Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane

2020 ◽  
Author(s):  
Mariana De Niz
Keyword(s):  
Nuclear Envelope ◽  
Cellular Membrane ◽  
Spatiotemporal Dynamics

scholarly journals Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane

2020 ◽  
Author(s):  
Domingos Castro ◽  
Vanessa Nunes ◽  
Joana T. Lima ◽  
Jorge G. Ferreira ◽  
Paulo Aguiar
Keyword(s):  
Nuclear Envelope ◽  
Cellular Membrane ◽  
Spatiotemporal Dynamics ◽  
Imaging Analysis ◽  
Imaging Data ◽  
Analysis Software ◽  
Model Free ◽  
Centrosome Separation ◽  
Efficient Access ◽  
Spatiotemporal Relations

AbstractDuring the initial stages of mitosis, multiple mechanisms drive centrosome separation and positioning. How they are functionally coordinated to promote centrosome migration to opposite sides of the nucleus remains unclear. Imaging analysis software has been used to quantitatively study centrosome dynamics at this stage. However, available tracking tools are generic and not fine-tuned for the constrains and motion dynamics of centrosome pairs. Such generality limits the tracking performance and may require exhaustive optimization of parameters. Here, we present Trackosome, a freely available open-source computational tool to track the centrosomes and reconstruct the nuclear and cellular membranes, based on volumetric live-imaging data. The toolbox runs in MATLAB and provides a graphical user interface for easy and efficient access to the tracking and analysis algorithms. It outputs key metrics describing the spatiotemporal relations between centrosomes, nucleus and cellular membrane. Trackosome can also be used to measure the dynamic fluctuations of the nuclear envelope. A fine description of these fluctuations is important because they are correlated with the mechanical forces exerted on the nucleus by its adjacent cytoskeletal structures. Unlike previous algorithms based on circular/elliptical approximations of the nucleus, Trackosome measures membrane movement in a model-free condition, making it viable for irregularly shaped nuclei. Using Trackosome, we demonstrate significant correlations between the movements of the two centrosomes, and identify specific modes of oscillation of the nuclear envelope. Overall, Trackosome is a powerful tool to help unravel new elements in the spatiotemporal dynamics of subcellular structures.

scholarly journals Trackosome: a computational toolbox to study the spatiotemporal dynamics of centrosomes, nuclear envelope and cellular membrane

2020 ◽  
Vol 133 (24) ◽  
pp. jcs252254
Author(s):  
Domingos Castro ◽  
Vanessa Nunes ◽  
Joana T. Lima ◽  
Jorge G. Ferreira ◽  
Paulo Aguiar
Keyword(s):  
Nuclear Envelope ◽  
Cellular Membrane ◽  
Spatiotemporal Dynamics ◽  
Easy Access ◽  
Source Image ◽  
Imaging Data ◽  
Analysis Software ◽  
Model Free ◽  
Centrosome Separation ◽  
Oscillation Modes

ABSTRACTDuring the initial stages of mitosis, multiple mechanisms drive centrosome separation and positioning. How they are coordinated to promote centrosome migration to opposite sides of the nucleus remains unclear. Here, we present Trackosome, an open-source image analysis software for tracking centrosomes and reconstructing nuclear and cellular membranes, based on volumetric live-imaging data. The toolbox runs in MATLAB and provides a graphical user interface for easy access to the tracking and analysis algorithms. It provides detailed quantification of the spatiotemporal relationships between centrosomes, nuclear envelope and cellular membrane, and can also be used to measure the dynamic fluctuations of the nuclear envelope. These fluctuations are important because they are related to the mechanical forces exerted on the nucleus by its adjacent cytoskeletal structures. Unlike previous algorithms based on circular or elliptical approximations, Trackosome measures membrane movement in a model-free condition, making it viable for irregularly shaped nuclei. Using Trackosome, we demonstrate significant correlations between the movements of the centrosomes, and identify specific oscillation modes of the nuclear envelope. Overall, Trackosome is a powerful tool that can be used to help unravel new elements in the spatiotemporal dynamics of subcellular structures.

The Ultrastructure of the Nuclear Events of Binary Fission in Paramecium bursaria and the Effects of Colchicine on Cell Division

1974 ◽  
Vol 32 ◽  
pp. 276-277
Author(s):  
L. M. Lewis
Keyword(s):  
Cell Division ◽  
Nuclear Envelope ◽  
Condensed Chromatin ◽  
Binary Fission ◽  
Paramecium Bursaria ◽  
Nuclear Events ◽  
Division Axis

The effects of colchicine on extranuclear microtubules associated with the macronucleus of Paramecium bursaria were studied to determine the possible role that these microtubules play in controlling the shape of the macronucleus. In the course of this study, the ultrastructure of the nuclear events of binary fission in control cells was also studied.During interphase in control cells, the micronucleus contains randomly distributed clumps of condensed chromatin and microtubular fragments. Throughout mitosis the nuclear envelope remains intact. During micronuclear prophase, cup-shaped microfilamentous structures appear that are filled with condensing chromatin. Microtubules are also present and are parallel to the division axis.

