Quantum-yield-optimized fluorophores for site-specific labeling and super-resolution imaging

Single-molecule applications, saturated pattern excitation microscopy, and stimulated emission depletion (STED) microscopy demand bright as well as highly stable fluorescent dyes. Here we describe the synthesis of quantum-yield-optimized fluorophores for reversible, site-specific labeling of proteins or macromolecular complexes. We used polyproline-II (PPII) helices as sufficiently rigid spacers with various lengths to improve the fluorescence signals of a set of different trisNTA-fluorophores. The improved quantum yields were demonstrated by steady-state and fluorescence lifetime analyses. As a proof of principle, we characterized the trisNTA-PPII-fluorophores with respect to in vivo protein labeling and super-resolution imaging at synapses of living neurons. The distribution of His-tagged AMPA receptors (GluA1) in spatially restricted synaptic clefts was imaged by confocal and STED microscopy. The comparison of fluorescence intensity profiles revealed the superior resolution of STED microscopy. These results highlight the advantages of biocompatible and, in particular, small and photostable trisNTA-PPII-fluorophores in super-resolution microscopy.     

Confocal/TEM overlay microscopy: a simple method for correlating confocal and electron microscopy of cells expressing GFP/YFP fusion proteins.

Genetic manipulation allows simultaneous expression of green fluorescent protein (GFP) and its derivatives with a wide variety of cellular proteins in a variety of living systems. Epifluorescent and confocal laser scanning microscopy (confocal) localization of GFP constructs within living tissue and cell cultures has become routine, but correlation of light microscopy and high resolution transmission electron microscopy (TEM) on components within identical cells has been problematic. In this study, we describe an approach that specifically localizes the position of GFP/yellow fluorescent protein (YFP) constructs within the same cultured cell imaged in the confocal and transmission electron microscopes. We present a simplified method for delivering cell cultures expressing fluorescent fusion proteins into LR White embedding media, which allows excellent GFP/YFP detection and also high-resolution imaging in the TEM. Confocal images from 0.5-microm-thick sections are overlaid atop TEM images of the same cells collected from the next serial ultrathin section. The overlay is achieved in Adobe Photoshop by making the confocal image somewhat transparent, then carefully aligning features within the confocal image over the same features visible in the TEM image. The method requires no specialized specimen preparation equipment; specimens are taken from live cultures to embedding within 8 h, and confocal transmission overlay microscopy can be completed within a few hours.     

Three-dimensional imaging of proton gradients at microelectrode surfaces using confocal laser scanning microscopy

The first use of fluorescence confocal laser scanning microscopy (CLSM) to image three-dimensional pH gradients at electrode surfaces is described, using the reduction of benzoquinone (BQ) to hydroquinone in aqueous solution as an example. The associated local pH changes accompanying the process have been imaged using a trace amount of fluorescein, which has a pH-dependent fluorescent signal. Images recorded in x–y–z space, allow pH profiles to be obtained as a function of applied electrode potential. Experimentally determined profiles measured when BQ is reduced at a diffusion-limited rate are shown to be in good agreement with predictions from numerical simulation. Future applications of CLSM for pH imaging at electrode surfaces and its use in scanning electrochemical microscopy (SECM) are highlighted briefly.     

Confocal imaging of the embryonic heart: how deep?

Confocal microscopy allows for optical sectioning of tissues, thus obviating the need for physical sectioning and subsequent registration to obtain a three-dimensional representation of tissue architecture. However, practicalities such as tissue opacity, light penetration, and detector sensitivity have usually limited the available depth of imaging to 200 microm. With the emergence of newer, more powerful systems, we attempted to push these limits to those dictated by the working distance of the objective. We used whole-mount immunohistochemical staining followed by clearing with benzyl alcohol-benzyl benzoate (BABB) to visualize three-dimensional myocardial architecture. Confocal imaging of entire chick embryonic hearts up to a depth of 1.5 mm with voxel dimensions of 3 microm was achieved with a 10x dry objective. For the purpose of screening for congenital heart defects, we used endocardial painting with fluorescently labeled poly-L-lysine and imaged BABB-cleared hearts with a 5x objective up to a depth of 2 mm. Two-photon imaging of whole-mount specimens stained with Hoechst nuclear dye produced clear images all the way through stage 29 hearts without significant signal attenuation. Thus, currently available systems allow confocal imaging of fixed samples to previously unattainable depths, the current limiting factors being objective working distance, antibody penetration, specimen autofluorescence, and incomplete clearing.     

