1
|
Abstract
The number of (TTAGGG)n repeats at the ends of chromosomes is highly variable between individual chromosomes, between different cells and between species. Progressive loss of telomere repeats limits the proliferation of pre-malignant human cells but also contributes to aging by inducing apoptosis and senescence in normal cells. Despite enormous progress in understanding distinct pathways that result in loss and gain of telomeric DNA in different cell types, many questions remain. Further studies are needed to delineate the role of damage to telomeric DNA, replication errors, chromatin structure, liquid-liquid phase transition, telomeric transcripts (TERRA) and secondary DNA structures such as guanine quadruplex structures, R-loops and T-loops in inducing gains and losses of telomere repeats in different cell types. Limitations of current telomere length measurements techniques and differences in telomere biology between species and different cell types complicate generalizations about the role of telomeres in aging and cancer. Here some of the factors regulating the telomere length in embryonic and adult cells in mammals are discussed from a mechanistic and evolutionary perspective.
Collapse
Affiliation(s)
- Peter Lansdorp
- Terry Fox Laboratory, British Columbia (BC) Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Peter Lansdorp,
| |
Collapse
|
2
|
Holmes TJ, Liu YH, Khosla D, Agard DA. Increased depth of field and stereo pairs of fluorescence micrographs via inverse filtering and maximum-likelihood estimation. J Microsc 2011. [DOI: 10.1111/j.1365-2818.1991.tb03209.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
3
|
Houtsmuller AB, Oud JL, Voort HTM, Baarslag MW, Krol JJ, Mosterd B, Mans A, Brakenhoff GJ, Nanninga N. Image processing techniques for 3-D chromosome analysis. J Microsc 2011. [DOI: 10.1111/j.1365-2818.1990.tb02997.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
4
|
Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
5
|
Houtsmuller AB, Smeulders AW, van der Voort HT, Oud JL, Nanninga N. The homing cursor: a tool for three-dimensional chromosome analysis. CYTOMETRY 1993; 14:501-9. [PMID: 8354123 DOI: 10.1002/cyto.990140509] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
When studying the three-dimensional shape of prophase chromosomes (or any other tubular structure), it is useful to represent these structures as a string of three-dimensional Cartesian coordinates along the medial axis. This procedure was automated in order to limit the number of human interactions and to improve reproducibility. In this paper the design, implementation, and validation of the automated method is presented. From the data presented it can be concluded that the cursor algorithm provides an objective and therefore reproducible method to trace the medial axes of prophase chromosomes automatically. This method could allow a more extensive understanding of the (changes in) chromosome organisation throughout the cell cycle, its relation to cell function, and the complex process of chromosome condensation.
Collapse
Affiliation(s)
- A B Houtsmuller
- Department of Molecular Cell Biology, University of Amsterdam, The Netherlands
| | | | | | | | | |
Collapse
|
6
|
Three-dimensional organization of ribosomal DNA in interphase nuclei ofPisum sativum by in situ hybridization and optical tomography. Chromosoma 1990. [DOI: 10.1007/bf01735331] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
7
|
Abstract
The combination of the specificity provided by fluorescence microscopy and the ability to quantitatively analyze specimens in three dimensions allows the fundamental organization of cells to be probed as never before. Key features in this emergent technology have been the development of a wide variety of fluorescent dyes or fluorescently labeled probes to provide the requisite specificity. High-quality, cooled charge-coupled devices have recently become available. Functioning as nearly ideal imagers or "electronic film," they are more sensitive than photomultipliers and provide extraordinarily accurate direct digital readout from the microscope. Not only is this precision crucial for accurate quantitative imaging such as that required for the ratioing necessary to determine intracellular ion concentrations, but it also opens the way for sophisticated image processing. It is important to realize that image processing isn't simply a means to improve image aesthetics, but can directly provide new, biologically important information. The impact of modern video microscopy techniques (Allen, 1985; Inoué, 1986) attests to the fact that many biologically relevant phenomena take place at the limits of conventional microscopy. Image processing can be used to substantially enhance the resolution and contrast obtainable in two dimensions, enabling the invisible to be seen and quantitated. Cells are intrinsically three-dimensional. This can simply be a nuisance because of limited depth of focus of the microscope or it could be a fundamental aspect of the problem being studied. In either case, image processing techniques can be used to rapidly provide the desired representation of the data. In this chapter we have discussed the nature of image formation in three dimensions and dealt with several means to remove contaminating out-of-focus information. The most straightforward of these methods uses only information from adjacent focal planes to correct the central one. This approach can be readily applied to virtually any problem and with most commonly available image processing hardware to provide a substantially deblurred image in almost real time. In addition to covering more sophisticated algorithms where the utmost in three-dimensional imaging is required, we have developed a method for extremely rapidly and accurately producing an in-focus, high-resolution "synthetic projection" image from a thick specimen. This is equivalent to that produced by a microscope having the impossible combination of a high-NA objective lens and an infinite depth of focus. A variation on this method allows efficient calculation of stereo pairs.(ABSTRACT TRUNCATED AT 400 WORDS)
Collapse
Affiliation(s)
- D A Agard
- Howard Hughes Medical Institute, University of California, San Francisco 94143
| | | | | | | |
Collapse
|
8
|
Rykowski MC, Parmelee SJ, Agard DA, Sedat JW. Precise determination of the molecular limits of a polytene chromosome band: regulatory sequences for the Notch gene are in the interband. Cell 1988; 54:461-72. [PMID: 3135939 DOI: 10.1016/0092-8674(88)90067-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have aligned the molecular map of the Notch locus to the cytological features of the salivary gland polytene chromosomes of D. melanogaster in order to determine the interphase chromatin structure of this gene. Using high-resolution in situ hybridization and computer-aided optical microscope data collection and image analysis, we have determined that the coding portions and introns of the Notch gene, which is not expressed in this tissue, are all contained within the polytene chromosome band 3C7. The portion of the Notch gene that resides 5' to the start of transcription lies in an open chromatin conformation, the interband between bands 3C6 and 3C7. Our data are most consistent with condensation of the chromosomal DNA into 30 nm fibers in this polytene band.