Ultra-Rapid Freezing of Isolated Skeletal Muscle Fibers

1977 ◽  
Vol 35 ◽  
pp. 576-577
Author(s):  
Joachim R. Sommer ◽  
Nancy R. Wallace
Keyword(s):  
Skeletal Muscle ◽  
Sarcoplasmic Reticulum ◽  
Granular Material ◽  
Nuclear Envelope ◽  
Intracellular Calcium ◽  
Ruthenium Red ◽  
Threshold Concentration ◽  
Rapid Freezing ◽  
Frog Skeletal Muscle ◽  
Electrical Isolation

After Howell (1) had shown that ruthenium red treatment of fixed frog skeletal muscle caused collapse of the intermediate cisternae of the sarcoplasmic reticulum (SR), forming a pentalaminate structure by obi iterating the SR lumen, we demonstrated that the phenomenon involves the entire SR including the nuclear envelope and that it also occurs after treatment with other cations, including calcium (2,3,4).From these observations we have formulated a hypothesis which states that intracellular calcium taken up by the SR at the end of contraction causes the M rete to collapse at a certain threshold concentration as the first step in a subsequent centrifugal zippering of the free SR toward the junctional SR (JSR). This would cause a) bulk transport of SR contents, such as calcium and granular material (4) into the JSR and, b) electrical isolation of the free SR from the JSR.

Membranous alterations in the cytoplasm and nucleus in a primitive neuroectodermal tumor of the brain

1978 ◽  
Vol 36 (2) ◽  
pp. 628-629
Author(s):  
C. N. Sun ◽  
C. Araoz ◽  
H. J. White
Keyword(s):  
Nuclear Envelope ◽  
Tumor Cells ◽  
Osmium Tetroxide ◽  
Primitive Neuroectodermal Tumor ◽  
Uranyl Acetate ◽  
Neuroectodermal Tumor ◽  
Annulate Lamellae ◽  
Lead Citrate ◽  
Thin Sections ◽  
The Brain

The ultrastructure of a cerebral primitive neuroectodermal tumor has been reported previously. In the present case, we will present some unusual previously unreported membranous structures and alterations in the cytoplasm and nucleus of the tumor cells.Specimens were cut into small pieces about 1 mm3 and immediately fixed in 4% glutaraldehyde in phosphate buffer for two hours, then post-fixed in 1% buffered osmium tetroxide for one hour. After dehydration, tissues were embedded in Epon 812. Thin sections were stained with uranyl acetate and lead citrate.In the cytoplasm of the tumor cells, we found paired cisternae (Fig. 1) and annulate lamellae (Fig. 2) noting that the annulate lamellae were sometimes associated with the outer nuclear envelope (Fig. 3). These membranous structures have been reported in other tumor cells. In our case, mitochondrial to nuclear envelope fusions were often noted (Fig. 4). Although this phenomenon was reported in an oncocytoma, their frequency in the present study is quite striking.

Compound Symbiosis in Peridinium Balticum

1973 ◽  
Vol 31 ◽  
pp. 500-501
Author(s):  
R. N. Tomas
Keyword(s):  
Endoplasmic Reticulum ◽  
Nuclear Envelope ◽  
The Other ◽  
Exact Nature ◽  
Symbiotic Relationship

Peridinium balticum appears to be unusual among the dinoflagellates in that it possesses two DNA-containing structures as determined by histochemical techniques. Ultrastructurally, the two dissimilar nuclei are contained within different protoplasts; one of the nuclei is characteristically dinophycean in nature, while the other is characteristically eucaryotic. The chloroplasts observed within P. balticum are intrinsic to an eucaryotic photosynthetic endosymbiont and not to the dinoflagellate. These organelles are surrounded by outpocketings of endoplasmic reticulum which are continuous with the eucaryotic nuclear envelope and are characterized by thylakoids composed of three apposed lamellae. Girdle lamellae and membranebounded interlamellar pyrenoids are also present. Only the plasmalemma of the endosymbiont segregates its protoplast from that of the dinophycean cytoplasm. The exact nature of this symbiotic relationship is at present not known.