Three-dimensional imaging of sulfides in silicate rocks at submicron resolution with multiphoton microscopy

We report the first application of multiphoton microscopy (MPM) to generate three-dimensional (3D) images of natural minerals (micron-sized sulfides) in thick (～120 μm) rock sections. First, reflection mode (RM) using confocal laser scanning microscopy (CLSM), combined with differential interference contrast (DIC), was tested on polished sections. Second, two-photon fluorescence (TPF) and second harmonic signal (SHG) images were generated using a femtosecond-laser on the same rock section without impregnation by a fluorescent dye. CSLM results show that the silicate matrix is revealed with DIC and RM, while sulfides can be imaged in 3D at low resolution by RM. Sulfides yield strong autofluorescence from 392 to 715 nm with TPF, while SHG is only produced by the embedding medium. Simultaneous recording of TPF and SHG images enables efficient discrimination between different components of silicate rocks. Image stacks obtained with MPM enable complete reconstruction of the 3D structure of a rock slice and of sulfide morphology at submicron resolution, which has not been previously reported for 3D imaging of minerals. Our work suggests that MPM is a highly efficient tool for 3D studies of microstructures and morphologies of minerals in silicate rocks, which may find other applications in geosciences.     

FSiNPs mediated improved double immunofluorescence staining for gastric cancer cells imaging

A fluorescent silica nanoparticles (FSiNPs) mediated double immunofluorescence staining technique has been proposed for MGC-803 gastric cancer cells imaging by confocal laser scanning microscopy. Anti-CEA antibody and anti-CK19 antibody which can be both bonded to MGC-803 gastric cancer cells were first conjugated to fluorescein isothiocyanate (FITC) doped fluorescent silica nanoparticles (FFSiNPs) and RuBPY doped fluorescent silica nanoparticles (RFSiNPs), respectively. The MGC-803 gastric cancer cells were incubated with the mixture of anti-CEA antibody-conjugated FFSiNPs and anti-CK19 antibody-conjugated RFSiNPs, and subsequently imaged using confocal laser scanning microscopy. With this method, the in vitro cultured MGC-803 gastric cancer cells lines were successfully doubled labeled and distinguished through antigen-antibody recognition, together with the green and red signal of FFSiNPs and RFSiNPs simultaneously obtained without crossreactivity by confocal laser scanning microscopy imaging. By comparison with the conventional double immunofluorescence staining using green-emitting and red-emitting dyes, the photostability of this proposed method for confocal laser scanning microscopy imaging has been greatly improved. Furthermore, the ex vivo imaging of primary MGC-803 gastric cancer cells samples came from the tumor tissues of mice bearing the MGC gastric cancer tumor xenografts by this method have also been explored. The results demonstrate that the method offers potential advantage of photostability for the confocal laser scanning microscopy imaging of MGC-803 gastric cancer cells, and is applicable to the imaging of primary MGC-803 gastric cancer cells from the tumor tissues.     

Analysis of orientations of collagen fibers by novel fiber-tracking software.

Recent evidence supports the notion that biological functions of extracellular matrix (ECM) are highly correlated to not only its composition but also its structure. This article integrates confocal microscopy imaging and image-processing techniques to analyze the microstructural properties of ECM. This report describes a two- and three-dimensional fiber middle-line tracing algorithm that may be used to quantify collagen fibril organization. We utilized computer simulation and statistical analysis to validate the developed algorithm. These algorithms were applied to confocal images of collagen gels made with reconstituted bovine collagen type I, to demonstrate the computation of orientations of individual fibers.     

Robust automated three-dimensional segmentation of secondary ion mass spectrometry image sets

Three-dimensional (3-D) element distributions generated by scanning secondary ion mass spectrometry (SIMS) are usually noisy and blurred and contain objects which do not usually have sharp edges or may have noise induced boundaries. Additionally, there are local intensity differences due to sensitivity differences of the channelplate. As a result, traditional segmentation techniques become difficult and yield rather poor results. We present a novel methodology which combines a restoration process (using a combination of channelplate sensitivity compensation with a 3-D de-noising technique based on the wavelet transform) with a fuzzy logic 3-D gray level segmentation which can be used to successfully segment 3-D SIMS image sets. The restoration algorithm removes the artifacts produced by the channelplate inhomogeneities as well as noise aberrations from the image sets and the gray level thresholding algorithm segments their features. The algorithm is designed for minimal user interaction to achieve a high automation level. The methodology is discussed and experimental results using real 3-D images are presented.     

