Imaging of molecular surface dynamics in brain slices using single-particle tracking.

Organization of signalling molecules in biological membranes is crucial for cellular communication. Many receptors, ion channels and cell adhesion molecules are associated with proteins important for their trafficking, surface localization or function. These complexes are embedded in a lipid environment of varying composition. Binding affinities and stoichiometry of such complexes were so far experimentally accessible only in isolated systems or monolayers of cell culture. Visualization of molecular dynamics within signalling complexes and their correlation to specialized membrane compartments demand high temporal and spatial resolution and has been difficult to demonstrate in complex tissue like brain slices. Here we demonstrate the feasibility of single-particle tracking (SPT) in organotypic brain slices to measure molecular dynamics of lipids and transmembrane proteins in correlation to synaptic membrane compartments. This method will provide important information about the dynamics and organization of surface molecules in the complex environment of neuronal networks within brain slices.

Wavelet analysis for single molecule localization microscopy.

Localization of single molecules in microscopy images is a key step in quantitative single particle data analysis. Among them, single molecule based super-resolution optical microscopy techniques require high localization accuracy as well as computation of large data sets in the order of 10(5) single molecule detections to reconstruct a single image. We hereby present an algorithm based on image wavelet segmentation and single particle centroid determination, and compare its performance with the commonly used gaussian fitting of the point spread function. We performed realistic simulations at different signal-to-noise ratios and particle densities and show that the calculation time using the wavelet approach can be more than one order of magnitude faster than that of gaussian fitting without a significant degradation of the localization accuracy, from 1 nm to 4 nm in our range of study. We propose a simulation-based estimate of the resolution of an experimental single molecule acquisition.

Fast 4D Microscopy.

Many cellular processes involve fast movements of weakly labeled cellular structures in all directions, which should be recorded in 3D time-lapse microscopy (4D microscopy). This chapter introduces fast 4D imaging, which is used for sampling the cell's volume by collecting focal planes in time-lapse mode as rapidly as possible, without perturbing the sample by strong illumination. The final images should contain sufficient contrast allowing for the isolation of structures of interest by segmentation and the analysis of their intracellular movements by tracking. Because they are the most sensitive, systems using wide-field microscopy and deconvolution techniques are discussed in greater depth. We discuss important points to consider, including system components and multifunctionality, spatial resolution and sampling conditions, and mechanical and optical stability and how to test for it. We consider image formation using high numerical aperture optics and discuss the influence of optical blur and noise on image formation of living cells. Spherical aberrations, their consequences for axial image quality, and their impact on the success of deconvolution of low intensity image stacks are explained in detail. Simple protocols for acquiring and treating point spread functions (PSFs) and live cells are provided. A compromise for counteracting spherical aberration involving the use of a kit of immersion oils for PSF and cell acquisition is illustrated. Recommendations for evaluating acquisition conditions and deconvolution parameters are given. Finally, we discuss future developments based on the use of adaptive optics which will push back many of today's limits.

Nucleolar assembly of the rRNA processing machinery in living cells.

To understand how nuclear machineries are targeted to accurate locations during nuclear assembly, we investigated the pathway of the ribosomal RNA (rRNA) processing machinery towards ribosomal genes (nucleolar organizer regions [NORs]) at exit of mitosis. To follow in living cells two permanently transfected green fluorescence protein-tagged nucleolar proteins, fibrillarin and Nop52, from metaphase to G1, 4-D time-lapse microscopy was used. In early telophase, fibrillarin is concentrated simultaneously in prenucleolar bodies (PNBs) and NORs, whereas PNB-containing Nop52 forms later. These distinct PNBs assemble at the chromosome surface. Analysis of PNB movement does not reveal the migration of PNBs towards the nucleolus, but rather a directional flow between PNBs and between PNBs and the nucleolus, ensuring progressive delivery of proteins into nucleoli. This delivery appeared organized in morphologically distinct structures visible by electron microscopy, suggesting transfer of large complexes. We propose that the temporal order of PNB assembly and disassembly controls nucleolar delivery of these proteins, and that accumulation of processing complexes in the nucleolus is driven by pre-rRNA concentration. Initial nucleolar formation around competent NORs appears to be followed by regroupment of the NORs into a single nucleolus 1 h later to complete the nucleolar assembly. This demonstrates the formation of one functional domain by cooperative interactions between different chromosome territories.

