C. Cremer

Three-dimensional spectral precision distance microscopy of chromatin nanostructures after triple-colour DNA labelling: a study of the BCR region on chromosome 22 and the Philadelphia chromosome

Topological analysis of the three‐dimensional (3D) chromatin nanostructure and its function in intact cell nuclei implies the use of high resolution far field light microscopy, e.g. confocal laser scanning microscopy (CLSM). However, experimental evidence indicates that, in practice, under biologically relevant conditions, the spatial resolution of CLSM is limited to about 300 nm in the lateral direction and about 700 nm in the axial direction. To overcome this shortcoming, the use of a recently developed light microscopical approach, spectral precision distance microscopy (SPDM) is established. This approach is based on the precise localization of small labelling sites of a given target in spectrally differential images. By means of quantitative image analysis, the bary centres (intensity weighted centroid analogous to the centre of mass) of these independently registered labelling sites can be used as point markers for distance and angle measurements after appropriate calibration of optical aberrations (here, polychromatic shifts). In combination with specific labelling of very small chromatin target sites with dyes of different spectral signatures by fluorescence in situ hybridization (FISH), SPDM presently allows us to analyse the nuclear topology in three‐dimensionally conserved nuclei with a ‘resolution equivalent’, many times smaller than the conventional optical resolution.

Axial tomographic confocal fluorescence microscopy

By physical rotation of the sample, axial tomography enables the acquisition of otherwise inaccessible spatial information from an object. In combination with confocal microscopy, the method can fundamentally improve the effective three‐dimensional (3D) resolution. In this report we present a novel method for high resolution reconstruction of confocal axial tomographic data. The method automatically determines the relative angles of rotation, aligns the data from different rotational views and reconstructs a single high resolution 3D dataset. The reconstruction makes use of a known point spread function and is based on an unconstrained maximum likelihood deconvolution performed simultaneously from multiple (in our case three) angular views. It was applied to simulated as well as to experimental confocal datasets. The gain in resolution was quantified and the effect of choice of overrelaxation factors on the speed of convergence was investigated. A clearly improved 3D resolution was obtained by axial tomography together with reconstruction as compared with reconstruction of confocal data from only a single angular view.

Application of confocal laser microscopy and three-dimensional Voronoi diagrams for volume and surface estimates of interphase chromosomes

This study demonstrates the use of Voronoi tessellation procedures to obtain quantitative morphological data for chromosome territories in the cell nucleus. As a model system, chromosomes 7 and X were visualized in human female amniotic fluid cell nuclei by chromosomal in situ suppression hybridization with chromosome‐specific composite probes. Light optical serial sections of 18 nuclei were obtained with a confocal scanning laser fluorescence microscope. A three‐dimensional (3‐D) tessellation of the image volumes defined by the stack of serial sections was then performed. For this purpose a Voronoi diagram, which consists of convex polyhedra structured in a graph environment, was built for each nucleus. The chromosome territories were extracted by applying the Delaunay graph, the dual of the Voronoi diagram, which describes the neighbourhood in the Voronoi diagram. The chromosome territories were then described by three morphological parameters, i.e. volume, surface area and a roundness factor (shape factor). The complete evaluation of a nucleus, including the calculation of the Voronoi diagram, 3‐D visualization of extracted territories using computer graphic methods and parameterization was carried out on a Silicon Graphics workstation and was generally completed within 5 min. The geometric information obtained by this procedure revealed that both X‐ and 7‐chromosome territories were similar in volume. Roundness factors indicated a pronounced variability in interphase shape for both pairs of chromosomes. Surface estimates showed a significant difference between the two X‐territories but not between chromosome 7‐territories.

A versatile 2π-tilting device for fluorescence microscopes

A tilting device for biological specimens (rotation angle up to 2π), especially fluorescence‐labelled cell nuclei, was developed. It consists of a quartz glass capillary and a mounting adapter for the microscope stage. The applicability of the device was tested for several epifluorescence and confocal scanning laser fluorescence microscopes. The axis of rotation is perpendicular to the optical axis of the microscope. The capillary can be tilted around its axis at any desired angle or in equiangular steps. This can be done manually or by remote control using a stepping motor.

Real-time multiprocessing of slit scan chromosome profiles.

The multiprocessor NERV and its application to slit scan flow cytometry is described. Up to 320 processors and 640 MBytes of RAM may be used in one VME crate, providing a computing power of less than or equal to 1300 MIPS. The multiprocessor is controlled by a host computer that provides a friendly user interface and comfortable program development tools. All hardware and software has been tested on a prototype NERV system with 5 processors. For a real-time classification/detection of normal and aberrant chromosomes, the centromeric index or the number of centromeres are computed or specifically labeled DNA sequences are detected. The program is partitioned into 60 tasks that can be executed concurrently. A total analysis time of less than 600 microseconds including system overhead will be achieved according to timing measurements which have been done for all individual tasks.

Denaturation behaviour of DNA-protein-complexes detected in situ in metaphase chromosomes in. suspension by Hoechst 33258 fluorescence

The denaturation behaviour of DNA-protein complexes in metaphase chromosomes in suspension was analysed in situ by Hoechst 33258 fluorescence. The results indicate that due to the stability of the dye molecule and the product of the molecular extinction coefficient and the quantum yield at different temperatures, Hoechst 33258 is a suitable probe for the detection of double-stranded DNA. Thus, it is possible to monitor the concentration of double-stranded DNA in a suspension by measuring the total fluorescence intensity. The fluorescence denaturation profiles of DNA (calf thymus) were found to be comparable to absorption measurements. The decrease in fluorescence of metaphase chromosomes in suspension with increasing temperature may therefore be used to detect conformational changes of DNA in situ.

Real-time classification of chromosomes in slit scan flow cytometry using NERV-a MIMD supercomputer

Presently, profile evaluation can be done at a rate of 10 chromosomes/s using the reflection algorithm. To measure, for example, radiation-induced aberrations in the low dose range or to sort chromosomes according to their slit scan data, it is desired that the analysis speed increase by a factor of 100. It is shown that the data analysis rate allowed by the on-line computer may be increased by implementing the analysis algorithm on a multiprocessor system consisting of 60 microprocessors. The authors discuss an evaluation done on a parallel processing system that may consist of a high number (<or=320) of 32-b microprocessors (NERV). The NERV system was developed as a prototype with a small number of slave processors. Its hardware has been tested completely.<<ETX>>