In-plane stacking disorder in polydisperse hard sphere crystals

We demonstrate that in random-stacking hard-sphere colloidal crystals the stacking disorder not only exists in the direction perpendicular to the close-packed layers, but also extends in the lateral direction. The existence of such in-plane stacking disorder is suggested by a recent observation of lateral broadening of the Bragg scattering rods in microradian X-ray diffraction and is further confirmed here by real-space confocal microscopy in two hard-sphere colloidal systems with different relative gravity effects. Due to the in-plane stacking disorder, the hexagonal planes consist of islands with different lateral A, B, and C positions with characteristic line defects in between them. The real-space layer-by-layer stacks of images also reveal the 3-D structure of the defects. The chance zeta to find another line-defect above a line-defect in the layer below turns out to be close to 1/2--independent of relative gravity--which can be explained by the two different stacking options above a defect. The stacking of a few sets of several line defects situated on top of each other turns out to be predominantly FCC-like.     

Self-assembly of 1-D organic semiconductor nanostructures

This review focuses on the molecular design and self-assembly of a new class of crowded aromatics that form 1-D nanostructures via hydrogen bonding and pi-pi interactions. These molecules have a permanent dipole moment that sums as the subunits self assemble into molecular stacks. The assembly of these molecular stacks can be directed with electric fields. Depending on the nature of the side-chains, molecules can obtain the face-on or edge-on orientation upon the deposition onto a surface via spin cast technique. Site-selective steady state fluorescence, time-resolved fluorescence, and various types of scanning probe microscopy measurements detail the intermolecular interactions that drive the aromatic molecules to self-assemble in solution to form well-ordered columnar stacks. These nanostructures, formed in solution, vary in their number, size, and structure depending on the functional groups, solvent, and concentration used. Thus, the substituents/side-groups and the proper choice of the solvent can be used to tune the intermolecular interactions. The 1-D stacks and their aggregates can be easily transferred by solution casting, thus allowing a simple preparation of molecular nanostructures on different surfaces.     

Nonrigid registration of CLSM images of physical sections with discontinuous deformations

When biological specimens are cut into physical sections for three-dimensional (3D) imaging by confocal laser scanning microscopy, the slices may get distorted or ruptured. For subsequent 3D reconstruction, images from different physical sections need to be spatially aligned by optimization of a function composed of a data fidelity term evaluating similarity between the reference and target images, and a regularization term enforcing transformation smoothness. A regularization term evaluating the total variation (TV), which enables the registration algorithm to account for discontinuities in slice deformation (ruptures), while enforcing smoothness on continuously deformed regions, was proposed previously. The function with TV regularization was optimized using a graph-cut (GC) based iterative solution. However, GC may generate visible registration artifacts, which impair the 3D reconstruction. We present an alternative, multilabel TV optimization algorithm, which in the examined samples prevents the artifacts produced by GC. The algorithm is slower than GC but can be sped up several times when implemented in a multiprocessor computing environment. For image pairs with uneven brightness distribution, we introduce a reformulation of the TV-based registration, in which intensity-based data terms are replaced by comparison of salient features in the reference and target images quantified by local image entropies.     

Real space observation of silica monoliths in the formation process

The macropore structure evolution of a silica monolith during the formation process was observed by laser scanning confocal microscopy (LSCM) for two kinds of systems. The obtained LSCM images were further subjected to image analysis, and the geometrical parameters were calculated. On the basis of the parameters obtained, improved compositions for high efficiency preparation of macroporous monoliths are discussed.     

On 3-D graphical representation of proteomics maps and their numerical characterization

We consider numerical characterization of proteomics maps by representing a map as a three-dimensional graphical object based on x, y coordinates of the spots and using their relative abundance as the z coordinate. In our representation the protein spots are first ordered based on their relative abundance and labeled accordingly. In the next step a 3-D path is constructed connecting spots having adjacent labels. Finally a matrix is constructed by assigning to each pairs of labels (i, j) matrix element, the numerical value of which is based on the quotients of the Euclidean distance and the distance along the 3-D zigzag between the two points. The approach has been illustrated on a fragment of a proteomics map and compared with 2-D graphical representation of proteomics maps.     

