezing method, we transform spherical core–shell polymethyl-methacrylate (PMMA) particles into oblate ellipsoids. We show how the shape polydispersity as well as the aspect ratio of the obtained oblate ellipsoids can be controlled. In addition, we discuss how the core–shell geometry limits the range of aspect ratios because of the different viscoelastic properties of the cross-linked PMMA core and linear PMMA shell. We further demonstrate imaging of the core–shell oblate dispersions on a single-particle level in real space and time and the tracking of position and orientation using our recently developed tracking algorithm for anisotropic core–shell colloids. Our results thus provide the tools for the future investigation of the behavior of oblate ellipsoids, especially in dense suspensions.

Suspensions of hard ellipsoidal particles exhibit complex phase behavior as shown by theoretical predictions and simulations of phase diagrams. Here, we report quantitative confocal microscopy experiments of hard prolate colloidal ellipsoids with different aspect ratio a/b. We studied different volume fractions φ of ellipsoids in density and refractive index matched suspensions. Large 3D sample volumes were investigated and the positions as well as the orientations of all ellipsoids were extracted by image analysis routines. By evaluating the translational and orientational order in the system we determined the presence of isotropic and nematic phases. For ellipsoids with a/b = 2.0 we found that isotropic phases form at all φ, while ellipsoids with a/b = 7.0 formed nematic phases at high φ, as expected from theory and simulations. For a/b = 3.5 and a/b = 4.1, however, we observed the absence of long-range orientational order even at φ where nematic phases are expected. We show that local orientational order formed with the emergence of nematic precursors for a/b = 3.5 and short-ranged nematic domains for a/b = 4.1. Our results provide novel insight into the phase behavior and orientational order of ellipsoids with different aspect ratios.

The hydrolysis of nucleotides is of paramount importance as an energy source for cellular processes. In addition, the transfer of phosphates from nucleotides onto proteins is important as a post-translational protein modification. Monitoring the enzymatic turnover of nucleotides therefore offers great potential as a tool to follow enzymatic activity. While a number of fluorescence sensors are known, so far, there are no methods available for the real-time monitoring of ATP hydrolysis inside live cells. We present the synthesis and application of a novel fluorogenic adenosine 5'-tetraphosphate (Ap4) analog suited for this task. Upon enzymatic hydrolysis, the molecule displays an increase in fluorescence intensity, which provides a readout of its turnover. We demonstrate how this can be used for monitoring cellular processes involving Ap4 hydrolysis. To this end, we visualized the enzymatic activity in live cells using confocal fluorescence microscopy of the Ap4 analog. Our results demonstrate that the Ap4 analog is hydrolyzed in lysosomes. We show that this approach is suited to visualize the lysosome distribution profiles within the live cell and discuss how it can be employed to gather information regarding autophagic flux. ispartof: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES vol:22 issue:16 ispartof: location:Switzerland status: published

In the quest to decipher the chain of life from molecules to cells, the biological and biophysical questions being asked increasingly demand techniques that are capable of identifying specific biomolecules in their native environment, and can measure biomolecular interactions quantitatively, at the smallest possible scale in space and time, without perturbing the system under observation. The interaction of light with biomolecules offers a wealth of phenomena and tools that can be exploited to drive this progress. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of bio-nano-photonics, spanning from the development of optical micro/nano-spectroscopy technologies for quantitative bioimaging and biosensing to the fundamental understanding of light–matter interaction phenomena with biomolecules at the nanoscale. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

During the adipogenic differentiation process of mesenchymal stem cells, lipid droplets (LDs) grow slowly by transferring lipids between each other. Recent findings hint at the possibility that a fusion pore is involved. In this study, we analyze lipid transfer data obtained in long-term label-free microscopy studies in the framework of a Hagen-Poiseuille model. The data obtained show a LD fusion process in which the lipid transfer directionality depends on the size difference between LDs, whereas the respective rates depend on the size difference and additionally on the diameter of the smaller LDs. For the data analysis, the viscosity of the transferred material has to be known. We demonstrate that a viscosity-dependent molecular rotor dye can be used to measure LD viscosities in live cells. On this basis, we calculate the diameter of a putative lipid transfer channel which appears to have a direct dependence on the diameter of the smaller of the two participating LDs.