Collapse
Affiliation(s)
- M C Rykowski
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0554
| | | | | | | |
Collapse
|
9
|
Agard DA, Hiraoka Y, Sedat JW. Three-dimensional light microscopy of diploid Drosophila chromosomes. CELL MOTILITY AND THE CYTOSKELETON 1988; 10:18-27. [PMID: 3141069 DOI: 10.1002/cm.970100106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fluorescence microscopy, uniquely, provides the ability to examine specific components within intact, even living, cells. Unfortunately, high-resolution conventional fluorescence microscopy is intrinsically a two-dimensional technique and performs poorly with specimens thicker than about 0.5 micron. Probing the spatial organization of components within cells has required the development of new methods optimized for three-dimensional data collection, processing, display, and interpretation. Our interest in understanding the relationship between chromosome structure and function has led us to develop the necessary methodology for exploring cell structures in three dimensions. It is now possible to determine directly the three-dimensional spatial organization of diploid chromosomes within intact nuclei throughout most of the mitotic the cell cycle.
Collapse
Affiliation(s)
- D A Agard
- Howard Hughes Medical Institute, Department of Biochemistry, University of California, San Francisco 94143-0448
| | | | | |
Collapse
|
10
|
Abstract
The microworld was revealed to investigators through a glass bead or a hanging water droplet long before optics was understood. The cellular structure of plants was well resolved by such simple magnifying glasses, van Leeuwenhoek, the Dutch merchant and amateur microscopist, was the first to report to the English Royal Society his observations of bacteria with his single-lens microscope in 1665.
Collapse
Affiliation(s)
- Z Kam
- Polymer Research Department, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
11
|
Hiraoka Y, Sedat JW, Agard DA. The use of a charge-coupled device for quantitative optical microscopy of biological structures. Science 1987; 238:36-41. [PMID: 3116667 DOI: 10.1126/science.3116667] [Citation(s) in RCA: 237] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The properties of a charge-coupled device (CCD) and its application to the high-resolution analysis of biological structures by optical microscopy are described. The CCD, with its high resolution, high sensitivity, wide dynamic range, photometric accuracy, and geometric stability, can provide data of such high quality that quantitative analysis on two- and three-dimensional microscopic images is possible. For example, the three-dimensional imaging properties of an epifluorescence microscope have been quantitatively determined with the CCD. This description of the imaging properties of the microscope, and the high-quality image data provided by the CCD, allow sophisticated computational image processing methods to be used that greatly improve the effective resolution obtainable for biological structures. Image processing techniques revealed fine substructures in Drosophila embryonic diploid chromosomes in two and three dimensions. The same approach can be extended to structures as small as yeast chromosomes or to other problems in structural cell biology.
Collapse
Affiliation(s)
- Y Hiraoka
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448
| | | | | |
Collapse
|
12
|
Hochstrasser M, Sedat JW. Three-dimensional organization of Drosophila melanogaster interphase nuclei. I. Tissue-specific aspects of polytene nuclear architecture. J Cell Biol 1987; 104:1455-70. [PMID: 3108264 PMCID: PMC2114489 DOI: 10.1083/jcb.104.6.1455] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Interphase chromosome organization in four different Drosophila melanogaster tissues, covering three to four levels of polyteny, has been analyzed. The results are based primarily on three-dimensional reconstructions from unfixed tissues using a computer-based data collection and modeling system. A characteristic organization of chromosomes in each cell type is observed, independent of polyteny, with some packing motifs common to several or all tissues and others tissue-specific. All chromosomes display a right-handed coiling chirality, despite large differences in size and degree of coiling. Conversely, in each cell type, the heterochromatic centromeric regions have a unique structure, tendency to associate, and intranuclear location. The organization of condensed nucleolar chromatin is also tissue-specific. The tightly coiled prothoracic gland chromosomes are arrayed in a similar fashion to the much larger salivary gland chromosomes described previously, having polarized orientations, nonintertwined spatial domains, and close packing of the arms of each autosome, whereas hindgut and especially the unusually straight midgut chromosomes display striking departures from these regularities. Surprisingly, gut chromosomes often appear to be broken in the centric heterochromatin. Severe deformations of midgut nuclei observed during gut contractions in living larvae may account for their unusual properties. Finally, morphometric measurements of chromosome and nuclear dimensions provide insights into chromosome growth and substructure and also suggest an unexpected parallel with diploid chromatin organization.