Sum frequency generation vibrational spectroscopic and high-pressure scanning tunneling microscopic studies of benzene hydrogenation on Pt(111)

Sum frequency generation (SFG) vibrational spectroscopy and high-pressure scanning tunneling microscopy (HP-STM) have been used in combination for the first time to study a catalytic reaction. These techniques have been able to identify surface intermediates in situ during benzene hydrogenation on a Pt(111) single-crystal surface at Torr pressures. In a background of 10 Torr of benzene, STM is able to image small ordered regions corresponding to the c(2 radical3 x 3)rect structure in which each molecule is chemisorbed at a bridge site. In addition, individual benzene molecules are also observed between the ordered regions. These individual molecules are assumed to be physisorbed benzene on the basis of the SFG results showing both chemisorbed and physisorbed molecules. The surface becomes too mobile to image upon addition of hydrogen but is determined to have physisorbed and chemisorbed benzene present by SFG. It was spectroscopically determined that heating the platinum surface after poisoning with CO displaces benzene molecules. The high-coverage pure CO structure of (radical19 x radical19)R23.4 degrees imaged with STM is a verification of spectroscopic measurements.     

Automatic registration for images of two-dimensional protein gels.

Two-dimensional polyacrylamide gel electrophoresis 1 (2-D PAGE 1) is currently the method of choice for separating complex mixtures of cellular proteins. Despite its usefulness, 2-D PAGE is not being applied to its full potential because of difficulties with both the method and analysis of the results. One of the key problems is the difficulty and slowness of image analysis, especially registration (image alignment), which is laborious and the results unsatisfactory. We have developed a novel system for analysis of 2-D PAGE images, called Z3, that performs the analysis faster and more precisely. The Z3 system employs novel approaches to image registration, image display, computation of differential expression, and the design and analysis of 2-D gel experiments. This paper describes in detail the registration algorithm, and briefly discusses the merits of complementary pseudocolor display. The registration algorithm is novel in that for the first time raw-image-based registration technology is applied to 2-D gel analysis.     

Structural diversity of the oxovanadium organodiphosphonate system: a platform for the design of void channels

The hydrothermal reactions of a vanadium source, an appropriate diphosphonate ligand, and water in the presence of HF provide a series of compounds with neutral V-P-O networks as the recurring structural motif. When the {O3P(CH2)(n)PO3}4- diphosphonate tether length n is 2-5, metal-oxide hybrids of type 1, [V2O2(H2O){O3P(CH2)(n)PO3}] x xH2O, are isolated. The type 1 oxides exhibit the prototypical three-dimensional (3-D) "pillared" layer architecture. When n is increased to 6-8, the two-dimensional (2-D) "pillared" slab structure of the type 2 oxides [V2O2(H2O)4{O3P(CH2)6PO3}] is encountered. Further lengthening of the spacer to n = 9 provides another 3-D structure, type 3, constructed from the condensation of pillared slabs to give V-P-O double layers as the network substructure. When organic cations are introduced to provide charge balance for anionic V-P-O networks, oxides of types 4-7 are observed. For spacer length n = 3, a range of organodiammonium cations are accommodated by the same 3-D "pillared" layer oxovanadium diphosphonate framework in the type 4 materials [H3N(CH2)(n)NH3][V4O4(OH)2 {O3P(CH)3PO3}2] x xH2O [n = 2, x = 6 (4a); n = 3, x = 3 (4b); n = 4, x = 2 (4c); n = 5, x = 1 (4d); n = 6, x = 0.5 (4e); n = 7, x = 0 (4f)] and [H3NR]y[V4O4(OH)2 {O3P(CH)3PO3}2] x xH2O [R = -CH2(NH3)CH2CH3, y = 1, x = 0 (4g); R = -CH3, n = 2, x = 3 (4h); R = -CH2CH3, y = 2, x = 1 (4i); R = -CH2CH2CH3, y = 2, x = 0 (4j); cation = [H2N(CH2CH3)2], y = 2, x = 0 (4k)]. These oxides exhibit two distinct interlamellar domains, one occupied by the cations and the second by water of crystallization. Furthermore, as the length of the cation increases, the organodiammonium component spills over into the hydrophilic domain to displace the water of crystallization. When the diphosphonate tether length is increased to n = 5, structure type 5, [H3N(CH2)2NH3][V4O4(OH)2(H2O){O3P(CH2)5PO3}2] x H2O, is obtained. This oxide possesses a 2-D "pillared" network or slab structure, similar in gross profile to that of type 2 oxides and with the cations occupying the interlamellar domain. In contrast, shortening the diphosphonate tether length to n = 2 results in the 3-D oxovanadium organophosphonate structure of the type 7 oxide [H3N(CH2)5NH3][V3O3{O3P(CH2)2PO3}2]. The ethylenediphosphonate ligand does not pillar V-P-O networks in this instance but rather chelates to a vanadium center in the construction of complex polyhedral connectivity of 7. Substitution of piperazinium cations for the simple alkyl chains of types 4, 5, and 7 provides the 2-D pillared layer structure of the type 6 oxides, [H2N(CH2CH2)NH2][V2O2{O3P(CH)(n)PO3H}2] [n = 2 (6a); n = 4 (6b); n = 6 (6c)]. The structural diversity of the system is reflected in the magnetic properties and thermal behavior of the oxides, which are also discussed.     