Poly(ADP-ribos)ylation (PARylation) is an important posttranslational protein modification, and is involved in major cellular processes such as gene regulation and DNA repair. Its dysregulation has been linked to several diseases, including cancer. Despite its importance, methods to observe PARylation dynamics within cells are rare. By following a chemical biology approach, we developed a fluorescent NAD(+) analogue that proved to be a competitive building block for protein PARylation in vitro and in cells. This allowed us to directly monitor the turnover of PAR in living cells at DNA damage sites after near-infrared (NIR) microirradiation. Additionally, covalent and noncovalent interactions of selected target proteins with PAR chains were visualized in cells by using FLIM-FRET microscopy. Our results open up new opportunities for the study of protein PARylation in real time and in live cells, and will thus contribute to a better understanding of its significance in a cellular context. published

Poly(ADP-ribos)ylation (PARylation) is a major posttranslational modification and signaling event in most eukaryotes. Fundamental processes like DNA repair and transcription are coordinated by this transient polymer and its binding to proteins. ADP-ribosyltransferases (ARTs) build complex ADP-ribose chains from NAD+ onto various acceptor proteins. Molecular studies of PARylation thus remain challenging. Herein, we present the development of bioorthogonally functionalized NAD+ analogues for the imaging of PARylation in vitro and in cells. Our results show that 2-modified NAD+ analogues perform remarkably well and can be applied to the in-cell visualization of PARylation simultaneously in two colors. This tool gives insight into the substrate scope of ARTs and will help to further elucidate the biological role of PARylation by offering fast optical, multichannel read-outs. published

Intercellular communication is a fundamental process in the development and functioning of multicellular organisms. Recently, an essentially new type of intercellular communication, based on thin membrane channels between cells, has been reported. These structures, termed intercellular or tunnelling nanotubes (TNTs), permit the direct exchange of various components or signals (e.g., ions, proteins, or organelles) between non-adjacent cells at distances over 100 μm. Our studies revealed the presence of tunnelling nanotubes in microvascular endothelial cells (HMEC-1). The TNTs were studied with live cell imaging, environmental scanning electron microscopy (ESEM) and coherent anti-Stokes Raman scattering spectroscopy (CARS). Tunneling nanotubes showed marked persistence: the TNTs could connect cells over long distances (up to 150 μm) for several hours. Several cellular organelles were present in TNTs, such as lysosomes and mitochondria. Moreover, we could identify lipid droplets as a novel type of cargo in the TNTs. Under angiogenic conditions (VEGF treatment) the number of lipid droplets increased significantly. Arachidonic acid application not only increased the number of lipid droplets but also tripled the extent of TNT formation. Taken together, our results provide the first demonstration of lipid droplets as a cargo of TNTs and thereby open a new field in intercellular communication research.

Polymer chemistry 5(8), 2700-2703 (2014). doi:10.1039/c3py01684f, Published by RSC Publ., Cambridge

Water-soluble derivatives of pyrrolopyrrole cyanines (PPCys) have been synthesized by a post-synthetic modification route. In highly polar media, these dyes are excellent NIR fluorophores. Labeling experiments show how these novel dyes are internalized into mammalian cells.

Polymeric nano- and microparticles are finding widespread applications in materials and biological science. In all preparation methods pursued to date, the chemical stability of the particles is determined by the polymer system chosen. Usually, after particle synthesis, postprocessing with the aim of changing their stability is not possible. Therefore, one only has two choices: the synthesis of crosslinked polymer particles with high solvent and heat resistance and limited formability, or the synthesis of polymer particles consisting of linear polymer chains exhibiting low stability and high formability. In this contribution, we describe a new class of colloids which combine the advantages of both particle systems. The particles are composed of linear PMMA chains which are functionalized with photo-crosslinkable moieties. After preparation, the particles can be deformed before they are crosslinked by UV illumination. This offers unique possibilities for particle modification with a broad range of possible applications. Three examples are given. First, we show that the particles can be thermo-mechanically deformed into anisotropic shapes, in which they can be locked by subsequent crosslinking. Relaxation into the thermodynamically favorable spherical shape is thus suppressed, even in harsh environments. Second, we describe how the difference in solvent stability between illuminated and non-illuminated particles can be exploited for photolithography. Third, we demonstrate how photo-crosslinked anisotropic particles can be loaded with functional compounds, e.g. fluorophores.

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.

