Measuring murine chromosome orientation in interphase nuclei

Abstract

The nuclear architecture of a cell may change as a result of various diseases, including cancer. A variety of nuclear features are, therefore, of interest to cell biologists. Recently, several studies have investigated the orientation of chromosomes in the interphase nucleus either visually or semi-automatically. In this article an automated method to measure this orientation is presented. The theoretical difference between performing these measurements in two and three dimensions is discussed and experimentally verified. The results computed from measurements of murine nuclei correspond with results from visual inspection. We found significant differences in the orientation of chromosome 11 between nuclei from a PreB cell line of BALB/c origin and primary B nuclei from congenic [T38HxBALB/c]N wild-type mice. Since our new automatic method concurs with both the visual and semi-automatic methods, we conclude that the automatic method can replace these methods in assessing chromosome orientation. V C 2015 International Society for Advancement of Cytometry

A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions

“…Sample preparation, FISH procedure, image capturing, deconvolution, 3D model rendering, and data analysis may all potentially contribute to small variations between cells and experiments. However, these variables were minimized by ensuring all of these steps for the 3D aspect of this study were performed by the same experienced operator following the same procedures and through the use of established and accepted methodologies 45 46 47 48 49 . Similar approaches to the longitudinal method of analysis performed in this study has been previously published by several groups 39 40 50 51 .…”

Changes in Nuclear Orientation Patterns of Chromosome 11 during Mouse Plasmacytoma Development

“…In addition, we used novel automated software to confirm our visual results [30] . In short, the nucleus was segmented first with an isodata threshold after some smoothing and out-of-focus blur subtraction.…”

Distinct and shared three‐dimensional chromosome organization patterns in lymphocytes, monoclonal gammopathy of undetermined significance and multiple myeloma

“…(2015) with some minor modifications for these cells. The chromosome channels are individually segmented from their respective images . The image is first band‐filtered with a difference of Gaussians filter, the negative values arising from this filter are clipped to zero.…”

“…Second, the relevant features were measured. The nucleus was segmented as described by Righolt et al (2015) with some minor modifications for these cells. The chromosome channels are individually segmented from their respective images.…”

“…The chromosome channels are individually segmented from their respective images. 49 The image is first band-filtered with a difference of Gaussians filter, the negative values arising from this filter are clipped to zero. The product of the original image and the clipped band-pass filtered image is subsequently thresholded over the nuclear mask with the isodata algorithm.…”