Cytochemical analysis of mast cell granules after poly-dl-lysine action

1978 ◽  
Vol 36 (2) ◽  
pp. 278-279
Author(s):  
R. Courtoy ◽  
L.J. Simar ◽  
J. Christophe
Keyword(s):  
Mast Cell ◽  
Mast Cells ◽  
Chemical Compounds ◽  
Cellular Membrane ◽  
Thin Sections ◽  
Organic Bases ◽  
Ferric Thiocyanate ◽  
Cytochemical Analysis ◽  
Mast Cell Granule ◽  
Amine Liberation

Several chemical compounds induce amine liberation from mast cells but do not necessarily provoque the granule expulsion. For example, poly-dl-lysine induces modifications of the cellular membrane permeability which promotes ion exchange at the level of mast cell granules. Few of them are expulsed but the majority remains in the cytoplasm and appears less dense to the electrons. A cytochemical analysis has been performed to determine the composition of these granules after the polylysine action.We have previously reported that it was possible to demonstrate polyanions on epon thin sections using a cetylpyridinium ferric thiocyanate method. Organic bases are selectively stained with cobalt thiocyanate and the sulfhydryle groups are characterized with a silver methenamine reaction. These techniques permit to reveal the mast cell granule constituents, i.e. heparin, biogenic amines and basic proteins.

Contributions to the mechanisms of mitosis and roles of cytoplasmic microtubules from ultrastructural analyses of fungi

1978 ◽  
Vol 36 (2) ◽  
pp. 266-267
Author(s):  
I. Brent Heath
Keyword(s):  
Nuclear Envelope ◽  
Direct Application ◽  
Ultrastructural Analysis ◽  
General Interest ◽  
Research Results ◽  
Organelle Motility ◽  
Cytoplasmic Microtubules

Detailed ultrastructural analysis of fungal mitotic systems and cytoplasmic microtubules might be expected to contribute to a number of areas of general interest in addition to the direct application to the organisms of study. These areas include possibly fundamental general mechanisms of mitosis; evolution of mitosis; phylogeny of organisms; mechanisms of organelle motility and positioning; characterization of cellular aspects of microtubule properties and polymerization control features. This communication is intended to outline our current research results relating to selected parts of the above questions.Mitosis in the oomycetes Saprolegnia and Thraustotheca has been described previously. These papers described simple kinetochores and showed that the kineto- chores could probably be used as markers for the poorly defined chromosomes. Kineto- chore counts from serially sectioned prophase mitotic nuclei show that kinetochore replication precedes centriole replication to yield a single hemispherical array containing approximately the 4 n number of kinetochore microtubules diverging from the centriole associated "pocket" region of the nuclear envelope (Fig. 1).

Nuclear Envelope Dynamics During Mitosis

1988 ◽  
Vol 46 ◽  
pp. 224-225
Author(s):  
Brian Burke
Keyword(s):  
Nuclear Envelope ◽  
Membrane Vesicles ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Animal Cells ◽  
Interphase Chromosome ◽  
Lamin B ◽  
Chromosome Architecture ◽  
Complex Membrane ◽  
Pore Complexes

The nuclear envelope is a complex membrane structure that forms the boundary of the nuclear compartment in eukaryotes. It regulates the passage of macromolecules between the two compartments and may be important for organizing interphase chromosome architecture. In interphase animal cells it forms a remarkably stable structure consisting of a double membrane ouerlying a protein meshwork or lamina and penetrated by nuclear pore complexes. The latter form the channels for nucleocytoplasmic exchange of macromolecules, At the onset of mitosis, however, it rapidly disassembles, the membranes fragment to yield small vesicles and the lamina, which is composed of predominantly three polypeptides, lamins R, B and C (MW approx. 74, 68 and 65 kDa respectiuely), breaks down. Lamins B and C are dispersed as monomers throughout the mitotic cytoplasm, while lamin B remains associated with the nuclear membrane vesicles.

Detection and mapping of interactions between chromatin and the nuclear envelope in drosophila embryos

1995 ◽  
Vol 53 ◽  
pp. 764-765
Author(s):  
W.F. Marshall ◽  
A.F. Dernburg ◽  
B. Harmon ◽  
J.W. Sedat
Keyword(s):  
Nuclear Envelope ◽  
Chromatin Condensation ◽  
Three Dimensional ◽  
Physiological Role ◽  
Nuclear Surface ◽  
Intact Cells ◽  
Molecular Determinants ◽  
Surface Harmonic ◽  
Drosophila Embryos

Interactions between chromatin and nuclear envelope (NE) have been implicated in chromatin condensation, gene regulation, nuclear reassembly, and organization of chromosomes within the nucleus. To further investigate the physiological role played by such interactions, it will be necessary to determine which loci specifically interact with the nuclear envelope. This will not only facilitate identification of the molecular determinants of this interaction, but will also allow manipulation of the pattern of chromatin-NE interactions to probe possible functions. We have developed a microscopic approach to detect and map chromatin-NE interactions inside intact cells.Fluorescence in situ hybridization (FISH) is used to localize specific chromosomal regions within the nucleus of Drosophila embryos and anti-lamin immunofluorescence is used to detect the nuclear envelope. Widefield deconvolution microscopy is then used to obtain a three-dimensional image of the sample (Fig. 1). The nuclear surface is represented by a surface-harmonic expansion (Fig 2). A statistical test for association of the FISH spot with the surface is then performed.

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