Estimation of protein secondary structure and error analysis from circular dichroism spectra.

The estimation of protein secondary structure from circular dichroism spectra is described by a multivariate linear model with noise (Gauss-Markoff model). With this formalism the adequacy of the linear model is investigated, paying special attention to the estimation of the error in the secondary structure estimates. It is shown that the linear model is only adequate for the alpha-helix class. Since the failure of the linear model is most likely due to nonlinear effects, a locally linearized model is introduced. This model is combined with the selection of the estimate whose fractions of secondary structure summate to approximately one. Comparing the estimation from the CD spectra with the X-ray data (by using the data set of W.C. Johnson Jr., 1988, Annu. Rev. Biophys. Chem. 17, 145-166) the root mean square residuals are 0.09 (alpha-helix), 0.12 (anti-parallel beta-sheet), 0.08 (parallel beta-sheet), 0.07 (beta-turn), and 0.09 (other). These residuals are somewhat larger than the errors estimated from the locally linearized model. In addition to alpha-helix, in this model the beta-turn and "other" class are estimated adequately. But the estimation of the antiparallel and parallel beta-sheet class remains unsatisfactory. We compared the linear model and the locally linearized model with two other methods (S. W. Provencher and J. Glöckner, 1981, Biochemistry 20, 1085-1094; P. Manavalan and W. C. Johnson Jr., 1988, Anal. Biochem. 167, 76-85). The locally linearized model and the Provencher and Glöckner method provided the smallest residuals. However, an advantage of the locally linearized model is the estimation of the error in the secondary structure estimates.

A comparison of different focus functions for use in autofocus algorithms.

A number of functions for the autofocusing of microscopes and other optical instruments are to be found in the literature. In this article we compare 11 of them to determine, in an objective manner, which functions are most suitable for implementation with real-time video acquisition systems. Three different images, each representing a typical class of image, are used in the comparison. Among the best focus functions found in our study are the squared magnitude gradient, the squared Laplacian, and the normalized image standard deviation.

Three-dimensional skeletonization: principle and algorithm.

An algorithm is proposed for skeletonization of 3-D images. The criterion to preserve connectivity is given in two versions: global and local. The latter allows local decisions in the erosion process. A table of the decisions for all possible configurations is given in this paper. The algorithm using this table can be directly implemented both on general purpose computers and on dedicated machinery.

DNA content and chromosome number of a heteroploid human tumour cell line.

In this paper investigations concerning the relation between variability of chromosome number and variability of DNA content within the cells of a tumour stemline are reported. A highly heteroploid human tumour cell line was used, which was derived from a chondrosarcoma. Flow cytometrical and scanning cytophotometrical measurements confirmed the heteroploid nature of the original cell line and of several subclones. Measurement of the DNA content per metaphase showed a linear relation between chromosome number and DNA content of heteroploid cells. This finding is discussed with regard to its implications for the mechanism of heteroploidy in tumour cells.

DNA cytophotometry of human chromosomes.

The applicability of Feulgen-based parameters to detect variant metaphase chromosomes involved in deletions or translocations, was investigated and algorithms developed to compute such parameters. This report is focused primarily on the magnitude of the errors involved during the prerequisite procedures of photography, measurement and computation. Measurements were performed by stage-scanning of photographic negatives of Feulgen-stained metaphases. In the scanned images the initial chromosome boundaries were obtained by thresholding, while definite chromosomal areas and local background values were obtained by expansion of the initial boundaries. The integrated density profiles and the relative DNA content were computed for the individual chromosomes (straight as well as bent). Total DNA content, DNA arm ratio, as well as length and centromere index can be obtained from the profile. It was shown that under such conditions the experimental errors associated with the measurements are small compared to biologic variations (e.g., differences between homologues) and that the procedures applied allow to detect polymorphisms. In addition to this, mean and standard deviations of both DNA and length parameters are given for metaphases of five subjects. Comparison of the applicability of DNA and length parameters is realized by a classification experiment.