Optical microscopy is an indispensable tool that is driving progress in cell biology. It still is the only practical means of obtaining spatial and temporal resolution within living cells and tissues. Most prominently, fluorescence microscopy based on dye-labeling or protein fusions with fluorescent tags is a highly sensitive and specific method of visualizing biomolecules within sub-cellular structures. It is however severely limited by labeling artifacts, photo-bleaching and cytotoxicity of the labels. Coherent Raman Scattering (CRS) has emerged in the last decade as a new multiphoton microscopy technique suited for imaging unlabeled living cells in real time with high three-dimensional spatial resolution and chemical specificity. This technique has proven to be particularly successful in imaging unstained lipids from artificial membrane model systems, to living cells and tissues to whole organisms. In this article, we will review the experimental implementations of CRS microscopy and their application to imaging lipids. We will cover the theoretical background of linear and non-linear vibrational micro-spectroscopy necessary for the understanding of CRS microscopy. The different experimental implementations of CRS will be compared in terms of sensitivity limits and excitation and detection methods. Finally, we will provide an overview of the applications of CRS microscopy to lipid biology.

We demonstrate a method for broadband laser pulse characterization based on a spectrally resolved cross-correlation with a narrowband flat-top gate pulse. Excellent phase-matching by collinear excitation in a microscope focus is exploited by degenerate four-wave mixing in a microscope slide. Direct group delay extraction of an octave spanning spectrum which is generated in a highly nonlinear fiber allows for spectral phase retrieval. The validity of the technique is supported by the comparison with an independent second-harmonic fringe-resolved autocorrelation measurement for an 11 fs laser pulse.

A series of novel pyrrolopyrrole cyanines (PPCys) bearing various aminophenyl substituents at the diketopyrrolopyrrole (DPP) core are presented. Compared to their alkoxyphenyl substituted analogues, these dyes feature additional intense electronic transitions of charge-transfer character which give detailed insight into the optical properties of PPCys. The energetic mixing of the involved orbitals has pronounced effects on the absorption and fluorescence behavior. Protonation of the amino function suppresses these effects and leads to a pronounced increase in fluorescence quantum yield. The photophysics of the dyes can be rationalized by means of a simple energy scheme.

We present experimental results regarding the effects of electric pulses on giant unilamellar vesicles (GUVs). We have used phase contrast and coherent anti-Stokes Raman scattering (CARS) microscopy as relevant optical approaches to gain insight into membrane changes under electropermeabilization. No addition of exogenous molecules (lipid analogue, fluorescent dye) was needed. Therefore, experiments were performed on pure lipid systems avoiding possible artefacts linked to their use. Structural membrane changes were assessed by loss of contrast inside the GUVs due to sucrose and glucose mixing. Our observations, performed at the single vesicle level, indicate these changes are under the control of the number of pulses and field intensity. Larger number of pulses enhances membrane alterations. A threshold value of the field intensity must be applied to allow exchange of molecules between GUVs and the external medium. This threshold depends on the size of the vesicles, the larger GUVs being affected at lower electric field strengths than the smaller ones. Our experimental data are well described by a simple model in which molecule entry is driven by direct exchange. The CARS microscopic study of the effect of pulse duration confirms that pulses, in the ms time range, induce loss of lipids and membrane deformations facing the electrodes.

Electrotransfer of molecules is a well established technique which finds extensive use for gene transfer and holds great promise for anticancer treatment. Despite its widespread application, the mechanisms governing the entry of DNA into the cell and its intracellular trafficking are not yet known. The aim of this study is to unravel the role of the actin cytoskeleton during gene electrotransfer in cells. We performed single-cell level approaches to observe the organization of the actin cytoskeleton in Chinese hamster ovary (CHO) cells. In addition, we performed experiments at the multiple-cell level to evaluate the efficiency of DNA transfer after alteration of the actin cytoskeleton using the drug latrunculin B. Actin patches colocalizing with the DNA at the plasma membrane were observed with additional characteristics similar to those of the DNA aggregates in terms of time, number, and size. The disruption of the microfilaments reduces the DNA accumulation at the plasma membrane and the gene expression. This is the first direct experimental evidence of the participation of the actin cytoskeleton in DNA electrotransfer.

We demonstrate a compact pulse compression scheme that offers flexible chirp control for improved conversion efficiencies in high resolution nonlinear optical microscopy. An Er:fiber laser combined with a highly nonlinear optical fiber yields pulses centered at 1100 nm with a bandwidth of 500 nm. The compressed pulses with a duration of 7.6 fs enable simultaneous second-harmonic generation, third-harmonic generation, and four-wave mixing microscopy. The spectrum is tailored for an ideal compromise between conversion efficiency and spectral discrimination between the three types of broadband nonlinear signals. Distinct differences in structural contrast obtained from the simultaneous read-out of the three nonlinear signals are demonstrated in a biological sample.