The dynamic nature of amyloid beta (1-40) aggregation

In this paper, we characterize the dynamic nature of the full amyloid beta (1-40) (Aβ (1-40)) aggregates. We labeled the peptide with either 5-carboxytetramethylrhodamine (TAMRA) or with fluorescein-isothiocyanate (FITC). The labeled peptides were mixed after separate fibrillization, and the dynamic changes in the structure of the fibrils were imaged using confocal microscopy. Fluorescence resonance energy transfer (FRET) measurements showed that the Aβ (1-40) peptides detach from and reattach to the fibrils in a biologically relevant timescale (days). With time, the two peptides mix at the molecular level. This process is concentration dependent and occurs primarily in the external parts of the aggregates with a half time between 4 and 7 days. This study shows that the combination of confocal microscopy and FRET analysis is a facile method for studying dynamic processes in supra-molecular aggregates.     

Circular dichroism probed by two-photon fluorescence microscopy in enantiopure chiral polyfluorene thin films

Two-photon fluorescence scanning confocal microscopy sensitive to circular dichroism with a diffraction-limited resolution well below 500 nm is demonstrated. With this method, the spatial variation of the circular dichroism of thermally annealed chiral polyfluorene thin films has been imaged. We observed circular dichroism associated with submicrometer-sized domains showing helicoidally twisted macromolecular organization. Domains with opposite chiroptical properties, corresponding to left- or right-handed molecular organization, coexist in the film. Our results are consistent with those obtained by one-photon imaging and illustrate the potential of two-photon imaging for use in studying helical macromolecular organization.     

Direct visualization of colloidal rod assembly by confocal microscopy

The development of model materials and image processing methods to directly visualize and quantify colloidal rod assembly by means of confocal laser scanning microscopy (CLSM) is reported. Monodisperse fluorescent colloidal rods are prepared by the uniaxial extensional deformation of sterically stabilized microspheres at elevated temperatures. The particles are stably dispersed in refractive index matching mixed organic solvents for CLSM. An image processing algorithm is developed to detect rod backbones and extract particle centroids and orientation angles from the CLSM image volumes. By means of these methods we quantify the distribution of rod orientation angles in self-assembled structures of rods formed by sedimentation. We find the observations to be consistent with aspect-ratio-dependent jamming and orientational order/disorder transition in the rod sediments.     

Contact angle measurements by confocal microscopy for non-destructive microscale surface characterization

Contact angle measurements are of great importance in surface characterization but the practical use has often been limited to macroscopic dimensions (millimeters). Therefore, we have developed a confocal microscopy method that allows non-destructive measurements of both low (<30 degrees ) and high (30 degrees -90 degrees ) contact angles. Low contact angles were measured by reconstructing the drop profile from the interference patterns in droplets condensed from atmospheric humidity. At higher contact angles water droplets with a small amount of fluorescein were sprayed onto the surfaces and 3D-image stacks were recorded and used to extract the contact angle. Suitable drop sizes were between a few up to about 50 mum radius, using a 40x magnification objective. Using drops >10 micrometers radius for microcontact angle measurements a good correlation was obtained between measured micro- and macrocontact angles. After microcontact angle measurements the surfaces were rinsed and heavy meromyosin motor fragments were adsorbed to the surface. Importantly, the sensitive actin propelling function of these motor proteins was not affected by the previous contact angle measurements using fluorescent droplets. This suggests that the methodology should be suitable for non-destructive characterization of different parts of micropatterned surfaces being developed for biological assays.