Duplication and maintenance of heterochromatin domains.

To investigate the mechanisms that assure the maintenance of heterochromatin regions, we took advantage of the fact that clusters of heterochromatin DNA replicate late in S phase and are processed in discrete foci with a characteristic nuclear distribution. At the light microscopy level, within these entities, we followed DNA synthesis, histone H4 acetylation, heterochromatin protein 1 (Hp1alpha and -beta), and chromatin assembly factor 1 (CAF-1). During replication, Hp1alpha and -beta domains of concentration are stably maintained, whereas heterochromatin regions are enriched in both CAF-1 and replication-specific acetylated isoforms of histone H4 (H4Ac 5 and 12). We defined a time window of 20 min for the maintenance of this state. Furthermore, treatment with Trichostatin A (TSA), during and after replication, sustains the H4Ac 5 and 12 state in heterochromatin excluding H4Ac 8 and 16. In comparison, early replication foci, at the same level, did not display any specific enrichment in H4Ac 5 and 12. These data emphasize the specific importance for heterochromatin of the replication-associated H4 isoforms. We propose that perpetuation of heterochromatin involves self-maintenance factors, including local concentration of Hp1alpha and -beta, and that a degree of plasticity is provided by the cycle of H4 acetylation/deacetylation assisted by CAF-1.

Relationship between cell migration and cell cycle during the initiation of epithelial to fibroblastoid transition.

The NBT-II rat bladder carcinoma cell line, which displays epithelial to mesenchymal transition or EMT in response to FGF-1 stimulation, was used to study the interrelationships between cell cycle and cell scattering and locomotion. Time-lapse video microscopy experiments were performed with asynchronous growing cells and lovastatin-arrested cells. FGF-1 stimulation induced cell movement in cells in all phases of the cell cycle, except G2 + M phase, in which cells did not respond to stimulation. The delay between cell stimulation and cell movement depended on the age of the cell at the beginning of cell stimulation: cells less than 4 h old when stimulated by FGF-1 had a 1-h delay whereas cells more than 4 h old had a 3-h delay. Cells stimulated before they were 4 h old were temporarily arrested in their cell cycle progression. Older cells underwent mitosis on schedule. Lovastatin-treated cells were shown to be synchronized in the G1 phase and to migrate simultaneously after FGF-1 stimulation. These results indicate that the G1 phase was a critical phase for FGF-1 induced cell migration during epithelial to fibroblastoid transition.

Image restoration in X-ray microscopy: PSF determination and biological applications.

In this work, we show that digital image processing methods can be applied to enhance the quality of X-ray microscopic images. One application of X-ray microscopy is imaging of biological specimens in their natural aqueous environment. Since X radiation can introduce structural changes in these objects when observing them at room temperature, it is sometimes necessary to take images with short exposure time. The image quality can thus be reduced due to low signal-to-noise ratio (SNR). Digital image processing methods can be applied to reduce image degradation caused by noise. Another example of a digital image processing method we applied to X-ray microscopy images is contrast enhancement of structures near the resolution limit of the microscope. Structures of 20 nm in size, which show weak contrast in the original image, become more clearly visible after restoration. Since image restoration methods are based on the knowledge of the optical transfer function (OTF) or the point spread function (PSF), a handy method for quick PSF determination is presented. An iterative image-restoration method was applied to pictures obtained with the Gottingen transmission X-ray microscope at BESSY. Results of image quality enhancement by this method are shown for images of polytene chromosomes of Chironomus Thummi larvae, test-structures and in situ hybridization on Xist RNA using biotinilated DNA probe.