We present a compact coherent anti-Stokes Raman scattering microscope based on a widely tunable picosecond Er:fiber laser. Intense and bandwidth-limited 1 ps pump pulses at a center wavelength of 775 nm are generated via frequency mixing within the broadband fundamental at 1.55 microm. Narrowband Stokes pulses are obtained by frequency shifting of solitons in a highly nonlinear bulk fiber and subsequent second-harmonic generation. The tuning range from 850 nm to 1100 nm gives access to vibrational resonances between 1150 cm(-1) and 3800 cm(-1). A first imaging application in the spectral region of CH stretch vibrations is demonstrated.

Our research activities over the last few decades have concerned correlations between molecular structure and fluorescence. 2] A central theme of the research has been the synthesis and spectroscopic investigations of near-infrared (NIR) dyes to get insights into what degree the obtainable fluorescence quantum yields are restricted by the S0$S1 energy gap. Our results on the condensation of 1,4phthalazinediones with heteroarylacetonitriles in POCl3 prompted us to carry out the reaction with diketopyrrolopyrroles (DPPs) 1. Herein we report the results of the investigations. To date, attempts to activate the carbonyl group of DPPs with POCl3, and to subsequently convert the intermediates with nucleophiles, only led to monosubstitution or to ring opening. 10] The reaction of 1 and 2 in refluxing toluene with an excess of POCl3 according to Scheme 1 afforded disubstituted NIR dyes 3. The progress of the reaction was controlled by recording absorption spectra and stopping the heating as soon as the DPP was used up and/or products absorbing at short wavelengths appeared. Purification was carried out by digesting the product in acetone and subsequent flash chromatography (silica gel/CHCl3 or CH2Cl2). The NIR dyes 3a–3h (the structures and spectroscopic data of 3b–3h can be found in the Supporting Information) were synthesized according to this procedure (Scheme 1) from the reaction of 1 and 2. The course of the reactions was the same in all cases and side-products with strong absorptions below 350 nm were observed. These side-products are most likely compounds formed by the opening of the DPPs pentalene ring system. Prerequisite for the reactions is a certain solubility of the DPPs. This is a feature of all of the DPPs used here with the exception of the 4-methoxy derivative 1b. Remarkably, the 4(N-methyl-N-octyl amino) derivative 1e has a much better solubility than all the other DPPs used. Only in the case of the reaction of 1e with 2a were we able to isolate the 1:1 condensation product (13% yield). The heteroarylacetonitriles 2a and 2b substituted with a tert-butyl group were used to improve the solubility of the condensation products 3. In general, satisfying yields were obtained only if the solubility of both condensation partners was improved by having longer alkyl groups (Table 1). From these observations we draw the following conclusion concerning the reaction pathway: DPP reacts with POCl3 to form a monophosphorylated intermediate, which reacts with the Scheme 1. Reagents and conditions: a) absolute toluene/POCl3, reflux; b) 1,2-dichlorobenzene/BF3·Et2O, reflux, diisopropylethylamine; c) xylene/chlorodiphenylborane, reflux; DPPs 1: R=4-octyloxy (1a), R=4-methoxy (1b), R=4-butyloxy (1c), R=4-(hex-5-enyloxy) (1d), R=4-(N-methyl-N-octylamino) (1e); heteroarylacetonitriles 2 : 2-(6tert-butylquinolin-2-yl)acetonitrile (2a), 2-(6-tert-butylbenzothiazol-2yl)acetonitrile (2b), 2-(quinoxalin-2-yl)acetonitrile (2c), 2-(6-methylpyridin-2-yl)acetonitrile (2d). A: aromatic ring.

Fluorescence lifetime (FLT) properties of organic molecules provide a new reporting strategy for molecular imaging in the near infrared (NIR) spectral region. Unfortunately, most of the NIR fluorescent dyes have short FLT typically clustered below 1.5 ns. In this study, we demonstrate that a new class of NIR fluorescent dyes, pyrrolopyrrole cyanine dyes, have exceptionally long FLTs ranging from 3 to 4 ns, both in vitro (dimethyl sulfoxide and albumin/water solutions) and in vivo (mice). These results provide a new window for imaging molecular processes, rejecting backscattered light and autofluorescence, and multiplexing imaging information with conventional NIR fluorescent dyes that absorb and emit light at similar wavelengths.