Collapse
|
13
|
Hochstrasser M, Mathog D, Gruenbaum Y, Saumweber H, Sedat JW. Spatial organization of chromosomes in the salivary gland nuclei of Drosophila melanogaster. J Cell Biol 1986; 102:112-23. [PMID: 3079766 PMCID: PMC2114037 DOI: 10.1083/jcb.102.1.112] [Citation(s) in RCA: 196] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Using a computer-based system for model building and analysis, three-dimensional models of 24 Drosophila melanogaster salivary gland nuclei have been constructed from optically or physically sectioned glands, allowing several generalizations about chromosome folding and packaging in these nuclei. First and most surprising, the prominent coiling of the chromosomes is strongly chiral, with right-handed gyres predominating. Second, high frequency appositions between certain loci and the nuclear envelope appear almost exclusively at positions of intercalary heterochromatin; in addition, the chromocenter is always apposed to the envelope. Third, chromosomes are invariably separated into mutually exclusive spatial domains while usually extending across the nucleus in a polarized (Rabl) orientation. Fourth, the arms of each autosome are almost always juxtaposed, but no other relative arm positions are strongly favored. Finally, despite these nonrandom structural features, each chromosome is found to fold into a wide variety of different configurations. In addition, a set of nuclei has been analyzed in which the normally aggregrated centromeric regions of the chromosomes are located far apart from one another. These nuclei have the same architectural motifs seen in normal nuclei. This implies that such characteristics as separate chromosome domains and specific chromosome-nuclear envelope contacts are largely independent of the relative placement of the different chromosomes within the nucleus.
Collapse
|
14
|
Arndt-Jovin DJ, Robert-Nicoud M, Kaufman SJ, Jovin TM. Fluorescence digital imaging microscopy in cell biology. Science 1985; 230:247-56. [PMID: 4048934 DOI: 10.1126/science.4048934] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Developments in microscope, sensor, and image-processing technologies have led to integrated systems for the quantification of low-light-level emission signals from biological samples. Specificity is provided in the form of monoclonal antibodies and other ligands or enzyme substrates conjugated with efficient fluorophores. Fluorescent probes are also available for cellular macromolecular constituents and for free ions of biological interest such as H+ and Ca2+. The entire spectrum of photophysical phenomena can be exploited. Representative data are presented from studies of DNA conformation and architecture in polytene chromosomes and from studies of receptor-mediated endocytosis, calcium distribution, and the organization of the contractile apparatus in muscle cells.
Collapse
|
15
|
Mathog D. Light microscope based analysis of three-dimensional structure: applications to the study of Drosophila salivary gland nuclei. II. Algorithms for model analysis. J Microsc 1985; 137:253-73. [PMID: 3923201 DOI: 10.1111/j.1365-2818.1985.tb02583.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In Drosophila melanogaster there are significant differences in the way the polytene chromosomes are arranged in different nuclei from the same salivary gland (Mathog et al., 1984). Visual inspection of the models of these nuclei was inadequate to delineate all of the features conserved in their structures. In order to bypass this limitation, models of these nuclei were constructed in a format compatible with computational manipulation (Mathog et al., 1985). By applying some simple algorithms to these models, quantitative comparisons were made which revealed otherwise cryptic features common to many nuclei. Given here are the details of several algorithms for describing and comparing the arrangement of the chromosomes within the nuclei.
Collapse
|
16
|
Mathog D, Hochstrasser M, Sedat JW. Light microscope based analysis of three-dimensional structure: applications to the study of Drosophila salivary gland nuclei. I. Data collection and analysis. J Microsc 1985; 137:241-52. [PMID: 3999131 DOI: 10.1111/j.1365-2818.1985.tb02582.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Many biological structures of interest are large enough that they may be viewed by light microscope methods, yet they are sufficiently complicated that interpretation of what is seen is quite difficult. The salivary gland nuclei from Dipterans are an example of this. Previous attempts at determining the path of the giant chromosomes in these nuclei have depended on the laborious construction of models by hand. A unified Computer Aided Modelling and Analysis system (CAMA) has been implemented, allowing data collection and analysis of structures visible by light microscopy. This system is extendible to the analysis of electron micrographs of serial sections or of other data consisting of images present in a stack.
Collapse
|